From ac89abaa4f061539afeae472003d4a223486aae4 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Thu, 5 Jun 2025 15:08:48 -0700 Subject: [PATCH 001/101] feat: nf-core modules bump-version supports specifying the toolkit Tools like picard, fgbio, and samtools all have sub-commands. It is onerous to have to update them all individually using nf-core modules bump-version. This change allows the module name to update to have a trailing forward slash, which will be interpreted as specifying that all subcommands should be updated. E.g. nf-core modules bump-version samtools/ --- nf_core/modules/bump_versions.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index d98eac7cd6..90a1a26f13 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -105,7 +105,10 @@ def bump_versions( raise nf_core.modules.modules_utils.ModuleExceptionError( "You cannot specify a tool and request all tools to be bumped." ) - nfcore_modules = [m for m in nfcore_modules if m.component_name == module] + if module.endswith("/"): + nfcore_modules = [m for m in nfcore_modules if m.component_name.startswith(module)] + else: + nfcore_modules = [m for m in nfcore_modules if m.component_name == module] if len(nfcore_modules) == 0: raise nf_core.modules.modules_utils.ModuleExceptionError( f"Could not find the specified module: '{module}'" From a5b9730da05ae8a0782e0c2e0bf5a59d7d1a2e77 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Fri, 6 Jun 2025 17:50:41 -0700 Subject: [PATCH 002/101] chore: add unit test --- tests/modules/test_bump_versions.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index d46b8747c8..b0e9e4e066 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -29,6 +29,12 @@ def test_modules_bump_versions_all_modules(self): version_bumper.bump_versions(all_modules=True) assert len(version_bumper.failed) == 0 + def test_modules_bump_versions_toolkit(self): + """Test updating a single toolkit""" + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) + version_bumper.bump_versions(module="fgbio/") + assert len(version_bumper.failed) == 0 + def test_modules_bump_versions_fail(self): """Fail updating a module with wrong name""" version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) From c595d2ed17606302e4b8503704d7fcbedf022fa4 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Sun, 8 Jun 2025 12:54:37 -0700 Subject: [PATCH 003/101] update tests --- nf_core/modules/bump_versions.py | 18 +++++++- tests/modules/test_bump_versions.py | 68 ++++++++++++++++++++++++++--- 2 files changed, 77 insertions(+), 9 deletions(-) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 90a1a26f13..715e0404b4 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -46,8 +46,12 @@ def __init__( self.tools_config: Optional[NFCoreYamlConfig] def bump_versions( - self, module: Union[str, None] = None, all_modules: bool = False, show_uptodate: bool = False - ) -> None: + self, + module: Union[str, None] = None, + all_modules: bool = False, + show_uptodate: bool = False, + _dryrun: bool = False, + ) -> List[NFCoreComponent]: """ Bump the container and conda version of single module or all modules @@ -59,6 +63,10 @@ def bump_versions( Args: module: a specific module to update all_modules: whether to bump versions for all modules + show_uptodate: whether to show up-to-date modules as well + + Returns: + the modules updated """ self.up_to_date = [] self.updated = [] @@ -114,6 +122,10 @@ def bump_versions( f"Could not find the specified module: '{module}'" ) + # mainly used for testing, return the list of nfcore_modules selected + if _dryrun: + return nfcore_modules + progress_bar = Progress( "[bold blue]{task.description}", BarColumn(bar_width=None), @@ -133,6 +145,8 @@ def bump_versions( self._print_results() + return nfcore_modules + def bump_module_version(self, module: NFCoreComponent) -> bool: """ Bump the bioconda and container version of a single NFCoreComponent diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index b0e9e4e066..18eb40d737 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -1,10 +1,16 @@ import os import re +import tempfile +from pathlib import Path +from typing import List import pytest +import ruamel.yaml import nf_core.modules.bump_versions +from nf_core import __version__ from nf_core.modules.modules_utils import ModuleExceptionError +from nf_core.utils import NFCoreYamlConfig from ..test_modules import TestModules @@ -20,20 +26,68 @@ def test_modules_bump_versions_single_module(self): with open(env_yml_path, "w") as fh: fh.write(new_content) version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(module="bpipe/test") + modules = version_bumper.bump_versions(module="bpipe/test") assert len(version_bumper.failed) == 0 + assert [m.component_name for m in modules] == ["bpipe/test"] def test_modules_bump_versions_all_modules(self): """Test updating all modules""" version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(all_modules=True) + modules = version_bumper.bump_versions(all_modules=True) assert len(version_bumper.failed) == 0 + assert [m.component_name for m in modules] == ["bpipe/test"] - def test_modules_bump_versions_toolkit(self): - """Test updating a single toolkit""" - version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=self.nfcore_modules) - version_bumper.bump_versions(module="fgbio/") - assert len(version_bumper.failed) == 0 + @staticmethod + def _mock_nf_core_yml(root_dir: Path) -> None: + """Mock the .nf_core.yml""" + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + yaml.indent(mapping=2, sequence=2, offset=0) + nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core") + with open(Path(root_dir, ".nf-core.yml"), "w") as fh: + yaml.dump(nf_core_yml.model_dump(), fh) + + @staticmethod + def _mock_modules(root_dir: Path, modules: List[str]) -> None: + """Mock the directory for a given module (or sub-module) for use with `_dryrun`""" + nf_core_dir = root_dir / "modules" / "nf-core" + for module in modules: + if "/" in module: + module, sub_module = module.split("/") + module_dir = nf_core_dir / module / sub_module + else: + module_dir = nf_core_dir / module + module_dir.mkdir(parents=True) + module_main = module_dir / "main.nf" + with module_main.open("w"): + pass + + def test_modules_bump_versions_multiple_modules(self): + """Test updating all modules when multiple modules are present""" + # mock the fgbio directory + root_dir = Path(tempfile.TemporaryDirectory().name) + self._mock_modules(root_dir=root_dir, modules=["fqgrep", "fqtk"]) + # mock the ".nf-core.yml" + self._mock_nf_core_yml(root_dir=root_dir) + + # run it with dryrun to return the modules that it found + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) + modules = version_bumper.bump_versions(all_modules=True, _dryrun=True) + assert [m.component_name for m in modules] == ["fqgrep", "fqtk"] + + def test_modules_bump_versions_submodules(self): + """Test updating a submodules""" + # mock the fgbio directory + root_dir = Path(tempfile.TemporaryDirectory().name) + in_modules = ["fgbio/callduplexconsensusreads", "fgbio/groupreadsbyumi"] + self._mock_modules(root_dir=root_dir, modules=in_modules) + # mock the ".nf-core.yml" + self._mock_nf_core_yml(root_dir=root_dir) + + # run it with dryrun to return the modules that it found + version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) + out_modules = version_bumper.bump_versions(module="fgbio/", _dryrun=True) + assert [m.component_name for m in out_modules] == in_modules def test_modules_bump_versions_fail(self): """Fail updating a module with wrong name""" From 279daf2160237aecad7cd2b221d4a0bdd3cf3e10 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Sun, 8 Jun 2025 13:00:26 -0700 Subject: [PATCH 004/101] fix --- tests/modules/test_bump_versions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index 18eb40d737..4fe1943296 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -87,7 +87,7 @@ def test_modules_bump_versions_submodules(self): # run it with dryrun to return the modules that it found version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) out_modules = version_bumper.bump_versions(module="fgbio/", _dryrun=True) - assert [m.component_name for m in out_modules] == in_modules + assert sorted([m.component_name for m in out_modules]) == sorted(in_modules) def test_modules_bump_versions_fail(self): """Fail updating a module with wrong name""" From 5f27df337410dc34d780d856b83e1fb21d6c4148 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Sun, 8 Jun 2025 13:00:51 -0700 Subject: [PATCH 005/101] fix --- tests/modules/test_bump_versions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index 4fe1943296..d0747acaf0 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -73,7 +73,7 @@ def test_modules_bump_versions_multiple_modules(self): # run it with dryrun to return the modules that it found version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) modules = version_bumper.bump_versions(all_modules=True, _dryrun=True) - assert [m.component_name for m in modules] == ["fqgrep", "fqtk"] + assert sorted([m.component_name for m in modules]) == sorted(["fqgrep", "fqtk"]) def test_modules_bump_versions_submodules(self): """Test updating a submodules""" From 05c52e6c158eecddc053f3f0e487128850509b55 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Fri, 20 Jun 2025 16:46:31 +0100 Subject: [PATCH 006/101] Support modules with exec: blocks --- nf_core/modules/lint/main_nf.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index d5a174237e..063fc354fa 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -90,6 +90,7 @@ def main_nf( process_lines = [] script_lines = [] shell_lines = [] + exec_lines = [] when_lines = [] iter_lines = iter(lines) for line in iter_lines: @@ -110,6 +111,9 @@ def main_nf( if re.search(r"^\s*shell\s*:", line) and state in ["input", "output", "when", "process"]: state = "shell" continue + if re.search(r"^\s*exec\s*:", line) and state in ["input", "output", "when", "process"]: + state = "exec" + continue # Perform state-specific linting checks if state == "process" and not _is_empty(line): @@ -132,6 +136,8 @@ def main_nf( script_lines.append(line) if state == "shell" and not _is_empty(line): shell_lines.append(line) + if state == "exec" and not _is_empty(line): + exec_lines.append(line) # Check that we have required sections if not len(outputs): @@ -149,8 +155,10 @@ def main_nf( check_when_section(module, when_lines) # Check that we have script or shell, not both - if len(script_lines) and len(shell_lines): - module.failed.append(("main_nf_script_shell", "Script and Shell found, should use only one", module.main_nf)) + if sum(bool(block_lines) for block_lines in (script_lines, shell_lines, exec_lines)) > 1: + module.failed.append( + ("main_nf_script_shell", "Multiple script:/shell:/exec: blocks found, should use only one", module.main_nf) + ) # Check the script definition if len(script_lines): From 6975c28c9f6686ac147030c5c1749be85b39ce22 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 20 Jun 2025 15:49:54 +0000 Subject: [PATCH 007/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e305850c4..cf2d781f09 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ ### Modules - Remove args stub from module template to satisfy language server ([#3403](https://github.com/nf-core/tools/pull/3403)) +- Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633)) ### Subworkflows From 2cff862d32ce7036a1035694f5c193216d4f592f Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 1 Jul 2025 10:29:42 +0200 Subject: [PATCH 008/101] fix variable names and make dry_run a valid paramter --- nf_core/__main__.py | 5 +++-- nf_core/commands_modules.py | 4 ++-- nf_core/modules/bump_versions.py | 29 +++++++++++++++-------------- 3 files changed, 20 insertions(+), 18 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index d1dcc77260..532125e529 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1333,12 +1333,13 @@ def command_modules_info(ctx, tool, directory): ) @click.option("-a", "--all", is_flag=True, help="Run on all modules") @click.option("-s", "--show-all", is_flag=True, help="Show up-to-date modules in results too") -def command_modules_bump_versions(ctx, tool, directory, all, show_all): +@click.option("-r", "--dry-run", is_flag=True, help="Dry run the command") +def command_modules_bump_versions(ctx, tool, directory, all, show_all, dry_run): """ Bump versions for one or more modules in a clone of the nf-core/modules repo. """ - modules_bump_versions(ctx, tool, directory, all, show_all) + modules_bump_versions(ctx, tool, directory, all, show_all, dry_run) # nf-core subworkflows click command diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py index 33b1f75160..151ee5d205 100644 --- a/nf_core/commands_modules.py +++ b/nf_core/commands_modules.py @@ -334,7 +334,7 @@ def modules_info(ctx, tool, directory): sys.exit(1) -def modules_bump_versions(ctx, tool, directory, all, show_all): +def modules_bump_versions(ctx, tool, directory, all, show_all, dry_run): """ Bump versions for one or more modules in a clone of the nf-core/modules repo. @@ -349,7 +349,7 @@ def modules_bump_versions(ctx, tool, directory, all, show_all): ctx.obj["modules_repo_branch"], ctx.obj["modules_repo_no_pull"], ) - version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all) + version_bumper.bump_versions(module=tool, all_modules=all, show_up_to_date=show_all, dry_run=dry_run) except ModuleExceptionError as e: log.error(e) sys.exit(1) diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index 715e0404b4..f6ce55869a 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -38,20 +38,20 @@ def __init__( ): super().__init__("modules", pipeline_dir, remote_url, branch, no_pull) - self.up_to_date: List[Tuple[str, str]] = [] - self.updated: List[Tuple[str, str]] = [] - self.failed: List[Tuple[str, str]] = [] - self.ignored: List[Tuple[str, str]] = [] + self.up_to_date: list[tuple[str, str]] = [] + self.updated: list[tuple[str, str]] = [] + self.failed: list[tuple[str, str]] = [] + self.ignored: list[tuple[str, str]] = [] self.show_up_to_date: Optional[bool] = None self.tools_config: Optional[NFCoreYamlConfig] def bump_versions( self, - module: Union[str, None] = None, + module: Optional[str] = None, all_modules: bool = False, - show_uptodate: bool = False, - _dryrun: bool = False, - ) -> List[NFCoreComponent]: + show_up_to_date: bool = False, + dry_run: bool = False, + ) -> list[NFCoreComponent]: """ Bump the container and conda version of single module or all modules @@ -63,7 +63,8 @@ def bump_versions( Args: module: a specific module to update all_modules: whether to bump versions for all modules - show_uptodate: whether to show up-to-date modules as well + show_up_to_date: whether to show up-to-date modules as well + Returns: the modules updated @@ -72,7 +73,7 @@ def bump_versions( self.updated = [] self.failed = [] self.ignored = [] - self.show_up_to_date = show_uptodate + self.show_up_to_date = show_up_to_date # Check modules directory structure self.check_modules_structure() @@ -123,7 +124,7 @@ def bump_versions( ) # mainly used for testing, return the list of nfcore_modules selected - if _dryrun: + if dry_run: return nfcore_modules progress_bar = Progress( @@ -177,9 +178,9 @@ def bump_module_version(self, module: NFCoreComponent) -> bool: return False # Don't update if blocked in blacklist - self.bump_versions_config = getattr(self.tools_config, "bump-versions", {}) or {} - if module.component_name in self.bump_versions_config: - config_version = self.bump_versions_config[module.component_name] + bump_versions_config: dict[str, str] = getattr(self.tools_config, "bump-versions", {}) or {} + if module.component_name in bump_versions_config: + config_version = bump_versions_config[module.component_name] if not config_version: self.ignored.append(("Omitting module due to config.", module.component_name)) return False From c08e81fea03516b1d40f0930411d51decc7115de Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 1 Jul 2025 10:33:16 +0200 Subject: [PATCH 009/101] switch logic: no need for trailing backslash --- nf_core/__main__.py | 9 ++++++++- nf_core/modules/bump_versions.py | 18 ++++++++++++------ 2 files changed, 20 insertions(+), 7 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 532125e529..09d7d9a0ed 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1322,7 +1322,14 @@ def command_modules_info(ctx, tool, directory): # nf-core modules bump-versions @modules.command("bump-versions") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + help="Module to bump versions for. If is provided and exists, all subtools will be bumped.", +) @click.option( "-d", "--dir", diff --git a/nf_core/modules/bump_versions.py b/nf_core/modules/bump_versions.py index f6ce55869a..d5ea915856 100644 --- a/nf_core/modules/bump_versions.py +++ b/nf_core/modules/bump_versions.py @@ -53,7 +53,9 @@ def bump_versions( dry_run: bool = False, ) -> list[NFCoreComponent]: """ - Bump the container and conda version of single module or all modules + Bump the container and conda version of single module or all modules. + + If module is the name of a directory in the modules directory, all modules in that directory will be bumped. Looks for a bioconda tool version in the `main.nf` file of the module and checks whether are more recent version is available. If yes, then tries to get docker/singularity @@ -64,10 +66,10 @@ def bump_versions( module: a specific module to update all_modules: whether to bump versions for all modules show_up_to_date: whether to show up-to-date modules as well - + dry_run: whether to dry run the command Returns: - the modules updated + list[NFCoreComponent]: the updated modules """ self.up_to_date = [] self.updated = [] @@ -114,10 +116,14 @@ def bump_versions( raise nf_core.modules.modules_utils.ModuleExceptionError( "You cannot specify a tool and request all tools to be bumped." ) - if module.endswith("/"): - nfcore_modules = [m for m in nfcore_modules if m.component_name.startswith(module)] + # First try to find an exact match + exact_matches = [m for m in nfcore_modules if m.component_name == module] + if exact_matches: + nfcore_modules = exact_matches else: - nfcore_modules = [m for m in nfcore_modules if m.component_name == module] + # If no exact match, look for modules that start with the given name (subtools) + nfcore_modules = [m for m in nfcore_modules if m.component_name.startswith(module + "/")] + if len(nfcore_modules) == 0: raise nf_core.modules.modules_utils.ModuleExceptionError( f"Could not find the specified module: '{module}'" From 6dccb6dd8a7f0e042ac2da7dc3bdc257ae1b9cb3 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 1 Jul 2025 10:39:19 +0200 Subject: [PATCH 010/101] fix argument syntax --- nf_core/__main__.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 09d7d9a0ed..f9e25a886b 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1327,8 +1327,7 @@ def command_modules_info(ctx, tool, directory): type=str, callback=normalize_case, required=False, - metavar=" or ", - help="Module to bump versions for. If is provided and exists, all subtools will be bumped.", + metavar=" or . Module to bump versions for. If is provided and exists, all subtools will be bumped.", ) @click.option( "-d", From 1896876d01d4ad7639df49ed8d4f0ad65ca9529e Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 1 Jul 2025 10:48:17 +0200 Subject: [PATCH 011/101] fix ruff linting --- tests/modules/test_bump_versions.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/tests/modules/test_bump_versions.py b/tests/modules/test_bump_versions.py index d0747acaf0..f3b377be33 100644 --- a/tests/modules/test_bump_versions.py +++ b/tests/modules/test_bump_versions.py @@ -2,7 +2,6 @@ import re import tempfile from pathlib import Path -from typing import List import pytest import ruamel.yaml @@ -48,8 +47,8 @@ def _mock_nf_core_yml(root_dir: Path) -> None: yaml.dump(nf_core_yml.model_dump(), fh) @staticmethod - def _mock_modules(root_dir: Path, modules: List[str]) -> None: - """Mock the directory for a given module (or sub-module) for use with `_dryrun`""" + def _mock_modules(root_dir: Path, modules: list[str]) -> None: + """Mock the directory for a given module (or sub-module) for use with `dry_run`""" nf_core_dir = root_dir / "modules" / "nf-core" for module in modules: if "/" in module: @@ -72,7 +71,7 @@ def test_modules_bump_versions_multiple_modules(self): # run it with dryrun to return the modules that it found version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) - modules = version_bumper.bump_versions(all_modules=True, _dryrun=True) + modules = version_bumper.bump_versions(all_modules=True, dry_run=True) assert sorted([m.component_name for m in modules]) == sorted(["fqgrep", "fqtk"]) def test_modules_bump_versions_submodules(self): @@ -86,7 +85,7 @@ def test_modules_bump_versions_submodules(self): # run it with dryrun to return the modules that it found version_bumper = nf_core.modules.bump_versions.ModuleVersionBumper(pipeline_dir=root_dir) - out_modules = version_bumper.bump_versions(module="fgbio/", _dryrun=True) + out_modules = version_bumper.bump_versions(module="fgbio", dry_run=True) assert sorted([m.component_name for m in out_modules]) == sorted(in_modules) def test_modules_bump_versions_fail(self): From cdda107c23578e4e2e4bb4e6e3bd0bcc1229071b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 17:18:34 -0500 Subject: [PATCH 012/101] test(#3590): Copy tests over from env sorter --- tests/modules/lint/test_environment_yml.py | 123 +++++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 tests/modules/lint/test_environment_yml.py diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py new file mode 100644 index 0000000000..d1252ceabf --- /dev/null +++ b/tests/modules/lint/test_environment_yml.py @@ -0,0 +1,123 @@ +import ruamel.yaml +from nf_core.modules.lint.environment_yml import environment_yml +from nf_core.components.lint import ComponentLint, LintExceptionError +from nf_core.components.nfcore_component import NFCoreComponent +import pytest + +yaml = ruamel.yaml.YAML() +yaml.indent(mapping=2, sequence=2, offset=2) + + +@pytest.mark.parametrize( + "input_content,expected", + [ + # Test basic sorting + ("dependencies:\n - zlib\n - python\n", ["python", "zlib"]), + # Test dict sorting + ("dependencies:\n - pip:\n - b\n - a\n - python\n", ["python", {"pip": ["a", "b"]}]), + # Test existing headers + ("---\n# yaml-language-server: $schema=...\ndependencies:\n - b\n - a\n", ["a", "b"]), + # Test channel sorting + ( + "channels:\n - conda-forge\n - bioconda\ndependencies:\n - python\n", + {"channels": ["conda-forge", "bioconda"], "dependencies": ["python"]}, + ), + # Test channel sorting with additional channels + ( + "channels:\n - bioconda\n - conda-forge\n - defaults\n - r\n", + {"channels": ["conda-forge", "bioconda", "defaults", "r"]}, + ), + # Test namespaced dependencies + ( + "dependencies:\n - bioconda::ngscheckmate=1.0.1\n - bioconda::bcftools=1.21\n", + ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1"], + ), + # Test mixed dependencies + ( + "dependencies:\n - bioconda::ngscheckmate=1.0.1\n - python\n - bioconda::bcftools=1.21\n", + ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1", "python"], + ), + # Test full environment with channels and namespaced dependencies + ( + """ + channels: + - conda-forge + - bioconda + dependencies: + - bioconda::ngscheckmate=1.0.1 + - bioconda::bcftools=1.21 + """, + { + "channels": ["conda-forge", "bioconda"], + "dependencies": ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1"], + }, + ), + ], + ids=[ + "basic_dependency_sorting", + "dict_dependency_sorting", + "existing_headers", + "channel_sorting", + "channel_sorting_with_additional_channels", + "namespaced_dependencies", + "mixed_dependencies", + "full_environment", + ], +) +def test_conda_sorter(tmp_path, input_content, expected): + test_file = tmp_path / "environment.yml" + test_file.write_text(input_content) + + # Run our sorter on the test file + main([str(test_file)]) + + # Read back the sorted file + result = test_file.read_text() + + # Check schema headers are present + assert result.startswith("---\n# yaml-language-server: $schema=") + + # Parse the sorted content (skip first 2 header lines) + parsed = yaml.load("".join(result.splitlines(True)[2:])) + + # Compare the actual dependencies structure + if isinstance(expected, list): + assert parsed["dependencies"] == expected + else: + # For comparing dictionaries, only compare the keys that are in the expected dictionary + for key, value in expected.items(): + assert key in parsed + assert parsed[key] == value + + +def test_invalid_file(tmp_path): + test_file = tmp_path / "bad.yml" + test_file.write_text("invalid: yaml: here") + + with pytest.raises(ruamel.yaml.scanner.ScannerError): + main([str(test_file)]) + + +def test_empty_file(tmp_path): + """Test handling of empty files.""" + test_file = tmp_path / "empty.yml" + test_file.write_text("") + + with pytest.raises(ruamel.yaml.scanner.ScannerError): + main([str(test_file)]) + + +def test_missing_dependencies(tmp_path): + """Test handling of files without dependencies section.""" + test_file = tmp_path / "no_deps.yml" + test_file.write_text("channels:\n - conda-forge\n") + + # Run without error now that we handle missing dependencies + main([str(test_file)]) + + # Read back and verify channel is preserved + result = test_file.read_text() + parsed = yaml.load("".join(result.splitlines(True)[2:])) + assert "channels" in parsed + assert parsed["channels"] == ["conda-forge"] + assert "dependencies" not in parsed From 54925f96104bb1cc69780674f6fa4788d8b01562 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 17:37:07 -0500 Subject: [PATCH 013/101] test(#3590): Refactor tests for environment.yml sorting and error handling - Renamed test functions for clarity. - Introduced DummyModule and DummyLint classes to simulate module and lint behavior. - Enhanced tests for handling invalid, empty, and missing dependencies in environment.yml files. - Improved assertions to validate sorting and schema compliance. --- tests/modules/lint/test_environment_yml.py | 131 +++++++++++++++------ 1 file changed, 95 insertions(+), 36 deletions(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index d1252ceabf..b3a7844acc 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -3,6 +3,7 @@ from nf_core.components.lint import ComponentLint, LintExceptionError from nf_core.components.nfcore_component import NFCoreComponent import pytest +from ruamel.yaml.scanner import ScannerError yaml = ruamel.yaml.YAML() yaml.indent(mapping=2, sequence=2, offset=2) @@ -64,60 +65,118 @@ "full_environment", ], ) -def test_conda_sorter(tmp_path, input_content, expected): +def test_environment_yml_sorting(tmp_path, input_content, expected): test_file = tmp_path / "environment.yml" test_file.write_text(input_content) - - # Run our sorter on the test file - main([str(test_file)]) - - # Read back the sorted file + class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] + class DummyLint(ComponentLint): + def __init__(self): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] + module = DummyModule(test_file) + lint = DummyLint() + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") + environment_yml(lint, module) result = test_file.read_text() - - # Check schema headers are present - assert result.startswith("---\n# yaml-language-server: $schema=") - - # Parse the sorted content (skip first 2 header lines) - parsed = yaml.load("".join(result.splitlines(True)[2:])) - - # Compare the actual dependencies structure + lines = result.splitlines(True) + if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: + parsed = yaml.load("".join(lines[2:])) + else: + parsed = yaml.load(result) if isinstance(expected, list): assert parsed["dependencies"] == expected else: - # For comparing dictionaries, only compare the keys that are in the expected dictionary for key, value in expected.items(): assert key in parsed assert parsed[key] == value + # Check linter passed for sorting + assert any("environment_yml_sorted" in x for x in [p[0] for p in lint.passed]) -def test_invalid_file(tmp_path): +def test_environment_yml_invalid_file(tmp_path): test_file = tmp_path / "bad.yml" test_file.write_text("invalid: yaml: here") - - with pytest.raises(ruamel.yaml.scanner.ScannerError): - main([str(test_file)]) - - -def test_empty_file(tmp_path): - """Test handling of empty files.""" + class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] + class DummyLint(ComponentLint): + def __init__(self): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] + module = DummyModule(test_file) + lint = DummyLint() + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") + with pytest.raises(Exception): + environment_yml(lint, module) + + +def test_environment_yml_empty_file(tmp_path): test_file = tmp_path / "empty.yml" test_file.write_text("") - - with pytest.raises(ruamel.yaml.scanner.ScannerError): - main([str(test_file)]) - - -def test_missing_dependencies(tmp_path): - """Test handling of files without dependencies section.""" + class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] + class DummyLint(ComponentLint): + def __init__(self): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] + module = DummyModule(test_file) + lint = DummyLint() + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") + with pytest.raises(Exception): + environment_yml(lint, module) + + +def test_environment_yml_missing_dependencies(tmp_path): test_file = tmp_path / "no_deps.yml" test_file.write_text("channels:\n - conda-forge\n") - - # Run without error now that we handle missing dependencies - main([str(test_file)]) - - # Read back and verify channel is preserved + class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] + class DummyLint(ComponentLint): + def __init__(self): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] + module = DummyModule(test_file) + lint = DummyLint() + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") + environment_yml(lint, module) result = test_file.read_text() - parsed = yaml.load("".join(result.splitlines(True)[2:])) + lines = result.splitlines(True) + if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: + parsed = yaml.load("".join(lines[2:])) + else: + parsed = yaml.load(result) assert "channels" in parsed assert parsed["channels"] == ["conda-forge"] assert "dependencies" not in parsed From 806f9353abaf18b240f0c50050c1c5f8bfd992f1 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 20:10:57 -0500 Subject: [PATCH 014/101] fint(#3590): Enhance environment.yml handling and sorting - Replaced yaml library with ruamel.yaml for improved YAML processing. - Added schema validation for environment.yml files. - Implemented sorting for dependencies and channels, ensuring proper order. - Updated file writing to include schema lines and sorted content. - Enhanced logging for sorting actions and validation results. --- nf_core/modules/lint/environment_yml.py | 130 ++++++++++++++++++------ 1 file changed, 98 insertions(+), 32 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 37998fcc4b..238c8e5f3b 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -2,15 +2,18 @@ import logging from pathlib import Path -import yaml +import ruamel.yaml from jsonschema import exceptions, validators from nf_core.components.lint import ComponentLint, LintExceptionError from nf_core.components.nfcore_component import NFCoreComponent -from nf_core.utils import custom_yaml_dumper log = logging.getLogger(__name__) +# Configure ruamel.yaml for proper formatting +yaml = ruamel.yaml.YAML() +yaml.indent(mapping=2, sequence=2, offset=2) + def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None: """ @@ -34,8 +37,26 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, return raise LintExceptionError("Module does not have an `environment.yml` file") try: + # Read the entire file content to handle headers properly with open(module.environment_yml) as fh: - env_yml = yaml.safe_load(fh) + lines = fh.readlines() + + # Define the schema lines to be added if missing + schema_lines = [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ] + + # Check if the first two lines match the expected schema lines + if len(lines) >= 2 and lines[:2] == schema_lines: + content = "".join(lines[2:]) # Skip schema lines when reading content + else: + content = "".join(lines) # Use all content if no schema lines present + + # Parse the YAML content + env_yml = yaml.load(content) + if env_yml is None: + raise ruamel.yaml.scanner.ScannerError("Empty YAML file") module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml)) @@ -82,41 +103,86 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, ) if valid_env_yml: - # Check that the dependencies section is sorted alphabetically - def sort_recursively(obj): - """Simple recursive sort for nested structures.""" - if isinstance(obj, list): - - def get_key(x): - if isinstance(x, dict): - # For dicts like {"pip": [...]}, use the key "pip" - return (list(x.keys())[0], 1) - else: - # For strings like "pip=23.3.1", use "pip" and for bioconda::samtools=1.15.1, use "bioconda::samtools" - return (str(x).split("=")[0], 0) - - return sorted([sort_recursively(item) for item in obj], key=get_key) - elif isinstance(obj, dict): - return {k: sort_recursively(v) for k, v in obj.items()} - else: - return obj - - sorted_dependencies = sort_recursively(env_yml["dependencies"]) - - # Direct comparison of sorted vs original dependencies - if sorted_dependencies == env_yml["dependencies"]: - module.passed.append( + # Define channel priority order + channel_order = { + "conda-forge": 0, + "bioconda": 1, + } + + # Sort dependencies if they exist + if "dependencies" in env_yml: + dicts = [] + others = [] + + for term in env_yml["dependencies"]: + if isinstance(term, dict): + dicts.append(term) + else: + others.append(term) + + # Sort non-dict dependencies (strings) alphabetically + others.sort(key=str) + + # Sort any lists within dict dependencies + for dict_term in dicts: + for value in dict_term.values(): + if isinstance(value, list): + value.sort(key=str) + + # Sort dict dependencies alphabetically + dicts.sort(key=str) + + # Combine sorted dependencies + sorted_deps = others + dicts + + # Check if dependencies are already sorted + is_sorted = env_yml["dependencies"] == sorted_deps and all( + not isinstance(term, dict) + or all(not isinstance(value, list) or value == sorted(value, key=str) for value in term.values()) + for term in env_yml["dependencies"] + ) + else: + sorted_deps = None + is_sorted = True + + # Check if channels are sorted + channels_sorted = True + if "channels" in env_yml: + sorted_channels = sorted(env_yml["channels"], key=lambda x: (channel_order.get(x, 2), str(x))) + channels_sorted = env_yml["channels"] == sorted_channels + + if is_sorted and channels_sorted: + module_lint_object.passed.append( ( "environment_yml_sorted", - "The dependencies in the module's `environment.yml` are sorted alphabetically", + "The dependencies and channels in the module's `environment.yml` are sorted correctly", module.environment_yml, ) ) else: - # sort it and write it back to the file log.info( - f"Dependencies in {module.component_name}'s environment.yml were not sorted alphabetically. Sorting them now." + f"Dependencies or channels in {module.component_name}'s environment.yml were not sorted. Sorting them now." ) - env_yml["dependencies"] = sorted_dependencies + + # Update dependencies if they need sorting + if sorted_deps is not None: + env_yml["dependencies"] = sorted_deps + + # Update channels if they need sorting + if "channels" in env_yml: + env_yml["channels"] = sorted(env_yml["channels"], key=lambda x: (channel_order.get(x, 2), str(x))) + + # Write back to file with headers with open(Path(module.component_dir, "environment.yml"), "w") as fh: - yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper()) + # Always write schema lines first + fh.writelines(schema_lines) + # Then dump the sorted YAML + yaml.dump(env_yml, fh) + + module_lint_object.passed.append( + ( + "environment_yml_sorted", + "The dependencies and channels in the module's `environment.yml` have been sorted", + module.environment_yml, + ) + ) From 945c1158ef044208e6a0db1fb4c94393b3a7ec22 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 20:17:45 -0500 Subject: [PATCH 015/101] refactor(#3590): Replace ruamel.yaml with PyYAML for environment.yml processing - Updated the YAML library from ruamel.yaml to PyYAML for improved compatibility. - Changed YAML loading to use safe_load for better security. - Enhanced YAML dumping with specific formatting options for clarity. - Adjusted error handling to reflect the new library usage. --- nf_core/modules/lint/environment_yml.py | 20 +++++++++++--------- tests/modules/lint/test_environment_yml.py | 15 ++++++--------- 2 files changed, 17 insertions(+), 18 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 238c8e5f3b..b1bbd17a52 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -2,7 +2,7 @@ import logging from pathlib import Path -import ruamel.yaml +import yaml from jsonschema import exceptions, validators from nf_core.components.lint import ComponentLint, LintExceptionError @@ -10,10 +10,6 @@ log = logging.getLogger(__name__) -# Configure ruamel.yaml for proper formatting -yaml = ruamel.yaml.YAML() -yaml.indent(mapping=2, sequence=2, offset=2) - def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None: """ @@ -54,9 +50,9 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, content = "".join(lines) # Use all content if no schema lines present # Parse the YAML content - env_yml = yaml.load(content) + env_yml = yaml.safe_load(content) if env_yml is None: - raise ruamel.yaml.scanner.ScannerError("Empty YAML file") + raise yaml.scanner.ScannerError("Empty YAML file") module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml)) @@ -176,8 +172,14 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, with open(Path(module.component_dir, "environment.yml"), "w") as fh: # Always write schema lines first fh.writelines(schema_lines) - # Then dump the sorted YAML - yaml.dump(env_yml, fh) + # Then dump the sorted YAML with proper formatting + yaml.dump( + env_yml, + fh, + default_flow_style=False, + indent=2, + sort_keys=False + ) module_lint_object.passed.append( ( diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index b3a7844acc..0137d66f54 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -1,12 +1,9 @@ -import ruamel.yaml +import yaml from nf_core.modules.lint.environment_yml import environment_yml from nf_core.components.lint import ComponentLint, LintExceptionError from nf_core.components.nfcore_component import NFCoreComponent import pytest -from ruamel.yaml.scanner import ScannerError - -yaml = ruamel.yaml.YAML() -yaml.indent(mapping=2, sequence=2, offset=2) +from yaml.scanner import ScannerError @pytest.mark.parametrize( @@ -89,9 +86,9 @@ def __init__(self): result = test_file.read_text() lines = result.splitlines(True) if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: - parsed = yaml.load("".join(lines[2:])) + parsed = yaml.safe_load("".join(lines[2:])) else: - parsed = yaml.load(result) + parsed = yaml.safe_load(result) if isinstance(expected, list): assert parsed["dependencies"] == expected else: @@ -174,9 +171,9 @@ def __init__(self): result = test_file.read_text() lines = result.splitlines(True) if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: - parsed = yaml.load("".join(lines[2:])) + parsed = yaml.safe_load("".join(lines[2:])) else: - parsed = yaml.load(result) + parsed = yaml.safe_load(result) assert "channels" in parsed assert parsed["channels"] == ["conda-forge"] assert "dependencies" not in parsed From c62ccb9ba3c3681f7e1721c7a064138eea173d3c Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 22:00:36 -0500 Subject: [PATCH 016/101] test(#3590): Move integration tests to new lint test file --- tests/modules/lint/__init__.py | 1 + tests/modules/lint/test_environment_yml.py | 112 +++++++++++++++++++++ tests/modules/test_lint.py | 102 ------------------- 3 files changed, 113 insertions(+), 102 deletions(-) create mode 100644 tests/modules/lint/__init__.py diff --git a/tests/modules/lint/__init__.py b/tests/modules/lint/__init__.py new file mode 100644 index 0000000000..0519ecba6e --- /dev/null +++ b/tests/modules/lint/__init__.py @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index 0137d66f54..d84db3d344 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -4,6 +4,10 @@ from nf_core.components.nfcore_component import NFCoreComponent import pytest from yaml.scanner import ScannerError +from pathlib import Path + +import nf_core.modules.lint +from ...test_modules import TestModules @pytest.mark.parametrize( @@ -177,3 +181,111 @@ def __init__(self): assert "channels" in parsed assert parsed["channels"] == ["conda-forge"] assert "dependencies" not in parsed + + +# Integration tests using the full ModuleLint class + +class TestModulesEnvironmentYml(TestModules): + """Integration tests for environment.yml linting using real modules""" + + def test_modules_environment_yml_file_doesnt_exists(self): + """Test linting a module with an environment.yml file""" + (self.bpipe_test_module_path / "environment.yml").rename(self.bpipe_test_module_path / "environment.yml.bak") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + (self.bpipe_test_module_path / "environment.yml.bak").rename(self.bpipe_test_module_path / "environment.yml") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_exists" + + def test_modules_environment_yml_file_sorted_correctly(self): + """Test linting a module with a correctly sorted environment.yml file""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_sorted_incorrectly(self): + """Test linting a module with an incorrectly sorted environment.yml file""" + with open(self.bpipe_test_module_path / "environment.yml") as fh: + yaml_content = yaml.safe_load(fh) + # Add a new dependency to the environment.yml file and reverse the order + yaml_content["dependencies"].append("z=0.0.0") + yaml_content["dependencies"].reverse() + yaml_content = yaml.dump(yaml_content) + with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + fh.write(yaml_content) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + # we fix the sorting on the fly, so this should pass + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_not_array(self): + """Test linting a module with an incorrectly formatted environment.yml file""" + with open(self.bpipe_test_module_path / "environment.yml") as fh: + yaml_content = yaml.safe_load(fh) + yaml_content["dependencies"] = "z" + with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + fh.write(yaml.dump(yaml_content)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_valid" + + def test_modules_environment_yml_file_mixed_dependencies(self): + """Test linting a module with mixed-type dependencies (strings and pip dict)""" + with open(self.bpipe_test_module_path / "environment.yml") as fh: + yaml_content = yaml.safe_load(fh) + + # Create mixed dependencies with strings and pip dict in wrong order + yaml_content["dependencies"] = [ + "python=3.8", + {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]}, + "bioconda::samtools=1.15.1", + "bioconda::fastqc=0.12.1", + "pip=23.3.1", + ] + + with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + fh.write(yaml.dump(yaml_content)) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Check that the dependencies were sorted correctly + with open(self.bpipe_test_module_path / "environment.yml") as fh: + sorted_yaml = yaml.safe_load(fh) + + expected_deps = [ + "bioconda::fastqc=0.12.1", + "bioconda::samtools=1.15.1", + "pip=23.3.1", + {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]}, + "python=3.8", + ] + + assert sorted_yaml["dependencies"] == expected_deps + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_environment_yml_file_default_channel_fails(self): + """Test linting a module with a default channel set in the environment.yml file, which should fail""" + with open(self.bpipe_test_module_path / "environment.yml") as fh: + yaml_content = yaml.safe_load(fh) + yaml_content["channels"] = ["bioconda", "default"] + with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + fh.write(yaml.dump(yaml_content)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_valid" diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index b586b4d57a..af393fdbfc 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -392,108 +392,6 @@ def test_modules_lint_snapshot_file_not_needed(self): assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - def test_modules_environment_yml_file_doesnt_exists(self): - """Test linting a module with an environment.yml file""" - (self.bpipe_test_module_path / "environment.yml").rename(self.bpipe_test_module_path / "environment.yml.bak") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - (self.bpipe_test_module_path / "environment.yml.bak").rename(self.bpipe_test_module_path / "environment.yml") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_exists" - - def test_modules_environment_yml_file_sorted_correctly(self): - """Test linting a module with a correctly sorted environment.yml file""" - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_environment_yml_file_sorted_incorrectly(self): - """Test linting a module with an incorrectly sorted environment.yml file""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) - # Add a new dependency to the environment.yml file and reverse the order - yaml_content["dependencies"].append("z=0.0.0") - yaml_content["dependencies"].reverse() - yaml_content = yaml.dump(yaml_content) - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml_content) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - # we fix the sorting on the fly, so this should pass - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_environment_yml_file_not_array(self): - """Test linting a module with an incorrectly formatted environment.yml file""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) - yaml_content["dependencies"] = "z" - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_valid" - - def test_modules_environment_yml_file_mixed_dependencies(self): - """Test linting a module with mixed-type dependencies (strings and pip dict)""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) - - # Create mixed dependencies with strings and pip dict in wrong order - yaml_content["dependencies"] = [ - "python=3.8", - {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]}, - "bioconda::samtools=1.15.1", - "bioconda::fastqc=0.12.1", - "pip=23.3.1", - ] - - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) - - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - # Check that the dependencies were sorted correctly - with open(self.bpipe_test_module_path / "environment.yml") as fh: - sorted_yaml = yaml.safe_load(fh) - - expected_deps = [ - "bioconda::fastqc=0.12.1", - "bioconda::samtools=1.15.1", - "pip=23.3.1", - {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]}, - "python=3.8", - ] - - assert sorted_yaml["dependencies"] == expected_deps - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_environment_yml_file_default_channel_fails(self): - """Test linting a module with a default channel set in the environment.yml file, which should fail""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) - yaml_content["channels"] = ["bioconda", "default"] - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_valid" - def test_modules_meta_yml_incorrect_licence_field(self): """Test linting a module with an incorrect Licence field in meta.yml""" with open(self.bpipe_test_module_path / "meta.yml") as fh: From feabc6836cedd23566498f0a08a98cb3770fb414 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 22:01:44 -0500 Subject: [PATCH 017/101] test(#3590): Update dependency order on a test --- tests/modules/lint/test_environment_yml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index d84db3d344..f42e4e2ea3 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -266,8 +266,8 @@ def test_modules_environment_yml_file_mixed_dependencies(self): "bioconda::fastqc=0.12.1", "bioconda::samtools=1.15.1", "pip=23.3.1", - {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]}, "python=3.8", + {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]}, ] assert sorted_yaml["dependencies"] == expected_deps From e4026f3e41dbed7524d57ac899750de5c6b90f8a Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 10:39:18 -0500 Subject: [PATCH 018/101] Revert "refactor(#3590): Replace ruamel.yaml with PyYAML for environment.yml processing" This reverts commit 34d5b006eb97880381806e683548ce88b07b0bce. Co-authored-by: mashehu --- nf_core/modules/lint/environment_yml.py | 20 +++--- tests/modules/lint/test_environment_yml.py | 72 +++++++++++++++------- 2 files changed, 60 insertions(+), 32 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index b1bbd17a52..238c8e5f3b 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -2,7 +2,7 @@ import logging from pathlib import Path -import yaml +import ruamel.yaml from jsonschema import exceptions, validators from nf_core.components.lint import ComponentLint, LintExceptionError @@ -10,6 +10,10 @@ log = logging.getLogger(__name__) +# Configure ruamel.yaml for proper formatting +yaml = ruamel.yaml.YAML() +yaml.indent(mapping=2, sequence=2, offset=2) + def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None: """ @@ -50,9 +54,9 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, content = "".join(lines) # Use all content if no schema lines present # Parse the YAML content - env_yml = yaml.safe_load(content) + env_yml = yaml.load(content) if env_yml is None: - raise yaml.scanner.ScannerError("Empty YAML file") + raise ruamel.yaml.scanner.ScannerError("Empty YAML file") module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml)) @@ -172,14 +176,8 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, with open(Path(module.component_dir, "environment.yml"), "w") as fh: # Always write schema lines first fh.writelines(schema_lines) - # Then dump the sorted YAML with proper formatting - yaml.dump( - env_yml, - fh, - default_flow_style=False, - indent=2, - sort_keys=False - ) + # Then dump the sorted YAML + yaml.dump(env_yml, fh) module_lint_object.passed.append( ( diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index f42e4e2ea3..cdec89707e 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -1,14 +1,25 @@ -import yaml -from nf_core.modules.lint.environment_yml import environment_yml -from nf_core.components.lint import ComponentLint, LintExceptionError -from nf_core.components.nfcore_component import NFCoreComponent +import io + import pytest -from yaml.scanner import ScannerError -from pathlib import Path +import ruamel.yaml import nf_core.modules.lint +from nf_core.components.lint import ComponentLint +from nf_core.components.nfcore_component import NFCoreComponent +from nf_core.modules.lint.environment_yml import environment_yml + from ...test_modules import TestModules +yaml = ruamel.yaml.YAML() +yaml.indent(mapping=2, sequence=2, offset=2) + + +def yaml_dump_to_string(data): + """Helper function to dump YAML data to string using ruamel.yaml""" + stream = io.StringIO() + yaml.dump(data, stream) + return stream.getvalue() + @pytest.mark.parametrize( "input_content,expected", @@ -69,6 +80,7 @@ def test_environment_yml_sorting(tmp_path, input_content, expected): test_file = tmp_path / "environment.yml" test_file.write_text(input_content) + class DummyModule(NFCoreComponent): def __init__(self, path): self.environment_yml = path @@ -77,11 +89,13 @@ def __init__(self, path): self.passed = [] self.failed = [] self.warned = [] + class DummyLint(ComponentLint): def __init__(self): self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) self.passed = [] self.failed = [] + module = DummyModule(test_file) lint = DummyLint() (tmp_path / "modules").mkdir(exist_ok=True) @@ -89,10 +103,13 @@ def __init__(self): environment_yml(lint, module) result = test_file.read_text() lines = result.splitlines(True) - if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: - parsed = yaml.safe_load("".join(lines[2:])) + if lines[:2] == [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ]: + parsed = yaml.load("".join(lines[2:])) else: - parsed = yaml.safe_load(result) + parsed = yaml.load(result) if isinstance(expected, list): assert parsed["dependencies"] == expected else: @@ -106,6 +123,7 @@ def __init__(self): def test_environment_yml_invalid_file(tmp_path): test_file = tmp_path / "bad.yml" test_file.write_text("invalid: yaml: here") + class DummyModule(NFCoreComponent): def __init__(self, path): self.environment_yml = path @@ -114,11 +132,13 @@ def __init__(self, path): self.passed = [] self.failed = [] self.warned = [] + class DummyLint(ComponentLint): def __init__(self): self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) self.passed = [] self.failed = [] + module = DummyModule(test_file) lint = DummyLint() (tmp_path / "modules").mkdir(exist_ok=True) @@ -130,6 +150,7 @@ def __init__(self): def test_environment_yml_empty_file(tmp_path): test_file = tmp_path / "empty.yml" test_file.write_text("") + class DummyModule(NFCoreComponent): def __init__(self, path): self.environment_yml = path @@ -138,11 +159,13 @@ def __init__(self, path): self.passed = [] self.failed = [] self.warned = [] + class DummyLint(ComponentLint): def __init__(self): self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) self.passed = [] self.failed = [] + module = DummyModule(test_file) lint = DummyLint() (tmp_path / "modules").mkdir(exist_ok=True) @@ -154,6 +177,7 @@ def __init__(self): def test_environment_yml_missing_dependencies(tmp_path): test_file = tmp_path / "no_deps.yml" test_file.write_text("channels:\n - conda-forge\n") + class DummyModule(NFCoreComponent): def __init__(self, path): self.environment_yml = path @@ -162,11 +186,13 @@ def __init__(self, path): self.passed = [] self.failed = [] self.warned = [] + class DummyLint(ComponentLint): def __init__(self): self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) self.passed = [] self.failed = [] + module = DummyModule(test_file) lint = DummyLint() (tmp_path / "modules").mkdir(exist_ok=True) @@ -174,10 +200,13 @@ def __init__(self): environment_yml(lint, module) result = test_file.read_text() lines = result.splitlines(True) - if lines[:2] == ["---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n"]: - parsed = yaml.safe_load("".join(lines[2:])) + if lines[:2] == [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ]: + parsed = yaml.load("".join(lines[2:])) else: - parsed = yaml.safe_load(result) + parsed = yaml.load(result) assert "channels" in parsed assert parsed["channels"] == ["conda-forge"] assert "dependencies" not in parsed @@ -185,6 +214,7 @@ def __init__(self): # Integration tests using the full ModuleLint class + class TestModulesEnvironmentYml(TestModules): """Integration tests for environment.yml linting using real modules""" @@ -210,11 +240,11 @@ def test_modules_environment_yml_file_sorted_correctly(self): def test_modules_environment_yml_file_sorted_incorrectly(self): """Test linting a module with an incorrectly sorted environment.yml file""" with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) + yaml_content = yaml.load(fh) # Add a new dependency to the environment.yml file and reverse the order yaml_content["dependencies"].append("z=0.0.0") yaml_content["dependencies"].reverse() - yaml_content = yaml.dump(yaml_content) + yaml_content = yaml_dump_to_string(yaml_content) with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: fh.write(yaml_content) module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) @@ -227,10 +257,10 @@ def test_modules_environment_yml_file_sorted_incorrectly(self): def test_modules_environment_yml_file_not_array(self): """Test linting a module with an incorrectly formatted environment.yml file""" with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) + yaml_content = yaml.load(fh) yaml_content["dependencies"] = "z" with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) + fh.write(yaml_dump_to_string(yaml_content)) module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" @@ -241,7 +271,7 @@ def test_modules_environment_yml_file_not_array(self): def test_modules_environment_yml_file_mixed_dependencies(self): """Test linting a module with mixed-type dependencies (strings and pip dict)""" with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) + yaml_content = yaml.load(fh) # Create mixed dependencies with strings and pip dict in wrong order yaml_content["dependencies"] = [ @@ -253,14 +283,14 @@ def test_modules_environment_yml_file_mixed_dependencies(self): ] with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) + fh.write(yaml_dump_to_string(yaml_content)) module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # Check that the dependencies were sorted correctly with open(self.bpipe_test_module_path / "environment.yml") as fh: - sorted_yaml = yaml.safe_load(fh) + sorted_yaml = yaml.load(fh) expected_deps = [ "bioconda::fastqc=0.12.1", @@ -278,10 +308,10 @@ def test_modules_environment_yml_file_mixed_dependencies(self): def test_modules_environment_yml_file_default_channel_fails(self): """Test linting a module with a default channel set in the environment.yml file, which should fail""" with open(self.bpipe_test_module_path / "environment.yml") as fh: - yaml_content = yaml.safe_load(fh) + yaml_content = yaml.load(fh) yaml_content["channels"] = ["bioconda", "default"] with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml.dump(yaml_content)) + fh.write(yaml_dump_to_string(yaml_content)) module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") From d8eff3c43cfc9afa85099dbe56517bce96d4fb24 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 11:22:22 -0500 Subject: [PATCH 019/101] fix(#3590): Having first pip and then immediately followed by pip dependencies Co-authored-by: mashehu --- nf_core/modules/lint/environment_yml.py | 13 +++++++++++-- tests/modules/lint/test_environment_yml.py | 4 ++-- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 238c8e5f3b..bce800322c 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -120,8 +120,17 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, else: others.append(term) - # Sort non-dict dependencies (strings) alphabetically - others.sort(key=str) + # Sort non-dict dependencies with special handling for pip + def sort_key(x): + # Convert to string for comparison + str_x = str(x) + # If it's a pip package (but not pip itself), put it after other conda packages + if str_x.startswith('pip=') or str_x == 'pip': + return (1, str_x) # pip comes after other conda packages + else: + return (0, str_x) # regular conda packages come first + + others.sort(key=sort_key) # Sort any lists within dict dependencies for dict_term in dicts: diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index cdec89707e..3f74a30f91 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -276,10 +276,10 @@ def test_modules_environment_yml_file_mixed_dependencies(self): # Create mixed dependencies with strings and pip dict in wrong order yaml_content["dependencies"] = [ "python=3.8", - {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]}, "bioconda::samtools=1.15.1", "bioconda::fastqc=0.12.1", "pip=23.3.1", + {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]}, ] with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: @@ -295,8 +295,8 @@ def test_modules_environment_yml_file_mixed_dependencies(self): expected_deps = [ "bioconda::fastqc=0.12.1", "bioconda::samtools=1.15.1", - "pip=23.3.1", "python=3.8", + "pip=23.3.1", {"pip": ["aaa-package==2.0.0", "zzz-package==1.0.0"]}, ] From 1d06957d839c037ec0cde0d003e2926df26484de Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 11:34:31 -0500 Subject: [PATCH 020/101] refactor(#3590): Simplify environment.yml handling by removing channel sorting - Removed channel sorting logic from environment.yml processing. - Updated related tests to reflect channel preservation instead of sorting. - Adjusted logging messages to focus solely on dependency sorting. Co-authored-by: mashehu --- nf_core/modules/lint/environment_yml.py | 24 ++++------------------ tests/modules/lint/test_environment_yml.py | 12 +++++------ 2 files changed, 10 insertions(+), 26 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index bce800322c..c7239269bb 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -103,12 +103,6 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, ) if valid_env_yml: - # Define channel priority order - channel_order = { - "conda-forge": 0, - "bioconda": 1, - } - # Sort dependencies if they exist if "dependencies" in env_yml: dicts = [] @@ -154,33 +148,23 @@ def sort_key(x): sorted_deps = None is_sorted = True - # Check if channels are sorted - channels_sorted = True - if "channels" in env_yml: - sorted_channels = sorted(env_yml["channels"], key=lambda x: (channel_order.get(x, 2), str(x))) - channels_sorted = env_yml["channels"] == sorted_channels - - if is_sorted and channels_sorted: + if is_sorted: module_lint_object.passed.append( ( "environment_yml_sorted", - "The dependencies and channels in the module's `environment.yml` are sorted correctly", + "The dependencies in the module's `environment.yml` are sorted correctly", module.environment_yml, ) ) else: log.info( - f"Dependencies or channels in {module.component_name}'s environment.yml were not sorted. Sorting them now." + f"Dependencies in {module.component_name}'s environment.yml were not sorted. Sorting them now." ) # Update dependencies if they need sorting if sorted_deps is not None: env_yml["dependencies"] = sorted_deps - # Update channels if they need sorting - if "channels" in env_yml: - env_yml["channels"] = sorted(env_yml["channels"], key=lambda x: (channel_order.get(x, 2), str(x))) - # Write back to file with headers with open(Path(module.component_dir, "environment.yml"), "w") as fh: # Always write schema lines first @@ -191,7 +175,7 @@ def sort_key(x): module_lint_object.passed.append( ( "environment_yml_sorted", - "The dependencies and channels in the module's `environment.yml` have been sorted", + "The dependencies in the module's `environment.yml` have been sorted", module.environment_yml, ) ) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index 3f74a30f91..cbf82923e6 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -30,15 +30,15 @@ def yaml_dump_to_string(data): ("dependencies:\n - pip:\n - b\n - a\n - python\n", ["python", {"pip": ["a", "b"]}]), # Test existing headers ("---\n# yaml-language-server: $schema=...\ndependencies:\n - b\n - a\n", ["a", "b"]), - # Test channel sorting + # Test channel preservation (no sorting) - channels order preserved as per nf-core/modules#8554 ( "channels:\n - conda-forge\n - bioconda\ndependencies:\n - python\n", {"channels": ["conda-forge", "bioconda"], "dependencies": ["python"]}, ), - # Test channel sorting with additional channels + # Test channel preservation with additional channels - channels order preserved as per nf-core/modules#8554 ( "channels:\n - bioconda\n - conda-forge\n - defaults\n - r\n", - {"channels": ["conda-forge", "bioconda", "defaults", "r"]}, + {"channels": ["bioconda", "conda-forge", "defaults", "r"]}, ), # Test namespaced dependencies ( @@ -50,7 +50,7 @@ def yaml_dump_to_string(data): "dependencies:\n - bioconda::ngscheckmate=1.0.1\n - python\n - bioconda::bcftools=1.21\n", ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1", "python"], ), - # Test full environment with channels and namespaced dependencies + # Test full environment with channels and namespaced dependencies - channels order preserved as per nf-core/modules#8554 ( """ channels: @@ -70,8 +70,8 @@ def yaml_dump_to_string(data): "basic_dependency_sorting", "dict_dependency_sorting", "existing_headers", - "channel_sorting", - "channel_sorting_with_additional_channels", + "channel_preservation", + "channel_preservation_with_additional_channels", "namespaced_dependencies", "mixed_dependencies", "full_environment", From 8c4839c267f9e38fa2cb1a550ba23dba9c02279b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 11:39:11 -0500 Subject: [PATCH 021/101] style: Clean up parameterized tests --- tests/modules/lint/test_environment_yml.py | 62 ++++++++++++++++++---- 1 file changed, 52 insertions(+), 10 deletions(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index cbf82923e6..d30ff75d9c 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -24,30 +24,72 @@ def yaml_dump_to_string(data): @pytest.mark.parametrize( "input_content,expected", [ - # Test basic sorting - ("dependencies:\n - zlib\n - python\n", ["python", "zlib"]), - # Test dict sorting - ("dependencies:\n - pip:\n - b\n - a\n - python\n", ["python", {"pip": ["a", "b"]}]), + # Test basic dependency sorting + ( + """ + dependencies: + - zlib + - python + """, + ["python", "zlib"], + ), + # Test dict dependency sorting + ( + """ + dependencies: + - pip: + - b + - a + - python + """, + ["python", {"pip": ["a", "b"]}], + ), # Test existing headers ("---\n# yaml-language-server: $schema=...\ndependencies:\n - b\n - a\n", ["a", "b"]), # Test channel preservation (no sorting) - channels order preserved as per nf-core/modules#8554 ( - "channels:\n - conda-forge\n - bioconda\ndependencies:\n - python\n", - {"channels": ["conda-forge", "bioconda"], "dependencies": ["python"]}, + """ + channels: + - conda-forge + - bioconda + dependencies: + - python + """, + { + "channels": ["conda-forge", "bioconda"], + "dependencies": ["python"], + }, ), # Test channel preservation with additional channels - channels order preserved as per nf-core/modules#8554 ( - "channels:\n - bioconda\n - conda-forge\n - defaults\n - r\n", - {"channels": ["bioconda", "conda-forge", "defaults", "r"]}, + """ + channels: + - bioconda + - conda-forge + - defaults + - r + """, + { + "channels": ["bioconda", "conda-forge", "defaults", "r"], + }, ), # Test namespaced dependencies ( - "dependencies:\n - bioconda::ngscheckmate=1.0.1\n - bioconda::bcftools=1.21\n", + """ + dependencies: + - bioconda::ngscheckmate=1.0.1 + - bioconda::bcftools=1.21 + """, ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1"], ), # Test mixed dependencies ( - "dependencies:\n - bioconda::ngscheckmate=1.0.1\n - python\n - bioconda::bcftools=1.21\n", + """ + dependencies: + - bioconda::ngscheckmate=1.0.1 + - python + - bioconda::bcftools=1.21 + """, ["bioconda::bcftools=1.21", "bioconda::ngscheckmate=1.0.1", "python"], ), # Test full environment with channels and namespaced dependencies - channels order preserved as per nf-core/modules#8554 From b6803c319d0d89f4c8a87b77fda8461ae600fc72 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 12:56:54 -0500 Subject: [PATCH 022/101] test(#3590): Refactor environment.yml tests with factory fixtures - Introduced factory fixtures for creating DummyModule and DummyLint instances to streamline test setup. - Updated tests to utilize the new setup_lint_environment fixture for improved clarity and maintainability. - Enhanced assertions for YAML parsing results in the environment.yml sorting tests. - Added parameterized tests for handling invalid and empty YAML files. --- tests/modules/lint/test_environment_yml.py | 296 ++++++++++----------- 1 file changed, 147 insertions(+), 149 deletions(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index d30ff75d9c..731479dbb0 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -21,6 +21,76 @@ def yaml_dump_to_string(data): return stream.getvalue() +@pytest.fixture +def dummy_module_factory(): + """Factory fixture for creating DummyModule instances""" + def _create_dummy_module(path): + class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] + return DummyModule(path) + return _create_dummy_module + + +@pytest.fixture +def dummy_lint_factory(): + """Factory fixture for creating DummyLint instances""" + def _create_dummy_lint(tmp_path): + class DummyLint(ComponentLint): + def __init__(self): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] + return DummyLint() + return _create_dummy_lint + + +@pytest.fixture +def setup_lint_environment(tmp_path, dummy_module_factory, dummy_lint_factory): + """Setup function that creates the necessary directory structure and dummy objects for linting""" + def _setup(test_file_content, filename="environment.yml"): + test_file = tmp_path / filename + test_file.write_text(test_file_content) + + # Create required directory structure + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") + + module = dummy_module_factory(test_file) + lint = dummy_lint_factory(tmp_path) + + return test_file, module, lint + return _setup + + +def assert_yaml_result(test_file, expected, check_sorting=True): + """Helper function to assert YAML parsing results""" + result = test_file.read_text() + lines = result.splitlines(True) + + # Handle YAML with schema headers + if lines[:2] == [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ]: + parsed = yaml.load("".join(lines[2:])) + else: + parsed = yaml.load(result) + + # Assert expected content + if isinstance(expected, list): + assert parsed["dependencies"] == expected + else: + for key, value in expected.items(): + assert key in parsed + assert parsed[key] == value + + @pytest.mark.parametrize( "input_content,expected", [ @@ -110,7 +180,7 @@ def yaml_dump_to_string(data): ], ids=[ "basic_dependency_sorting", - "dict_dependency_sorting", + "dict_dependency_sorting", "existing_headers", "channel_preservation", "channel_preservation_with_additional_channels", @@ -119,157 +189,66 @@ def yaml_dump_to_string(data): "full_environment", ], ) -def test_environment_yml_sorting(tmp_path, input_content, expected): - test_file = tmp_path / "environment.yml" - test_file.write_text(input_content) - - class DummyModule(NFCoreComponent): - def __init__(self, path): - self.environment_yml = path - self.component_dir = path.parent - self.component_name = "dummy" - self.passed = [] - self.failed = [] - self.warned = [] - - class DummyLint(ComponentLint): - def __init__(self): - self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) - self.passed = [] - self.failed = [] - - module = DummyModule(test_file) - lint = DummyLint() - (tmp_path / "modules").mkdir(exist_ok=True) - (tmp_path / "modules" / "environment-schema.json").write_text("{}") +def test_environment_yml_sorting(setup_lint_environment, input_content, expected): + """Test that environment.yml files are sorted correctly""" + test_file, module, lint = setup_lint_environment(input_content) + environment_yml(lint, module) - result = test_file.read_text() - lines = result.splitlines(True) - if lines[:2] == [ - "---\n", - "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", - ]: - parsed = yaml.load("".join(lines[2:])) - else: - parsed = yaml.load(result) - if isinstance(expected, list): - assert parsed["dependencies"] == expected - else: - for key, value in expected.items(): - assert key in parsed - assert parsed[key] == value + + assert_yaml_result(test_file, expected) # Check linter passed for sorting assert any("environment_yml_sorted" in x for x in [p[0] for p in lint.passed]) -def test_environment_yml_invalid_file(tmp_path): - test_file = tmp_path / "bad.yml" - test_file.write_text("invalid: yaml: here") - - class DummyModule(NFCoreComponent): - def __init__(self, path): - self.environment_yml = path - self.component_dir = path.parent - self.component_name = "dummy" - self.passed = [] - self.failed = [] - self.warned = [] - - class DummyLint(ComponentLint): - def __init__(self): - self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) - self.passed = [] - self.failed = [] - - module = DummyModule(test_file) - lint = DummyLint() - (tmp_path / "modules").mkdir(exist_ok=True) - (tmp_path / "modules" / "environment-schema.json").write_text("{}") - with pytest.raises(Exception): - environment_yml(lint, module) - - -def test_environment_yml_empty_file(tmp_path): - test_file = tmp_path / "empty.yml" - test_file.write_text("") - - class DummyModule(NFCoreComponent): - def __init__(self, path): - self.environment_yml = path - self.component_dir = path.parent - self.component_name = "dummy" - self.passed = [] - self.failed = [] - self.warned = [] - - class DummyLint(ComponentLint): - def __init__(self): - self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) - self.passed = [] - self.failed = [] - - module = DummyModule(test_file) - lint = DummyLint() - (tmp_path / "modules").mkdir(exist_ok=True) - (tmp_path / "modules" / "environment-schema.json").write_text("{}") +@pytest.mark.parametrize( + "invalid_content,filename", + [ + ("invalid: yaml: here", "bad.yml"), + ("", "empty.yml"), + ], + ids=["invalid_yaml", "empty_file"] +) +def test_environment_yml_invalid_files(setup_lint_environment, invalid_content, filename): + """Test that invalid YAML files raise exceptions""" + test_file, module, lint = setup_lint_environment(invalid_content, filename) + with pytest.raises(Exception): environment_yml(lint, module) -def test_environment_yml_missing_dependencies(tmp_path): - test_file = tmp_path / "no_deps.yml" - test_file.write_text("channels:\n - conda-forge\n") - - class DummyModule(NFCoreComponent): - def __init__(self, path): - self.environment_yml = path - self.component_dir = path.parent - self.component_name = "dummy" - self.passed = [] - self.failed = [] - self.warned = [] - - class DummyLint(ComponentLint): - def __init__(self): - self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) - self.passed = [] - self.failed = [] - - module = DummyModule(test_file) - lint = DummyLint() - (tmp_path / "modules").mkdir(exist_ok=True) - (tmp_path / "modules" / "environment-schema.json").write_text("{}") +def test_environment_yml_missing_dependencies(setup_lint_environment): + """Test handling of environment.yml without dependencies section""" + content = "channels:\n - conda-forge\n" + test_file, module, lint = setup_lint_environment(content) + environment_yml(lint, module) - result = test_file.read_text() - lines = result.splitlines(True) - if lines[:2] == [ - "---\n", - "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", - ]: - parsed = yaml.load("".join(lines[2:])) - else: - parsed = yaml.load(result) - assert "channels" in parsed - assert parsed["channels"] == ["conda-forge"] - assert "dependencies" not in parsed + + expected = {"channels": ["conda-forge"]} + assert_yaml_result(test_file, expected, check_sorting=False) # Integration tests using the full ModuleLint class - - -class TestModulesEnvironmentYml(TestModules): +@pytest.mark.integration +class TestModulesEnvironmentYmlIntegration(TestModules): """Integration tests for environment.yml linting using real modules""" def test_modules_environment_yml_file_doesnt_exists(self): """Test linting a module with an environment.yml file""" - (self.bpipe_test_module_path / "environment.yml").rename(self.bpipe_test_module_path / "environment.yml.bak") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - (self.bpipe_test_module_path / "environment.yml.bak").rename(self.bpipe_test_module_path / "environment.yml") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "environment_yml_exists" + # Use context manager for file manipulation + backup_path = self.bpipe_test_module_path / "environment.yml.bak" + env_path = self.bpipe_test_module_path / "environment.yml" + + env_path.rename(backup_path) + try: + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "environment_yml_exists" + finally: + backup_path.rename(env_path) def test_modules_environment_yml_file_sorted_correctly(self): """Test linting a module with a correctly sorted environment.yml file""" @@ -281,30 +260,42 @@ def test_modules_environment_yml_file_sorted_correctly(self): def test_modules_environment_yml_file_sorted_incorrectly(self): """Test linting a module with an incorrectly sorted environment.yml file""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: + env_path = self.bpipe_test_module_path / "environment.yml" + + # Read, modify, and write back + with open(env_path) as fh: yaml_content = yaml.load(fh) + # Add a new dependency to the environment.yml file and reverse the order yaml_content["dependencies"].append("z=0.0.0") yaml_content["dependencies"].reverse() - yaml_content = yaml_dump_to_string(yaml_content) - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: - fh.write(yaml_content) + + with open(env_path, "w") as fh: + fh.write(yaml_dump_to_string(yaml_content)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") + # we fix the sorting on the fly, so this should pass assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - def test_modules_environment_yml_file_not_array(self): - """Test linting a module with an incorrectly formatted environment.yml file""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: + def test_modules_environment_yml_file_dependencies_not_array(self): + """Test linting a module with dependencies not as an array""" + env_path = self.bpipe_test_module_path / "environment.yml" + + with open(env_path) as fh: yaml_content = yaml.load(fh) + yaml_content["dependencies"] = "z" - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -312,7 +303,9 @@ def test_modules_environment_yml_file_not_array(self): def test_modules_environment_yml_file_mixed_dependencies(self): """Test linting a module with mixed-type dependencies (strings and pip dict)""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: + env_path = self.bpipe_test_module_path / "environment.yml" + + with open(env_path) as fh: yaml_content = yaml.load(fh) # Create mixed dependencies with strings and pip dict in wrong order @@ -324,14 +317,14 @@ def test_modules_environment_yml_file_mixed_dependencies(self): {"pip": ["zzz-package==1.0.0", "aaa-package==2.0.0"]}, ] - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") # Check that the dependencies were sorted correctly - with open(self.bpipe_test_module_path / "environment.yml") as fh: + with open(env_path) as fh: sorted_yaml = yaml.load(fh) expected_deps = [ @@ -348,12 +341,17 @@ def test_modules_environment_yml_file_mixed_dependencies(self): assert len(module_lint.warned) >= 0 def test_modules_environment_yml_file_default_channel_fails(self): - """Test linting a module with a default channel set in the environment.yml file, which should fail""" - with open(self.bpipe_test_module_path / "environment.yml") as fh: + """Test linting a module with invalid default channel in the environment.yml file""" + env_path = self.bpipe_test_module_path / "environment.yml" + + with open(env_path) as fh: yaml_content = yaml.load(fh) + yaml_content["channels"] = ["bioconda", "default"] - with open(self.bpipe_test_module_path / "environment.yml", "w") as fh: + + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") From c758dafeb6868dc9780f12a440be6d4c390077c2 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 13:10:05 -0500 Subject: [PATCH 023/101] style: Fix code linting --- nf_core/modules/lint/environment_yml.py | 10 ++-- tests/modules/lint/__init__.py | 1 - tests/modules/lint/test_environment_yml.py | 68 ++++++++++++---------- 3 files changed, 44 insertions(+), 35 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index c7239269bb..6f165ee10b 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -5,7 +5,7 @@ import ruamel.yaml from jsonschema import exceptions, validators -from nf_core.components.lint import ComponentLint, LintExceptionError +from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult from nf_core.components.nfcore_component import NFCoreComponent log = logging.getLogger(__name__) @@ -119,7 +119,7 @@ def sort_key(x): # Convert to string for comparison str_x = str(x) # If it's a pip package (but not pip itself), put it after other conda packages - if str_x.startswith('pip=') or str_x == 'pip': + if str_x.startswith("pip=") or str_x == "pip": return (1, str_x) # pip comes after other conda packages else: return (0, str_x) # regular conda packages come first @@ -150,7 +150,8 @@ def sort_key(x): if is_sorted: module_lint_object.passed.append( - ( + LintResult( + module, "environment_yml_sorted", "The dependencies in the module's `environment.yml` are sorted correctly", module.environment_yml, @@ -173,7 +174,8 @@ def sort_key(x): yaml.dump(env_yml, fh) module_lint_object.passed.append( - ( + LintResult( + module, "environment_yml_sorted", "The dependencies in the module's `environment.yml` have been sorted", module.environment_yml, diff --git a/tests/modules/lint/__init__.py b/tests/modules/lint/__init__.py index 0519ecba6e..e69de29bb2 100644 --- a/tests/modules/lint/__init__.py +++ b/tests/modules/lint/__init__.py @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index 731479dbb0..aa35da8c34 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -24,6 +24,7 @@ def yaml_dump_to_string(data): @pytest.fixture def dummy_module_factory(): """Factory fixture for creating DummyModule instances""" + def _create_dummy_module(path): class DummyModule(NFCoreComponent): def __init__(self, path): @@ -33,38 +34,45 @@ def __init__(self, path): self.passed = [] self.failed = [] self.warned = [] + return DummyModule(path) + return _create_dummy_module -@pytest.fixture +@pytest.fixture def dummy_lint_factory(): """Factory fixture for creating DummyLint instances""" + def _create_dummy_lint(tmp_path): class DummyLint(ComponentLint): def __init__(self): self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) self.passed = [] self.failed = [] + return DummyLint() + return _create_dummy_lint @pytest.fixture def setup_lint_environment(tmp_path, dummy_module_factory, dummy_lint_factory): """Setup function that creates the necessary directory structure and dummy objects for linting""" + def _setup(test_file_content, filename="environment.yml"): test_file = tmp_path / filename test_file.write_text(test_file_content) - + # Create required directory structure (tmp_path / "modules").mkdir(exist_ok=True) (tmp_path / "modules" / "environment-schema.json").write_text("{}") - + module = dummy_module_factory(test_file) lint = dummy_lint_factory(tmp_path) - + return test_file, module, lint + return _setup @@ -72,7 +80,7 @@ def assert_yaml_result(test_file, expected, check_sorting=True): """Helper function to assert YAML parsing results""" result = test_file.read_text() lines = result.splitlines(True) - + # Handle YAML with schema headers if lines[:2] == [ "---\n", @@ -81,7 +89,7 @@ def assert_yaml_result(test_file, expected, check_sorting=True): parsed = yaml.load("".join(lines[2:])) else: parsed = yaml.load(result) - + # Assert expected content if isinstance(expected, list): assert parsed["dependencies"] == expected @@ -180,7 +188,7 @@ def assert_yaml_result(test_file, expected, check_sorting=True): ], ids=[ "basic_dependency_sorting", - "dict_dependency_sorting", + "dict_dependency_sorting", "existing_headers", "channel_preservation", "channel_preservation_with_additional_channels", @@ -192,9 +200,9 @@ def assert_yaml_result(test_file, expected, check_sorting=True): def test_environment_yml_sorting(setup_lint_environment, input_content, expected): """Test that environment.yml files are sorted correctly""" test_file, module, lint = setup_lint_environment(input_content) - + environment_yml(lint, module) - + assert_yaml_result(test_file, expected) # Check linter passed for sorting assert any("environment_yml_sorted" in x for x in [p[0] for p in lint.passed]) @@ -206,12 +214,12 @@ def test_environment_yml_sorting(setup_lint_environment, input_content, expected ("invalid: yaml: here", "bad.yml"), ("", "empty.yml"), ], - ids=["invalid_yaml", "empty_file"] + ids=["invalid_yaml", "empty_file"], ) def test_environment_yml_invalid_files(setup_lint_environment, invalid_content, filename): """Test that invalid YAML files raise exceptions""" test_file, module, lint = setup_lint_environment(invalid_content, filename) - + with pytest.raises(Exception): environment_yml(lint, module) @@ -220,9 +228,9 @@ def test_environment_yml_missing_dependencies(setup_lint_environment): """Test handling of environment.yml without dependencies section""" content = "channels:\n - conda-forge\n" test_file, module, lint = setup_lint_environment(content) - + environment_yml(lint, module) - + expected = {"channels": ["conda-forge"]} assert_yaml_result(test_file, expected, check_sorting=False) @@ -237,12 +245,12 @@ def test_modules_environment_yml_file_doesnt_exists(self): # Use context manager for file manipulation backup_path = self.bpipe_test_module_path / "environment.yml.bak" env_path = self.bpipe_test_module_path / "environment.yml" - + env_path.rename(backup_path) try: module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -261,21 +269,21 @@ def test_modules_environment_yml_file_sorted_correctly(self): def test_modules_environment_yml_file_sorted_incorrectly(self): """Test linting a module with an incorrectly sorted environment.yml file""" env_path = self.bpipe_test_module_path / "environment.yml" - + # Read, modify, and write back with open(env_path) as fh: yaml_content = yaml.load(fh) - + # Add a new dependency to the environment.yml file and reverse the order yaml_content["dependencies"].append("z=0.0.0") yaml_content["dependencies"].reverse() - + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) - + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - + # we fix the sorting on the fly, so this should pass assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 @@ -284,18 +292,18 @@ def test_modules_environment_yml_file_sorted_incorrectly(self): def test_modules_environment_yml_file_dependencies_not_array(self): """Test linting a module with dependencies not as an array""" env_path = self.bpipe_test_module_path / "environment.yml" - + with open(env_path) as fh: yaml_content = yaml.load(fh) - + yaml_content["dependencies"] = "z" - + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) - + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -304,7 +312,7 @@ def test_modules_environment_yml_file_dependencies_not_array(self): def test_modules_environment_yml_file_mixed_dependencies(self): """Test linting a module with mixed-type dependencies (strings and pip dict)""" env_path = self.bpipe_test_module_path / "environment.yml" - + with open(env_path) as fh: yaml_content = yaml.load(fh) @@ -343,15 +351,15 @@ def test_modules_environment_yml_file_mixed_dependencies(self): def test_modules_environment_yml_file_default_channel_fails(self): """Test linting a module with invalid default channel in the environment.yml file""" env_path = self.bpipe_test_module_path / "environment.yml" - + with open(env_path) as fh: yaml_content = yaml.load(fh) - + yaml_content["channels"] = ["bioconda", "default"] - + with open(env_path, "w") as fh: fh.write(yaml_dump_to_string(yaml_content)) - + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") From c901b4c42045d97afc36536a7cfc33a8597191e5 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 3 Jun 2025 09:13:50 -0500 Subject: [PATCH 024/101] chore: Add integration marker to pytest configuration - Updated pytest.ini_options in pyproject.toml to include a new "integration" marker for better test categorization. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d66797163d..42da317707 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ build-backend = "setuptools.build_meta" requires = ["setuptools>=40.6.0", "wheel"] [tool.pytest.ini_options] -markers = ["datafiles: load datafiles"] +markers = ["datafiles: load datafiles", "integration"] testpaths = ["tests"] python_files = ["test_*.py"] asyncio_mode = "auto" From 4b8226da61f9e8f73dbf4115b72a047945c8a122 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 3 Jun 2025 09:22:14 -0500 Subject: [PATCH 025/101] fix(test): Update assertion in environment.yml sorting test to use lint_test attribute - Changed the assertion to check for the "environment_yml_sorted" in the lint.passed list using the lint_test attribute instead of the previous tuple structure. --- tests/modules/lint/test_environment_yml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index aa35da8c34..a0f2354ea0 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -205,7 +205,7 @@ def test_environment_yml_sorting(setup_lint_environment, input_content, expected assert_yaml_result(test_file, expected) # Check linter passed for sorting - assert any("environment_yml_sorted" in x for x in [p[0] for p in lint.passed]) + assert any("environment_yml_sorted" in x for x in [p.lint_test for p in lint.passed]) @pytest.mark.parametrize( From ede037ba424bf2fd20e60df0e157e52b87145c17 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 1 Jul 2025 09:15:37 -0500 Subject: [PATCH 026/101] fix(modules): Check if they are not the exact same lines but it is a link to another json file --- nf_core/modules/lint/environment_yml.py | 40 +++++++++++++++++-------- 1 file changed, 28 insertions(+), 12 deletions(-) diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py index 6f165ee10b..b0ee636426 100644 --- a/nf_core/modules/lint/environment_yml.py +++ b/nf_core/modules/lint/environment_yml.py @@ -24,6 +24,15 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, is sorted alphabetically. """ env_yml = None + has_schema_header = False + lines = [] + + # Define the schema lines to be added if missing + schema_lines = [ + "---\n", + "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", + ] + # load the environment.yml file if module.environment_yml is None: if allow_missing: @@ -41,17 +50,14 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, with open(module.environment_yml) as fh: lines = fh.readlines() - # Define the schema lines to be added if missing - schema_lines = [ - "---\n", - "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", - ] + # Check if the first two lines contain schema configuration + content_start = 0 - # Check if the first two lines match the expected schema lines - if len(lines) >= 2 and lines[:2] == schema_lines: - content = "".join(lines[2:]) # Skip schema lines when reading content - else: - content = "".join(lines) # Use all content if no schema lines present + if len(lines) >= 2 and lines[0] == "---\n" and lines[1].startswith("# yaml-language-server: $schema="): + has_schema_header = True + content_start = 2 + + content = "".join(lines[content_start:]) # Skip schema lines when reading content # Parse the YAML content env_yml = yaml.load(content) @@ -168,8 +174,18 @@ def sort_key(x): # Write back to file with headers with open(Path(module.component_dir, "environment.yml"), "w") as fh: - # Always write schema lines first - fh.writelines(schema_lines) + # If file had a schema header, check if it's pointing to a different URL + if has_schema_header and len(lines) >= 2: + existing_schema_line = lines[1] + # If the existing schema URL is different, update it + if not existing_schema_line.endswith("/modules/master/modules/environment-schema.json\n"): + fh.writelines(schema_lines) + else: + # Keep the existing schema lines + fh.writelines(lines[:2]) + else: + # No schema header present, add the default one + fh.writelines(schema_lines) # Then dump the sorted YAML yaml.dump(env_yml, fh) From 2f3d2365a580d38903e3158b466dafc9ab088850 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 7 Jul 2025 22:20:57 +0200 Subject: [PATCH 027/101] Add module install autocompletion --- nf_core/__main__.py | 7 ++++++- nf_core/modules/_completion.py | 37 ++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+), 1 deletion(-) create mode 100644 nf_core/modules/_completion.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index d1dcc77260..3f69e6bc7f 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -62,6 +62,7 @@ from nf_core.components.constants import NF_CORE_MODULES_REMOTE from nf_core.pipelines.download import DownloadError from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir +from nf_core.modules._completion import autocomplete_modules # Set up logging as the root logger # Submodules should all traverse back to this @@ -944,7 +945,11 @@ def command_modules_list_local(ctx, keywords, json, directory): # pylint: disab # nf-core modules install @modules.command("install") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", diff --git a/nf_core/modules/_completion.py b/nf_core/modules/_completion.py new file mode 100644 index 0000000000..0439f4bfe3 --- /dev/null +++ b/nf_core/modules/_completion.py @@ -0,0 +1,37 @@ +import rich_click as click +import sys + + +def autocomplete_modules(ctx, param, incomplete: str): + # Provide fallback/defaults if ctx.obj is not available + modules_repo_url = "https://github.com/nf-core/modules" + modules_repo_branch = "master" + modules_repo_no_pull = False + + try: + if ctx.obj is not None: + modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url) + modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) + modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) + + from nf_core.modules.list import ModuleList + module_list = ModuleList( + ".", + True, + modules_repo_url, + modules_repo_branch, + modules_repo_no_pull, + ) + + available_modules = module_list.modules_repo.get_avail_components("modules") + + matches = [ + click.shell_completion.CompletionItem(mod) + for mod in available_modules + if mod.startswith(incomplete) + ] + + return matches + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] From e906671cdb744d113c91f83e4aef6424c030bd2b Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Mon, 7 Jul 2025 22:25:04 +0200 Subject: [PATCH 028/101] Add completion for all modules subcommand --- nf_core/__main__.py | 42 +++++++++++++++++++++++++++++++++++------- 1 file changed, 35 insertions(+), 7 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 3f69e6bc7f..790f774521 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -983,7 +983,11 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha): # nf-core modules update @modules.command("update") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", @@ -1060,7 +1064,11 @@ def command_modules_update( # nf-core modules patch @modules.command("patch") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", @@ -1080,7 +1088,11 @@ def command_modules_patch(ctx, tool, directory, remove): # nf-core modules remove @modules.command("remove") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", @@ -1199,7 +1211,11 @@ def command_modules_create( # nf-core modules test @modules.command("test") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-v", "--verbose", @@ -1254,7 +1270,11 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile # nf-core modules lint @modules.command("lint") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", @@ -1308,7 +1328,11 @@ def command_modules_lint( # nf-core modules info @modules.command("info") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", @@ -1327,7 +1351,11 @@ def command_modules_info(ctx, tool, directory): # nf-core modules bump-versions @modules.command("bump-versions") @click.pass_context -@click.argument("tool", type=str, callback=normalize_case, required=False, metavar=" or ") +@click.argument( + "tool", type=str, callback=normalize_case, + required=False, metavar=" or ", + shell_complete=autocomplete_modules +) @click.option( "-d", "--dir", From ebafbfeb57b71c0bf45d8db9d768ab1471bb4753 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 10:12:44 +0200 Subject: [PATCH 029/101] Add completion and test --- nf_core/__main__.py | 81 ++++++++++++++++++++++----- nf_core/modules/_completion.py | 7 ++- nf_core/pipelines/_completion.py | 33 +++++++++++ nf_core/subworkflows/_completion.py | 39 +++++++++++++ tests/modules/test_completion.py | 37 ++++++++++++ tests/pipelines/test_completion.py | 37 ++++++++++++ tests/subworkflows/test_completion.py | 37 ++++++++++++ 7 files changed, 254 insertions(+), 17 deletions(-) create mode 100644 nf_core/pipelines/_completion.py create mode 100644 nf_core/subworkflows/_completion.py create mode 100644 tests/modules/test_completion.py create mode 100644 tests/pipelines/test_completion.py create mode 100644 tests/subworkflows/test_completion.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 790f774521..876d1ff4f6 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -63,6 +63,8 @@ from nf_core.pipelines.download import DownloadError from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir from nf_core.modules._completion import autocomplete_modules +from nf_core.subworkflows._completion import autocomplete_subworkflows +from nf_core.pipelines._completion import autocomplete_pipelines # Set up logging as the root logger # Submodules should all traverse back to this @@ -355,7 +357,11 @@ def command_pipelines_lint( # nf-core pipelines download @pipelines.command("download") -@click.argument("pipeline", required=False, metavar="") +@click.argument( + "pipeline", + required=False, metavar="", + shell_complete=autocomplete_pipelines, +) @click.option( "-r", "--revision", @@ -462,7 +468,11 @@ def command_pipelines_download( # nf-core pipelines create-params-file @pipelines.command("create-params-file") -@click.argument("pipeline", required=False, metavar="") +@click.argument( + "pipeline", + required=False, metavar="", + shell_complete=autocomplete_pipelines, +) @click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") @click.option( "-o", @@ -490,7 +500,11 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force, # nf-core pipelines launch @pipelines.command("launch") -@click.argument("pipeline", required=False, metavar="") +@click.argument( + "pipeline", + required=False, metavar="", + shell_complete=autocomplete_pipelines, +) @click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") @click.option("-i", "--id", help="ID for web-gui launch parameter set") @click.option( @@ -746,7 +760,11 @@ def pipeline_schema(): default=".", help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) -@click.argument("pipeline", required=True, metavar="") +@click.argument( + "pipeline", + required=False, metavar="", + shell_complete=autocomplete_pipelines, +) @click.argument("params", type=click.Path(exists=True), required=True, metavar="") def command_pipelines_schema_validate(directory, pipeline, params): """ @@ -1447,7 +1465,12 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr # nf-core subworkflows test @subworkflows.command("test") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1535,7 +1558,12 @@ def command_subworkflows_list_local(ctx, keywords, json, directory): # pylint: # nf-core subworkflows lint @subworkflows.command("lint") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1584,7 +1612,12 @@ def command_subworkflows_lint( # nf-core subworkflows info @subworkflows.command("info") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1603,7 +1636,12 @@ def command_subworkflows_info(ctx, subworkflow, directory): # nf-core subworkflows install @subworkflows.command("install") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1643,7 +1681,12 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha # nf-core subworkflows patch @subworkflows.command("patch") @click.pass_context -@click.argument("tool", type=str, required=False, metavar=" or ") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1652,7 +1695,7 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha help=r"Pipeline directory. [dim]\[default: current working directory][/]", ) @click.option("-r", "--remove", is_flag=True, default=False, help="Remove an existent patch file and regenerate it.") -def subworkflows_patch(ctx, tool, dir, remove): +def subworkflows_patch(ctx, subworkflow, dir, remove): """ Create a patch file for minor changes in a subworkflow @@ -1669,9 +1712,9 @@ def subworkflows_patch(ctx, tool, dir, remove): ctx.obj["modules_repo_no_pull"], ) if remove: - subworkflow_patch.remove(tool) + subworkflow_patch.remove(subworkflow) else: - subworkflow_patch.patch(tool) + subworkflow_patch.patch(subworkflow) except (UserWarning, LookupError) as e: log.error(e) sys.exit(1) @@ -1680,7 +1723,12 @@ def subworkflows_patch(ctx, tool, dir, remove): # nf-core subworkflows remove @subworkflows.command("remove") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", @@ -1699,7 +1747,12 @@ def command_subworkflows_remove(ctx, directory, subworkflow): # nf-core subworkflows update @subworkflows.command("update") @click.pass_context -@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name") +@click.argument( + "subworkflow", + type=str, callback=normalize_case, + required=False, metavar="subworkflow name", + shell_complete=autocomplete_subworkflows +) @click.option( "-d", "--dir", diff --git a/nf_core/modules/_completion.py b/nf_core/modules/_completion.py index 0439f4bfe3..92a76dc89b 100644 --- a/nf_core/modules/_completion.py +++ b/nf_core/modules/_completion.py @@ -1,6 +1,8 @@ -import rich_click as click +from click.shell_completion import CompletionItem import sys +from nf_core.modules.list import ModuleList + def autocomplete_modules(ctx, param, incomplete: str): # Provide fallback/defaults if ctx.obj is not available @@ -14,7 +16,6 @@ def autocomplete_modules(ctx, param, incomplete: str): modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) - from nf_core.modules.list import ModuleList module_list = ModuleList( ".", True, @@ -26,7 +27,7 @@ def autocomplete_modules(ctx, param, incomplete: str): available_modules = module_list.modules_repo.get_avail_components("modules") matches = [ - click.shell_completion.CompletionItem(mod) + CompletionItem(mod) for mod in available_modules if mod.startswith(incomplete) ] diff --git a/nf_core/pipelines/_completion.py b/nf_core/pipelines/_completion.py new file mode 100644 index 0000000000..79a97857f8 --- /dev/null +++ b/nf_core/pipelines/_completion.py @@ -0,0 +1,33 @@ +from unittest.mock import MagicMock, patch + +from nf_core.pipelines._completion import autocomplete_pipelines + + +class DummyParam: + pass + +class DummyCtx: + def __init__(self, obj=None): + self.obj = obj + +@patch("nf_core.pipelines._completion.Workflows") +def test_autocomplete_pipelines_mocked(mock_workflows_class): + # Mock instance + mock_instance = mock_workflows_class.return_value + + # Mock local and remote workflows + mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] + mock_instance.remote_workflows = [MagicMock(name="awesome-remote"), MagicMock(name="other-remote")] + + ctx = DummyCtx() + param = DummyParam() + + completions = autocomplete_pipelines(ctx, param, "awesome") + + # Extract values from CompletionItem + values = [c.value for c in completions] + + # Assertions + assert "awesome/localpipeline" in values + assert "awesome-remote" in values + assert "other-remote" not in values \ No newline at end of file diff --git a/nf_core/subworkflows/_completion.py b/nf_core/subworkflows/_completion.py new file mode 100644 index 0000000000..02c004d724 --- /dev/null +++ b/nf_core/subworkflows/_completion.py @@ -0,0 +1,39 @@ +import sys + +from click.shell_completion import CompletionItem + +from nf_core.subworkflows.list import SubworkflowList + + +def autocomplete_subworkflows(ctx, param, incomplete: str): + # Provide fallback/defaults if ctx.obj is not available + modules_repo_url = "https://github.com/nf-core/modules" + modules_repo_branch = "master" + modules_repo_no_pull = False + + try: + if ctx.obj is not None: + modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url) + modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) + modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) + + subworkflow_list = SubworkflowList( + ".", + True, + modules_repo_url, + modules_repo_branch, + modules_repo_no_pull, + ) + + available_subworkflows = subworkflow_list.modules_repo.get_avail_components("subworkflows") + + matches = [ + CompletionItem(sub) + for sub in available_subworkflows + if sub.startswith(incomplete) + ] + + return matches + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] diff --git a/tests/modules/test_completion.py b/tests/modules/test_completion.py new file mode 100644 index 0000000000..551f08c595 --- /dev/null +++ b/tests/modules/test_completion.py @@ -0,0 +1,37 @@ +from unittest.mock import MagicMock, patch + +from nf_core.modules._completion import autocomplete_modules + + +class DummyParam: + # Minimal mock object for Click parameter (not used in the function) + pass + +class DummyCtx: + def __init__(self, obj=None): + self.obj = obj + +@patch("nf_core.modules._completion.CompletionItem") +@patch("nf_core.modules._completion.ModuleList") +def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): + # Setup mock for module list + mock_instance = mock_module_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "fastqc", "bcftools/call", "bcftools/index" + ] + + # Setup mock for CompletionItem + def mock_completion(value): + mock_item = MagicMock() + mock_item.value = value + return mock_item + + mock_completion_item_class.side_effect = mock_completion + + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_modules(ctx, param, "bcf") + + values = [c.value for c in completions] + assert "bcftools/call" in values + assert "fastqc" not in values diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py new file mode 100644 index 0000000000..3f74b8f618 --- /dev/null +++ b/tests/pipelines/test_completion.py @@ -0,0 +1,37 @@ +from unittest.mock import MagicMock, patch + +from nf_core.subworkflows._completion import autocomplete_subworkflows + + +class DummyParam: + # Minimal mock object for Click parameter (not used in the function) + pass + +class DummyCtx: + def __init__(self, obj=None): + self.obj = obj + +@patch("nf_core.subworkflows._completion.CompletionItem") +@patch("nf_core.subworkflows._completion.ModuleList") +def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): + # Setup mock for module list + mock_instance = mock_subworkflows_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "vcf_gather_bcftools", "fastq_align_star", "utils_nextflow_pipeline" + ] + + # Setup mock for CompletionItem + def mock_completion(value): + mock_item = MagicMock() + mock_item.value = value + return mock_item + + mock_completion_item_class.side_effect = mock_completion + + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py new file mode 100644 index 0000000000..3f74b8f618 --- /dev/null +++ b/tests/subworkflows/test_completion.py @@ -0,0 +1,37 @@ +from unittest.mock import MagicMock, patch + +from nf_core.subworkflows._completion import autocomplete_subworkflows + + +class DummyParam: + # Minimal mock object for Click parameter (not used in the function) + pass + +class DummyCtx: + def __init__(self, obj=None): + self.obj = obj + +@patch("nf_core.subworkflows._completion.CompletionItem") +@patch("nf_core.subworkflows._completion.ModuleList") +def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): + # Setup mock for module list + mock_instance = mock_subworkflows_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "vcf_gather_bcftools", "fastq_align_star", "utils_nextflow_pipeline" + ] + + # Setup mock for CompletionItem + def mock_completion(value): + mock_item = MagicMock() + mock_item.value = value + return mock_item + + mock_completion_item_class.side_effect = mock_completion + + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values From 115ac7776c08a10167dc87aa4551c95b446dd36d Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 10:17:32 +0200 Subject: [PATCH 030/101] Update Changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 34f22775d1..204ea38083 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,6 +45,7 @@ - Update `nf-core modules info` command after `meta.yml` restructuring ([#3659](https://github.com/nf-core/tools/pull/3659)) - Enable parsing of multi-line config values ([#3629](https://github.com/nf-core/tools/pull/3629)) - Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.2 ([#3661](https://github.com/nf-core/tools/pull/3661)) +- Add modules / subworkflows and pipelines names autocompletion to the CLI ([#3660](https://github.com/nf-core/tools/pull/3660)) ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02] From 485c4e71057c0d69f43698ea5f9cbb8172844268 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 10:19:26 +0200 Subject: [PATCH 031/101] Fix code --- nf_core/pipelines/_completion.py | 47 +++++++++++++----------------- tests/pipelines/test_completion.py | 36 ++++++++++------------- 2 files changed, 36 insertions(+), 47 deletions(-) diff --git a/nf_core/pipelines/_completion.py b/nf_core/pipelines/_completion.py index 79a97857f8..bc9175963f 100644 --- a/nf_core/pipelines/_completion.py +++ b/nf_core/pipelines/_completion.py @@ -1,33 +1,26 @@ -from unittest.mock import MagicMock, patch +import sys -from nf_core.pipelines._completion import autocomplete_pipelines +from click.shell_completion import CompletionItem +from nf_core.pipelines.list import Workflows -class DummyParam: - pass -class DummyCtx: - def __init__(self, obj=None): - self.obj = obj +def autocomplete_pipelines(ctx, param, incomplete: str): + try: + wfs = Workflows() + wfs.get_remote_workflows() + wfs.get_local_nf_workflows() + local_workflows = [wf.full_name for wf in wfs.local_workflows] + remote_workflows = [wf.name for wf in wfs.remote_workflows] + available_workflows = local_workflows + remote_workflows -@patch("nf_core.pipelines._completion.Workflows") -def test_autocomplete_pipelines_mocked(mock_workflows_class): - # Mock instance - mock_instance = mock_workflows_class.return_value + matches = [ + CompletionItem(wor) + for wor in available_workflows + if wor.startswith(incomplete) + ] - # Mock local and remote workflows - mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] - mock_instance.remote_workflows = [MagicMock(name="awesome-remote"), MagicMock(name="other-remote")] - - ctx = DummyCtx() - param = DummyParam() - - completions = autocomplete_pipelines(ctx, param, "awesome") - - # Extract values from CompletionItem - values = [c.value for c in completions] - - # Assertions - assert "awesome/localpipeline" in values - assert "awesome-remote" in values - assert "other-remote" not in values \ No newline at end of file + return matches + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 3f74b8f618..79a97857f8 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -1,37 +1,33 @@ from unittest.mock import MagicMock, patch -from nf_core.subworkflows._completion import autocomplete_subworkflows +from nf_core.pipelines._completion import autocomplete_pipelines class DummyParam: - # Minimal mock object for Click parameter (not used in the function) pass class DummyCtx: def __init__(self, obj=None): self.obj = obj -@patch("nf_core.subworkflows._completion.CompletionItem") -@patch("nf_core.subworkflows._completion.ModuleList") -def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): - # Setup mock for module list - mock_instance = mock_subworkflows_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", "fastq_align_star", "utils_nextflow_pipeline" - ] +@patch("nf_core.pipelines._completion.Workflows") +def test_autocomplete_pipelines_mocked(mock_workflows_class): + # Mock instance + mock_instance = mock_workflows_class.return_value - # Setup mock for CompletionItem - def mock_completion(value): - mock_item = MagicMock() - mock_item.value = value - return mock_item - - mock_completion_item_class.side_effect = mock_completion + # Mock local and remote workflows + mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] + mock_instance.remote_workflows = [MagicMock(name="awesome-remote"), MagicMock(name="other-remote")] ctx = DummyCtx() param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") + completions = autocomplete_pipelines(ctx, param, "awesome") + + # Extract values from CompletionItem values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values + + # Assertions + assert "awesome/localpipeline" in values + assert "awesome-remote" in values + assert "other-remote" not in values \ No newline at end of file From cba8dce3094035609cb25efae6ac26b53cf9b278 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 10:27:33 +0200 Subject: [PATCH 032/101] Fix order import --- nf_core/__main__.py | 6 +++--- nf_core/modules/_completion.py | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 876d1ff4f6..f9af1d1caa 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -60,11 +60,11 @@ test_datasets_search, ) from nf_core.components.constants import NF_CORE_MODULES_REMOTE -from nf_core.pipelines.download import DownloadError -from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir from nf_core.modules._completion import autocomplete_modules -from nf_core.subworkflows._completion import autocomplete_subworkflows from nf_core.pipelines._completion import autocomplete_pipelines +from nf_core.pipelines.download import DownloadError +from nf_core.subworkflows._completion import autocomplete_subworkflows +from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir # Set up logging as the root logger # Submodules should all traverse back to this diff --git a/nf_core/modules/_completion.py b/nf_core/modules/_completion.py index 92a76dc89b..34756272a0 100644 --- a/nf_core/modules/_completion.py +++ b/nf_core/modules/_completion.py @@ -1,6 +1,7 @@ -from click.shell_completion import CompletionItem import sys +from click.shell_completion import CompletionItem + from nf_core.modules.list import ModuleList From de2f8006819290b1ed8f8f2fdcfcef3a92fe53f1 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 10:28:33 +0200 Subject: [PATCH 033/101] Fix linting --- nf_core/__main__.py | 140 +++++++++++++++++--------- nf_core/modules/_completion.py | 6 +- nf_core/pipelines/_completion.py | 6 +- nf_core/subworkflows/_completion.py | 6 +- tests/modules/test_completion.py | 6 +- tests/pipelines/test_completion.py | 4 +- tests/subworkflows/test_completion.py | 6 +- 7 files changed, 105 insertions(+), 69 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index f9af1d1caa..26b2b1ddf6 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -359,7 +359,8 @@ def command_pipelines_lint( @pipelines.command("download") @click.argument( "pipeline", - required=False, metavar="", + required=False, + metavar="", shell_complete=autocomplete_pipelines, ) @click.option( @@ -470,7 +471,8 @@ def command_pipelines_download( @pipelines.command("create-params-file") @click.argument( "pipeline", - required=False, metavar="", + required=False, + metavar="", shell_complete=autocomplete_pipelines, ) @click.option("-r", "--revision", help="Release/branch/SHA of the pipeline (if remote)") @@ -502,7 +504,8 @@ def command_pipelines_create_params_file(ctx, pipeline, revision, output, force, @pipelines.command("launch") @click.argument( "pipeline", - required=False, metavar="", + required=False, + metavar="", shell_complete=autocomplete_pipelines, ) @click.option("-r", "--revision", help="Release/branch/SHA of the project to run (if remote)") @@ -762,7 +765,8 @@ def pipeline_schema(): ) @click.argument( "pipeline", - required=False, metavar="", + required=False, + metavar="", shell_complete=autocomplete_pipelines, ) @click.argument("params", type=click.Path(exists=True), required=True, metavar="") @@ -964,9 +968,12 @@ def command_modules_list_local(ctx, keywords, json, directory): # pylint: disab @modules.command("install") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1002,9 +1009,12 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha): @modules.command("update") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1083,9 +1093,12 @@ def command_modules_update( @modules.command("patch") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1107,9 +1120,12 @@ def command_modules_patch(ctx, tool, directory, remove): @modules.command("remove") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1230,9 +1246,12 @@ def command_modules_create( @modules.command("test") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-v", @@ -1289,9 +1308,12 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile @modules.command("lint") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1347,9 +1369,12 @@ def command_modules_lint( @modules.command("info") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1370,9 +1395,12 @@ def command_modules_info(ctx, tool, directory): @modules.command("bump-versions") @click.pass_context @click.argument( - "tool", type=str, callback=normalize_case, - required=False, metavar=" or ", - shell_complete=autocomplete_modules + "tool", + type=str, + callback=normalize_case, + required=False, + metavar=" or ", + shell_complete=autocomplete_modules, ) @click.option( "-d", @@ -1467,9 +1495,11 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1560,9 +1590,11 @@ def command_subworkflows_list_local(ctx, keywords, json, directory): # pylint: @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1614,9 +1646,11 @@ def command_subworkflows_lint( @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1638,9 +1672,11 @@ def command_subworkflows_info(ctx, subworkflow, directory): @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1683,9 +1719,11 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1725,9 +1763,11 @@ def subworkflows_patch(ctx, subworkflow, dir, remove): @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", @@ -1749,9 +1789,11 @@ def command_subworkflows_remove(ctx, directory, subworkflow): @click.pass_context @click.argument( "subworkflow", - type=str, callback=normalize_case, - required=False, metavar="subworkflow name", - shell_complete=autocomplete_subworkflows + type=str, + callback=normalize_case, + required=False, + metavar="subworkflow name", + shell_complete=autocomplete_subworkflows, ) @click.option( "-d", diff --git a/nf_core/modules/_completion.py b/nf_core/modules/_completion.py index 34756272a0..8713c16e87 100644 --- a/nf_core/modules/_completion.py +++ b/nf_core/modules/_completion.py @@ -27,11 +27,7 @@ def autocomplete_modules(ctx, param, incomplete: str): available_modules = module_list.modules_repo.get_avail_components("modules") - matches = [ - CompletionItem(mod) - for mod in available_modules - if mod.startswith(incomplete) - ] + matches = [CompletionItem(mod) for mod in available_modules if mod.startswith(incomplete)] return matches except Exception as e: diff --git a/nf_core/pipelines/_completion.py b/nf_core/pipelines/_completion.py index bc9175963f..9a0597fe21 100644 --- a/nf_core/pipelines/_completion.py +++ b/nf_core/pipelines/_completion.py @@ -14,11 +14,7 @@ def autocomplete_pipelines(ctx, param, incomplete: str): remote_workflows = [wf.name for wf in wfs.remote_workflows] available_workflows = local_workflows + remote_workflows - matches = [ - CompletionItem(wor) - for wor in available_workflows - if wor.startswith(incomplete) - ] + matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] return matches except Exception as e: diff --git a/nf_core/subworkflows/_completion.py b/nf_core/subworkflows/_completion.py index 02c004d724..a3fd9c4bce 100644 --- a/nf_core/subworkflows/_completion.py +++ b/nf_core/subworkflows/_completion.py @@ -27,11 +27,7 @@ def autocomplete_subworkflows(ctx, param, incomplete: str): available_subworkflows = subworkflow_list.modules_repo.get_avail_components("subworkflows") - matches = [ - CompletionItem(sub) - for sub in available_subworkflows - if sub.startswith(incomplete) - ] + matches = [CompletionItem(sub) for sub in available_subworkflows if sub.startswith(incomplete)] return matches except Exception as e: diff --git a/tests/modules/test_completion.py b/tests/modules/test_completion.py index 551f08c595..955a433137 100644 --- a/tests/modules/test_completion.py +++ b/tests/modules/test_completion.py @@ -7,18 +7,18 @@ class DummyParam: # Minimal mock object for Click parameter (not used in the function) pass + class DummyCtx: def __init__(self, obj=None): self.obj = obj + @patch("nf_core.modules._completion.CompletionItem") @patch("nf_core.modules._completion.ModuleList") def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): # Setup mock for module list mock_instance = mock_module_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "fastqc", "bcftools/call", "bcftools/index" - ] + mock_instance.modules_repo.get_avail_components.return_value = ["fastqc", "bcftools/call", "bcftools/index"] # Setup mock for CompletionItem def mock_completion(value): diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 79a97857f8..0911ac18b0 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -6,10 +6,12 @@ class DummyParam: pass + class DummyCtx: def __init__(self, obj=None): self.obj = obj + @patch("nf_core.pipelines._completion.Workflows") def test_autocomplete_pipelines_mocked(mock_workflows_class): # Mock instance @@ -30,4 +32,4 @@ def test_autocomplete_pipelines_mocked(mock_workflows_class): # Assertions assert "awesome/localpipeline" in values assert "awesome-remote" in values - assert "other-remote" not in values \ No newline at end of file + assert "other-remote" not in values diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py index 3f74b8f618..9d8b8578c9 100644 --- a/tests/subworkflows/test_completion.py +++ b/tests/subworkflows/test_completion.py @@ -7,17 +7,21 @@ class DummyParam: # Minimal mock object for Click parameter (not used in the function) pass + class DummyCtx: def __init__(self, obj=None): self.obj = obj + @patch("nf_core.subworkflows._completion.CompletionItem") @patch("nf_core.subworkflows._completion.ModuleList") def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): # Setup mock for module list mock_instance = mock_subworkflows_list_class.return_value mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", "fastq_align_star", "utils_nextflow_pipeline" + "vcf_gather_bcftools", + "fastq_align_star", + "utils_nextflow_pipeline", ] # Setup mock for CompletionItem From 253aed10d57d2305a385a17737531f201b7b4080 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 11:24:35 +0200 Subject: [PATCH 034/101] Update test --- nf_core/pipelines/_completion.py | 2 +- tests/pipelines/test_completion.py | 2 +- tests/subworkflows/test_completion.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipelines/_completion.py b/nf_core/pipelines/_completion.py index 9a0597fe21..065b6c73f9 100644 --- a/nf_core/pipelines/_completion.py +++ b/nf_core/pipelines/_completion.py @@ -11,7 +11,7 @@ def autocomplete_pipelines(ctx, param, incomplete: str): wfs.get_remote_workflows() wfs.get_local_nf_workflows() local_workflows = [wf.full_name for wf in wfs.local_workflows] - remote_workflows = [wf.name for wf in wfs.remote_workflows] + remote_workflows = [wf.full_name for wf in wfs.remote_workflows] available_workflows = local_workflows + remote_workflows matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 0911ac18b0..03c9bea6fd 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -19,7 +19,7 @@ def test_autocomplete_pipelines_mocked(mock_workflows_class): # Mock local and remote workflows mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] - mock_instance.remote_workflows = [MagicMock(name="awesome-remote"), MagicMock(name="other-remote")] + mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] ctx = DummyCtx() param = DummyParam() diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py index 9d8b8578c9..6458c734bf 100644 --- a/tests/subworkflows/test_completion.py +++ b/tests/subworkflows/test_completion.py @@ -14,7 +14,7 @@ def __init__(self, obj=None): @patch("nf_core.subworkflows._completion.CompletionItem") -@patch("nf_core.subworkflows._completion.ModuleList") +@patch("nf_core.subworkflows._completion.SubworkflowList") def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): # Setup mock for module list mock_instance = mock_subworkflows_list_class.return_value From 81e58c592df80c12069d9a7037643b04786e5cbe Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 11:26:34 +0200 Subject: [PATCH 035/101] Update changelog --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a1c5362e5..b789c92a95 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,10 +40,8 @@ - Update error message for rocrate_readme_sync ([#3652](https://github.com/nf-core/tools/pull/3652)) - Update `nf-core modules info` command after `meta.yml` restructuring ([#3659](https://github.com/nf-core/tools/pull/3659)) - Enable parsing of multi-line config values ([#3629](https://github.com/nf-core/tools/pull/3629)) -- Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.2 ([#3661](https://github.com/nf-core/tools/pull/3661)) - Add modules / subworkflows and pipelines names autocompletion to the CLI ([#3660](https://github.com/nf-core/tools/pull/3660)) - #### Version updates - Drop python 3.8, add tests with python 3.13 ([#3538](https://github.com/nf-core/tools/pull/3538)) From b501f4123c94392c47fb98a26f70ae379b3a3cf3 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 12:00:12 +0200 Subject: [PATCH 036/101] Check for error --- tests/modules/test_completion.py | 12 ++++++++++++ tests/pipelines/test_completion.py | 12 ++++++++++++ tests/subworkflows/test_completion.py | 12 ++++++++++++ 3 files changed, 36 insertions(+) diff --git a/tests/modules/test_completion.py b/tests/modules/test_completion.py index 955a433137..5467f4c3b7 100644 --- a/tests/modules/test_completion.py +++ b/tests/modules/test_completion.py @@ -1,5 +1,7 @@ from unittest.mock import MagicMock, patch +import pytest + from nf_core.modules._completion import autocomplete_modules @@ -35,3 +37,13 @@ def mock_completion(value): values = [c.value for c in completions] assert "bcftools/call" in values assert "fastqc" not in values + + +def test_autocomplete_modules_missing_argument(capfd): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_modules(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 03c9bea6fd..f2372b2b34 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -1,5 +1,7 @@ from unittest.mock import MagicMock, patch +import pytest + from nf_core.pipelines._completion import autocomplete_pipelines @@ -33,3 +35,13 @@ def test_autocomplete_pipelines_mocked(mock_workflows_class): assert "awesome/localpipeline" in values assert "awesome-remote" in values assert "other-remote" not in values + + +def test_autocomplete_pipelines_missing_argument(capfd): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_pipelines(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py index 6458c734bf..f94803ccc2 100644 --- a/tests/subworkflows/test_completion.py +++ b/tests/subworkflows/test_completion.py @@ -1,5 +1,7 @@ from unittest.mock import MagicMock, patch +import pytest + from nf_core.subworkflows._completion import autocomplete_subworkflows @@ -39,3 +41,13 @@ def mock_completion(value): values = [c.value for c in completions] assert "utils_nextflow_pipeline" in values assert "vcf_gather_bcftools" not in values + + +def test_autocomplete_subworkflows_missing_argument(): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_subworkflows(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) From 318b216d1c0ae11ea176a5dddbc62239b0f28a03 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 8 Jul 2025 13:49:00 +0200 Subject: [PATCH 037/101] Add test with ctx object --- tests/modules/test_completion.py | 27 ++++++++++++++++++++++++ tests/subworkflows/test_completion.py | 30 +++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) diff --git a/tests/modules/test_completion.py b/tests/modules/test_completion.py index 5467f4c3b7..3018c8df89 100644 --- a/tests/modules/test_completion.py +++ b/tests/modules/test_completion.py @@ -39,6 +39,33 @@ def mock_completion(value): assert "fastqc" not in values +@patch("nf_core.modules._completion.ModuleList") +def test_autocomplete_modules_with_ctx_obj(mock_module_list_class): + # Setup mock return value + mock_instance = mock_module_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = ["custommodule/a", "custommodule/b", "othermodule/x"] + + # Provide ctx.obj with custom values + ctx = DummyCtx( + obj={ + "modules_repo_url": "https://custom.url/modules", + "modules_repo_branch": "custom-branch", + "modules_repo_no_pull": True, + } + ) + + param = DummyParam() + completions = autocomplete_modules(ctx, param, "custom") + + # Assertions + mock_module_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) + + values = [c.value for c in completions] + assert "custommodule/a" in values + assert "custommodule/b" in values + assert "othermodule/x" not in values + + def test_autocomplete_modules_missing_argument(capfd): ctx = DummyCtx() param = DummyParam() diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py index f94803ccc2..52b0c230c5 100644 --- a/tests/subworkflows/test_completion.py +++ b/tests/subworkflows/test_completion.py @@ -43,6 +43,36 @@ def mock_completion(value): assert "vcf_gather_bcftools" not in values +@patch("nf_core.subworkflows._completion.SubworkflowList") +def test_autocomplete_subworkflows_with_ctx_obj(mock_subworkflows_list_class): + # Setup mock return value + mock_instance = mock_subworkflows_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "vcf_gather_bcftools", + "fastq_align_star", + "utils_nextflow_pipeline", + ] + + # Provide ctx.obj with custom values + ctx = DummyCtx( + obj={ + "modules_repo_url": "https://custom.url/modules", + "modules_repo_branch": "custom-branch", + "modules_repo_no_pull": True, + } + ) + + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + + # Assertions + mock_subworkflows_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values + + def test_autocomplete_subworkflows_missing_argument(): ctx = DummyCtx() param = DummyParam() From 4f9d937cb2dc2e4445fba5359a3a7d9c50ec6bd9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 8 Jul 2025 13:40:28 +0200 Subject: [PATCH 038/101] bump to 3.4.0dev # Conflicts: # CHANGELOG.md --- .gitpod.yml | 2 +- CHANGELOG.md | 12 ++++++++++++ setup.py | 2 +- 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index db31d01bed..d5948695bf 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:latest +image: nfcore/gitpod:dev tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/CHANGELOG.md b/CHANGELOG.md index a1f151fb8b..7e4a7ffd51 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,17 @@ # nf-core/tools: Changelog +## v3.4.0dev + +### Template + +### Linting + +### Modules + +### Subworkflows + +### General + ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] ### Template diff --git a/setup.py b/setup.py index bdccab3ae7..56f073442c 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.3.2" +version = "3.4.0dev" with open("README.md") as f: readme = f.read() From 81484bb64042b959f3a2652d1f54055f4af71fef Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Tue, 8 Jul 2025 19:24:23 +0200 Subject: [PATCH 039/101] Move all script to component_completion --- nf_core/__main__.py | 4 +- nf_core/components/components_completion.py | 55 ++++++ nf_core/components/components_utils.py | 2 + nf_core/modules/_completion.py | 35 ---- nf_core/pipelines/_completion.py | 22 --- nf_core/subworkflows/_completion.py | 35 ---- tests/components/test_completion.py | 204 ++++++++++++++++++++ tests/modules/test_completion.py | 76 -------- tests/pipelines/test_completion.py | 47 ----- tests/subworkflows/test_completion.py | 83 -------- 10 files changed, 262 insertions(+), 301 deletions(-) create mode 100644 nf_core/components/components_completion.py delete mode 100644 nf_core/modules/_completion.py delete mode 100644 nf_core/pipelines/_completion.py delete mode 100644 nf_core/subworkflows/_completion.py create mode 100644 tests/components/test_completion.py delete mode 100644 tests/modules/test_completion.py delete mode 100644 tests/pipelines/test_completion.py delete mode 100644 tests/subworkflows/test_completion.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 26b2b1ddf6..b00a7b4714 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -60,10 +60,8 @@ test_datasets_search, ) from nf_core.components.constants import NF_CORE_MODULES_REMOTE -from nf_core.modules._completion import autocomplete_modules -from nf_core.pipelines._completion import autocomplete_pipelines +from nf_core.components.components_utils import autocomplete_modules, autocomplete_subworkflows, autocomplete_pipelines from nf_core.pipelines.download import DownloadError -from nf_core.subworkflows._completion import autocomplete_subworkflows from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir # Set up logging as the root logger diff --git a/nf_core/components/components_completion.py b/nf_core/components/components_completion.py new file mode 100644 index 0000000000..dff7f3f0ea --- /dev/null +++ b/nf_core/components/components_completion.py @@ -0,0 +1,55 @@ +from click.shell_completion import CompletionItem +from nf_core.modules.list import ModuleList +from nf_core.subworkflows.list import SubworkflowList +from nf_core.pipelines.list import Workflows + + +def autocomplete_components(ctx, param, incomplete: str, component_type: str, list_class): + # Defaults + modules_repo_url = "https://github.com/nf-core/modules" + modules_repo_branch = "master" + modules_repo_no_pull = False + dir_folder = ctx.params.get("dir", ".") + + try: + if ctx.obj is not None: + modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url) + modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) + modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) + + components_list = list_class( + dir_folder, True, modules_repo_url, modules_repo_branch, modules_repo_no_pull + ) + + available_components = components_list.modules_repo.get_avail_components(component_type) + + return [ + CompletionItem(comp) + for comp in available_components + if comp.startswith(incomplete) + ] + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] + +def autocomplete_modules(ctx, param, incomplete: str): + return autocomplete_components(ctx, param, incomplete, "modules", ModuleList) + +def autocomplete_subworkflows(ctx, param, incomplete: str): + return autocomplete_components(ctx, param, incomplete, "subworkflows", SubworkflowList) + +def autocomplete_pipelines(ctx, param, incomplete: str): + try: + wfs = Workflows() + wfs.get_remote_workflows() + wfs.get_local_nf_workflows() + local_workflows = [wf.full_name for wf in wfs.local_workflows] + remote_workflows = [wf.full_name for wf in wfs.remote_workflows] + available_workflows = local_workflows + remote_workflows + + matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] + + return matches + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index f381f0fd55..1e86650f4d 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -1,5 +1,7 @@ import logging import re +import sys + from pathlib import Path from typing import Optional, Union diff --git a/nf_core/modules/_completion.py b/nf_core/modules/_completion.py deleted file mode 100644 index 8713c16e87..0000000000 --- a/nf_core/modules/_completion.py +++ /dev/null @@ -1,35 +0,0 @@ -import sys - -from click.shell_completion import CompletionItem - -from nf_core.modules.list import ModuleList - - -def autocomplete_modules(ctx, param, incomplete: str): - # Provide fallback/defaults if ctx.obj is not available - modules_repo_url = "https://github.com/nf-core/modules" - modules_repo_branch = "master" - modules_repo_no_pull = False - - try: - if ctx.obj is not None: - modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url) - modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) - modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) - - module_list = ModuleList( - ".", - True, - modules_repo_url, - modules_repo_branch, - modules_repo_no_pull, - ) - - available_modules = module_list.modules_repo.get_avail_components("modules") - - matches = [CompletionItem(mod) for mod in available_modules if mod.startswith(incomplete)] - - return matches - except Exception as e: - print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) - return [] diff --git a/nf_core/pipelines/_completion.py b/nf_core/pipelines/_completion.py deleted file mode 100644 index 065b6c73f9..0000000000 --- a/nf_core/pipelines/_completion.py +++ /dev/null @@ -1,22 +0,0 @@ -import sys - -from click.shell_completion import CompletionItem - -from nf_core.pipelines.list import Workflows - - -def autocomplete_pipelines(ctx, param, incomplete: str): - try: - wfs = Workflows() - wfs.get_remote_workflows() - wfs.get_local_nf_workflows() - local_workflows = [wf.full_name for wf in wfs.local_workflows] - remote_workflows = [wf.full_name for wf in wfs.remote_workflows] - available_workflows = local_workflows + remote_workflows - - matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] - - return matches - except Exception as e: - print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) - return [] diff --git a/nf_core/subworkflows/_completion.py b/nf_core/subworkflows/_completion.py deleted file mode 100644 index a3fd9c4bce..0000000000 --- a/nf_core/subworkflows/_completion.py +++ /dev/null @@ -1,35 +0,0 @@ -import sys - -from click.shell_completion import CompletionItem - -from nf_core.subworkflows.list import SubworkflowList - - -def autocomplete_subworkflows(ctx, param, incomplete: str): - # Provide fallback/defaults if ctx.obj is not available - modules_repo_url = "https://github.com/nf-core/modules" - modules_repo_branch = "master" - modules_repo_no_pull = False - - try: - if ctx.obj is not None: - modules_repo_url = ctx.obj.get("modules_repo_url", modules_repo_url) - modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) - modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) - - subworkflow_list = SubworkflowList( - ".", - True, - modules_repo_url, - modules_repo_branch, - modules_repo_no_pull, - ) - - available_subworkflows = subworkflow_list.modules_repo.get_avail_components("subworkflows") - - matches = [CompletionItem(sub) for sub in available_subworkflows if sub.startswith(incomplete)] - - return matches - except Exception as e: - print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) - return [] diff --git a/tests/components/test_completion.py b/tests/components/test_completion.py new file mode 100644 index 0000000000..f82185c515 --- /dev/null +++ b/tests/components/test_completion.py @@ -0,0 +1,204 @@ +from unittest.mock import MagicMock, patch + +import pytest + +from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows, autocomplete_pipelines + +class DummyParam: + # Minimal mock object for Click parameter (not used in the function) + pass + + +class DummyCtx: + def __init__(self, obj=None, params=None): + self.obj = obj + self.params = params if params is not None else {} + +def test_autocomplete_modules(): + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_modules(ctx, param, "bcf") + + values = [c.value for c in completions] + assert "bcftools/call" in values + assert "fastqc" not in values + +@patch("nf_core.components.components_completion.CompletionItem") +@patch("nf_core.components.components_completion.ModuleList") +def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): + # Setup mock for module list + mock_instance = mock_module_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = ["fastqc", "bcftools/call", "bcftools/index"] + + # Setup mock for CompletionItem + def mock_completion(value): + mock_item = MagicMock() + mock_item.value = value + return mock_item + + mock_completion_item_class.side_effect = mock_completion + + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_modules(ctx, param, "bcf") + + values = [c.value for c in completions] + assert "bcftools/call" in values + assert "fastqc" not in values + + +@patch("nf_core.components.components_completion.ModuleList") +def test_autocomplete_modules_with_ctx_obj(mock_module_list_class): + # Setup mock return value + mock_instance = mock_module_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = ["custommodule/a", "custommodule/b", "othermodule/x"] + + # Provide ctx.obj with custom values + ctx = DummyCtx( + obj={ + "modules_repo_url": "https://custom.url/modules", + "modules_repo_branch": "custom-branch", + "modules_repo_no_pull": True, + } + ) + + param = DummyParam() + completions = autocomplete_modules(ctx, param, "custom") + + # Assertions + mock_module_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) + + values = [c.value for c in completions] + assert "custommodule/a" in values + assert "custommodule/b" in values + assert "othermodule/x" not in values + + +def test_autocomplete_modules_missing_argument(capfd): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_modules(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) + + +def test_autocomplete_subworkflows(): + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + print(completions) + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values + +@patch("nf_core.components.components_completion.CompletionItem") +@patch("nf_core.components.components_completion.SubworkflowList") +def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): + # Setup mock for module list + mock_instance = mock_subworkflows_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "vcf_gather_bcftools", + "fastq_align_star", + "utils_nextflow_pipeline", + ] + + # Setup mock for CompletionItem + def mock_completion(value): + mock_item = MagicMock() + mock_item.value = value + return mock_item + + mock_completion_item_class.side_effect = mock_completion + + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values + + +@patch("nf_core.components.components_completion.SubworkflowList") +def test_autocomplete_subworkflows_with_ctx_obj(mock_subworkflows_list_class): + # Setup mock return value + mock_instance = mock_subworkflows_list_class.return_value + mock_instance.modules_repo.get_avail_components.return_value = [ + "vcf_gather_bcftools", + "fastq_align_star", + "utils_nextflow_pipeline", + ] + + # Provide ctx.obj with custom values + ctx = DummyCtx( + obj={ + "modules_repo_url": "https://custom.url/modules", + "modules_repo_branch": "custom-branch", + "modules_repo_no_pull": True, + } + ) + + param = DummyParam() + completions = autocomplete_subworkflows(ctx, param, "utils") + + # Assertions + mock_subworkflows_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) + + values = [c.value for c in completions] + assert "utils_nextflow_pipeline" in values + assert "vcf_gather_bcftools" not in values + + +def test_autocomplete_subworkflows_missing_argument(): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_subworkflows(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) + +def test_autocomplete_pipelines(): + ctx = DummyCtx() + param = DummyParam() + completions = autocomplete_pipelines(ctx, param, "sar") + print(completions) + + values = [c.value for c in completions] + assert "sarek" in values + assert "rnasek" not in values + +@patch("nf_core.components.components_completion.Workflows") +def test_autocomplete_pipelines_mocked(mock_workflows_class): + # Mock instance + mock_instance = mock_workflows_class.return_value + + # Mock local and remote workflows + mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] + mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] + + ctx = DummyCtx() + param = DummyParam() + + completions = autocomplete_pipelines(ctx, param, "awesome") + + # Extract values from CompletionItem + values = [c.value for c in completions] + + # Assertions + assert "awesome/localpipeline" in values + assert "awesome-remote" in values + assert "other-remote" not in values + + +def test_autocomplete_pipelines_missing_argument(capfd): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_pipelines(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/modules/test_completion.py b/tests/modules/test_completion.py deleted file mode 100644 index 3018c8df89..0000000000 --- a/tests/modules/test_completion.py +++ /dev/null @@ -1,76 +0,0 @@ -from unittest.mock import MagicMock, patch - -import pytest - -from nf_core.modules._completion import autocomplete_modules - - -class DummyParam: - # Minimal mock object for Click parameter (not used in the function) - pass - - -class DummyCtx: - def __init__(self, obj=None): - self.obj = obj - - -@patch("nf_core.modules._completion.CompletionItem") -@patch("nf_core.modules._completion.ModuleList") -def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): - # Setup mock for module list - mock_instance = mock_module_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = ["fastqc", "bcftools/call", "bcftools/index"] - - # Setup mock for CompletionItem - def mock_completion(value): - mock_item = MagicMock() - mock_item.value = value - return mock_item - - mock_completion_item_class.side_effect = mock_completion - - ctx = DummyCtx() - param = DummyParam() - completions = autocomplete_modules(ctx, param, "bcf") - - values = [c.value for c in completions] - assert "bcftools/call" in values - assert "fastqc" not in values - - -@patch("nf_core.modules._completion.ModuleList") -def test_autocomplete_modules_with_ctx_obj(mock_module_list_class): - # Setup mock return value - mock_instance = mock_module_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = ["custommodule/a", "custommodule/b", "othermodule/x"] - - # Provide ctx.obj with custom values - ctx = DummyCtx( - obj={ - "modules_repo_url": "https://custom.url/modules", - "modules_repo_branch": "custom-branch", - "modules_repo_no_pull": True, - } - ) - - param = DummyParam() - completions = autocomplete_modules(ctx, param, "custom") - - # Assertions - mock_module_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) - - values = [c.value for c in completions] - assert "custommodule/a" in values - assert "custommodule/b" in values - assert "othermodule/x" not in values - - -def test_autocomplete_modules_missing_argument(capfd): - ctx = DummyCtx() - param = DummyParam() - - with pytest.raises(TypeError) as exc_info: - autocomplete_modules(ctx, param) # Missing 'incomplete' argument - - assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py deleted file mode 100644 index f2372b2b34..0000000000 --- a/tests/pipelines/test_completion.py +++ /dev/null @@ -1,47 +0,0 @@ -from unittest.mock import MagicMock, patch - -import pytest - -from nf_core.pipelines._completion import autocomplete_pipelines - - -class DummyParam: - pass - - -class DummyCtx: - def __init__(self, obj=None): - self.obj = obj - - -@patch("nf_core.pipelines._completion.Workflows") -def test_autocomplete_pipelines_mocked(mock_workflows_class): - # Mock instance - mock_instance = mock_workflows_class.return_value - - # Mock local and remote workflows - mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] - mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] - - ctx = DummyCtx() - param = DummyParam() - - completions = autocomplete_pipelines(ctx, param, "awesome") - - # Extract values from CompletionItem - values = [c.value for c in completions] - - # Assertions - assert "awesome/localpipeline" in values - assert "awesome-remote" in values - assert "other-remote" not in values - - -def test_autocomplete_pipelines_missing_argument(capfd): - ctx = DummyCtx() - param = DummyParam() - - with pytest.raises(TypeError) as exc_info: - autocomplete_pipelines(ctx, param) # Missing 'incomplete' argument - - assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/subworkflows/test_completion.py b/tests/subworkflows/test_completion.py deleted file mode 100644 index 52b0c230c5..0000000000 --- a/tests/subworkflows/test_completion.py +++ /dev/null @@ -1,83 +0,0 @@ -from unittest.mock import MagicMock, patch - -import pytest - -from nf_core.subworkflows._completion import autocomplete_subworkflows - - -class DummyParam: - # Minimal mock object for Click parameter (not used in the function) - pass - - -class DummyCtx: - def __init__(self, obj=None): - self.obj = obj - - -@patch("nf_core.subworkflows._completion.CompletionItem") -@patch("nf_core.subworkflows._completion.SubworkflowList") -def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): - # Setup mock for module list - mock_instance = mock_subworkflows_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", - "fastq_align_star", - "utils_nextflow_pipeline", - ] - - # Setup mock for CompletionItem - def mock_completion(value): - mock_item = MagicMock() - mock_item.value = value - return mock_item - - mock_completion_item_class.side_effect = mock_completion - - ctx = DummyCtx() - param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") - - values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values - - -@patch("nf_core.subworkflows._completion.SubworkflowList") -def test_autocomplete_subworkflows_with_ctx_obj(mock_subworkflows_list_class): - # Setup mock return value - mock_instance = mock_subworkflows_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", - "fastq_align_star", - "utils_nextflow_pipeline", - ] - - # Provide ctx.obj with custom values - ctx = DummyCtx( - obj={ - "modules_repo_url": "https://custom.url/modules", - "modules_repo_branch": "custom-branch", - "modules_repo_no_pull": True, - } - ) - - param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") - - # Assertions - mock_subworkflows_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) - - values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values - - -def test_autocomplete_subworkflows_missing_argument(): - ctx = DummyCtx() - param = DummyParam() - - with pytest.raises(TypeError) as exc_info: - autocomplete_subworkflows(ctx, param) # Missing 'incomplete' argument - - assert "missing 1 required positional argument" in str(exc_info.value) From bc50d837b21821399fa7f9d3813c296ed4b221b6 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Tue, 8 Jul 2025 19:28:42 +0200 Subject: [PATCH 040/101] Add pipeline real completion test --- tests/components/test_completion.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/components/test_completion.py b/tests/components/test_completion.py index f82185c515..95532fa9b2 100644 --- a/tests/components/test_completion.py +++ b/tests/components/test_completion.py @@ -164,12 +164,11 @@ def test_autocomplete_subworkflows_missing_argument(): def test_autocomplete_pipelines(): ctx = DummyCtx() param = DummyParam() - completions = autocomplete_pipelines(ctx, param, "sar") - print(completions) + completions = autocomplete_pipelines(ctx, param, "next") values = [c.value for c in completions] - assert "sarek" in values - assert "rnasek" not in values + assert "nextflow-io/hello" in values + assert "nf-core/rnasek" not in values @patch("nf_core.components.components_completion.Workflows") def test_autocomplete_pipelines_mocked(mock_workflows_class): From d1a6d4f5df6e14dd47abacf491115e8156e6c18f Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 18:24:59 +0200 Subject: [PATCH 041/101] Change location pipeline autocompletion and use gitlab dummy --- nf_core/__main__.py | 3 +- nf_core/components/components_completion.py | 32 ++------- nf_core/components/components_utils.py | 2 - nf_core/pipelines/list.py | 19 +++++ tests/components/test_completion.py | 77 ++++++++------------- tests/pipelines/test_completion.py | 68 ++++++++++++++++++ 6 files changed, 123 insertions(+), 78 deletions(-) create mode 100644 tests/pipelines/test_completion.py diff --git a/nf_core/__main__.py b/nf_core/__main__.py index b00a7b4714..b811244288 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -59,9 +59,10 @@ test_datasets_list_remote, test_datasets_search, ) +from nf_core.components.components_utils import autocomplete_modules, autocomplete_subworkflows from nf_core.components.constants import NF_CORE_MODULES_REMOTE -from nf_core.components.components_utils import autocomplete_modules, autocomplete_subworkflows, autocomplete_pipelines from nf_core.pipelines.download import DownloadError +from nf_core.pipelines.list import autocomplete_pipelines from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir # Set up logging as the root logger diff --git a/nf_core/components/components_completion.py b/nf_core/components/components_completion.py index dff7f3f0ea..191fa32e21 100644 --- a/nf_core/components/components_completion.py +++ b/nf_core/components/components_completion.py @@ -1,7 +1,9 @@ +import sys + from click.shell_completion import CompletionItem + from nf_core.modules.list import ModuleList from nf_core.subworkflows.list import SubworkflowList -from nf_core.pipelines.list import Workflows def autocomplete_components(ctx, param, incomplete: str, component_type: str, list_class): @@ -17,39 +19,19 @@ def autocomplete_components(ctx, param, incomplete: str, component_type: str, li modules_repo_branch = ctx.obj.get("modules_repo_branch", modules_repo_branch) modules_repo_no_pull = ctx.obj.get("modules_repo_no_pull", modules_repo_no_pull) - components_list = list_class( - dir_folder, True, modules_repo_url, modules_repo_branch, modules_repo_no_pull - ) + components_list = list_class(dir_folder, True, modules_repo_url, modules_repo_branch, modules_repo_no_pull) available_components = components_list.modules_repo.get_avail_components(component_type) - return [ - CompletionItem(comp) - for comp in available_components - if comp.startswith(incomplete) - ] + return [CompletionItem(comp) for comp in available_components if comp.startswith(incomplete)] except Exception as e: print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) return [] + def autocomplete_modules(ctx, param, incomplete: str): return autocomplete_components(ctx, param, incomplete, "modules", ModuleList) + def autocomplete_subworkflows(ctx, param, incomplete: str): return autocomplete_components(ctx, param, incomplete, "subworkflows", SubworkflowList) - -def autocomplete_pipelines(ctx, param, incomplete: str): - try: - wfs = Workflows() - wfs.get_remote_workflows() - wfs.get_local_nf_workflows() - local_workflows = [wf.full_name for wf in wfs.local_workflows] - remote_workflows = [wf.full_name for wf in wfs.remote_workflows] - available_workflows = local_workflows + remote_workflows - - matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] - - return matches - except Exception as e: - print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) - return [] diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py index 1e86650f4d..f381f0fd55 100644 --- a/nf_core/components/components_utils.py +++ b/nf_core/components/components_utils.py @@ -1,7 +1,5 @@ import logging import re -import sys - from pathlib import Path from typing import Optional, Union diff --git a/nf_core/pipelines/list.py b/nf_core/pipelines/list.py index 658f4dc6d2..ec2c9636de 100644 --- a/nf_core/pipelines/list.py +++ b/nf_core/pipelines/list.py @@ -4,6 +4,7 @@ import logging import os import re +import sys from datetime import datetime from pathlib import Path from typing import Union @@ -12,6 +13,7 @@ import requests import rich.console import rich.table +from click.shell_completion import CompletionItem import nf_core.utils @@ -40,6 +42,23 @@ def list_workflows(filter_by=None, sort_by="release", as_json=False, show_archiv return wfs.print_summary() +def autocomplete_pipelines(ctx, param, incomplete: str): + try: + wfs = Workflows() + wfs.get_remote_workflows() + wfs.get_local_nf_workflows() + local_workflows = [wf.full_name for wf in wfs.local_workflows] + remote_workflows = [wf.full_name for wf in wfs.remote_workflows] + available_workflows = local_workflows + remote_workflows + + matches = [CompletionItem(wor) for wor in available_workflows if wor.startswith(incomplete)] + + return matches + except Exception as e: + print(f"[ERROR] Autocomplete failed: {e}", file=sys.stderr) + return [] + + def get_local_wf(workflow: Union[str, Path], revision=None) -> Union[str, None]: """ Check if this workflow has a local copy and use nextflow to pull it if not diff --git a/tests/components/test_completion.py b/tests/components/test_completion.py index 95532fa9b2..79a6cd0fa0 100644 --- a/tests/components/test_completion.py +++ b/tests/components/test_completion.py @@ -2,7 +2,10 @@ import pytest -from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows, autocomplete_pipelines +from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows + +from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + class DummyParam: # Minimal mock object for Click parameter (not used in the function) @@ -14,15 +17,24 @@ def __init__(self, obj=None, params=None): self.obj = obj self.params = params if params is not None else {} + def test_autocomplete_modules(): - ctx = DummyCtx() + ctx = DummyCtx( + obj={ + "modules_repo_url": GITLAB_URL, + "modules_repo_branch": GITLAB_NFTEST_BRANCH, + "modules_repo_no_pull": True, + } + ) param = DummyParam() - completions = autocomplete_modules(ctx, param, "bcf") + completions = autocomplete_modules(ctx, param, "samt") values = [c.value for c in completions] - assert "bcftools/call" in values + assert "samtools/stats" in values + assert "samtools/idxstats" in values assert "fastqc" not in values + @patch("nf_core.components.components_completion.CompletionItem") @patch("nf_core.components.components_completion.ModuleList") def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): @@ -85,14 +97,20 @@ def test_autocomplete_modules_missing_argument(capfd): def test_autocomplete_subworkflows(): - ctx = DummyCtx() + ctx = DummyCtx( + obj={ + "modules_repo_url": GITLAB_URL, + "modules_repo_branch": GITLAB_NFTEST_BRANCH, + "modules_repo_no_pull": True, + } + ) param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") - print(completions) + completions = autocomplete_subworkflows(ctx, param, "bam_stats") values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values + assert "bam_stats_samtools" in values + assert "bam_sort_stats_samtools" not in values + @patch("nf_core.components.components_completion.CompletionItem") @patch("nf_core.components.components_completion.SubworkflowList") @@ -160,44 +178,3 @@ def test_autocomplete_subworkflows_missing_argument(): autocomplete_subworkflows(ctx, param) # Missing 'incomplete' argument assert "missing 1 required positional argument" in str(exc_info.value) - -def test_autocomplete_pipelines(): - ctx = DummyCtx() - param = DummyParam() - completions = autocomplete_pipelines(ctx, param, "next") - - values = [c.value for c in completions] - assert "nextflow-io/hello" in values - assert "nf-core/rnasek" not in values - -@patch("nf_core.components.components_completion.Workflows") -def test_autocomplete_pipelines_mocked(mock_workflows_class): - # Mock instance - mock_instance = mock_workflows_class.return_value - - # Mock local and remote workflows - mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] - mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] - - ctx = DummyCtx() - param = DummyParam() - - completions = autocomplete_pipelines(ctx, param, "awesome") - - # Extract values from CompletionItem - values = [c.value for c in completions] - - # Assertions - assert "awesome/localpipeline" in values - assert "awesome-remote" in values - assert "other-remote" not in values - - -def test_autocomplete_pipelines_missing_argument(capfd): - ctx = DummyCtx() - param = DummyParam() - - with pytest.raises(TypeError) as exc_info: - autocomplete_pipelines(ctx, param) # Missing 'incomplete' argument - - assert "missing 1 required positional argument" in str(exc_info.value) diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py new file mode 100644 index 0000000000..49bcbb04c5 --- /dev/null +++ b/tests/pipelines/test_completion.py @@ -0,0 +1,68 @@ +from unittest.mock import MagicMock, patch + +import pytest + +from nf_core.pipelines.list import autocomplete_pipelines + +from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +class DummyParam: + # Minimal mock object for Click parameter + pass + + +class DummyCtx: + def __init__(self, obj=None, params=None): + self.obj = obj + self.params = params if params is not None else {} + + +def test_autocomplete_pipelines(): + ctx = DummyCtx( + obj={ + "modules_repo_url": GITLAB_URL, + "modules_repo_branch": GITLAB_NFTEST_BRANCH, + "modules_repo_no_pull": True, + } + ) + param = DummyParam() + completions = autocomplete_pipelines(ctx, param, "next") + + values = [c.value for c in completions] + + assert "nextflow-io/hello" in values + assert "nf-core/rnaseq" not in values + + +@patch("nf_core.pipelines.list.Workflows") +def test_autocomplete_pipelines_mocked(mock_workflows_class): + # Mock instance + mock_instance = mock_workflows_class.return_value + + # Mock local and remote workflows + mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] + mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] + + ctx = DummyCtx() + param = DummyParam() + + completions = autocomplete_pipelines(ctx, param, "awesome") + + # Extract values from CompletionItem + values = [c.value for c in completions] + + # Assertions + assert "awesome/localpipeline" in values + assert "awesome-remote" in values + assert "other-remote" not in values + + +def test_autocomplete_pipelines_missing_argument(capfd): + ctx = DummyCtx() + param = DummyParam() + + with pytest.raises(TypeError) as exc_info: + autocomplete_pipelines(ctx, param) # Missing 'incomplete' argument + + assert "missing 1 required positional argument" in str(exc_info.value) From fb6414e045761d73d791f748865144520954678c Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 18:50:50 +0200 Subject: [PATCH 042/101] Fix import --- nf_core/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index b811244288..07fc476ded 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -59,7 +59,7 @@ test_datasets_list_remote, test_datasets_search, ) -from nf_core.components.components_utils import autocomplete_modules, autocomplete_subworkflows +from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows from nf_core.components.constants import NF_CORE_MODULES_REMOTE from nf_core.pipelines.download import DownloadError from nf_core.pipelines.list import autocomplete_pipelines From 9ac6dd8d811e9f44b08f6ef71f183de11e1456d0 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 19:06:20 +0200 Subject: [PATCH 043/101] Update pipelines completion test --- tests/pipelines/test_completion.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 49bcbb04c5..cbd559e6e6 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -19,17 +19,12 @@ def __init__(self, obj=None, params=None): def test_autocomplete_pipelines(): - ctx = DummyCtx( - obj={ - "modules_repo_url": GITLAB_URL, - "modules_repo_branch": GITLAB_NFTEST_BRANCH, - "modules_repo_no_pull": True, - } - ) + ctx = DummyCtx() param = DummyParam() completions = autocomplete_pipelines(ctx, param, "next") values = [c.value for c in completions] + print(values) # For debugging purposes assert "nextflow-io/hello" in values assert "nf-core/rnaseq" not in values From 85177582c58206bf9f449ab06a7e8d8c16a9b491 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 19:24:31 +0200 Subject: [PATCH 044/101] Update test --- nf_core/pipelines/list.py | 6 ++++++ tests/pipelines/test_completion.py | 1 - 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/nf_core/pipelines/list.py b/nf_core/pipelines/list.py index ec2c9636de..2a4d35a4fe 100644 --- a/nf_core/pipelines/list.py +++ b/nf_core/pipelines/list.py @@ -125,6 +125,12 @@ def get_remote_workflows(self): repos = response.json()["remote_workflows"] for repo in repos: self.remote_workflows.append(RemoteWorkflow(repo)) + else: + print( + f"Could not fetch remote workflows from {nfcore_url} - " + f"HTTP status code: {response.status_code}" + ) + sys.exit(1) def get_local_nf_workflows(self): """Retrieves local Nextflow workflows. diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index cbd559e6e6..772d6f536e 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -24,7 +24,6 @@ def test_autocomplete_pipelines(): completions = autocomplete_pipelines(ctx, param, "next") values = [c.value for c in completions] - print(values) # For debugging purposes assert "nextflow-io/hello" in values assert "nf-core/rnaseq" not in values From 9c887aaa1983deadf853fc62145c96043b598929 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 19:38:57 +0200 Subject: [PATCH 045/101] Update test --- nf_core/pipelines/list.py | 6 ------ tests/pipelines/test_completion.py | 3 ++- 2 files changed, 2 insertions(+), 7 deletions(-) diff --git a/nf_core/pipelines/list.py b/nf_core/pipelines/list.py index 2a4d35a4fe..ec2c9636de 100644 --- a/nf_core/pipelines/list.py +++ b/nf_core/pipelines/list.py @@ -125,12 +125,6 @@ def get_remote_workflows(self): repos = response.json()["remote_workflows"] for repo in repos: self.remote_workflows.append(RemoteWorkflow(repo)) - else: - print( - f"Could not fetch remote workflows from {nfcore_url} - " - f"HTTP status code: {response.status_code}" - ) - sys.exit(1) def get_local_nf_workflows(self): """Retrieves local Nextflow workflows. diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 772d6f536e..805bae2b9f 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -21,9 +21,10 @@ def __init__(self, obj=None, params=None): def test_autocomplete_pipelines(): ctx = DummyCtx() param = DummyParam() - completions = autocomplete_pipelines(ctx, param, "next") + completions = autocomplete_pipelines(ctx, param, "") values = [c.value for c in completions] + print(values) # For debugging purposes assert "nextflow-io/hello" in values assert "nf-core/rnaseq" not in values From 3b4e4996c1a46b95c73ad70470d8ba9933d840d7 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Wed, 9 Jul 2025 19:46:21 +0200 Subject: [PATCH 046/101] Fix test --- tests/pipelines/test_completion.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 805bae2b9f..10879ef9ce 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -4,8 +4,6 @@ from nf_core.pipelines.list import autocomplete_pipelines -from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL - class DummyParam: # Minimal mock object for Click parameter @@ -21,13 +19,14 @@ def __init__(self, obj=None, params=None): def test_autocomplete_pipelines(): ctx = DummyCtx() param = DummyParam() - completions = autocomplete_pipelines(ctx, param, "") + completions = autocomplete_pipelines(ctx, param, "nf-core/bac") values = [c.value for c in completions] print(values) # For debugging purposes - assert "nextflow-io/hello" in values - assert "nf-core/rnaseq" not in values + assert "nf-core/bacass" in values + assert "nf-core/bactmap" in values + assert "nf-core/abotyper" not in values @patch("nf_core.pipelines.list.Workflows") From ef427b5dd263e3ce5990517ff4c8384d6dd578e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 10 Jul 2025 10:36:10 +0200 Subject: [PATCH 047/101] don't read param expressions with spaces as params --- nf_core/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index f9a3413ef9..278865bb23 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -326,7 +326,7 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict: if result is not None: nfconfig_raw, _ = result nfconfig = nfconfig_raw.decode("utf-8") - multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL) + multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=\s]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL) for config_match in multiline_key_value_pattern.finditer(nfconfig): k = config_match.group(2).strip() From bb13b044df0a4d1ee8837c2b016cb9fc11fd5a3d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 10 Jul 2025 08:39:22 +0000 Subject: [PATCH 048/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e4a7ffd51..63e871a19f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ ### General +- don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) + ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] ### Template From 587b816d89b03589584b8c01657b30e6a0d4bc7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 10 Jul 2025 16:40:01 +0200 Subject: [PATCH 049/101] add test for fetch_wf_config utils --- tests/test_utils.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/tests/test_utils.py b/tests/test_utils.py index b7761253a3..d8e9eb4351 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -216,3 +216,11 @@ def test_set_wd_revert_on_raise(self): with nf_core.utils.set_wd(self.tmp_dir): raise Exception assert wd_before_context == Path().resolve() + + @mock.patch("nf_core.utils.run_cmd") + def test_fetch_wf_config(self, mock_run_cmd): + """Test the fetch_wf_config() regular expression to read config params.""" + mock_run_cmd.return_value = (b"params.param1 ? 'a=b' : ''\nparams.param2 = foo", b"mock") + config = nf_core.utils.fetch_wf_config(".", False) + assert len(config.keys()) == 1 + assert "params.param2" in list(config.keys()) From 92e1325914b39451913db72d5e1f86b90851e735 Mon Sep 17 00:00:00 2001 From: Louis Le Nezet Date: Tue, 15 Jul 2025 16:41:17 +0200 Subject: [PATCH 050/101] Remove unecessary mocked test --- tests/components/test_completion.py | 111 ---------------------------- tests/pipelines/test_completion.py | 25 ------- 2 files changed, 136 deletions(-) diff --git a/tests/components/test_completion.py b/tests/components/test_completion.py index 79a6cd0fa0..c465e8bd18 100644 --- a/tests/components/test_completion.py +++ b/tests/components/test_completion.py @@ -1,5 +1,3 @@ -from unittest.mock import MagicMock, patch - import pytest from nf_core.components.components_completion import autocomplete_modules, autocomplete_subworkflows @@ -35,57 +33,6 @@ def test_autocomplete_modules(): assert "fastqc" not in values -@patch("nf_core.components.components_completion.CompletionItem") -@patch("nf_core.components.components_completion.ModuleList") -def test_autocomplete_modules_mocked(mock_module_list_class, mock_completion_item_class): - # Setup mock for module list - mock_instance = mock_module_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = ["fastqc", "bcftools/call", "bcftools/index"] - - # Setup mock for CompletionItem - def mock_completion(value): - mock_item = MagicMock() - mock_item.value = value - return mock_item - - mock_completion_item_class.side_effect = mock_completion - - ctx = DummyCtx() - param = DummyParam() - completions = autocomplete_modules(ctx, param, "bcf") - - values = [c.value for c in completions] - assert "bcftools/call" in values - assert "fastqc" not in values - - -@patch("nf_core.components.components_completion.ModuleList") -def test_autocomplete_modules_with_ctx_obj(mock_module_list_class): - # Setup mock return value - mock_instance = mock_module_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = ["custommodule/a", "custommodule/b", "othermodule/x"] - - # Provide ctx.obj with custom values - ctx = DummyCtx( - obj={ - "modules_repo_url": "https://custom.url/modules", - "modules_repo_branch": "custom-branch", - "modules_repo_no_pull": True, - } - ) - - param = DummyParam() - completions = autocomplete_modules(ctx, param, "custom") - - # Assertions - mock_module_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) - - values = [c.value for c in completions] - assert "custommodule/a" in values - assert "custommodule/b" in values - assert "othermodule/x" not in values - - def test_autocomplete_modules_missing_argument(capfd): ctx = DummyCtx() param = DummyParam() @@ -112,64 +59,6 @@ def test_autocomplete_subworkflows(): assert "bam_sort_stats_samtools" not in values -@patch("nf_core.components.components_completion.CompletionItem") -@patch("nf_core.components.components_completion.SubworkflowList") -def test_autocomplete_subworkflows_mocked(mock_subworkflows_list_class, mock_completion_item_class): - # Setup mock for module list - mock_instance = mock_subworkflows_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", - "fastq_align_star", - "utils_nextflow_pipeline", - ] - - # Setup mock for CompletionItem - def mock_completion(value): - mock_item = MagicMock() - mock_item.value = value - return mock_item - - mock_completion_item_class.side_effect = mock_completion - - ctx = DummyCtx() - param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") - - values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values - - -@patch("nf_core.components.components_completion.SubworkflowList") -def test_autocomplete_subworkflows_with_ctx_obj(mock_subworkflows_list_class): - # Setup mock return value - mock_instance = mock_subworkflows_list_class.return_value - mock_instance.modules_repo.get_avail_components.return_value = [ - "vcf_gather_bcftools", - "fastq_align_star", - "utils_nextflow_pipeline", - ] - - # Provide ctx.obj with custom values - ctx = DummyCtx( - obj={ - "modules_repo_url": "https://custom.url/modules", - "modules_repo_branch": "custom-branch", - "modules_repo_no_pull": True, - } - ) - - param = DummyParam() - completions = autocomplete_subworkflows(ctx, param, "utils") - - # Assertions - mock_subworkflows_list_class.assert_called_once_with(".", True, "https://custom.url/modules", "custom-branch", True) - - values = [c.value for c in completions] - assert "utils_nextflow_pipeline" in values - assert "vcf_gather_bcftools" not in values - - def test_autocomplete_subworkflows_missing_argument(): ctx = DummyCtx() param = DummyParam() diff --git a/tests/pipelines/test_completion.py b/tests/pipelines/test_completion.py index 10879ef9ce..8a9cf8f38f 100644 --- a/tests/pipelines/test_completion.py +++ b/tests/pipelines/test_completion.py @@ -1,5 +1,3 @@ -from unittest.mock import MagicMock, patch - import pytest from nf_core.pipelines.list import autocomplete_pipelines @@ -29,29 +27,6 @@ def test_autocomplete_pipelines(): assert "nf-core/abotyper" not in values -@patch("nf_core.pipelines.list.Workflows") -def test_autocomplete_pipelines_mocked(mock_workflows_class): - # Mock instance - mock_instance = mock_workflows_class.return_value - - # Mock local and remote workflows - mock_instance.local_workflows = [MagicMock(full_name="awesome/localpipeline")] - mock_instance.remote_workflows = [MagicMock(full_name="awesome-remote"), MagicMock(full_name="other-remote")] - - ctx = DummyCtx() - param = DummyParam() - - completions = autocomplete_pipelines(ctx, param, "awesome") - - # Extract values from CompletionItem - values = [c.value for c in completions] - - # Assertions - assert "awesome/localpipeline" in values - assert "awesome-remote" in values - assert "other-remote" not in values - - def test_autocomplete_pipelines_missing_argument(capfd): ctx = DummyCtx() param = DummyParam() From 50814803e9e549f0d65862e7992e909ff99d87e7 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 21 Jul 2025 09:25:50 +0200 Subject: [PATCH 051/101] Update marocchino/sticky-pull-request-comment digest to 7737449 (#3681) * Update marocchino/sticky-pull-request-comment digest to 7737449 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot --- CHANGELOG.md | 1 + nf_core/pipeline-template/.github/workflows/linting_comment.yml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6f30dbb70..e6890d5ea3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ ### General - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) +- Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml index ccf3e4f01e..63ec136aa4 100644 --- a/nf_core/pipeline-template/.github/workflows/linting_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/linting_comment.yml @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} From e6cc401fb9f93b3d428bf5c5218557c66f26d73e Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Tue, 15 Jul 2025 22:45:38 +0100 Subject: [PATCH 052/101] With cross-org repos, components can be dictionaries whose (only) key is the component name --- nf_core/subworkflows/lint/meta_yml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py index 0e62cccfc9..416f0d630d 100644 --- a/nf_core/subworkflows/lint/meta_yml.py +++ b/nf_core/subworkflows/lint/meta_yml.py @@ -115,7 +115,7 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False): # join included modules and included subworkflows in a single list included_components_names = [component["name"] for component in included_components] if "components" in meta_yaml: - meta_components = [x for x in meta_yaml["components"]] + meta_components = [x if isinstance(x, str) else list(x)[0] for x in meta_yaml["components"]] for component in set(included_components_names): if component in meta_components: subworkflow.passed.append( From ae7ca23469bf5326da97c89f2d41ac0583fc449f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Jul 2025 21:58:25 +0000 Subject: [PATCH 053/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6890d5ea3..6c7a9a8adf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 7f2b96be9a7f6862b78c2ea2bb10e1d15f5e31ea Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 21 Jul 2025 13:40:18 +0000 Subject: [PATCH 054/101] Migrate config .github/renovate.json5 --- .github/renovate.json5 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/renovate.json5 b/.github/renovate.json5 index 5af6502e95..83402f239f 100644 --- a/.github/renovate.json5 +++ b/.github/renovate.json5 @@ -2,7 +2,7 @@ $schema: "https://docs.renovatebot.com/renovate-schema.json", extends: ["github>nf-core/ops//.github/renovate/default.json5"], ignorePaths: ["**/nf_core/pipeline-template/modules/nf-core/**"], - baseBranches: ["dev"], + baseBranchPatterns: ["dev"], packageRules: [ { matchDatasources: ["docker"], From 186ca114ea9a3de31e4efa96294336f8bd62ad57 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 21 Jul 2025 17:05:59 +0200 Subject: [PATCH 055/101] make the tests more similar to the rest of the testing structure --- tests/modules/lint/test_environment_yml.py | 99 +++++++--------------- 1 file changed, 29 insertions(+), 70 deletions(-) diff --git a/tests/modules/lint/test_environment_yml.py b/tests/modules/lint/test_environment_yml.py index a0f2354ea0..02a963e68f 100644 --- a/tests/modules/lint/test_environment_yml.py +++ b/tests/modules/lint/test_environment_yml.py @@ -15,73 +15,45 @@ def yaml_dump_to_string(data): - """Helper function to dump YAML data to string using ruamel.yaml""" stream = io.StringIO() yaml.dump(data, stream) return stream.getvalue() -@pytest.fixture -def dummy_module_factory(): - """Factory fixture for creating DummyModule instances""" +class DummyModule(NFCoreComponent): + def __init__(self, path): + self.environment_yml = path + self.component_dir = path.parent + self.component_name = "dummy" + self.passed = [] + self.failed = [] + self.warned = [] - def _create_dummy_module(path): - class DummyModule(NFCoreComponent): - def __init__(self, path): - self.environment_yml = path - self.component_dir = path.parent - self.component_name = "dummy" - self.passed = [] - self.failed = [] - self.warned = [] - return DummyModule(path) +class DummyLint(ComponentLint): + def __init__(self, tmp_path): + self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) + self.passed = [] + self.failed = [] - return _create_dummy_module +def setup_test_environment(tmp_path, content, filename="environment.yml"): + test_file = tmp_path / filename + test_file.write_text(content) -@pytest.fixture -def dummy_lint_factory(): - """Factory fixture for creating DummyLint instances""" + (tmp_path / "modules").mkdir(exist_ok=True) + (tmp_path / "modules" / "environment-schema.json").write_text("{}") - def _create_dummy_lint(tmp_path): - class DummyLint(ComponentLint): - def __init__(self): - self.modules_repo = type("repo", (), {"local_repo_dir": tmp_path}) - self.passed = [] - self.failed = [] + module = DummyModule(test_file) + lint = DummyLint(tmp_path) - return DummyLint() + return test_file, module, lint - return _create_dummy_lint - -@pytest.fixture -def setup_lint_environment(tmp_path, dummy_module_factory, dummy_lint_factory): - """Setup function that creates the necessary directory structure and dummy objects for linting""" - - def _setup(test_file_content, filename="environment.yml"): - test_file = tmp_path / filename - test_file.write_text(test_file_content) - - # Create required directory structure - (tmp_path / "modules").mkdir(exist_ok=True) - (tmp_path / "modules" / "environment-schema.json").write_text("{}") - - module = dummy_module_factory(test_file) - lint = dummy_lint_factory(tmp_path) - - return test_file, module, lint - - return _setup - - -def assert_yaml_result(test_file, expected, check_sorting=True): - """Helper function to assert YAML parsing results""" +def assert_yaml_result(test_file, expected): result = test_file.read_text() lines = result.splitlines(True) - # Handle YAML with schema headers if lines[:2] == [ "---\n", "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json\n", @@ -90,7 +62,6 @@ def assert_yaml_result(test_file, expected, check_sorting=True): else: parsed = yaml.load(result) - # Assert expected content if isinstance(expected, list): assert parsed["dependencies"] == expected else: @@ -186,25 +157,14 @@ def assert_yaml_result(test_file, expected, check_sorting=True): }, ), ], - ids=[ - "basic_dependency_sorting", - "dict_dependency_sorting", - "existing_headers", - "channel_preservation", - "channel_preservation_with_additional_channels", - "namespaced_dependencies", - "mixed_dependencies", - "full_environment", - ], ) -def test_environment_yml_sorting(setup_lint_environment, input_content, expected): +def test_environment_yml_sorting(tmp_path, input_content, expected): """Test that environment.yml files are sorted correctly""" - test_file, module, lint = setup_lint_environment(input_content) + test_file, module, lint = setup_test_environment(tmp_path, input_content) environment_yml(lint, module) assert_yaml_result(test_file, expected) - # Check linter passed for sorting assert any("environment_yml_sorted" in x for x in [p.lint_test for p in lint.passed]) @@ -214,25 +174,24 @@ def test_environment_yml_sorting(setup_lint_environment, input_content, expected ("invalid: yaml: here", "bad.yml"), ("", "empty.yml"), ], - ids=["invalid_yaml", "empty_file"], ) -def test_environment_yml_invalid_files(setup_lint_environment, invalid_content, filename): +def test_environment_yml_invalid_files(tmp_path, invalid_content, filename): """Test that invalid YAML files raise exceptions""" - test_file, module, lint = setup_lint_environment(invalid_content, filename) + test_file, module, lint = setup_test_environment(tmp_path, invalid_content, filename) with pytest.raises(Exception): environment_yml(lint, module) -def test_environment_yml_missing_dependencies(setup_lint_environment): +def test_environment_yml_missing_dependencies(tmp_path): """Test handling of environment.yml without dependencies section""" content = "channels:\n - conda-forge\n" - test_file, module, lint = setup_lint_environment(content) + test_file, module, lint = setup_test_environment(tmp_path, content) environment_yml(lint, module) expected = {"channels": ["conda-forge"]} - assert_yaml_result(test_file, expected, check_sorting=False) + assert_yaml_result(test_file, expected) # Integration tests using the full ModuleLint class From 30ad3031391d9c26e972a7eed59596f893fd436a Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Tue, 22 Jul 2025 22:31:31 +0200 Subject: [PATCH 056/101] Update .nftignore --- nf_core/pipeline-template/tests/.nftignore | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipeline-template/tests/.nftignore b/nf_core/pipeline-template/tests/.nftignore index 5870048f24..3019b6e197 100644 --- a/nf_core/pipeline-template/tests/.nftignore +++ b/nf_core/pipeline-template/tests/.nftignore @@ -8,6 +8,7 @@ multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/llms-full.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html {%- endif %} From 8a6484083c93995b4e9f882b2eae8979a7f1eb34 Mon Sep 17 00:00:00 2001 From: Jonas Scheid Date: Wed, 23 Jul 2025 12:21:04 +0000 Subject: [PATCH 057/101] update multiQC to 1.30 --- nf_core/pipeline-template/modules.json | 2 +- .../modules/nf-core/multiqc/environment.yml | 2 +- .../modules/nf-core/multiqc/main.nf | 4 ++-- .../nf-core/multiqc/tests/main.nf.test.snap | 20 +++++++++---------- .../modules/nf-core/multiqc/tests/tags.yml | 2 -- 5 files changed, 14 insertions(+), 16 deletions(-) delete mode 100644 nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 8e0f67eb2c..ae8429ec10 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -13,7 +13,7 @@ }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "c9a31c472ef2d86802eb44f27322955849859361", "installed_by": ["modules"] } {%- endif %} diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml index 812fc4c5e5..f893704836 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.29 + - bioconda::multiqc=1.30 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 0ac3c36996..a508541ba0 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : - 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.30--pyhdfd78af_0' : + 'biocontainers/multiqc:1.30--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap index 88e90571c7..0d3f288bd9 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:50:41.182332996" + "timestamp": "2025-07-10T08:06:23.563041241" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:22.448739369" + "timestamp": "2025-07-10T08:06:48.96226832" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:06.198928424" + "timestamp": "2025-07-10T08:06:40.627008706" } -} \ No newline at end of file +} diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d37f..0000000000 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** From a6c148f554c7bee6a59e350859808ab06a1791d4 Mon Sep 17 00:00:00 2001 From: Jonas Scheid Date: Thu, 24 Jul 2025 05:55:54 +0000 Subject: [PATCH 058/101] update pipelien template default snapshot with new mqc llm.txt output --- .github/snapshots/default.nf.test.snap | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index be24cb1e74..31ea202d6a 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", From ec47974d4d40246917a2f1afa5debf3207aa4a15 Mon Sep 17 00:00:00 2001 From: Jonas Scheid Date: Thu, 24 Jul 2025 07:43:49 +0000 Subject: [PATCH 059/101] update snapshots --- .github/snapshots/adaptivecard.nf.test.snap | 1 + .github/snapshots/changelog.nf.test.snap | 1 + .github/snapshots/ci.nf.test.snap | 1 + .github/snapshots/citations.nf.test.snap | 1 + .github/snapshots/code_linters.nf.test.snap | 1 + .github/snapshots/codespaces.nf.test.snap | 1 + .github/snapshots/documentation.nf.test.snap | 1 + .github/snapshots/email.nf.test.snap | 1 + .github/snapshots/fastqc.nf.test.snap | 1 + .github/snapshots/github_badges.nf.test.snap | 1 + .github/snapshots/gitpod.nf.test.snap | 1 + .github/snapshots/gpu.nf.test.snap | 1 + .github/snapshots/igenomes.nf.test.snap | 1 + .github/snapshots/license.nf.test.snap | 1 + .github/snapshots/nf_core_configs.nf.test.snap | 1 + .github/snapshots/nf_schema.nf.test.snap | 1 + .github/snapshots/rocrate.nf.test.snap | 1 + .github/snapshots/seqera_platform.nf.test.snap | 1 + .github/snapshots/slackreport.nf.test.snap | 1 + .github/snapshots/vscode.nf.test.snap | 1 + 20 files changed, 20 insertions(+) diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/adaptivecard.nf.test.snap +++ b/.github/snapshots/adaptivecard.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap index f0c9d64c23..3989533f59 100644 --- a/.github/snapshots/changelog.nf.test.snap +++ b/.github/snapshots/changelog.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap index 1f12b211d4..39f8719f76 100644 --- a/.github/snapshots/ci.nf.test.snap +++ b/.github/snapshots/ci.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap index 815c73deef..292367b69f 100644 --- a/.github/snapshots/citations.nf.test.snap +++ b/.github/snapshots/citations.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap index 815c73deef..292367b69f 100644 --- a/.github/snapshots/code_linters.nf.test.snap +++ b/.github/snapshots/code_linters.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap index 815c73deef..292367b69f 100644 --- a/.github/snapshots/codespaces.nf.test.snap +++ b/.github/snapshots/codespaces.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/documentation.nf.test.snap +++ b/.github/snapshots/documentation.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/email.nf.test.snap +++ b/.github/snapshots/email.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap index 3a29057a03..66184b7b84 100644 --- a/.github/snapshots/fastqc.nf.test.snap +++ b/.github/snapshots/fastqc.nf.test.snap @@ -11,6 +11,7 @@ "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/BETA-multiqc.parquet", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap index 655cefc5ec..e671050699 100644 --- a/.github/snapshots/github_badges.nf.test.snap +++ b/.github/snapshots/github_badges.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap index 815c73deef..292367b69f 100644 --- a/.github/snapshots/gitpod.nf.test.snap +++ b/.github/snapshots/gitpod.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index d4d45910f5..eb83194a65 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap index ff5b0af023..e7425c2b11 100644 --- a/.github/snapshots/igenomes.nf.test.snap +++ b/.github/snapshots/igenomes.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/license.nf.test.snap +++ b/.github/snapshots/license.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap index 815c73deef..292367b69f 100644 --- a/.github/snapshots/nf_core_configs.nf.test.snap +++ b/.github/snapshots/nf_core_configs.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap index 6f5954020c..f0703db991 100644 --- a/.github/snapshots/nf_schema.nf.test.snap +++ b/.github/snapshots/nf_schema.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/rocrate.nf.test.snap +++ b/.github/snapshots/rocrate.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/seqera_platform.nf.test.snap +++ b/.github/snapshots/seqera_platform.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/slackreport.nf.test.snap +++ b/.github/snapshots/slackreport.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap index fe11743437..fd0f6fd295 100644 --- a/.github/snapshots/vscode.nf.test.snap +++ b/.github/snapshots/vscode.nf.test.snap @@ -38,6 +38,7 @@ "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/llms-full.txt", "multiqc/multiqc_data/multiqc.log", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", From 95ec76d6e9a7ee17d179066a1a31ec32192b3557 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 29 May 2025 22:29:48 -0500 Subject: [PATCH 060/101] refactor: Split up test_lint tests to match modules lint structure Did my best, and wanted to keep the code verbatim before things really start shifting. --- tests/modules/lint/test_lint.py | 137 ++++++ tests/modules/lint/test_main_nf.py | 185 +++++++ tests/modules/lint/test_meta_yml.py | 75 +++ tests/modules/lint/test_module_tests.py | 187 +++++++ tests/modules/lint/test_patch.py | 48 ++ tests/modules/test_lint.py | 630 ------------------------ 6 files changed, 632 insertions(+), 630 deletions(-) create mode 100644 tests/modules/lint/test_lint.py create mode 100644 tests/modules/lint/test_main_nf.py create mode 100644 tests/modules/lint/test_meta_yml.py create mode 100644 tests/modules/lint/test_module_tests.py create mode 100644 tests/modules/lint/test_patch.py delete mode 100644 tests/modules/test_lint.py diff --git a/tests/modules/lint/test_lint.py b/tests/modules/lint/test_lint.py new file mode 100644 index 0000000000..b70ad53307 --- /dev/null +++ b/tests/modules/lint/test_lint.py @@ -0,0 +1,137 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + +class TestModulesLint(TestModules): + + def test_modules_lint_trimgalore(self): + """Test linting the TrimGalore! module""" + self.mods_install.install("trimgalore") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="trimgalore") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_trinity(self): + """Test linting the Trinity module""" + self.mods_install.install("trinity") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="trinity") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_tabix_tabix(self): + """Test linting the tabix/tabix module""" + self.mods_install.install("tabix/tabix") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="tabix/tabix") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_empty(self): + """Test linting a pipeline with no modules installed""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text + + def test_modules_lint_new_modules(self): + """lint a new module""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_no_gitlab(self): + """Test linting a pipeline with no modules installed""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text + + def test_modules_lint_gitlab_modules(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("fastqc") + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 2 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_multiple_remotes(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 1 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + + def test_modules_lint_local(self): + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore") + shutil.move(installed, local) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_local_missing_files(self): + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore") + shutil.move(installed, local) + Path(self.pipeline_dir, "modules", "local", "trimgalore", "environment.yml").unlink() + Path(self.pipeline_dir, "modules", "local", "trimgalore", "meta.yml").unlink() + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + warnings = [x.message for x in module_lint.warned] + assert "Module's `environment.yml` does not exist" in warnings + assert "Module `meta.yml` does not exist" in warnings + + def test_modules_lint_local_old_format(self): + Path(self.pipeline_dir, "modules", "local").mkdir() + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore", "main.nf") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore.nf") + shutil.move(installed, local) + self.mods_remove.remove("trimgalore", force=True) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + + self.main_nf = "main_nf" diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py new file mode 100644 index 0000000000..a35ea1836c --- /dev/null +++ b/tests/modules/lint/test_main_nf.py @@ -0,0 +1,185 @@ +PROCESS_LABEL_GOOD = ( + """ + label 'process_high' + cpus 12 + """, + 1, + 0, + 0, +) +PROCESS_LABEL_NON_ALPHANUMERIC = ( + """ + label 'a:label:with:colons' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_GOOD_CONFLICTING = ( + """ + label 'process_high' + label 'process_low' + cpus 12 + """, + 0, + 1, + 0, +) +PROCESS_LABEL_GOOD_DUPLICATES = ( + """ + label 'process_high' + label 'process_high' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( + """ + label 'process_high' + label 'process_extra_label' + cpus 12 + """, + 1, + 1, + 0, +) +PROCESS_LABEL_NONSTANDARD = ( + """ + label 'process_extra_label' + cpus 12 + """, + 0, + 2, + 0, +) +PROCESS_LABEL_NONSTANDARD_DUPLICATES = ( + """ + label process_extra_label + label process_extra_label + cpus 12 + """, + 0, + 3, + 0, +) +PROCESS_LABEL_NONE_FOUND = ( + """ + cpus 12 + """, + 0, + 1, + 0, +) + +PROCESS_LABEL_TEST_CASES = [ + PROCESS_LABEL_GOOD, + PROCESS_LABEL_NON_ALPHANUMERIC, + PROCESS_LABEL_GOOD_CONFLICTING, + PROCESS_LABEL_GOOD_DUPLICATES, + PROCESS_LABEL_GOOD_AND_NONSTANDARD, + PROCESS_LABEL_NONSTANDARD, + PROCESS_LABEL_NONSTANDARD_DUPLICATES, + PROCESS_LABEL_NONE_FOUND, +] + + +# Test cases for linting the container definitions + +CONTAINER_SINGLE_GOOD = ( + "Single-line container definition should pass", + """ + container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package + """, + 2, # passed + 0, # warned + 0, # failed +) + +CONTAINER_TWO_LINKS_GOOD = ( + "Multi-line container definition should pass", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 6, + 0, + 0, +) + +CONTAINER_WITH_SPACE_BAD = ( + "Space in container URL should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 5, + 0, + 1, +) + +CONTAINER_MULTIPLE_DBLQUOTES_BAD = ( + "Incorrect quoting of container string should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" + """, + 4, + 0, + 1, +) + +CONTAINER_TEST_CASES = [ + CONTAINER_SINGLE_GOOD, + CONTAINER_TWO_LINKS_GOOD, + CONTAINER_WITH_SPACE_BAD, + CONTAINER_MULTIPLE_DBLQUOTES_BAD, +] + + + + def test_modules_lint_registry(self): + """Test linting the samtools module and alternative registry""" + assert self.mods_install.install("samtools/sort") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") + module_lint.lint(print_results=False, module="samtools/sort") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_check_process_labels(self): + for test_case in PROCESS_LABEL_TEST_CASES: + process, passed, warned, failed = test_case + mocked_ModuleLint = MockModuleLint() + check_process_labels(mocked_ModuleLint, process.splitlines()) + assert len(mocked_ModuleLint.passed) == passed + assert len(mocked_ModuleLint.warned) == warned + assert len(mocked_ModuleLint.failed) == failed + + def test_modules_lint_check_url(self): + for test_case in CONTAINER_TEST_CASES: + test, process, passed, warned, failed = test_case + mocked_ModuleLint = MockModuleLint() + for line in process.splitlines(): + if line.strip(): + check_container_link_line(mocked_ModuleLint, line, registry="quay.io") + + assert len(mocked_ModuleLint.passed) == passed, ( + f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}." + ) + assert len(mocked_ModuleLint.warned) == warned, ( + f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}." + ) + assert len(mocked_ModuleLint.failed) == failed, ( + f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." + ) \ No newline at end of file diff --git a/tests/modules/lint/test_meta_yml.py b/tests/modules/lint/test_meta_yml.py new file mode 100644 index 0000000000..7c59f1a5bf --- /dev/null +++ b/tests/modules/lint/test_meta_yml.py @@ -0,0 +1,75 @@ + + def test_modules_lint_update_meta_yml(self): + """update the meta.yml of a module""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules, fix=True) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_meta_yml_incorrect_licence_field(self): + """Test linting a module with an incorrect Licence field in meta.yml""" + with open(self.bpipe_test_module_path / "meta.yml") as fh: + meta_yml = yaml.safe_load(fh) + meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]" + with open( + self.bpipe_test_module_path / "meta.yml", + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # reset changes + meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "meta_yml_valid" + + def test_modules_meta_yml_output_mismatch(self): + """Test linting a module with an extra entry in output fields in meta.yml compared to module.output""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: + main_nf = fh.read() + main_nf_new = main_nf.replace("emit: sequence_report", "emit: bai") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf_new) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: + fh.write(main_nf) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert "Module `meta.yml` does not match `main.nf`" in module_lint.failed[0].message + + def test_modules_meta_yml_incorrect_name(self): + """Test linting a module with an incorrect name in meta.yml""" + with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: + meta_yml = yaml.safe_load(fh) + meta_yml["name"] = "bpipe/test" + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # reset changes + meta_yml["name"] = "bpipe_test" + with open( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), + "w", + ) as fh: + fh.write(yaml.dump(meta_yml)) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "meta_name" \ No newline at end of file diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py new file mode 100644 index 0000000000..7a7b676be5 --- /dev/null +++ b/tests/modules/lint/test_module_tests.py @@ -0,0 +1,187 @@ + + def test_modules_lint_snapshot_file(self): + """Test linting a module with a snapshot file""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_snapshot_file_missing_fail(self): + """Test linting a module with a snapshot file missing, which should fail""" + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).unlink() + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test.snap", + ).touch() + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snapshot_exists" + + def test_modules_lint_snapshot_file_not_needed(self): + """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ) + ) as fh: + content = fh.read() + new_content = content.replace("snapshot(", "snap (") + with open( + Path( + self.nfcore_modules, + "modules", + "nf-core", + "bpipe", + "test", + "tests", + "main.nf.test", + ), + "w", + ) as fh: + fh.write(new_content) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_missing_test_dir(self): + """Test linting a module with a missing test directory""" + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") + ) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( + Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") + ) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_dir_exists" + + def test_modules_missing_test_main_nf(self): + """Test linting a module with a missing test/main.nf file""" + (self.bpipe_test_module_path / "tests" / "main.nf.test").rename( + self.bpipe_test_module_path / "tests" / "main.nf.test.bak" + ) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + (self.bpipe_test_module_path / "tests" / "main.nf.test.bak").rename( + self.bpipe_test_module_path / "tests" / "main.nf.test" + ) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_main_nf_exists" + + def test_modules_unused_pytest_files(self): + """Test linting a nf-test module with files still present in `tests/modules/`""" + Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_old_test_dir" + + def test_nftest_failing_linting(self): + """Test linting a module which includes other modules in nf-test tests. + Linting tests""" + # Clone modules repo with testing modules + tmp_dir = self.nfcore_modules.parent + self.nfcore_modules = Path(tmp_dir, "modules-test") + Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="kallisto/quant") + + assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "meta_yml_valid" + assert module_lint.failed[1].lint_test == "test_main_tags" + assert "kallisto/index" in module_lint.failed[1].message + + def test_modules_absent_version(self): + """Test linting a nf-test module if the versions is absent in the snapshot file `""" + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + with open(snap_file) as fh: + content = fh.read() + new_content = content.replace("versions", "foo") + with open(snap_file, "w") as fh: + fh.write(new_content) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + with open(snap_file, "w") as fh: + fh.write(content) + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) >= 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snap_versions" + + def test_modules_empty_file_in_snapshot(self): + """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert module_lint.failed[0].lint_test == "test_snap_md5sum" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + def test_modules_empty_file_in_stub_snapshot(self): + """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed) + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) \ No newline at end of file diff --git a/tests/modules/lint/test_patch.py b/tests/modules/lint/test_patch.py new file mode 100644 index 0000000000..7294438cdb --- /dev/null +++ b/tests/modules/lint/test_patch.py @@ -0,0 +1,48 @@ +import nf_core.modules.patch +from ..test_patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf + + def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): + install_obj = nf_core.modules.install.ModuleInstall( + pipeline_dir, + prompt=False, + force=False, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + sha=CORRECT_SHA, + ) + + # Install the module + install_obj.install(BISMARK_ALIGN) + + if modify_module: + # Modify the module + module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) + modify_main_nf(module_path / "main.nf") + + def test_modules_lint_patched_modules(self): + """ + Test creating a patch file and applying it to a new version of the the files + """ + self._setup_patch(str(self.pipeline_dir), True) + + # Create a patch file + patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) + patch_obj.patch(BISMARK_ALIGN) + + # change temporarily working directory to the pipeline directory + # to avoid error from try_apply_patch() during linting + with set_wd(self.pipeline_dir): + module_lint = nf_core.modules.lint.ModuleLint( + directory=self.pipeline_dir, + remote_url=GITLAB_URL, + branch=PATCH_BRANCH, + hide_progress=True, + ) + module_lint.lint( + print_results=False, + all_modules=True, + ) + + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py deleted file mode 100644 index 92cec6e6ed..0000000000 --- a/tests/modules/test_lint.py +++ /dev/null @@ -1,630 +0,0 @@ -import json -import shutil -from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo - -import nf_core.modules.lint -import nf_core.modules.patch -from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels -from nf_core.utils import set_wd - -from ..test_modules import TestModules -from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL -from .test_patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf - -PROCESS_LABEL_GOOD = ( - """ - label 'process_high' - cpus 12 - """, - 1, - 0, - 0, -) -PROCESS_LABEL_NON_ALPHANUMERIC = ( - """ - label 'a:label:with:colons' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_CONFLICTING = ( - """ - label 'process_high' - label 'process_low' - cpus 12 - """, - 0, - 1, - 0, -) -PROCESS_LABEL_GOOD_DUPLICATES = ( - """ - label 'process_high' - label 'process_high' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( - """ - label 'process_high' - label 'process_extra_label' - cpus 12 - """, - 1, - 1, - 0, -) -PROCESS_LABEL_NONSTANDARD = ( - """ - label 'process_extra_label' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_NONSTANDARD_DUPLICATES = ( - """ - label process_extra_label - label process_extra_label - cpus 12 - """, - 0, - 3, - 0, -) -PROCESS_LABEL_NONE_FOUND = ( - """ - cpus 12 - """, - 0, - 1, - 0, -) - -PROCESS_LABEL_TEST_CASES = [ - PROCESS_LABEL_GOOD, - PROCESS_LABEL_NON_ALPHANUMERIC, - PROCESS_LABEL_GOOD_CONFLICTING, - PROCESS_LABEL_GOOD_DUPLICATES, - PROCESS_LABEL_GOOD_AND_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD_DUPLICATES, - PROCESS_LABEL_NONE_FOUND, -] - - -# Test cases for linting the container definitions - -CONTAINER_SINGLE_GOOD = ( - "Single-line container definition should pass", - """ - container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package - """, - 2, # passed - 0, # warned - 0, # failed -) - -CONTAINER_TWO_LINKS_GOOD = ( - "Multi-line container definition should pass", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 6, - 0, - 0, -) - -CONTAINER_WITH_SPACE_BAD = ( - "Space in container URL should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 5, - 0, - 1, -) - -CONTAINER_MULTIPLE_DBLQUOTES_BAD = ( - "Incorrect quoting of container string should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" - """, - 4, - 0, - 1, -) - -CONTAINER_TEST_CASES = [ - CONTAINER_SINGLE_GOOD, - CONTAINER_TWO_LINKS_GOOD, - CONTAINER_WITH_SPACE_BAD, - CONTAINER_MULTIPLE_DBLQUOTES_BAD, -] - - -class TestModulesLint(TestModules): - def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): - install_obj = nf_core.modules.install.ModuleInstall( - pipeline_dir, - prompt=False, - force=False, - remote_url=GITLAB_URL, - branch=PATCH_BRANCH, - sha=CORRECT_SHA, - ) - - # Install the module - install_obj.install(BISMARK_ALIGN) - - if modify_module: - # Modify the module - module_path = Path(pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) - modify_main_nf(module_path / "main.nf") - - def test_modules_lint_trimgalore(self): - """Test linting the TrimGalore! module""" - self.mods_install.install("trimgalore") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="trimgalore") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_trinity(self): - """Test linting the Trinity module""" - self.mods_install.install("trinity") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="trinity") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_tabix_tabix(self): - """Test linting the tabix/tabix module""" - self.mods_install.install("tabix/tabix") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="tabix/tabix") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_empty(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text - - def test_modules_lint_new_modules(self): - """lint a new module""" - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_no_gitlab(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text - - def test_modules_lint_gitlab_modules(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("fastqc") - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_multiple_remotes(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_registry(self): - """Test linting the samtools module and alternative registry""" - assert self.mods_install.install("samtools/sort") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") - module_lint.lint(print_results=False, module="samtools/sort") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="samtools/sort") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_patched_modules(self): - """ - Test creating a patch file and applying it to a new version of the the files - """ - self._setup_patch(str(self.pipeline_dir), True) - - # Create a patch file - patch_obj = nf_core.modules.patch.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH) - patch_obj.patch(BISMARK_ALIGN) - - # change temporarily working directory to the pipeline directory - # to avoid error from try_apply_patch() during linting - with set_wd(self.pipeline_dir): - module_lint = nf_core.modules.lint.ModuleLint( - directory=self.pipeline_dir, - remote_url=GITLAB_URL, - branch=PATCH_BRANCH, - hide_progress=True, - ) - module_lint.lint( - print_results=False, - all_modules=True, - ) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_check_process_labels(self): - for test_case in PROCESS_LABEL_TEST_CASES: - process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - check_process_labels(mocked_ModuleLint, process.splitlines()) - assert len(mocked_ModuleLint.passed) == passed - assert len(mocked_ModuleLint.warned) == warned - assert len(mocked_ModuleLint.failed) == failed - - def test_modules_lint_check_url(self): - for test_case in CONTAINER_TEST_CASES: - test, process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - for line in process.splitlines(): - if line.strip(): - check_container_link_line(mocked_ModuleLint, line, registry="quay.io") - - assert len(mocked_ModuleLint.passed) == passed, ( - f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}." - ) - assert len(mocked_ModuleLint.warned) == warned, ( - f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}." - ) - assert len(mocked_ModuleLint.failed) == failed, ( - f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." - ) - - def test_modules_lint_update_meta_yml(self): - """update the meta.yml of a module""" - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules, fix=True) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_snapshot_file(self): - """Test linting a module with a snapshot file""" - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_snapshot_file_missing_fail(self): - """Test linting a module with a snapshot file missing, which should fail""" - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ).unlink() - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test.snap", - ).touch() - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snapshot_exists" - - def test_modules_lint_snapshot_file_not_needed(self): - """Test linting a module which doesn't need a snapshot file by removing the snapshot keyword in the main.nf.test file""" - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ) - ) as fh: - content = fh.read() - new_content = content.replace("snapshot(", "snap (") - with open( - Path( - self.nfcore_modules, - "modules", - "nf-core", - "bpipe", - "test", - "tests", - "main.nf.test", - ), - "w", - ) as fh: - fh.write(new_content) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_meta_yml_incorrect_licence_field(self): - """Test linting a module with an incorrect Licence field in meta.yml""" - with open(self.bpipe_test_module_path / "meta.yml") as fh: - meta_yml = yaml.safe_load(fh) - meta_yml["tools"][0]["bpipe"]["licence"] = "[MIT]" - with open( - self.bpipe_test_module_path / "meta.yml", - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - # reset changes - meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_yml_valid" - - def test_modules_meta_yml_output_mismatch(self): - """Test linting a module with an extra entry in output fields in meta.yml compared to module.output""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: - main_nf = fh.read() - main_nf_new = main_nf.replace("emit: sequence_report", "emit: bai") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf_new) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert "Module `meta.yml` does not match `main.nf`" in module_lint.failed[0].message - - def test_modules_meta_yml_incorrect_name(self): - """Test linting a module with an incorrect name in meta.yml""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml")) as fh: - meta_yml = yaml.safe_load(fh) - meta_yml["name"] = "bpipe/test" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - - # reset changes - meta_yml["name"] = "bpipe_test" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_name" - - def test_modules_missing_test_dir(self): - """Test linting a module with a missing test directory""" - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak") - ) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests.bak").rename( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "tests") - ) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_dir_exists" - - def test_modules_missing_test_main_nf(self): - """Test linting a module with a missing test/main.nf file""" - (self.bpipe_test_module_path / "tests" / "main.nf.test").rename( - self.bpipe_test_module_path / "tests" / "main.nf.test.bak" - ) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - (self.bpipe_test_module_path / "tests" / "main.nf.test.bak").rename( - self.bpipe_test_module_path / "tests" / "main.nf.test" - ) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_main_nf_exists" - - def test_modules_unused_pytest_files(self): - """Test linting a nf-test module with files still present in `tests/modules/`""" - Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").mkdir(parents=True, exist_ok=True) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - Path(self.nfcore_modules, "tests", "modules", "bpipe", "test").rmdir() - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_old_test_dir" - - def test_nftest_failing_linting(self): - """Test linting a module which includes other modules in nf-test tests. - Linting tests""" - # Clone modules repo with testing modules - tmp_dir = self.nfcore_modules.parent - self.nfcore_modules = Path(tmp_dir, "modules-test") - Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH) - - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="kallisto/quant") - - assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_yml_valid" - assert module_lint.failed[1].lint_test == "test_main_tags" - assert "kallisto/index" in module_lint.failed[1].message - - def test_modules_absent_version(self): - """Test linting a nf-test module if the versions is absent in the snapshot file `""" - snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" - with open(snap_file) as fh: - content = fh.read() - new_content = content.replace("versions", "foo") - with open(snap_file, "w") as fh: - fh.write(new_content) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(snap_file, "w") as fh: - fh.write(content) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snap_versions" - - def test_modules_empty_file_in_snapshot(self): - """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" - snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "test_snap_md5sum" - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - - def test_modules_empty_file_in_stub_snapshot(self): - """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" - snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" - snap = json.load(snap_file.open()) - content = snap_file.read_text() - snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} - - with open(snap_file, "w") as fh: - json.dump(snap, fh) - - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed) - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - - def test_modules_lint_local(self): - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore") - shutil.move(installed, local) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_local_missing_files(self): - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore") - shutil.move(installed, local) - Path(self.pipeline_dir, "modules", "local", "trimgalore", "environment.yml").unlink() - Path(self.pipeline_dir, "modules", "local", "trimgalore", "meta.yml").unlink() - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - warnings = [x.message for x in module_lint.warned] - assert "Module's `environment.yml` does not exist" in warnings - assert "Module `meta.yml` does not exist" in warnings - - def test_modules_lint_local_old_format(self): - Path(self.pipeline_dir, "modules", "local").mkdir() - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore", "main.nf") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore.nf") - shutil.move(installed, local) - self.mods_remove.remove("trimgalore", force=True) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - - self.main_nf = "main_nf" From 8d903066fb486089ce5eaa0addec8ffc702e552b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 08:11:54 -0500 Subject: [PATCH 061/101] test: Add new lint tests for module changes, deprecations, todos, and version handling - Introduced separate test files for module changes, deprecations, todos, and version functionalities. - Implemented basic structure and placeholder tests for each new test file to ensure future functionality can be added. - Removed the old test_lint.py file to streamline the test organization. --- tests/modules/lint/test_lint.py | 137 ------------------ tests/modules/lint/test_lint_utils.py | 46 ++++++ tests/modules/lint/test_module_changes.py | 66 +++++++++ .../modules/lint/test_module_deprecations.py | 54 +++++++ .../lint/test_module_lint_integration.py | 52 +++++++ tests/modules/lint/test_module_lint_local.py | 60 ++++++++ .../modules/lint/test_module_lint_remotes.py | 50 +++++++ tests/modules/lint/test_module_todos.py | 54 +++++++ tests/modules/lint/test_module_version.py | 66 +++++++++ 9 files changed, 448 insertions(+), 137 deletions(-) delete mode 100644 tests/modules/lint/test_lint.py create mode 100644 tests/modules/lint/test_lint_utils.py create mode 100644 tests/modules/lint/test_module_changes.py create mode 100644 tests/modules/lint/test_module_deprecations.py create mode 100644 tests/modules/lint/test_module_lint_integration.py create mode 100644 tests/modules/lint/test_module_lint_local.py create mode 100644 tests/modules/lint/test_module_lint_remotes.py create mode 100644 tests/modules/lint/test_module_todos.py create mode 100644 tests/modules/lint/test_module_version.py diff --git a/tests/modules/lint/test_lint.py b/tests/modules/lint/test_lint.py deleted file mode 100644 index b70ad53307..0000000000 --- a/tests/modules/lint/test_lint.py +++ /dev/null @@ -1,137 +0,0 @@ -import json -import shutil -from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo - -import nf_core.modules.lint -from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels -from nf_core.utils import set_wd - -from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL - -class TestModulesLint(TestModules): - - def test_modules_lint_trimgalore(self): - """Test linting the TrimGalore! module""" - self.mods_install.install("trimgalore") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="trimgalore") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_trinity(self): - """Test linting the Trinity module""" - self.mods_install.install("trinity") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="trinity") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_tabix_tabix(self): - """Test linting the tabix/tabix module""" - self.mods_install.install("tabix/tabix") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, module="tabix/tabix") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_empty(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text - - def test_modules_lint_new_modules(self): - """lint a new module""" - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_no_gitlab(self): - """Test linting a pipeline with no modules installed""" - self.mods_remove.remove("fastqc", force=True) - self.mods_remove.remove("multiqc", force=True) - nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text - - def test_modules_lint_gitlab_modules(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("fastqc") - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 2 - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_multiple_remotes(self): - """Lint modules from a different remote""" - self.mods_install_gitlab.install("multiqc") - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) - module_lint.lint(print_results=False, all_modules=True) - assert len(module_lint.failed) == 1 - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - - def test_modules_lint_local(self): - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore") - shutil.move(installed, local) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - def test_modules_lint_local_missing_files(self): - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore") - shutil.move(installed, local) - Path(self.pipeline_dir, "modules", "local", "trimgalore", "environment.yml").unlink() - Path(self.pipeline_dir, "modules", "local", "trimgalore", "meta.yml").unlink() - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - warnings = [x.message for x in module_lint.warned] - assert "Module's `environment.yml` does not exist" in warnings - assert "Module `meta.yml` does not exist" in warnings - - def test_modules_lint_local_old_format(self): - Path(self.pipeline_dir, "modules", "local").mkdir() - assert self.mods_install.install("trimgalore") - installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore", "main.nf") - local = Path(self.pipeline_dir, "modules", "local", "trimgalore.nf") - shutil.move(installed, local) - self.mods_remove.remove("trimgalore", force=True) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) - module_lint.lint(print_results=False, local=True) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - - -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - - self.main_nf = "main_nf" diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py new file mode 100644 index 0000000000..a54f6c7193 --- /dev/null +++ b/tests/modules/lint/test_lint_utils.py @@ -0,0 +1,46 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + + self.main_nf = "main_nf" + + +class TestModulesLint(TestModules): + """Core ModuleLint functionality tests""" + + def test_modules_lint_init(self): + """Test ModuleLint initialization""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + assert module_lint.directory == self.pipeline_dir + assert hasattr(module_lint, 'passed') + assert hasattr(module_lint, 'warned') + assert hasattr(module_lint, 'failed') + + def test_mock_module_lint(self): + """Test MockModuleLint utility class""" + mock_lint = MockModuleLint() + assert isinstance(mock_lint.passed, list) + assert isinstance(mock_lint.warned, list) + assert isinstance(mock_lint.failed, list) + assert mock_lint.main_nf == "main_nf" diff --git a/tests/modules/lint/test_module_changes.py b/tests/modules/lint/test_module_changes.py new file mode 100644 index 0000000000..7ec6695523 --- /dev/null +++ b/tests/modules/lint/test_module_changes.py @@ -0,0 +1,66 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import pytest +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.module_changes import module_changes +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + self.main_nf = "main_nf" + + +class TestModuleChanges(TestModules): + """Test module_changes.py functionality""" + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_unchanged(self): + """Test module changes when module is unchanged""" + # Test the functionality of module_changes.py when module is unchanged + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_modified(self): + """Test module changes when module is modified""" + # Test the functionality of module_changes.py when module is modified + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_patched(self): + """Test module changes when module is patched""" + # Test when module has patches applied + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_main_nf_modified(self): + """Test module changes when main.nf is modified""" + # Test when main.nf file is modified + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_meta_yml_modified(self): + """Test module changes when meta.yml is modified""" + # Test when meta.yml file is modified + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_changes_patch_apply_fail(self): + """Test module changes when patch application fails""" + # Test when patch cannot be applied in reverse + pass \ No newline at end of file diff --git a/tests/modules/lint/test_module_deprecations.py b/tests/modules/lint/test_module_deprecations.py new file mode 100644 index 0000000000..b4ca271c9a --- /dev/null +++ b/tests/modules/lint/test_module_deprecations.py @@ -0,0 +1,54 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import pytest +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.module_deprecations import module_deprecations +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + self.main_nf = "main_nf" + + +class TestModuleDeprecations(TestModules): + """Test module_deprecations.py functionality""" + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_deprecations_none(self): + """Test module deprecations when no deprecations exist""" + # Test the functionality of module_deprecations.py when no deprecated files exist + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_deprecations_found(self): + """Test module deprecations when deprecations are found""" + # Test the functionality of module_deprecations.py when deprecated files are found + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_deprecations_functions_nf(self): + """Test module deprecations when functions.nf exists""" + # Test when deprecated functions.nf file is found + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_deprecations_no_functions_nf(self): + """Test module deprecations when no functions.nf exists""" + # Test when no deprecated files are found + pass \ No newline at end of file diff --git a/tests/modules/lint/test_module_lint_integration.py b/tests/modules/lint/test_module_lint_integration.py new file mode 100644 index 0000000000..4eefb5cc27 --- /dev/null +++ b/tests/modules/lint/test_module_lint_integration.py @@ -0,0 +1,52 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +class TestModulesLintIntegration(TestModules): + """Test the overall ModuleLint functionality with different modules""" + + def test_modules_lint_trimgalore(self): + """Test linting the TrimGalore! module""" + self.mods_install.install("trimgalore") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="trimgalore") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_trinity(self): + """Test linting the Trinity module""" + self.mods_install.install("trinity") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="trinity") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_tabix_tabix(self): + """Test linting the tabix/tabix module""" + self.mods_install.install("tabix/tabix") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="tabix/tabix") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_new_modules(self): + """lint a new module""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 \ No newline at end of file diff --git a/tests/modules/lint/test_module_lint_local.py b/tests/modules/lint/test_module_lint_local.py new file mode 100644 index 0000000000..1d86bf933e --- /dev/null +++ b/tests/modules/lint/test_module_lint_local.py @@ -0,0 +1,60 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +class TestModulesLintLocal(TestModules): + """Test ModuleLint functionality with local modules""" + + def test_modules_lint_local(self): + """Test linting local modules""" + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore") + shutil.move(installed, local) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_local_missing_files(self): + """Test linting local modules with missing files""" + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore") + shutil.move(installed, local) + Path(self.pipeline_dir, "modules", "local", "trimgalore", "environment.yml").unlink() + Path(self.pipeline_dir, "modules", "local", "trimgalore", "meta.yml").unlink() + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + warnings = [x.message for x in module_lint.warned] + assert "Module's `environment.yml` does not exist" in warnings + assert "Module `meta.yml` does not exist" in warnings + + def test_modules_lint_local_old_format(self): + """Test linting local modules in old format""" + Path(self.pipeline_dir, "modules", "local").mkdir() + assert self.mods_install.install("trimgalore") + installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore", "main.nf") + local = Path(self.pipeline_dir, "modules", "local", "trimgalore.nf") + shutil.move(installed, local) + self.mods_remove.remove("trimgalore", force=True) + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, local=True) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 \ No newline at end of file diff --git a/tests/modules/lint/test_module_lint_remotes.py b/tests/modules/lint/test_module_lint_remotes.py new file mode 100644 index 0000000000..08c0c1184c --- /dev/null +++ b/tests/modules/lint/test_module_lint_remotes.py @@ -0,0 +1,50 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +class TestModulesLintRemotes(TestModules): + """Test ModuleLint functionality with different remote sources""" + + def test_modules_lint_empty(self): + """Test linting a pipeline with no modules installed""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + assert "No modules from https://github.com/nf-core/modules.git installed in pipeline" in self.caplog.text + + def test_modules_lint_no_gitlab(self): + """Test linting a pipeline with no modules installed from gitlab""" + self.mods_remove.remove("fastqc", force=True) + self.mods_remove.remove("multiqc", force=True) + nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + assert f"No modules from {GITLAB_URL} installed in pipeline" in self.caplog.text + + def test_modules_lint_gitlab_modules(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("fastqc") + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 2 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + + def test_modules_lint_multiple_remotes(self): + """Lint modules from a different remote""" + self.mods_install_gitlab.install("multiqc") + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL) + module_lint.lint(print_results=False, all_modules=True) + assert len(module_lint.failed) == 1 + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 \ No newline at end of file diff --git a/tests/modules/lint/test_module_todos.py b/tests/modules/lint/test_module_todos.py new file mode 100644 index 0000000000..860c1497b1 --- /dev/null +++ b/tests/modules/lint/test_module_todos.py @@ -0,0 +1,54 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import pytest +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.module_todos import module_todos +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + self.main_nf = "main_nf" + + +class TestModuleTodos(TestModules): + """Test module_todos.py functionality""" + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_todos_none(self): + """Test module todos when no TODOs exist""" + # Test the functionality of module_todos.py when no TODO statements are found + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_todos_found(self): + """Test module todos when TODOs are found""" + # Test the functionality of module_todos.py when TODO statements are found + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_todos_markdown(self): + """Test module todos when markdown TODOs exist""" + # Test finding TODO statements in markdown files + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_todos_groovy(self): + """Test module todos when groovy TODOs exist""" + # Test finding TODO statements in Nextflow/Groovy files + pass \ No newline at end of file diff --git a/tests/modules/lint/test_module_version.py b/tests/modules/lint/test_module_version.py new file mode 100644 index 0000000000..e8ff6f4811 --- /dev/null +++ b/tests/modules/lint/test_module_version.py @@ -0,0 +1,66 @@ +import json +import shutil +from pathlib import Path +from typing import Union + +import pytest +import yaml +from git.repo import Repo + +import nf_core.modules.lint +from nf_core.modules.lint.module_version import module_version +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +# A skeleton object with the passed/warned/failed list attrs +# Use this in place of a ModuleLint object to test behaviour of +# linting methods which don't need the full setup +class MockModuleLint: + def __init__(self): + self.passed = [] + self.warned = [] + self.failed = [] + self.main_nf = "main_nf" + + +class TestModuleVersion(TestModules): + """Test module_version.py functionality""" + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_valid(self): + """Test module version when version is valid""" + # Test the functionality of module_version.py when version is valid + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_invalid(self): + """Test module version when version is invalid""" + # Test the functionality of module_version.py when version is invalid + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_up_to_date(self): + """Test module version when module is up to date""" + # Test when module is at the latest version + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_outdated(self): + """Test module version when module is outdated""" + # Test when module has newer version available + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_no_git_sha(self): + """Test module version when no git_sha in modules.json""" + # Test when modules.json is missing git_sha entry + pass + + @pytest.mark.skip(reason="Test implementation pending") + def test_module_version_git_log_fail(self): + """Test module version when git log fetch fails""" + # Test when fetching git log fails + pass \ No newline at end of file From 8deb75aab55c7bced60fd08b5fe494e1e56d515e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 09:22:46 -0500 Subject: [PATCH 062/101] build: Set ruff as default editor --- .vscode/settings.json | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 5ffdff086c..5651d52e08 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -5,5 +5,12 @@ "python.testing.pytestArgs": ["tests", "-v", "--tb=short"], "python.testing.autoTestDiscoverOnSaveEnabled": true, "python.terminal.activateEnvInCurrentTerminal": true, - "python.terminal.shellIntegration.enabled": true + "python.terminal.shellIntegration.enabled": true, + "[python]": { + "editor.defaultFormatter": "charliermarsh.ruff", + "editor.codeActionsOnSave": { + "source.fixAll": "explicit", + "source.organizeImports": "explicit" + } + } } From 92e62b693b64efa2ea9c727c42814d7602b9ad09 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 09:25:05 -0500 Subject: [PATCH 063/101] style: Run ruff format --- tests/modules/lint/test_lint_utils.py | 17 +++-------------- tests/modules/lint/test_main_nf.py | 11 ++++++++++- tests/modules/lint/test_meta_yml.py | 13 ++++++++++++- tests/modules/lint/test_module_changes.py | 14 +------------- tests/modules/lint/test_module_deprecations.py | 14 +------------- .../lint/test_module_lint_integration.py | 12 +----------- tests/modules/lint/test_module_lint_local.py | 9 +-------- tests/modules/lint/test_module_lint_remotes.py | 13 ++----------- tests/modules/lint/test_module_tests.py | 16 +++++++++++++++- tests/modules/lint/test_module_todos.py | 14 +------------- tests/modules/lint/test_module_version.py | 14 +------------- tests/modules/lint/test_patch.py | 13 +++++++++++++ 12 files changed, 61 insertions(+), 99 deletions(-) diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py index a54f6c7193..006bec978a 100644 --- a/tests/modules/lint/test_lint_utils.py +++ b/tests/modules/lint/test_lint_utils.py @@ -1,17 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo - import nf_core.modules.lint -from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL # A skeleton object with the passed/warned/failed list attrs @@ -33,9 +22,9 @@ def test_modules_lint_init(self): """Test ModuleLint initialization""" module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) assert module_lint.directory == self.pipeline_dir - assert hasattr(module_lint, 'passed') - assert hasattr(module_lint, 'warned') - assert hasattr(module_lint, 'failed') + assert hasattr(module_lint, "passed") + assert hasattr(module_lint, "warned") + assert hasattr(module_lint, "failed") def test_mock_module_lint(self): """Test MockModuleLint utility class""" diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index a35ea1836c..4718a9d572 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -1,3 +1,10 @@ +import nf_core.modules.lint +import nf_core.modules.patch +from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels + +from ...test_modules import TestModules +from .test_lint_utils import MockModuleLint + PROCESS_LABEL_GOOD = ( """ label 'process_high' @@ -142,6 +149,8 @@ ] +class TestMainNf(TestModules): + """Test main.nf functionality""" def test_modules_lint_registry(self): """Test linting the samtools module and alternative registry""" @@ -182,4 +191,4 @@ def test_modules_lint_check_url(self): ) assert len(mocked_ModuleLint.failed) == failed, ( f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." - ) \ No newline at end of file + ) diff --git a/tests/modules/lint/test_meta_yml.py b/tests/modules/lint/test_meta_yml.py index 7c59f1a5bf..296e230fec 100644 --- a/tests/modules/lint/test_meta_yml.py +++ b/tests/modules/lint/test_meta_yml.py @@ -1,3 +1,14 @@ +from pathlib import Path + +import yaml + +import nf_core.modules.lint + +from ...test_modules import TestModules + + +class TestMetaYml(TestModules): + """Test meta.yml functionality""" def test_modules_lint_update_meta_yml(self): """update the meta.yml of a module""" @@ -72,4 +83,4 @@ def test_modules_meta_yml_incorrect_name(self): assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_name" \ No newline at end of file + assert module_lint.failed[0].lint_test == "meta_name" diff --git a/tests/modules/lint/test_module_changes.py b/tests/modules/lint/test_module_changes.py index 7ec6695523..a087947ba2 100644 --- a/tests/modules/lint/test_module_changes.py +++ b/tests/modules/lint/test_module_changes.py @@ -1,18 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - import pytest -import yaml -from git.repo import Repo - -import nf_core.modules.lint -from nf_core.modules.lint.module_changes import module_changes -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL # A skeleton object with the passed/warned/failed list attrs @@ -63,4 +51,4 @@ def test_module_changes_meta_yml_modified(self): def test_module_changes_patch_apply_fail(self): """Test module changes when patch application fails""" # Test when patch cannot be applied in reverse - pass \ No newline at end of file + pass diff --git a/tests/modules/lint/test_module_deprecations.py b/tests/modules/lint/test_module_deprecations.py index b4ca271c9a..7168d47f3a 100644 --- a/tests/modules/lint/test_module_deprecations.py +++ b/tests/modules/lint/test_module_deprecations.py @@ -1,18 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - import pytest -import yaml -from git.repo import Repo - -import nf_core.modules.lint -from nf_core.modules.lint.module_deprecations import module_deprecations -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL # A skeleton object with the passed/warned/failed list attrs @@ -51,4 +39,4 @@ def test_module_deprecations_functions_nf(self): def test_module_deprecations_no_functions_nf(self): """Test module deprecations when no functions.nf exists""" # Test when no deprecated files are found - pass \ No newline at end of file + pass diff --git a/tests/modules/lint/test_module_lint_integration.py b/tests/modules/lint/test_module_lint_integration.py index 4eefb5cc27..8a77a969dd 100644 --- a/tests/modules/lint/test_module_lint_integration.py +++ b/tests/modules/lint/test_module_lint_integration.py @@ -1,16 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo - import nf_core.modules.lint -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL class TestModulesLintIntegration(TestModules): @@ -49,4 +39,4 @@ def test_modules_lint_new_modules(self): module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 \ No newline at end of file + assert len(module_lint.warned) >= 0 diff --git a/tests/modules/lint/test_module_lint_local.py b/tests/modules/lint/test_module_lint_local.py index 1d86bf933e..8e1f0fa547 100644 --- a/tests/modules/lint/test_module_lint_local.py +++ b/tests/modules/lint/test_module_lint_local.py @@ -1,16 +1,9 @@ -import json import shutil from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo import nf_core.modules.lint -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL class TestModulesLintLocal(TestModules): @@ -57,4 +50,4 @@ def test_modules_lint_local_old_format(self): module_lint.lint(print_results=False, local=True) assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 \ No newline at end of file + assert len(module_lint.warned) >= 0 diff --git a/tests/modules/lint/test_module_lint_remotes.py b/tests/modules/lint/test_module_lint_remotes.py index 08c0c1184c..57cb797440 100644 --- a/tests/modules/lint/test_module_lint_remotes.py +++ b/tests/modules/lint/test_module_lint_remotes.py @@ -1,16 +1,7 @@ -import json -import shutil -from pathlib import Path -from typing import Union - -import yaml -from git.repo import Repo - import nf_core.modules.lint -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL +from ...utils import GITLAB_URL class TestModulesLintRemotes(TestModules): @@ -47,4 +38,4 @@ def test_modules_lint_multiple_remotes(self): module_lint.lint(print_results=False, all_modules=True) assert len(module_lint.failed) == 1 assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 \ No newline at end of file + assert len(module_lint.warned) >= 0 diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index 7a7b676be5..39ffed9e48 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -1,3 +1,17 @@ +import json +from pathlib import Path + +from git.repo import Repo + +import nf_core.modules.lint +import nf_core.modules.patch + +from ...test_modules import TestModules +from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL + + +class TestModuleTests(TestModules): + """Test module_tests.py functionality""" def test_modules_lint_snapshot_file(self): """Test linting a module with a snapshot file""" @@ -184,4 +198,4 @@ def test_modules_empty_file_in_stub_snapshot(self): # reset the file with open(snap_file, "w") as fh: - fh.write(content) \ No newline at end of file + fh.write(content) diff --git a/tests/modules/lint/test_module_todos.py b/tests/modules/lint/test_module_todos.py index 860c1497b1..9034d031ef 100644 --- a/tests/modules/lint/test_module_todos.py +++ b/tests/modules/lint/test_module_todos.py @@ -1,18 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - import pytest -import yaml -from git.repo import Repo - -import nf_core.modules.lint -from nf_core.modules.lint.module_todos import module_todos -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL # A skeleton object with the passed/warned/failed list attrs @@ -51,4 +39,4 @@ def test_module_todos_markdown(self): def test_module_todos_groovy(self): """Test module todos when groovy TODOs exist""" # Test finding TODO statements in Nextflow/Groovy files - pass \ No newline at end of file + pass diff --git a/tests/modules/lint/test_module_version.py b/tests/modules/lint/test_module_version.py index e8ff6f4811..c1fb5087c1 100644 --- a/tests/modules/lint/test_module_version.py +++ b/tests/modules/lint/test_module_version.py @@ -1,18 +1,6 @@ -import json -import shutil -from pathlib import Path -from typing import Union - import pytest -import yaml -from git.repo import Repo - -import nf_core.modules.lint -from nf_core.modules.lint.module_version import module_version -from nf_core.utils import set_wd from ...test_modules import TestModules -from ...utils import GITLAB_NFTEST_BRANCH, GITLAB_URL # A skeleton object with the passed/warned/failed list attrs @@ -63,4 +51,4 @@ def test_module_version_no_git_sha(self): def test_module_version_git_log_fail(self): """Test module version when git log fetch fails""" # Test when fetching git log fails - pass \ No newline at end of file + pass diff --git a/tests/modules/lint/test_patch.py b/tests/modules/lint/test_patch.py index 7294438cdb..1eb419755e 100644 --- a/tests/modules/lint/test_patch.py +++ b/tests/modules/lint/test_patch.py @@ -1,6 +1,19 @@ +from pathlib import Path +from typing import Union + +import nf_core.modules.install +import nf_core.modules.lint import nf_core.modules.patch +from nf_core.utils import set_wd + +from ...test_modules import TestModules +from ...utils import GITLAB_URL from ..test_patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf + +class TestPatch(TestModules): + """Test patch.py functionality""" + def _setup_patch(self, pipeline_dir: Union[str, Path], modify_module: bool): install_obj = nf_core.modules.install.ModuleInstall( pipeline_dir, From c041f82f2de1286ef7bfe6ed4bfcab485fdb471f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 30 May 2025 10:32:02 -0500 Subject: [PATCH 064/101] test: Enhance test for linting by checking for test_snap_md5sum in passed tests - Updated the assertion to verify the presence of "test_snap_md5sum" in the passed tests. - Improved handling to accommodate both LintResult objects and tuple formats for better robustness. --- tests/modules/lint/test_module_tests.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index 39ffed9e48..b5f361c7d8 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -194,7 +194,21 @@ def test_modules_empty_file_in_stub_snapshot(self): assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - assert any(x.lint_test == "test_snap_md5sum" for x in module_lint.passed) + + # Check for test_snap_md5sum in passed tests (handle both tuple and LintResult formats) + found_test = False + for x in module_lint.passed: + test_name = None + if hasattr(x, "lint_test"): + test_name = x.lint_test + elif isinstance(x, tuple) and len(x) > 0: + test_name = x[0] + + if test_name == "test_snap_md5sum": + found_test = True + break + + assert found_test, "test_snap_md5sum not found in passed tests" # reset the file with open(snap_file, "w") as fh: From 869a8a33f07d6848c4a3aa218358a64136674287 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 28 Jul 2025 14:29:51 +0200 Subject: [PATCH 065/101] clean up test_main_nf.py --- tests/modules/lint/test_main_nf.py | 336 ++++++++++++++--------------- 1 file changed, 167 insertions(+), 169 deletions(-) diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index 4718a9d572..d9194ff1df 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -1,3 +1,5 @@ +import pytest + import nf_core.modules.lint import nf_core.modules.patch from nf_core.modules.lint.main_nf import check_container_link_line, check_process_labels @@ -5,149 +7,6 @@ from ...test_modules import TestModules from .test_lint_utils import MockModuleLint -PROCESS_LABEL_GOOD = ( - """ - label 'process_high' - cpus 12 - """, - 1, - 0, - 0, -) -PROCESS_LABEL_NON_ALPHANUMERIC = ( - """ - label 'a:label:with:colons' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_CONFLICTING = ( - """ - label 'process_high' - label 'process_low' - cpus 12 - """, - 0, - 1, - 0, -) -PROCESS_LABEL_GOOD_DUPLICATES = ( - """ - label 'process_high' - label 'process_high' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_GOOD_AND_NONSTANDARD = ( - """ - label 'process_high' - label 'process_extra_label' - cpus 12 - """, - 1, - 1, - 0, -) -PROCESS_LABEL_NONSTANDARD = ( - """ - label 'process_extra_label' - cpus 12 - """, - 0, - 2, - 0, -) -PROCESS_LABEL_NONSTANDARD_DUPLICATES = ( - """ - label process_extra_label - label process_extra_label - cpus 12 - """, - 0, - 3, - 0, -) -PROCESS_LABEL_NONE_FOUND = ( - """ - cpus 12 - """, - 0, - 1, - 0, -) - -PROCESS_LABEL_TEST_CASES = [ - PROCESS_LABEL_GOOD, - PROCESS_LABEL_NON_ALPHANUMERIC, - PROCESS_LABEL_GOOD_CONFLICTING, - PROCESS_LABEL_GOOD_DUPLICATES, - PROCESS_LABEL_GOOD_AND_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD, - PROCESS_LABEL_NONSTANDARD_DUPLICATES, - PROCESS_LABEL_NONE_FOUND, -] - - -# Test cases for linting the container definitions - -CONTAINER_SINGLE_GOOD = ( - "Single-line container definition should pass", - """ - container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package - """, - 2, # passed - 0, # warned - 0, # failed -) - -CONTAINER_TWO_LINKS_GOOD = ( - "Multi-line container definition should pass", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 6, - 0, - 0, -) - -CONTAINER_WITH_SPACE_BAD = ( - "Space in container URL should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 5, - 0, - 1, -) - -CONTAINER_MULTIPLE_DBLQUOTES_BAD = ( - "Incorrect quoting of container string should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" - """, - 4, - 0, - 1, -) - -CONTAINER_TEST_CASES = [ - CONTAINER_SINGLE_GOOD, - CONTAINER_TWO_LINKS_GOOD, - CONTAINER_WITH_SPACE_BAD, - CONTAINER_MULTIPLE_DBLQUOTES_BAD, -] - class TestMainNf(TestModules): """Test main.nf functionality""" @@ -155,40 +14,179 @@ class TestMainNf(TestModules): def test_modules_lint_registry(self): """Test linting the samtools module and alternative registry""" assert self.mods_install.install("samtools/sort") + + # Test with alternative registry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 + + # Test with default registry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - def test_modules_lint_check_process_labels(self): - for test_case in PROCESS_LABEL_TEST_CASES: - process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - check_process_labels(mocked_ModuleLint, process.splitlines()) - assert len(mocked_ModuleLint.passed) == passed - assert len(mocked_ModuleLint.warned) == warned - assert len(mocked_ModuleLint.failed) == failed - - def test_modules_lint_check_url(self): - for test_case in CONTAINER_TEST_CASES: - test, process, passed, warned, failed = test_case - mocked_ModuleLint = MockModuleLint() - for line in process.splitlines(): - if line.strip(): - check_container_link_line(mocked_ModuleLint, line, registry="quay.io") - - assert len(mocked_ModuleLint.passed) == passed, ( - f"{test}: Expected {passed} PASS, got {len(mocked_ModuleLint.passed)}." - ) - assert len(mocked_ModuleLint.warned) == warned, ( - f"{test}: Expected {warned} WARN, got {len(mocked_ModuleLint.warned)}." - ) - assert len(mocked_ModuleLint.failed) == failed, ( - f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." - ) + @pytest.mark.parametrize( + "process_content,expected_passed,expected_warned,expected_failed", + [ + # Valid process label + ( + """ + label 'process_high' + cpus 12 + """, + 1, + 0, + 0, + ), + # Non-alphanumeric characters in label + ( + """ + label 'a:label:with:colons' + cpus 12 + """, + 0, + 2, + 0, + ), + # Conflicting labels + ( + """ + label 'process_high' + label 'process_low' + cpus 12 + """, + 0, + 1, + 0, + ), + # Duplicate labels + ( + """ + label 'process_high' + label 'process_high' + cpus 12 + """, + 0, + 2, + 0, + ), + # Valid and non-standard labels + ( + """ + label 'process_high' + label 'process_extra_label' + cpus 12 + """, + 1, + 1, + 0, + ), + # Non-standard label only + ( + """ + label 'process_extra_label' + cpus 12 + """, + 0, + 2, + 0, + ), + # Non-standard duplicates without quotes + ( + """ + label process_extra_label + label process_extra_label + cpus 12 + """, + 0, + 3, + 0, + ), + # No label found + ( + """ + cpus 12 + """, + 0, + 1, + 0, + ), + ], + ) + def test_process_labels(self, process_content, expected_passed, expected_warned, expected_failed): + """Test process label validation""" + mock_lint = MockModuleLint() + check_process_labels(mock_lint, process_content.splitlines()) + + assert len(mock_lint.passed) == expected_passed + assert len(mock_lint.warned) == expected_warned + assert len(mock_lint.failed) == expected_failed + + @pytest.mark.parametrize( + "test_name,process_content,expected_passed,expected_warned,expected_failed", + [ + ( + "Single-line container definition should pass", + """ + container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package + """, + 2, + 0, + 0, + ), + ( + "Multi-line container definition should pass", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 6, + 0, + 0, + ), + ( + "Space in container URL should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + """, + 5, + 0, + 1, + ), + ( + "Incorrect quoting of container string should fail", + """ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" + """, + 4, + 0, + 1, + ), + ], + ) + def test_container_links(self, test_name, process_content, expected_passed, expected_warned, expected_failed): + """Test container link validation""" + mock_lint = MockModuleLint() + + for line in process_content.splitlines(): + if line.strip(): + check_container_link_line(mock_lint, line, registry="quay.io") + + assert len(mock_lint.passed) == expected_passed, ( + f"{test_name}: Expected {expected_passed} PASS, got {len(mock_lint.passed)}." + ) + assert len(mock_lint.warned) == expected_warned, ( + f"{test_name}: Expected {expected_warned} WARN, got {len(mock_lint.warned)}." + ) + assert len(mock_lint.failed) == expected_failed, ( + f"{test_name}: Expected {expected_failed} FAIL, got {len(mock_lint.failed)}." + ) From 9a4f113b332f3d9320f89deaf9ebc66e2863eb1c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 28 Jul 2025 12:41:02 +0000 Subject: [PATCH 066/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6890d5ea3..cde0dff176 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ ### Modules +- feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608)) + ### Subworkflows ### General From 28192a0277a8357179ba1c86f9a4f1d1fb78cc72 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 28 Jul 2025 15:29:44 +0200 Subject: [PATCH 067/101] fix tests --- tests/modules/lint/test_main_nf.py | 240 ++++++++++------------------- 1 file changed, 78 insertions(+), 162 deletions(-) diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index d9194ff1df..9e2658ea74 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -8,6 +8,84 @@ from .test_lint_utils import MockModuleLint +@pytest.mark.parametrize( + "content,passed,warned,failed", + [ + # Valid process label + ("label 'process_high'\ncpus 12", 1, 0, 0), + # Non-alphanumeric characters in label + ("label 'a:label:with:colons'\ncpus 12", 0, 2, 0), + # Conflicting labels + ("label 'process_high'\nlabel 'process_low'\ncpus 12", 0, 1, 0), + # Duplicate labels + ("label 'process_high'\nlabel 'process_high'\ncpus 12", 0, 2, 0), + # Valid and non-standard labels + ("label 'process_high'\nlabel 'process_extra_label'\ncpus 12", 1, 1, 0), + # Non-standard label only + ("label 'process_extra_label'\ncpus 12", 0, 2, 0), + # Non-standard duplicates without quotes + ("label process_extra_label\nlabel process_extra_label\ncpus 12", 0, 3, 0), + # No label found + ("cpus 12", 0, 1, 0), + ], +) +def test_process_labels(content, passed, warned, failed): + """Test process label validation""" + mock_lint = MockModuleLint() + check_process_labels(mock_lint, content.splitlines()) + + assert len(mock_lint.passed) == passed + assert len(mock_lint.warned) == warned + assert len(mock_lint.failed) == failed + + +@pytest.mark.parametrize( + "content,passed,warned,failed", + [ + # Single-line container definition should pass + ('container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package', 2, 0, 0), + # Multi-line container definition should pass + ( + '''container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''', + 6, + 0, + 0, + ), + # Space in container URL should fail + ( + '''container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"''', + 5, + 0, + 1, + ), + # Incorrect quoting of container string should fail + ( + '''container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': + "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }"''', + 4, + 0, + 1, + ), + ], +) +def test_container_links(content, passed, warned, failed): + """Test container link validation""" + mock_lint = MockModuleLint() + + for line in content.splitlines(): + if line.strip(): + check_container_link_line(mock_lint, line, registry="quay.io") + + assert len(mock_lint.passed) == passed + assert len(mock_lint.warned) == warned + assert len(mock_lint.failed) == failed + + class TestMainNf(TestModules): """Test main.nf functionality""" @@ -28,165 +106,3 @@ def test_modules_lint_registry(self): assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - - @pytest.mark.parametrize( - "process_content,expected_passed,expected_warned,expected_failed", - [ - # Valid process label - ( - """ - label 'process_high' - cpus 12 - """, - 1, - 0, - 0, - ), - # Non-alphanumeric characters in label - ( - """ - label 'a:label:with:colons' - cpus 12 - """, - 0, - 2, - 0, - ), - # Conflicting labels - ( - """ - label 'process_high' - label 'process_low' - cpus 12 - """, - 0, - 1, - 0, - ), - # Duplicate labels - ( - """ - label 'process_high' - label 'process_high' - cpus 12 - """, - 0, - 2, - 0, - ), - # Valid and non-standard labels - ( - """ - label 'process_high' - label 'process_extra_label' - cpus 12 - """, - 1, - 1, - 0, - ), - # Non-standard label only - ( - """ - label 'process_extra_label' - cpus 12 - """, - 0, - 2, - 0, - ), - # Non-standard duplicates without quotes - ( - """ - label process_extra_label - label process_extra_label - cpus 12 - """, - 0, - 3, - 0, - ), - # No label found - ( - """ - cpus 12 - """, - 0, - 1, - 0, - ), - ], - ) - def test_process_labels(self, process_content, expected_passed, expected_warned, expected_failed): - """Test process label validation""" - mock_lint = MockModuleLint() - check_process_labels(mock_lint, process_content.splitlines()) - - assert len(mock_lint.passed) == expected_passed - assert len(mock_lint.warned) == expected_warned - assert len(mock_lint.failed) == expected_failed - - @pytest.mark.parametrize( - "test_name,process_content,expected_passed,expected_warned,expected_failed", - [ - ( - "Single-line container definition should pass", - """ - container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package - """, - 2, - 0, - 0, - ), - ( - "Multi-line container definition should pass", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 6, - 0, - 0, - ), - ( - "Space in container URL should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" - """, - 5, - 0, - 1, - ), - ( - "Incorrect quoting of container string should fail", - """ - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0 ': - "biocontainers/gatk4:4.4.0.0--py36hdfd78af_0" }" - """, - 4, - 0, - 1, - ), - ], - ) - def test_container_links(self, test_name, process_content, expected_passed, expected_warned, expected_failed): - """Test container link validation""" - mock_lint = MockModuleLint() - - for line in process_content.splitlines(): - if line.strip(): - check_container_link_line(mock_lint, line, registry="quay.io") - - assert len(mock_lint.passed) == expected_passed, ( - f"{test_name}: Expected {expected_passed} PASS, got {len(mock_lint.passed)}." - ) - assert len(mock_lint.warned) == expected_warned, ( - f"{test_name}: Expected {expected_warned} WARN, got {len(mock_lint.warned)}." - ) - assert len(mock_lint.failed) == expected_failed, ( - f"{test_name}: Expected {expected_failed} FAIL, got {len(mock_lint.failed)}." - ) From 378f522f533d1bc2003bf744d84cb6301a52adad Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Mon, 28 Jul 2025 13:53:32 -0500 Subject: [PATCH 068/101] feat\!: replace arm profile with arm64 and emulate_amd64 profiles MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit BREAKING CHANGE: The `arm` profile has been renamed to `arm64` and now provides native ARM64 support using Wave containers instead of x86 emulation. - Replace `arm` profile with `arm64` profile for native ARM64 execution - Add `emulate_amd64` profile for users who need x86 emulation on ARM hardware - The `arm64` profile works universally on Apple Silicon, AWS Graviton, and other ARM64 platforms - Users must update: `-profile arm` → `-profile arm64` (for native) or `-profile emulate_amd64` (for emulation) Fixes #3536 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/pipeline-template/nextflow.config | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index ea80dd8633..60e3934e9f 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -128,7 +128,18 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { + arm64 { + process.arch = 'arm64' + // TODO https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { From 6d10567bf5657dace3ed1a54e18bcd4cdaf2eca8 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 28 Jul 2025 18:59:15 +0000 Subject: [PATCH 069/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cde0dff176..28240a7978 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 1422ae14c9fc578ac80069c724919f3a37f760f5 Mon Sep 17 00:00:00 2001 From: Sol Shenker Date: Tue, 29 Jul 2025 15:25:01 -0400 Subject: [PATCH 070/101] add a description of allowed enum values to the docs --- nf_core/pipelines/schema.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 3a0077cc57..e8e551f47f 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -645,6 +645,9 @@ def markdown_param_table(self, properties, required, columns): out += f"| `{p_key}` " elif column == "description": desc = param.get("description", "").replace("\n", "
") + if "enum" in param: + enum_values = "\\|".join(f"`{e}`" for e in param["enum"]) + desc += f" (Allowed values: {enum_values})" out += f"| {desc} " if param.get("help_text", "") != "": help_txt = param["help_text"].replace("\n", "
") From 8749094b1e6652b1b92c945d1e276ca44c4078f3 Mon Sep 17 00:00:00 2001 From: Sol Shenker Date: Tue, 29 Jul 2025 15:32:21 -0400 Subject: [PATCH 071/101] add changelog update --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cde0dff176..4080596cb0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,6 +47,7 @@ ### General +- Add description of accepted enum values to `nf-core pipelines schema docs` output ([#3693](https://github.com/nf-core/tools/pull/3693)) - update id of ruff hook in pre-commit config ([#3621](https://github.com/nf-core/tools/pull/3621)) - Fixes a bug with the test-datasets subcommand [#3617](https://github.com/nf-core/tools/issues/3617) - Pin python Docker tag to f2fdaec ([#3623](https://github.com/nf-core/tools/pull/3623)) From ff2ba34b65a6e3500c9ec937d620151fe171a0d5 Mon Sep 17 00:00:00 2001 From: Sol Shenker Date: Wed, 30 Jul 2025 06:54:38 -0400 Subject: [PATCH 072/101] Update nf_core/pipelines/schema.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Change message to be consistent with --help Co-authored-by: Júlia Mir Pedrol --- nf_core/pipelines/schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index e8e551f47f..1164f0a8c5 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -647,7 +647,7 @@ def markdown_param_table(self, properties, required, columns): desc = param.get("description", "").replace("\n", "
") if "enum" in param: enum_values = "\\|".join(f"`{e}`" for e in param["enum"]) - desc += f" (Allowed values: {enum_values})" + desc += f" (accepted: {enum_values})" out += f"| {desc} " if param.get("help_text", "") != "": help_txt = param["help_text"].replace("\n", "
") From beb29d1f6e2b3256477b9961774fb53eeaed5334 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 1 Aug 2025 00:27:20 +0000 Subject: [PATCH 073/101] Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.7 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 71ba2b4a0c..9819c0d49d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.12.2 + rev: v0.12.7 hooks: - id: ruff-check # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 2e16fa5b2a84f0d2a41753de085409045c4c2b89 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 1 Aug 2025 00:27:25 +0000 Subject: [PATCH 074/101] Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 71ba2b4a0c..68be74749b 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -32,7 +32,7 @@ repos: tests/pipelines/__snapshots__/.* )$ - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.16.1" + rev: "v1.17.1" hooks: - id: mypy additional_dependencies: From b2043433bf9864c7c1860fc6f36f3af1fa973372 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 1 Aug 2025 00:27:29 +0000 Subject: [PATCH 075/101] Update dependency textual to v5 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 1e833f9fe8..15ae184b2d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -20,7 +20,7 @@ rich>=13.3.1 rocrate repo2rocrate tabulate -textual==3.5.0 +textual==5.1.1 trogon pdiff ruamel.yaml From c1044fc50df64406263b3baed710537fa7f26761 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 1 Aug 2025 00:28:15 +0000 Subject: [PATCH 076/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cde0dff176..20b568612b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Update pre-commit hook pre-commit/mirrors-mypy to v1.17.1 ([#3698](https://github.com/nf-core/tools/pull/3698)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From b3c6411883515250d13e29a884caea8fe228d5e5 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 1 Aug 2025 00:28:16 +0000 Subject: [PATCH 077/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cde0dff176..2fcaf3b4a2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Update pre-commit hook astral-sh/ruff-pre-commit to v0.12.7 ([#3697](https://github.com/nf-core/tools/pull/3697)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 8d0ad78eeabd8bf8e34725a7cfd5c53d64fadde7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 1 Aug 2025 00:28:21 +0000 Subject: [PATCH 078/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cde0dff176..6f0495c5fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Update dependency textual to v5 ([#3699](https://github.com/nf-core/tools/pull/3699)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 715508c7103cfaaad943a98cab4973da8ecf5910 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 12 Aug 2025 11:43:09 +0200 Subject: [PATCH 079/101] Update python:3.13-slim Docker digest to 4c2cf99 (#3700) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update python:3.13-slim Docker digest to 4c2cf99 * [automated] Update CHANGELOG.md --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: nf-core-bot Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 1 + Dockerfile | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d0afbc759c..8e87170afe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674)) - Update marocchino/sticky-pull-request-comment digest to 7737449 ([#3681](https://github.com/nf-core/tools/pull/3681)) +- Update python:3.13-slim Docker digest to 4c2cf99 ([#3700](https://github.com/nf-core/tools/pull/3700)) - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] diff --git a/Dockerfile b/Dockerfile index 526eb7e378..0c1cd51f00 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.13-slim@sha256:6544e0e002b40ae0f59bc3618b07c1e48064c4faed3a15ae2fbd2e8f663e8283 +FROM python:3.13-slim@sha256:4c2cf9917bd1cbacc5e9b07320025bdb7cdf2df7b0ceaccb55e9dd7e30987419 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for nf-core/tools" From 59b0e175a74145b7fb6e1279c16f65e52c54a15d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 12 Aug 2025 11:53:35 +0200 Subject: [PATCH 080/101] update textual snapshots --- .../test_basic_details_custom.svg | 244 ++++++++-------- .../test_basic_details_nfcore.svg | 252 ++++++++--------- .../test_create_app/test_choose_type.svg | 244 ++++++++-------- .../test_customisation_help.svg | 260 +++++++++--------- .../test_create_app/test_final_details.svg | 240 ++++++++-------- .../test_create_app/test_github_details.svg | 256 ++++++++--------- .../test_github_exit_message.svg | 246 ++++++++--------- .../test_create_app/test_github_question.svg | 234 ++++++++-------- .../test_create_app/test_type_custom.svg | 256 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 248 ++++++++--------- .../test_type_nfcore_validation.svg | 248 ++++++++--------- .../test_create_app/test_welcome.svg | 242 ++++++++-------- 12 files changed, 1485 insertions(+), 1485 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 3d74d0761e..1c47e8a52a 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-2233325667-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-2233325667-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #191919 } -.terminal-r9 { fill: #737373 } -.terminal-r10 { fill: #b93c5b } -.terminal-r11 { fill: #2d2d2d } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #e0e0e0;font-weight: bold } -.terminal-r14 { fill: #0a180e;font-weight: bold } -.terminal-r15 { fill: #0d0d0d } -.terminal-r16 { fill: #495259 } -.terminal-r17 { fill: #ffa62b;font-weight: bold } + .terminal-2233325667-r1 { fill: #c5c8c6 } +.terminal-2233325667-r2 { fill: #e0e0e0 } +.terminal-2233325667-r3 { fill: #a0a3a6 } +.terminal-2233325667-r4 { fill: #0178d4;font-weight: bold } +.terminal-2233325667-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-2233325667-r6 { fill: #121212 } +.terminal-2233325667-r7 { fill: #008139 } +.terminal-2233325667-r8 { fill: #191919 } +.terminal-2233325667-r9 { fill: #737373 } +.terminal-2233325667-r10 { fill: #b93c5b } +.terminal-2233325667-r11 { fill: #2d2d2d } +.terminal-2233325667-r12 { fill: #7ae998 } +.terminal-2233325667-r13 { fill: #e0e0e0;font-weight: bold } +.terminal-2233325667-r14 { fill: #0a180e;font-weight: bold } +.terminal-2233325667-r15 { fill: #0d0d0d } +.terminal-2233325667-r16 { fill: #495259 } +.terminal-2233325667-r17 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 8ccef7d421..d2b35ce0cd 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1850118853-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1850118853-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #084724 } -.terminal-r8 { fill: #0178d4 } -.terminal-r9 { fill: #a2a2a2 } -.terminal-r10 { fill: #797979 } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #191919 } -.terminal-r13 { fill: #737373 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #7ae998 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0a180e;font-weight: bold } -.terminal-r18 { fill: #0d0d0d } -.terminal-r19 { fill: #008139 } -.terminal-r20 { fill: #495259 } -.terminal-r21 { fill: #ffa62b;font-weight: bold } + .terminal-1850118853-r1 { fill: #c5c8c6 } +.terminal-1850118853-r2 { fill: #e0e0e0 } +.terminal-1850118853-r3 { fill: #a0a3a6 } +.terminal-1850118853-r4 { fill: #0178d4;font-weight: bold } +.terminal-1850118853-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-1850118853-r6 { fill: #121212 } +.terminal-1850118853-r7 { fill: #084724 } +.terminal-1850118853-r8 { fill: #0178d4 } +.terminal-1850118853-r9 { fill: #a2a2a2 } +.terminal-1850118853-r10 { fill: #797979 } +.terminal-1850118853-r11 { fill: #b93c5b } +.terminal-1850118853-r12 { fill: #191919 } +.terminal-1850118853-r13 { fill: #737373 } +.terminal-1850118853-r14 { fill: #2d2d2d } +.terminal-1850118853-r15 { fill: #7ae998 } +.terminal-1850118853-r16 { fill: #e0e0e0;font-weight: bold } +.terminal-1850118853-r17 { fill: #0a180e;font-weight: bold } +.terminal-1850118853-r18 { fill: #0d0d0d } +.terminal-1850118853-r19 { fill: #008139 } +.terminal-1850118853-r20 { fill: #495259 } +.terminal-1850118853-r21 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 8c7c257684..1b1bb0ba41 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3629807493-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3629807493-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #0178d4;text-decoration: underline; } -.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } -.terminal-r7 { fill: #e1e1e1;font-weight: bold } -.terminal-r8 { fill: #e0e0e0;font-style: italic; } -.terminal-r9 { fill: #7ae998 } -.terminal-r10 { fill: #6db2ff } -.terminal-r11 { fill: #55c076;font-weight: bold } -.terminal-r12 { fill: #ddedf9;font-weight: bold } -.terminal-r13 { fill: #008139 } -.terminal-r14 { fill: #004295 } -.terminal-r15 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r16 { fill: #ffa62b;font-weight: bold } -.terminal-r17 { fill: #495259 } + .terminal-3629807493-r1 { fill: #c5c8c6 } +.terminal-3629807493-r2 { fill: #e0e0e0 } +.terminal-3629807493-r3 { fill: #a0a3a6 } +.terminal-3629807493-r4 { fill: #0178d4;font-weight: bold } +.terminal-3629807493-r5 { fill: #0178d4;text-decoration: underline; } +.terminal-3629807493-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } +.terminal-3629807493-r7 { fill: #e1e1e1;font-weight: bold } +.terminal-3629807493-r8 { fill: #e0e0e0;font-style: italic; } +.terminal-3629807493-r9 { fill: #7ae998 } +.terminal-3629807493-r10 { fill: #6db2ff } +.terminal-3629807493-r11 { fill: #55c076;font-weight: bold } +.terminal-3629807493-r12 { fill: #ddedf9;font-weight: bold } +.terminal-3629807493-r13 { fill: #008139 } +.terminal-3629807493-r14 { fill: #004295 } +.terminal-3629807493-r15 { fill: #e1e1e1;text-decoration: underline; } +.terminal-3629807493-r16 { fill: #ffa62b;font-weight: bold } +.terminal-3629807493-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the● Your pipeline will never be part of nf-core -nf-core community● You want full control over all features that -● You think that there's an outside chanceare included from the template (including -that it ever could be part of nf-corethose that are mandatory for nf-core). - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the● Your pipeline will never be part of nf-core +nf-core community● You want full control over all features that +● You think that there's an outside chanceare included from the template (including +that it ever could be part of nf-corethose that are mandatory for nf-core). + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index e6bab82962..cc08768389 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,259 +19,259 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3014319722-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3014319722-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #191919 } -.terminal-r7 { fill: #1e1e1e } -.terminal-r8 { fill: #0178d4;text-decoration: underline; } -.terminal-r9 { fill: #6db2ff } -.terminal-r10 { fill: #808080 } -.terminal-r11 { fill: #ddedf9;font-weight: bold } -.terminal-r12 { fill: #000000 } -.terminal-r13 { fill: #004295 } -.terminal-r14 { fill: #0178d4 } -.terminal-r15 { fill: #2d2d2d } -.terminal-r16 { fill: #272727 } -.terminal-r17 { fill: #e0e0e0;font-weight: bold } -.terminal-r18 { fill: #0d0d0d } -.terminal-r19 { fill: #a5a5a5;font-weight: bold } -.terminal-r20 { fill: #e4e4e4;font-weight: bold } -.terminal-r21 { fill: #7ae998 } -.terminal-r22 { fill: #0a180e;font-weight: bold } -.terminal-r23 { fill: #008139 } -.terminal-r24 { fill: #ffa62b;font-weight: bold } -.terminal-r25 { fill: #495259 } + .terminal-3014319722-r1 { fill: #c5c8c6 } +.terminal-3014319722-r2 { fill: #e0e0e0 } +.terminal-3014319722-r3 { fill: #a0a3a6 } +.terminal-3014319722-r4 { fill: #0178d4;font-weight: bold } +.terminal-3014319722-r5 { fill: #121212 } +.terminal-3014319722-r6 { fill: #191919 } +.terminal-3014319722-r7 { fill: #1e1e1e } +.terminal-3014319722-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-3014319722-r9 { fill: #6db2ff } +.terminal-3014319722-r10 { fill: #808080 } +.terminal-3014319722-r11 { fill: #ddedf9;font-weight: bold } +.terminal-3014319722-r12 { fill: #000000 } +.terminal-3014319722-r13 { fill: #004295 } +.terminal-3014319722-r14 { fill: #0178d4 } +.terminal-3014319722-r15 { fill: #2d2d2d } +.terminal-3014319722-r16 { fill: #272727 } +.terminal-3014319722-r17 { fill: #e0e0e0;font-weight: bold } +.terminal-3014319722-r18 { fill: #0d0d0d } +.terminal-3014319722-r19 { fill: #a5a5a5;font-weight: bold } +.terminal-3014319722-r20 { fill: #e4e4e4;font-weight: bold } +.terminal-3014319722-r21 { fill: #7ae998 } +.terminal-3014319722-r22 { fill: #0a180e;font-weight: bold } +.terminal-3014319722-r23 { fill: #008139 } +.terminal-3014319722-r24 { fill: #ffa62b;font-weight: bold } +.terminal-3014319722-r25 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: - -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index 3e0fe54057..01a735e01c 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,249 +19,249 @@ font-weight: 700; } - .terminal-matrix { + .terminal-278309279-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-278309279-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #b93c5b } -.terminal-r9 { fill: #2d2d2d } -.terminal-r10 { fill: #7ae998 } -.terminal-r11 { fill: #e0e0e0;font-weight: bold } -.terminal-r12 { fill: #0a180e;font-weight: bold } -.terminal-r13 { fill: #0d0d0d } -.terminal-r14 { fill: #495259 } -.terminal-r15 { fill: #ffa62b;font-weight: bold } + .terminal-278309279-r1 { fill: #c5c8c6 } +.terminal-278309279-r2 { fill: #e0e0e0 } +.terminal-278309279-r3 { fill: #a0a3a6 } +.terminal-278309279-r4 { fill: #0178d4;font-weight: bold } +.terminal-278309279-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-278309279-r6 { fill: #121212 } +.terminal-278309279-r7 { fill: #008139 } +.terminal-278309279-r8 { fill: #b93c5b } +.terminal-278309279-r9 { fill: #2d2d2d } +.terminal-278309279-r10 { fill: #7ae998 } +.terminal-278309279-r11 { fill: #e0e0e0;font-weight: bold } +.terminal-278309279-r12 { fill: #0a180e;font-weight: bold } +.terminal-278309279-r13 { fill: #0d0d0d } +.terminal-278309279-r14 { fill: #495259 } +.terminal-278309279-r15 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Final details - - - - -First version of the pipelinePath to the output directory where the -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Final details + + + + +First version of the pipelinePath to the output directory where the +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 6c83c1497b..363074b566 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3615996459-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3615996459-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #2d2d2d } -.terminal-r7 { fill: #e0e0e0;font-weight: bold } -.terminal-r8 { fill: #121212 } -.terminal-r9 { fill: #008139 } -.terminal-r10 { fill: #0d0d0d } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #0f4b79 } -.terminal-r13 { fill: #a0a0a0;font-weight: bold } -.terminal-r14 { fill: #191919 } -.terminal-r15 { fill: #1e1e1e } -.terminal-r16 { fill: #808080 } -.terminal-r17 { fill: #7ae998 } -.terminal-r18 { fill: #6db2ff } -.terminal-r19 { fill: #0a180e;font-weight: bold } -.terminal-r20 { fill: #ddedf9;font-weight: bold } -.terminal-r21 { fill: #004295 } -.terminal-r22 { fill: #495259 } -.terminal-r23 { fill: #ffa62b;font-weight: bold } + .terminal-3615996459-r1 { fill: #c5c8c6 } +.terminal-3615996459-r2 { fill: #e0e0e0 } +.terminal-3615996459-r3 { fill: #a0a3a6 } +.terminal-3615996459-r4 { fill: #0178d4;font-weight: bold } +.terminal-3615996459-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-3615996459-r6 { fill: #2d2d2d } +.terminal-3615996459-r7 { fill: #e0e0e0;font-weight: bold } +.terminal-3615996459-r8 { fill: #121212 } +.terminal-3615996459-r9 { fill: #008139 } +.terminal-3615996459-r10 { fill: #0d0d0d } +.terminal-3615996459-r11 { fill: #b93c5b } +.terminal-3615996459-r12 { fill: #0f4b79 } +.terminal-3615996459-r13 { fill: #a0a0a0;font-weight: bold } +.terminal-3615996459-r14 { fill: #191919 } +.terminal-3615996459-r15 { fill: #1e1e1e } +.terminal-3615996459-r16 { fill: #808080 } +.terminal-3615996459-r17 { fill: #7ae998 } +.terminal-3615996459-r18 { fill: #6db2ff } +.terminal-3615996459-r19 { fill: #0a180e;font-weight: bold } +.terminal-3615996459-r20 { fill: #ddedf9;font-weight: bold } +.terminal-3615996459-r21 { fill: #004295 } +.terminal-3615996459-r22 { fill: #495259 } +.terminal-3615996459-r23 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - -Now that we have created a new pipeline locally, we can create a new GitHub repository and push -the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -The name of the organisation where theThe name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - -▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + +Now that we have created a new pipeline locally, we can create a new GitHub repository and push +the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +The name of the organisation where theThe name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index f28631fc53..79fefaa71b 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,252 +19,252 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3190985874-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3190985874-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #008000 } -.terminal-r6 { fill: #0000ff } -.terminal-r7 { fill: #ffff00 } -.terminal-r8 { fill: #e1e1e1;font-weight: bold } -.terminal-r9 { fill: #d2d2d2 } -.terminal-r10 { fill: #82aaff } -.terminal-r11 { fill: #eeffff } -.terminal-r12 { fill: #0f4b79 } -.terminal-r13 { fill: #a0a0a0;font-weight: bold } -.terminal-r14 { fill: #7ae998 } -.terminal-r15 { fill: #55c076;font-weight: bold } -.terminal-r16 { fill: #008139 } -.terminal-r17 { fill: #ffa62b;font-weight: bold } -.terminal-r18 { fill: #495259 } + .terminal-3190985874-r1 { fill: #c5c8c6 } +.terminal-3190985874-r2 { fill: #e0e0e0 } +.terminal-3190985874-r3 { fill: #a0a3a6 } +.terminal-3190985874-r4 { fill: #0178d4;font-weight: bold } +.terminal-3190985874-r5 { fill: #008000 } +.terminal-3190985874-r6 { fill: #0000ff } +.terminal-3190985874-r7 { fill: #ffff00 } +.terminal-3190985874-r8 { fill: #e1e1e1;font-weight: bold } +.terminal-3190985874-r9 { fill: #d2d2d2 } +.terminal-3190985874-r10 { fill: #82aaff } +.terminal-3190985874-r11 { fill: #eeffff } +.terminal-3190985874-r12 { fill: #0f4b79 } +.terminal-3190985874-r13 { fill: #a0a0a0;font-weight: bold } +.terminal-3190985874-r14 { fill: #7ae998 } +.terminal-3190985874-r15 { fill: #55c076;font-weight: bold } +.terminal-3190985874-r16 { fill: #008139 } +.terminal-3190985874-r17 { fill: #ffa62b;font-weight: bold } +.terminal-3190985874-r18 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -If you would like to create the GitHub repository later, you can do it manually by following -these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +If you would like to create the GitHub repository later, you can do it manually by following +these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 77494c0bfe..08aa0f1e15 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,246 +19,246 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1448878859-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1448878859-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #7ae998 } -.terminal-r6 { fill: #6db2ff } -.terminal-r7 { fill: #55c076;font-weight: bold } -.terminal-r8 { fill: #ddedf9;font-weight: bold } -.terminal-r9 { fill: #008139 } -.terminal-r10 { fill: #004295 } -.terminal-r11 { fill: #ffa62b;font-weight: bold } -.terminal-r12 { fill: #495259 } + .terminal-1448878859-r1 { fill: #c5c8c6 } +.terminal-1448878859-r2 { fill: #e0e0e0 } +.terminal-1448878859-r3 { fill: #a0a3a6 } +.terminal-1448878859-r4 { fill: #0178d4;font-weight: bold } +.terminal-1448878859-r5 { fill: #7ae998 } +.terminal-1448878859-r6 { fill: #6db2ff } +.terminal-1448878859-r7 { fill: #55c076;font-weight: bold } +.terminal-1448878859-r8 { fill: #ddedf9;font-weight: bold } +.terminal-1448878859-r9 { fill: #008139 } +.terminal-1448878859-r10 { fill: #004295 } +.terminal-1448878859-r11 { fill: #ffa62b;font-weight: bold } +.terminal-1448878859-r12 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - - -After creating the pipeline template locally, we can create a GitHub repository and push the -code to it. - -Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + + +After creating the pipeline template locally, we can create a GitHub repository and push the +code to it. + +Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index df8d2ee879..a254873ced 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3868623164-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3868623164-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #0178d4 } -.terminal-r7 { fill: #272727 } -.terminal-r8 { fill: #0178d4;text-decoration: underline; } -.terminal-r9 { fill: #191919 } -.terminal-r10 { fill: #6db2ff } -.terminal-r11 { fill: #1e1e1e } -.terminal-r12 { fill: #808080 } -.terminal-r13 { fill: #ddedf9;font-weight: bold } -.terminal-r14 { fill: #004295 } -.terminal-r15 { fill: #000000 } -.terminal-r16 { fill: #2d2d2d } -.terminal-r17 { fill: #7ae998 } -.terminal-r18 { fill: #e0e0e0;font-weight: bold } -.terminal-r19 { fill: #0a180e;font-weight: bold } -.terminal-r20 { fill: #0d0d0d } -.terminal-r21 { fill: #008139 } -.terminal-r22 { fill: #ffa62b;font-weight: bold } -.terminal-r23 { fill: #495259 } + .terminal-3868623164-r1 { fill: #c5c8c6 } +.terminal-3868623164-r2 { fill: #e0e0e0 } +.terminal-3868623164-r3 { fill: #a0a3a6 } +.terminal-3868623164-r4 { fill: #0178d4;font-weight: bold } +.terminal-3868623164-r5 { fill: #121212 } +.terminal-3868623164-r6 { fill: #0178d4 } +.terminal-3868623164-r7 { fill: #272727 } +.terminal-3868623164-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-3868623164-r9 { fill: #191919 } +.terminal-3868623164-r10 { fill: #6db2ff } +.terminal-3868623164-r11 { fill: #1e1e1e } +.terminal-3868623164-r12 { fill: #808080 } +.terminal-3868623164-r13 { fill: #ddedf9;font-weight: bold } +.terminal-3868623164-r14 { fill: #004295 } +.terminal-3868623164-r15 { fill: #000000 } +.terminal-3868623164-r16 { fill: #2d2d2d } +.terminal-3868623164-r17 { fill: #7ae998 } +.terminal-3868623164-r18 { fill: #e0e0e0;font-weight: bold } +.terminal-3868623164-r19 { fill: #0a180e;font-weight: bold } +.terminal-3868623164-r20 { fill: #0d0d0d } +.terminal-3868623164-r21 { fill: #008139 } +.terminal-3868623164-r22 { fill: #ffa62b;font-weight: bold } +.terminal-3868623164-r23 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Continuous Integration & Testing - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add testing profilesAdd two default testing Show help  -▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index f594d2348a..523356c03d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1870149918-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1870149918-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #191919 } -.terminal-r7 { fill: #6db2ff } -.terminal-r8 { fill: #1e1e1e } -.terminal-r9 { fill: #808080 } -.terminal-r10 { fill: #ddedf9;font-weight: bold } -.terminal-r11 { fill: #004295 } -.terminal-r12 { fill: #2d2d2d } -.terminal-r13 { fill: #7ae998 } -.terminal-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-r15 { fill: #0a180e;font-weight: bold } -.terminal-r16 { fill: #0d0d0d } -.terminal-r17 { fill: #008139 } -.terminal-r18 { fill: #ffa62b;font-weight: bold } -.terminal-r19 { fill: #495259 } + .terminal-1870149918-r1 { fill: #c5c8c6 } +.terminal-1870149918-r2 { fill: #e0e0e0 } +.terminal-1870149918-r3 { fill: #a0a3a6 } +.terminal-1870149918-r4 { fill: #0178d4;font-weight: bold } +.terminal-1870149918-r5 { fill: #121212 } +.terminal-1870149918-r6 { fill: #191919 } +.terminal-1870149918-r7 { fill: #6db2ff } +.terminal-1870149918-r8 { fill: #1e1e1e } +.terminal-1870149918-r9 { fill: #808080 } +.terminal-1870149918-r10 { fill: #ddedf9;font-weight: bold } +.terminal-1870149918-r11 { fill: #004295 } +.terminal-1870149918-r12 { fill: #2d2d2d } +.terminal-1870149918-r13 { fill: #7ae998 } +.terminal-1870149918-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-1870149918-r15 { fill: #0a180e;font-weight: bold } +.terminal-1870149918-r16 { fill: #0d0d0d } +.terminal-1870149918-r17 { fill: #008139 } +.terminal-1870149918-r18 { fill: #ffa62b;font-weight: bold } +.terminal-1870149918-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use GPUAdd GPU support to the Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use reference genomesThe pipeline will be Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +of the most common +reference genome files +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use multiqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +generates an HTML report +for quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use fastqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +performs quality control +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use nf-schemaUse the nf-schema Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use GPUAdd GPU support to the Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 4d3a837545..aaa8eebf67 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1227656248-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1227656248-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #084724 } -.terminal-r8 { fill: #762b3d } -.terminal-r9 { fill: #a2a2a2 } -.terminal-r10 { fill: #737373 } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #2d2d2d } -.terminal-r13 { fill: #7ae998 } -.terminal-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-r15 { fill: #55c076;font-weight: bold } -.terminal-r16 { fill: #0d0d0d } -.terminal-r17 { fill: #008139 } -.terminal-r18 { fill: #ffa62b;font-weight: bold } -.terminal-r19 { fill: #495259 } + .terminal-1227656248-r1 { fill: #c5c8c6 } +.terminal-1227656248-r2 { fill: #e0e0e0 } +.terminal-1227656248-r3 { fill: #a0a3a6 } +.terminal-1227656248-r4 { fill: #0178d4;font-weight: bold } +.terminal-1227656248-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-1227656248-r6 { fill: #121212 } +.terminal-1227656248-r7 { fill: #084724 } +.terminal-1227656248-r8 { fill: #762b3d } +.terminal-1227656248-r9 { fill: #a2a2a2 } +.terminal-1227656248-r10 { fill: #737373 } +.terminal-1227656248-r11 { fill: #b93c5b } +.terminal-1227656248-r12 { fill: #2d2d2d } +.terminal-1227656248-r13 { fill: #7ae998 } +.terminal-1227656248-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-1227656248-r15 { fill: #55c076;font-weight: bold } +.terminal-1227656248-r16 { fill: #0d0d0d } +.terminal-1227656248-r17 { fill: #008139 } +.terminal-1227656248-r18 { fill: #ffa62b;font-weight: bold } +.terminal-1227656248-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 875d7139cd..1c2172a66b 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,250 +19,250 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3327359260-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3327359260-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #008000 } -.terminal-r5 { fill: #0000ff } -.terminal-r6 { fill: #ffff00 } -.terminal-r7 { fill: #0178d4;font-weight: bold } -.terminal-r8 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r9 { fill: #0f4b79 } -.terminal-r10 { fill: #e2e2e2;text-decoration: underline; } -.terminal-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #55c076;font-weight: bold } -.terminal-r14 { fill: #008139 } -.terminal-r15 { fill: #ffa62b;font-weight: bold } -.terminal-r16 { fill: #495259 } + .terminal-3327359260-r1 { fill: #c5c8c6 } +.terminal-3327359260-r2 { fill: #e0e0e0 } +.terminal-3327359260-r3 { fill: #a0a3a6 } +.terminal-3327359260-r4 { fill: #008000 } +.terminal-3327359260-r5 { fill: #0000ff } +.terminal-3327359260-r6 { fill: #ffff00 } +.terminal-3327359260-r7 { fill: #0178d4;font-weight: bold } +.terminal-3327359260-r8 { fill: #e1e1e1;text-decoration: underline; } +.terminal-3327359260-r9 { fill: #0f4b79 } +.terminal-3327359260-r10 { fill: #e2e2e2;text-decoration: underline; } +.terminal-3327359260-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } +.terminal-3327359260-r12 { fill: #7ae998 } +.terminal-3327359260-r13 { fill: #55c076;font-weight: bold } +.terminal-3327359260-r14 { fill: #008139 } +.terminal-3327359260-r15 { fill: #ffa62b;font-weight: bold } +.terminal-3327359260-r16 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - + - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core -pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core +pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette From 784da0ee515a3d498bfa8a3373118f2919cd6a0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 12 Aug 2025 10:03:56 +0000 Subject: [PATCH 081/101] update textual snapshots --- .../test_basic_details_custom.svg | 246 ++++++++-------- .../test_basic_details_nfcore.svg | 254 ++++++++--------- .../test_create_app/test_choose_type.svg | 246 ++++++++-------- .../test_customisation_help.svg | 262 +++++++++--------- .../test_create_app/test_final_details.svg | 242 ++++++++-------- .../test_create_app/test_github_details.svg | 258 ++++++++--------- .../test_github_exit_message.svg | 248 ++++++++--------- .../test_create_app/test_github_question.svg | 236 ++++++++-------- .../test_create_app/test_type_custom.svg | 257 +++++++++-------- .../test_create_app/test_type_nfcore.svg | 250 ++++++++--------- .../test_type_nfcore_validation.svg | 250 ++++++++--------- .../test_create_app/test_welcome.svg | 244 ++++++++-------- 12 files changed, 1496 insertions(+), 1497 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 1c47e8a52a..e89f85c871 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-2233325667-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2233325667-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2233325667-r1 { fill: #c5c8c6 } -.terminal-2233325667-r2 { fill: #e0e0e0 } -.terminal-2233325667-r3 { fill: #a0a3a6 } -.terminal-2233325667-r4 { fill: #0178d4;font-weight: bold } -.terminal-2233325667-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-2233325667-r6 { fill: #121212 } -.terminal-2233325667-r7 { fill: #008139 } -.terminal-2233325667-r8 { fill: #191919 } -.terminal-2233325667-r9 { fill: #737373 } -.terminal-2233325667-r10 { fill: #b93c5b } -.terminal-2233325667-r11 { fill: #2d2d2d } -.terminal-2233325667-r12 { fill: #7ae998 } -.terminal-2233325667-r13 { fill: #e0e0e0;font-weight: bold } -.terminal-2233325667-r14 { fill: #0a180e;font-weight: bold } -.terminal-2233325667-r15 { fill: #0d0d0d } -.terminal-2233325667-r16 { fill: #495259 } -.terminal-2233325667-r17 { fill: #ffa62b;font-weight: bold } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #008139 } +.terminal-r8 { fill: #191919 } +.terminal-r9 { fill: #737373 } +.terminal-r10 { fill: #b93c5b } +.terminal-r11 { fill: #2d2d2d } +.terminal-r12 { fill: #7ae998 } +.terminal-r13 { fill: #e0e0e0;font-weight: bold } +.terminal-r14 { fill: #0a180e;font-weight: bold } +.terminal-r15 { fill: #0d0d0d } +.terminal-r16 { fill: #495259 } +.terminal-r17 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index d2b35ce0cd..9e26a85871 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-1850118853-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1850118853-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1850118853-r1 { fill: #c5c8c6 } -.terminal-1850118853-r2 { fill: #e0e0e0 } -.terminal-1850118853-r3 { fill: #a0a3a6 } -.terminal-1850118853-r4 { fill: #0178d4;font-weight: bold } -.terminal-1850118853-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-1850118853-r6 { fill: #121212 } -.terminal-1850118853-r7 { fill: #084724 } -.terminal-1850118853-r8 { fill: #0178d4 } -.terminal-1850118853-r9 { fill: #a2a2a2 } -.terminal-1850118853-r10 { fill: #797979 } -.terminal-1850118853-r11 { fill: #b93c5b } -.terminal-1850118853-r12 { fill: #191919 } -.terminal-1850118853-r13 { fill: #737373 } -.terminal-1850118853-r14 { fill: #2d2d2d } -.terminal-1850118853-r15 { fill: #7ae998 } -.terminal-1850118853-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-1850118853-r17 { fill: #0a180e;font-weight: bold } -.terminal-1850118853-r18 { fill: #0d0d0d } -.terminal-1850118853-r19 { fill: #008139 } -.terminal-1850118853-r20 { fill: #495259 } -.terminal-1850118853-r21 { fill: #ffa62b;font-weight: bold } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #084724 } +.terminal-r8 { fill: #0178d4 } +.terminal-r9 { fill: #a2a2a2 } +.terminal-r10 { fill: #797979 } +.terminal-r11 { fill: #b93c5b } +.terminal-r12 { fill: #191919 } +.terminal-r13 { fill: #737373 } +.terminal-r14 { fill: #2d2d2d } +.terminal-r15 { fill: #7ae998 } +.terminal-r16 { fill: #e0e0e0;font-weight: bold } +.terminal-r17 { fill: #0a180e;font-weight: bold } +.terminal-r18 { fill: #0d0d0d } +.terminal-r19 { fill: #008139 } +.terminal-r20 { fill: #495259 } +.terminal-r21 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 1b1bb0ba41..82bdfe49e5 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-3629807493-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3629807493-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3629807493-r1 { fill: #c5c8c6 } -.terminal-3629807493-r2 { fill: #e0e0e0 } -.terminal-3629807493-r3 { fill: #a0a3a6 } -.terminal-3629807493-r4 { fill: #0178d4;font-weight: bold } -.terminal-3629807493-r5 { fill: #0178d4;text-decoration: underline; } -.terminal-3629807493-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } -.terminal-3629807493-r7 { fill: #e1e1e1;font-weight: bold } -.terminal-3629807493-r8 { fill: #e0e0e0;font-style: italic; } -.terminal-3629807493-r9 { fill: #7ae998 } -.terminal-3629807493-r10 { fill: #6db2ff } -.terminal-3629807493-r11 { fill: #55c076;font-weight: bold } -.terminal-3629807493-r12 { fill: #ddedf9;font-weight: bold } -.terminal-3629807493-r13 { fill: #008139 } -.terminal-3629807493-r14 { fill: #004295 } -.terminal-3629807493-r15 { fill: #e1e1e1;text-decoration: underline; } -.terminal-3629807493-r16 { fill: #ffa62b;font-weight: bold } -.terminal-3629807493-r17 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #0178d4;text-decoration: underline; } +.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } +.terminal-r7 { fill: #57a5e2 } +.terminal-r8 { fill: #e0e0e0;font-style: italic; } +.terminal-r9 { fill: #7ae998 } +.terminal-r10 { fill: #6db2ff } +.terminal-r11 { fill: #55c076;font-weight: bold } +.terminal-r12 { fill: #ddedf9;font-weight: bold } +.terminal-r13 { fill: #008139 } +.terminal-r14 { fill: #004295 } +.terminal-r15 { fill: #e0e0e0;text-decoration: underline; } +.terminal-r16 { fill: #ffa62b;font-weight: bold } +.terminal-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the● Your pipeline will never be part of nf-core -nf-core community● You want full control over all features that -● You think that there's an outside chanceare included from the template (including -that it ever could be part of nf-corethose that are mandatory for nf-core). - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Choose pipeline type + + + +Choose "nf-core" if:Choose "Custom" if: + +• You want your pipeline to be part of the• Your pipeline will never be part of nf-core +nf-core community• You want full control over all features that +• You think that there's an outside chanceare included from the template (including +that it ever could be part of nf-corethose that are mandatory for nf-core). + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +Choosing "nf-core" effectively pre-selects the following template features: + +• GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +• Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index cc08768389..279d28601e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,259 +19,259 @@ font-weight: 700; } - .terminal-3014319722-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3014319722-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3014319722-r1 { fill: #c5c8c6 } -.terminal-3014319722-r2 { fill: #e0e0e0 } -.terminal-3014319722-r3 { fill: #a0a3a6 } -.terminal-3014319722-r4 { fill: #0178d4;font-weight: bold } -.terminal-3014319722-r5 { fill: #121212 } -.terminal-3014319722-r6 { fill: #191919 } -.terminal-3014319722-r7 { fill: #1e1e1e } -.terminal-3014319722-r8 { fill: #0178d4;text-decoration: underline; } -.terminal-3014319722-r9 { fill: #6db2ff } -.terminal-3014319722-r10 { fill: #808080 } -.terminal-3014319722-r11 { fill: #ddedf9;font-weight: bold } -.terminal-3014319722-r12 { fill: #000000 } -.terminal-3014319722-r13 { fill: #004295 } -.terminal-3014319722-r14 { fill: #0178d4 } -.terminal-3014319722-r15 { fill: #2d2d2d } -.terminal-3014319722-r16 { fill: #272727 } -.terminal-3014319722-r17 { fill: #e0e0e0;font-weight: bold } -.terminal-3014319722-r18 { fill: #0d0d0d } -.terminal-3014319722-r19 { fill: #a5a5a5;font-weight: bold } -.terminal-3014319722-r20 { fill: #e4e4e4;font-weight: bold } -.terminal-3014319722-r21 { fill: #7ae998 } -.terminal-3014319722-r22 { fill: #0a180e;font-weight: bold } -.terminal-3014319722-r23 { fill: #008139 } -.terminal-3014319722-r24 { fill: #ffa62b;font-weight: bold } -.terminal-3014319722-r25 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #121212 } +.terminal-r6 { fill: #191919 } +.terminal-r7 { fill: #1e1e1e } +.terminal-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-r9 { fill: #6db2ff } +.terminal-r10 { fill: #808080 } +.terminal-r11 { fill: #ddedf9;font-weight: bold } +.terminal-r12 { fill: #004295 } +.terminal-r13 { fill: #000000 } +.terminal-r14 { fill: #0178d4 } +.terminal-r15 { fill: #2d2d2d } +.terminal-r16 { fill: #272727 } +.terminal-r17 { fill: #e0e0e0;font-weight: bold } +.terminal-r18 { fill: #0d0d0d } +.terminal-r19 { fill: #f5bd6f } +.terminal-r20 { fill: #57a5e2 } +.terminal-r21 { fill: #7ae998 } +.terminal-r22 { fill: #0a180e;font-weight: bold } +.terminal-r23 { fill: #008139 } +.terminal-r24 { fill: #ffa62b;font-weight: bold } +.terminal-r25 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: - -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline.▅▅ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +• AWS CI Tests +• Zenodo DOI +• Nextflow +• nf-core template version +• Conda +• Docker +• Singularity +• Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index 01a735e01c..c91aa57f5a 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,249 +19,249 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Final details - - - - -First version of the pipelinePath to the output directory where the -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Final details + + + +First version of the pipelinePath to the output directory where the +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 363074b566..f677a9606e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,257 +19,257 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - -Now that we have created a new pipeline locally, we can create a new GitHub repository and push -the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -The name of the organisation where theThe name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + +Now that we have created a new pipeline locally, we can create a new GitHub repository and push +the code to it. + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +The name of the organisation where theThe name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index 79fefaa71b..ef245d5133 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,252 +19,252 @@ font-weight: 700; } - .terminal-3190985874-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3190985874-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3190985874-r1 { fill: #c5c8c6 } -.terminal-3190985874-r2 { fill: #e0e0e0 } -.terminal-3190985874-r3 { fill: #a0a3a6 } -.terminal-3190985874-r4 { fill: #0178d4;font-weight: bold } -.terminal-3190985874-r5 { fill: #008000 } -.terminal-3190985874-r6 { fill: #0000ff } -.terminal-3190985874-r7 { fill: #ffff00 } -.terminal-3190985874-r8 { fill: #e1e1e1;font-weight: bold } -.terminal-3190985874-r9 { fill: #d2d2d2 } -.terminal-3190985874-r10 { fill: #82aaff } -.terminal-3190985874-r11 { fill: #eeffff } -.terminal-3190985874-r12 { fill: #0f4b79 } -.terminal-3190985874-r13 { fill: #a0a0a0;font-weight: bold } -.terminal-3190985874-r14 { fill: #7ae998 } -.terminal-3190985874-r15 { fill: #55c076;font-weight: bold } -.terminal-3190985874-r16 { fill: #008139 } -.terminal-3190985874-r17 { fill: #ffa62b;font-weight: bold } -.terminal-3190985874-r18 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #008000 } +.terminal-r6 { fill: #0000ff } +.terminal-r7 { fill: #ffff00 } +.terminal-r8 { fill: #57a5e2 } +.terminal-r9 { fill: #ffc473 } +.terminal-r10 { fill: #ffffff } +.terminal-r11 { fill: #d2d2d2 } +.terminal-r12 { fill: #345b7a } +.terminal-r13 { fill: #f4bc6e } +.terminal-r14 { fill: #7ae998 } +.terminal-r15 { fill: #55c076;font-weight: bold } +.terminal-r16 { fill: #008139 } +.terminal-r17 { fill: #ffa62b;font-weight: bold } +.terminal-r18 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -If you would like to create the GitHub repository later, you can do it manually by following -these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +HowTo create a GitHub repository + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +If you would like to create the GitHub repository later, you can do it manually by following +these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 08aa0f1e15..7f7b3eaf71 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,246 +19,246 @@ font-weight: 700; } - .terminal-1448878859-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1448878859-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1448878859-r1 { fill: #c5c8c6 } -.terminal-1448878859-r2 { fill: #e0e0e0 } -.terminal-1448878859-r3 { fill: #a0a3a6 } -.terminal-1448878859-r4 { fill: #0178d4;font-weight: bold } -.terminal-1448878859-r5 { fill: #7ae998 } -.terminal-1448878859-r6 { fill: #6db2ff } -.terminal-1448878859-r7 { fill: #55c076;font-weight: bold } -.terminal-1448878859-r8 { fill: #ddedf9;font-weight: bold } -.terminal-1448878859-r9 { fill: #008139 } -.terminal-1448878859-r10 { fill: #004295 } -.terminal-1448878859-r11 { fill: #ffa62b;font-weight: bold } -.terminal-1448878859-r12 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #7ae998 } +.terminal-r6 { fill: #6db2ff } +.terminal-r7 { fill: #55c076;font-weight: bold } +.terminal-r8 { fill: #ddedf9;font-weight: bold } +.terminal-r9 { fill: #008139 } +.terminal-r10 { fill: #004295 } +.terminal-r11 { fill: #ffa62b;font-weight: bold } +.terminal-r12 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - - -After creating the pipeline template locally, we can create a GitHub repository and push the -code to it. - -Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + +After creating the pipeline template locally, we can create a GitHub repository and push the +code to it. + +Do you want to create a GitHub repository? + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index a254873ced..cbfb9d2d6e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,257 +19,256 @@ font-weight: 700; } - .terminal-3868623164-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3868623164-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3868623164-r1 { fill: #c5c8c6 } -.terminal-3868623164-r2 { fill: #e0e0e0 } -.terminal-3868623164-r3 { fill: #a0a3a6 } -.terminal-3868623164-r4 { fill: #0178d4;font-weight: bold } -.terminal-3868623164-r5 { fill: #121212 } -.terminal-3868623164-r6 { fill: #0178d4 } -.terminal-3868623164-r7 { fill: #272727 } -.terminal-3868623164-r8 { fill: #0178d4;text-decoration: underline; } -.terminal-3868623164-r9 { fill: #191919 } -.terminal-3868623164-r10 { fill: #6db2ff } -.terminal-3868623164-r11 { fill: #1e1e1e } -.terminal-3868623164-r12 { fill: #808080 } -.terminal-3868623164-r13 { fill: #ddedf9;font-weight: bold } -.terminal-3868623164-r14 { fill: #004295 } -.terminal-3868623164-r15 { fill: #000000 } -.terminal-3868623164-r16 { fill: #2d2d2d } -.terminal-3868623164-r17 { fill: #7ae998 } -.terminal-3868623164-r18 { fill: #e0e0e0;font-weight: bold } -.terminal-3868623164-r19 { fill: #0a180e;font-weight: bold } -.terminal-3868623164-r20 { fill: #0d0d0d } -.terminal-3868623164-r21 { fill: #008139 } -.terminal-3868623164-r22 { fill: #ffa62b;font-weight: bold } -.terminal-3868623164-r23 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #121212 } +.terminal-r6 { fill: #0178d4 } +.terminal-r7 { fill: #272727 } +.terminal-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-r9 { fill: #191919 } +.terminal-r10 { fill: #6db2ff } +.terminal-r11 { fill: #1e1e1e } +.terminal-r12 { fill: #808080 } +.terminal-r13 { fill: #ddedf9;font-weight: bold } +.terminal-r14 { fill: #004295 } +.terminal-r15 { fill: #2d2d2d } +.terminal-r16 { fill: #7ae998 } +.terminal-r17 { fill: #e0e0e0;font-weight: bold } +.terminal-r18 { fill: #0a180e;font-weight: bold } +.terminal-r19 { fill: #0d0d0d } +.terminal-r20 { fill: #008139 } +.terminal-r21 { fill: #ffa62b;font-weight: bold } +.terminal-r22 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Continuous Integration & Testing - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add testing profilesAdd two default testing Show help  -▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Continuous Integration & Testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add pipeline testingAdd pipeline testing Show help  +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 523356c03d..bf40178324 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,253 +19,253 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use GPUAdd GPU support to the Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + +Components & Modules + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use reference genomesThe pipeline will be Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +of the most common +reference genome files +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use multiqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +generates an HTML report +for quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use fastqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +performs quality control +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use nf-schemaUse the nf-schema Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +Configurations + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use GPUAdd GPU support to the Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index aaa8eebf67..32ff0cea49 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-1227656248-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1227656248-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1227656248-r1 { fill: #c5c8c6 } -.terminal-1227656248-r2 { fill: #e0e0e0 } -.terminal-1227656248-r3 { fill: #a0a3a6 } -.terminal-1227656248-r4 { fill: #0178d4;font-weight: bold } -.terminal-1227656248-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-1227656248-r6 { fill: #121212 } -.terminal-1227656248-r7 { fill: #084724 } -.terminal-1227656248-r8 { fill: #762b3d } -.terminal-1227656248-r9 { fill: #a2a2a2 } -.terminal-1227656248-r10 { fill: #737373 } -.terminal-1227656248-r11 { fill: #b93c5b } -.terminal-1227656248-r12 { fill: #2d2d2d } -.terminal-1227656248-r13 { fill: #7ae998 } -.terminal-1227656248-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-1227656248-r15 { fill: #55c076;font-weight: bold } -.terminal-1227656248-r16 { fill: #0d0d0d } -.terminal-1227656248-r17 { fill: #008139 } -.terminal-1227656248-r18 { fill: #ffa62b;font-weight: bold } -.terminal-1227656248-r19 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #084724 } +.terminal-r8 { fill: #762b3d } +.terminal-r9 { fill: #a2a2a2 } +.terminal-r10 { fill: #737373 } +.terminal-r11 { fill: #b93c5b } +.terminal-r12 { fill: #2d2d2d } +.terminal-r13 { fill: #7ae998 } +.terminal-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-r15 { fill: #55c076;font-weight: bold } +.terminal-r16 { fill: #0d0d0d } +.terminal-r17 { fill: #008139 } +.terminal-r18 { fill: #ffa62b;font-weight: bold } +.terminal-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 1c2172a66b..8d4d8174ae 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,250 +19,250 @@ font-weight: 700; } - .terminal-3327359260-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3327359260-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3327359260-r1 { fill: #c5c8c6 } -.terminal-3327359260-r2 { fill: #e0e0e0 } -.terminal-3327359260-r3 { fill: #a0a3a6 } -.terminal-3327359260-r4 { fill: #008000 } -.terminal-3327359260-r5 { fill: #0000ff } -.terminal-3327359260-r6 { fill: #ffff00 } -.terminal-3327359260-r7 { fill: #0178d4;font-weight: bold } -.terminal-3327359260-r8 { fill: #e1e1e1;text-decoration: underline; } -.terminal-3327359260-r9 { fill: #0f4b79 } -.terminal-3327359260-r10 { fill: #e2e2e2;text-decoration: underline; } -.terminal-3327359260-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } -.terminal-3327359260-r12 { fill: #7ae998 } -.terminal-3327359260-r13 { fill: #55c076;font-weight: bold } -.terminal-3327359260-r14 { fill: #008139 } -.terminal-3327359260-r15 { fill: #ffa62b;font-weight: bold } -.terminal-3327359260-r16 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #008000 } +.terminal-r5 { fill: #0000ff } +.terminal-r6 { fill: #ffff00 } +.terminal-r7 { fill: #0178d4;font-weight: bold } +.terminal-r8 { fill: #e0e0e0;text-decoration: underline; } +.terminal-r9 { fill: #345b7a } +.terminal-r10 { fill: #e1e1e1;text-decoration: underline; } +.terminal-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } +.terminal-r12 { fill: #7ae998 } +.terminal-r13 { fill: #55c076;font-weight: bold } +.terminal-r14 { fill: #008139 } +.terminal-r15 { fill: #ffa62b;font-weight: bold } +.terminal-r16 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core -pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core +pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette From 4cab74aa4c43a8509f1d8939ec76d42a78fdebf0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 12 Aug 2025 12:32:49 +0200 Subject: [PATCH 082/101] Update GitHub Actions to v5 (#3702) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/changelog.yml | 2 +- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- .github/workflows/create-test-wf.yml | 2 +- .github/workflows/deploy-pypi.yml | 2 +- .github/workflows/fix-linting.yml | 2 +- .github/workflows/lint-code.yml | 2 +- .github/workflows/nextflow-source-test.yml | 4 ++-- .github/workflows/push_dockerhub_dev.yml | 2 +- .github/workflows/push_dockerhub_release.yml | 2 +- .github/workflows/pytest.yml | 8 ++++---- .github/workflows/sync.yml | 4 ++-- .github/workflows/test_offline_configs.yml | 4 ++-- .github/workflows/update-textual-snapshots.yml | 2 +- .../pipeline-template/.github/workflows/fix_linting.yml | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 4 ++-- nf_core/pipeline-template/.github/workflows/nf-test.yml | 4 ++-- .../.github/workflows/template-version-comment.yml | 2 +- 18 files changed, 27 insertions(+), 27 deletions(-) diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index cc8f340782..981476d917 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -19,7 +19,7 @@ jobs: ) steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 0e1d30401f..52be4bcbd2 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -42,7 +42,7 @@ jobs: export NXF_WORK=$(pwd) # Get the repo code - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out source-code repository # Set up nf-core/tools diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 707f9607bb..8ca8a5f23c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -32,7 +32,7 @@ jobs: all_features: ${{ steps.create_matrix.outputs.matrix }} steps: - name: checkout - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Create Matrix id: create_matrix run: | @@ -56,7 +56,7 @@ jobs: steps: - name: Check out source-code repository - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index fcc6821552..a8788db9c5 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -41,7 +41,7 @@ jobs: cd create-test-wf export NXF_WORK=$(pwd) - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out source-code repository - name: Set up Python 3.13 diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index 67f3efc8a0..1d55e866e5 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out source-code repository - name: Set up Python 3.13 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index c4e34c8f56..4a15ec915d 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index e66108d741..214dc23779 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -20,7 +20,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml index c5dd9dd8de..d504169d78 100644 --- a/.github/workflows/nextflow-source-test.yml +++ b/.github/workflows/nextflow-source-test.yml @@ -14,12 +14,12 @@ jobs: steps: - name: Check out Nextflow - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: repository: nextflow-io/nextflow path: nextflow - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out nf-core/tools with: ref: dev diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml index 6409335ac7..4ec7a54e6c 100644 --- a/.github/workflows/push_dockerhub_dev.yml +++ b/.github/workflows/push_dockerhub_dev.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Build nfcore/tools:dev docker image run: docker build --no-cache . -t nfcore/tools:dev diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml index d29b03b687..495115a162 100644 --- a/.github/workflows/push_dockerhub_release.yml +++ b/.github/workflows/push_dockerhub_release.yml @@ -23,7 +23,7 @@ jobs: fail-fast: false steps: - name: Check out code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Build nfcore/tools:latest docker image run: docker build --no-cache . -t nfcore/tools:latest diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 59a98a7975..45b73bf94a 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -52,7 +52,7 @@ jobs: name: Get test file matrix runs-on: "ubuntu-latest" steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out source-code repository - name: List tests @@ -79,7 +79,7 @@ jobs: cd pytest export NXF_WORK=$(pwd) - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out source-code repository - name: Set up Python ${{ needs.setup.outputs.python-version }} @@ -153,7 +153,7 @@ jobs: - runs-on=${{ github.run_id }}-coverage - runner=2cpu-linux-x64 steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: @@ -169,7 +169,7 @@ jobs: mv .github/.coveragerc . - name: Download all artifacts - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4 + uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5 with: pattern: coverage_* diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index bba867b951..e5dc6087e6 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -58,12 +58,12 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out nf-core/tools with: ref: ${{ github.ref_name }} - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} diff --git a/.github/workflows/test_offline_configs.yml b/.github/workflows/test_offline_configs.yml index 78584d7b59..a6b8db320f 100644 --- a/.github/workflows/test_offline_configs.yml +++ b/.github/workflows/test_offline_configs.yml @@ -53,11 +53,11 @@ jobs: matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}} fail-fast: false steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out nf-core/tools with: ref: ${{ github.ref_name }} - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 name: Check out nf-core/${{ matrix.pipeline }} with: repository: nf-core/${{ matrix.pipeline }} diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index c4ad5fd37c..42033c3395 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/nf_core/pipeline-template/.github/workflows/fix_linting.yml b/nf_core/pipeline-template/.github/workflows/fix_linting.yml index 1977ba6743..35aa61c668 100644 --- a/nf_core/pipeline-template/.github/workflows/fix_linting.yml +++ b/nf_core/pipeline-template/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 2f304052cd..574cd7973e 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -11,7 +11,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index d399959faf..a11801499f 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -41,7 +41,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 @@ -87,7 +87,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 diff --git a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml index efdbbf13dd..95cb23d52b 100644 --- a/nf_core/pipeline-template/.github/workflows/template-version-comment.yml +++ b/nf_core/pipeline-template/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: ref: ${{ github.event.pull_request.head.sha }} From 92cce0b0eefdbdc8a1d7d2a3a77575ddd8eece8f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 12 Aug 2025 09:29:51 -0500 Subject: [PATCH 083/101] test: Implement module lint tests and consolidate MockModuleLint class MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Replace skeleton tests with actual implementations for module_changes, module_deprecations, module_version, and module_todos - Remove duplicate MockModuleLint class definitions and consolidate imports to test_lint_utils - Rename TestMainNf to TestMainNfLinting with improved documentation - Add comprehensive test coverage for lint functionality including edge cases and error conditions - Add CLAUDE.md to .gitignore 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- .gitignore | 3 + tests/modules/lint/test_main_nf.py | 12 +- tests/modules/lint/test_module_changes.py | 93 ++++++++----- .../modules/lint/test_module_deprecations.py | 78 +++++++---- tests/modules/lint/test_module_todos.py | 130 +++++++++++++----- tests/modules/lint/test_module_version.py | 68 ++++----- 6 files changed, 253 insertions(+), 131 deletions(-) diff --git a/.gitignore b/.gitignore index 7fe467abc9..d9e50d3989 100644 --- a/.gitignore +++ b/.gitignore @@ -117,3 +117,6 @@ pip-wheel-metadata # Textual snapshot_report.html + +# AI +CLAUDE.md diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index 9e2658ea74..62906dfa4b 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -86,8 +86,16 @@ def test_container_links(content, passed, warned, failed): assert len(mock_lint.failed) == failed -class TestMainNf(TestModules): - """Test main.nf functionality""" +class TestMainNfLinting(TestModules): + """ + Test main.nf linting functionality. + + This class tests various aspects of main.nf file linting including: + - Process label validation and standards compliance + - Container definition syntax and URL validation + - Integration testing with alternative registries + - General module linting workflow + """ def test_modules_lint_registry(self): """Test linting the samtools module and alternative registry""" diff --git a/tests/modules/lint/test_module_changes.py b/tests/modules/lint/test_module_changes.py index a087947ba2..50f7da7566 100644 --- a/tests/modules/lint/test_module_changes.py +++ b/tests/modules/lint/test_module_changes.py @@ -1,54 +1,75 @@ import pytest -from ...test_modules import TestModules - +import nf_core.modules.lint -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - self.main_nf = "main_nf" +from ...test_modules import TestModules class TestModuleChanges(TestModules): """Test module_changes.py functionality""" - @pytest.mark.skip(reason="Test implementation pending") def test_module_changes_unchanged(self): """Test module changes when module is unchanged""" - # Test the functionality of module_changes.py when module is unchanged - pass + # Install a module that should be unchanged from the repository + assert self.mods_install.install("samtools/sort") - @pytest.mark.skip(reason="Test implementation pending") - def test_module_changes_modified(self): - """Test module changes when module is modified""" - # Test the functionality of module_changes.py when module is modified - pass + # Run lint on the unchanged module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_changes"]) - @pytest.mark.skip(reason="Test implementation pending") - def test_module_changes_patched(self): - """Test module changes when module is patched""" - # Test when module has patches applied - pass + # Check that module_changes test passed (no changes detected) + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + + # Should have passed entries for files being up to date + passed_test_names = [test.lint_test for test in module_lint.passed] + assert "check_local_copy" in passed_test_names - @pytest.mark.skip(reason="Test implementation pending") - def test_module_changes_main_nf_modified(self): + def test_module_changes_modified_main_nf(self): """Test module changes when main.nf is modified""" - # Test when main.nf file is modified - pass + # Install a module + assert self.mods_install.install("samtools/sort") + + # Modify the main.nf file + main_nf_path = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" / "main.nf" + with open(main_nf_path, "a") as fh: + fh.write("\n// This is a test modification\n") - @pytest.mark.skip(reason="Test implementation pending") - def test_module_changes_meta_yml_modified(self): + # Run lint on the modified module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_changes"]) + + # Check that module_changes test failed (changes detected) + assert len(module_lint.failed) > 0, "Expected linting to fail due to modified file" + + # Should have failed entry for local copy not matching remote + failed_test_names = [test.lint_test for test in module_lint.failed] + assert "check_local_copy" in failed_test_names + + def test_module_changes_modified_meta_yml(self): """Test module changes when meta.yml is modified""" - # Test when meta.yml file is modified - pass + # Install a module + assert self.mods_install.install("samtools/sort") + + # Modify the meta.yml file + meta_yml_path = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" / "meta.yml" + with open(meta_yml_path, "a") as fh: + fh.write("\n# This is a test comment\n") - @pytest.mark.skip(reason="Test implementation pending") - def test_module_changes_patch_apply_fail(self): - """Test module changes when patch application fails""" - # Test when patch cannot be applied in reverse + # Run lint on the modified module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_changes"]) + + # Check that module_changes test failed (changes detected) + assert len(module_lint.failed) > 0, "Expected linting to fail due to modified file" + + # Should have failed entry for local copy not matching remote + failed_test_names = [test.lint_test for test in module_lint.failed] + assert "check_local_copy" in failed_test_names + + @pytest.mark.skip(reason="Patch testing requires complex setup - test framework needs improvement") + def test_module_changes_patched_module(self): + """Test module changes when module is patched""" + # This test would require creating a patched module which is complex + # in the current test framework. Skip for now until patch test infrastructure + # is improved. pass diff --git a/tests/modules/lint/test_module_deprecations.py b/tests/modules/lint/test_module_deprecations.py index 7168d47f3a..90db4b4cc8 100644 --- a/tests/modules/lint/test_module_deprecations.py +++ b/tests/modules/lint/test_module_deprecations.py @@ -1,42 +1,68 @@ -import pytest +import nf_core.modules.lint from ...test_modules import TestModules -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - self.main_nf = "main_nf" - - class TestModuleDeprecations(TestModules): """Test module_deprecations.py functionality""" - @pytest.mark.skip(reason="Test implementation pending") def test_module_deprecations_none(self): """Test module deprecations when no deprecations exist""" - # Test the functionality of module_deprecations.py when no deprecated files exist - pass + # Install a standard module that shouldn't have deprecated files + assert self.mods_install.install("samtools/sort") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_deprecations"]) - @pytest.mark.skip(reason="Test implementation pending") - def test_module_deprecations_found(self): - """Test module deprecations when deprecations are found""" - # Test the functionality of module_deprecations.py when deprecated files are found - pass + # Should not have any failures from deprecations + failed_test_names = [test.lint_test for test in module_lint.failed] + assert "module_deprecations" not in failed_test_names - @pytest.mark.skip(reason="Test implementation pending") def test_module_deprecations_functions_nf(self): """Test module deprecations when functions.nf exists""" - # Test when deprecated functions.nf file is found - pass + # Install a module first + assert self.mods_install.install("samtools/sort") + + # Create a deprecated functions.nf file + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + functions_nf_path = module_dir / "functions.nf" + + # Create the deprecated functions.nf file + with open(functions_nf_path, "w") as fh: + fh.write("// Deprecated functions.nf file\n") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_deprecations"]) + + # Should have failure for deprecated functions.nf file + assert len(module_lint.failed) > 0, "Expected linting to fail due to deprecated functions.nf file" + failed_test_names = [test.lint_test for test in module_lint.failed] + assert "module_deprecations" in failed_test_names + + # Check the specific failure message + deprecation_failure = [test for test in module_lint.failed if test.lint_test == "module_deprecations"][0] + assert "functions.nf" in deprecation_failure.message + assert "Deprecated" in deprecation_failure.message - @pytest.mark.skip(reason="Test implementation pending") def test_module_deprecations_no_functions_nf(self): """Test module deprecations when no functions.nf exists""" - # Test when no deprecated files are found - pass + # Install a module + assert self.mods_install.install("samtools/sort") + + # Ensure no functions.nf file exists (should be default) + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + functions_nf_path = module_dir / "functions.nf" + + # Remove functions.nf if it somehow exists + if functions_nf_path.exists(): + functions_nf_path.unlink() + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_deprecations"]) + + # Should not have any failures from deprecations + failed_test_names = [test.lint_test for test in module_lint.failed] + assert "module_deprecations" not in failed_test_names diff --git a/tests/modules/lint/test_module_todos.py b/tests/modules/lint/test_module_todos.py index 9034d031ef..dc18a50496 100644 --- a/tests/modules/lint/test_module_todos.py +++ b/tests/modules/lint/test_module_todos.py @@ -1,42 +1,106 @@ -import pytest +import nf_core.modules.lint from ...test_modules import TestModules -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - self.main_nf = "main_nf" - - class TestModuleTodos(TestModules): """Test module_todos.py functionality""" - @pytest.mark.skip(reason="Test implementation pending") def test_module_todos_none(self): """Test module todos when no TODOs exist""" - # Test the functionality of module_todos.py when no TODO statements are found - pass - - @pytest.mark.skip(reason="Test implementation pending") - def test_module_todos_found(self): - """Test module todos when TODOs are found""" - # Test the functionality of module_todos.py when TODO statements are found - pass - - @pytest.mark.skip(reason="Test implementation pending") - def test_module_todos_markdown(self): - """Test module todos when markdown TODOs exist""" - # Test finding TODO statements in markdown files - pass - - @pytest.mark.skip(reason="Test implementation pending") - def test_module_todos_groovy(self): - """Test module todos when groovy TODOs exist""" - # Test finding TODO statements in Nextflow/Groovy files - pass + # Install a module and remove any TODO statements + assert self.mods_install.install("samtools/sort") + + # Clean any TODO statements from files (they should be clean by default) + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + + # Ensure main.nf has no TODO statements + main_nf_path = module_dir / "main.nf" + with open(main_nf_path) as fh: + main_nf_content = fh.read() + + # Remove any TODO statements if they exist + main_nf_content = main_nf_content.replace("TODO", "") + with open(main_nf_path, "w") as fh: + fh.write(main_nf_content) + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_todos"]) + + # Should not have any warnings from TODOs + warned_test_names = [test.lint_test for test in module_lint.warned] + assert "module_todo" not in warned_test_names + + def test_module_todos_found_in_main_nf(self): + """Test module todos when TODOs are found in main.nf""" + # Install a module + assert self.mods_install.install("samtools/sort") + + # Add a TODO statement to main.nf + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + main_nf_path = module_dir / "main.nf" + + with open(main_nf_path, "a") as fh: + fh.write("\n// TODO nf-core: This is a test TODO statement\n") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_todos"]) + + # Should have warning for TODO statement + assert len(module_lint.warned) > 0, "Expected linting to warn due to TODO statement" + warned_test_names = [test.lint_test for test in module_lint.warned] + assert "module_todo" in warned_test_names + + # Check the specific warning message + todo_warning = [test for test in module_lint.warned if test.lint_test == "module_todo"][0] + assert "TODO" in todo_warning.message + + def test_module_todos_found_in_meta_yml(self): + """Test module todos when TODOs are found in meta.yml""" + # Install a module + assert self.mods_install.install("samtools/sort") + + # Add a TODO comment to meta.yml + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + meta_yml_path = module_dir / "meta.yml" + + with open(meta_yml_path, "a") as fh: + fh.write("\n# TODO nf-core: Add more detailed description\n") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_todos"]) + + # Should have warning for TODO statement + assert len(module_lint.warned) > 0, "Expected linting to warn due to TODO statement" + warned_test_names = [test.lint_test for test in module_lint.warned] + assert "module_todo" in warned_test_names + + def test_module_todos_multiple_found(self): + """Test module todos when multiple TODOs are found""" + # Install a module + assert self.mods_install.install("samtools/sort") + + # Add multiple TODO statements to different files + module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" + + # Add TODO to main.nf + main_nf_path = module_dir / "main.nf" + with open(main_nf_path, "a") as fh: + fh.write("\n// TODO nf-core: First TODO statement\n") + fh.write("// TODO nf-core: Second TODO statement\n") + + # Add TODO to meta.yml + meta_yml_path = module_dir / "meta.yml" + with open(meta_yml_path, "a") as fh: + fh.write("\n# TODO nf-core: Meta TODO statement\n") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_todos"]) + + # Should have multiple warnings for TODO statements + todo_warnings = [test for test in module_lint.warned if test.lint_test == "module_todo"] + assert len(todo_warnings) >= 3, f"Expected at least 3 TODO warnings, got {len(todo_warnings)}" diff --git a/tests/modules/lint/test_module_version.py b/tests/modules/lint/test_module_version.py index c1fb5087c1..1a9f73a813 100644 --- a/tests/modules/lint/test_module_version.py +++ b/tests/modules/lint/test_module_version.py @@ -1,54 +1,54 @@ import pytest -from ...test_modules import TestModules - +import nf_core.modules.lint -# A skeleton object with the passed/warned/failed list attrs -# Use this in place of a ModuleLint object to test behaviour of -# linting methods which don't need the full setup -class MockModuleLint: - def __init__(self): - self.passed = [] - self.warned = [] - self.failed = [] - self.main_nf = "main_nf" +from ...test_modules import TestModules class TestModuleVersion(TestModules): """Test module_version.py functionality""" - @pytest.mark.skip(reason="Test implementation pending") - def test_module_version_valid(self): - """Test module version when version is valid""" - # Test the functionality of module_version.py when version is valid - pass + def test_module_version_with_git_sha(self): + """Test module version when git_sha is present in modules.json""" + # Install a module + assert self.mods_install.install("samtools/sort") - @pytest.mark.skip(reason="Test implementation pending") - def test_module_version_invalid(self): - """Test module version when version is invalid""" - # Test the functionality of module_version.py when version is invalid - pass + # Run lint on the module - should have a git_sha entry + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) + + # Should pass git_sha test (git_sha entry exists) + passed_test_names = [test.lint_test for test in module_lint.passed] + assert "git_sha" in passed_test_names + + # Should have module_version test result (either passed or warned) + all_test_names = [test.lint_test for test in module_lint.passed + module_lint.warned + module_lint.failed] + assert "module_version" in all_test_names - @pytest.mark.skip(reason="Test implementation pending") def test_module_version_up_to_date(self): """Test module version when module is up to date""" - # Test when module is at the latest version - pass + # Install a module (should be latest by default) + assert self.mods_install.install("samtools/sort") + + # Run lint on the module + module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) + module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) - @pytest.mark.skip(reason="Test implementation pending") + # Should have a result for module_version (either passed if up-to-date or warned if newer available) + all_tests = module_lint.passed + module_lint.warned + module_lint.failed + version_test_names = [test.lint_test for test in all_tests] + assert "module_version" in version_test_names + + @pytest.mark.skip(reason="Testing outdated modules requires specific version setup") def test_module_version_outdated(self): """Test module version when module is outdated""" - # Test when module has newer version available - pass - - @pytest.mark.skip(reason="Test implementation pending") - def test_module_version_no_git_sha(self): - """Test module version when no git_sha in modules.json""" - # Test when modules.json is missing git_sha entry + # This test would require installing a specific older version of a module + # which is complex to set up reliably in the test framework pass - @pytest.mark.skip(reason="Test implementation pending") + @pytest.mark.skip(reason="Testing git log failure requires complex mocking setup") def test_module_version_git_log_fail(self): """Test module version when git log fetch fails""" - # Test when fetching git log fails + # This test would require mocking network failures or invalid repositories + # which is complex to set up in the current test framework pass From 4d812e44b55e7f21d735191dc5e89da8cfa828fb Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 13 Aug 2025 12:50:37 -0500 Subject: [PATCH 084/101] fix: Handle corrupted JSON cache files gracefully in utils MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Instead of raising a UserWarning when a cached JSON config file is corrupted, now logs a warning and attempts to delete the corrupted cache file, allowing the config to be regenerated. This prevents test failures in CI when cache files become corrupted. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/utils.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 278865bb23..191f9e32ce 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -313,12 +313,18 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict: cache_path = Path(cache_basedir, cache_fn) if cache_path.is_file() and cache_config is True: log.debug(f"Found a config cache, loading: {cache_path}") - with open(cache_path) as fh: - try: + try: + with open(cache_path) as fh: config = json.load(fh) - except json.JSONDecodeError as e: - raise UserWarning(f"Unable to load JSON file '{cache_path}' due to error {e}") - return config + return config + except json.JSONDecodeError as e: + # Log warning but don't raise - just regenerate the cache + log.warning(f"Unable to load cached JSON file '{cache_path}' due to error: {e}") + log.debug("Removing corrupted cache file and regenerating...") + try: + cache_path.unlink() + except OSError: + pass # If we can't delete it, just continue log.debug("No config cache found") # Call `nextflow config` From 83b62379c2b5d81eeabf9a6fd17505fb32b556ba Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Thu, 14 Aug 2025 15:50:26 -0500 Subject: [PATCH 085/101] refactor: Consolidate module installation in test setUp methods MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Move samtools/sort installation from individual test methods to setUp methods - Rename test_modules_lint_registry to test_main_nf_lint_with_alternative_registry to clarify scope - Eliminate redundant module installations across TestModuleChanges, TestModuleTodos, TestModuleDeprecations, TestModuleVersion, and TestMainNfLinting - Improve test performance by installing modules once per test class instead of per test method Addresses PR review comments about test setup optimization and method naming clarity. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- tests/modules/lint/test_main_nf.py | 8 ++++++-- tests/modules/lint/test_module_changes.py | 15 ++++++--------- tests/modules/lint/test_module_deprecations.py | 15 ++++++--------- tests/modules/lint/test_module_todos.py | 18 ++++++------------ tests/modules/lint/test_module_version.py | 12 ++++++------ 5 files changed, 30 insertions(+), 38 deletions(-) diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index 62906dfa4b..26990f9ccc 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -97,10 +97,14 @@ class TestMainNfLinting(TestModules): - General module linting workflow """ - def test_modules_lint_registry(self): - """Test linting the samtools module and alternative registry""" + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install samtools/sort module for all tests in this class assert self.mods_install.install("samtools/sort") + def test_main_nf_lint_with_alternative_registry(self): + """Test main.nf linting with alternative container registry""" # Test with alternative registry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") module_lint.lint(print_results=False, module="samtools/sort") diff --git a/tests/modules/lint/test_module_changes.py b/tests/modules/lint/test_module_changes.py index 50f7da7566..6b03dc67e9 100644 --- a/tests/modules/lint/test_module_changes.py +++ b/tests/modules/lint/test_module_changes.py @@ -8,11 +8,14 @@ class TestModuleChanges(TestModules): """Test module_changes.py functionality""" - def test_module_changes_unchanged(self): - """Test module changes when module is unchanged""" - # Install a module that should be unchanged from the repository + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install samtools/sort module for all tests in this class assert self.mods_install.install("samtools/sort") + def test_module_changes_unchanged(self): + """Test module changes when module is unchanged""" # Run lint on the unchanged module module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_changes"]) @@ -26,9 +29,6 @@ def test_module_changes_unchanged(self): def test_module_changes_modified_main_nf(self): """Test module changes when main.nf is modified""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Modify the main.nf file main_nf_path = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" / "main.nf" with open(main_nf_path, "a") as fh: @@ -47,9 +47,6 @@ def test_module_changes_modified_main_nf(self): def test_module_changes_modified_meta_yml(self): """Test module changes when meta.yml is modified""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Modify the meta.yml file meta_yml_path = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" / "meta.yml" with open(meta_yml_path, "a") as fh: diff --git a/tests/modules/lint/test_module_deprecations.py b/tests/modules/lint/test_module_deprecations.py index 90db4b4cc8..85c86030b6 100644 --- a/tests/modules/lint/test_module_deprecations.py +++ b/tests/modules/lint/test_module_deprecations.py @@ -6,11 +6,14 @@ class TestModuleDeprecations(TestModules): """Test module_deprecations.py functionality""" - def test_module_deprecations_none(self): - """Test module deprecations when no deprecations exist""" - # Install a standard module that shouldn't have deprecated files + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install samtools/sort module for all tests in this class assert self.mods_install.install("samtools/sort") + def test_module_deprecations_none(self): + """Test module deprecations when no deprecations exist""" # Run lint on the module module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_deprecations"]) @@ -21,9 +24,6 @@ def test_module_deprecations_none(self): def test_module_deprecations_functions_nf(self): """Test module deprecations when functions.nf exists""" - # Install a module first - assert self.mods_install.install("samtools/sort") - # Create a deprecated functions.nf file module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" functions_nf_path = module_dir / "functions.nf" @@ -48,9 +48,6 @@ def test_module_deprecations_functions_nf(self): def test_module_deprecations_no_functions_nf(self): """Test module deprecations when no functions.nf exists""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Ensure no functions.nf file exists (should be default) module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" functions_nf_path = module_dir / "functions.nf" diff --git a/tests/modules/lint/test_module_todos.py b/tests/modules/lint/test_module_todos.py index dc18a50496..2e5e896680 100644 --- a/tests/modules/lint/test_module_todos.py +++ b/tests/modules/lint/test_module_todos.py @@ -6,11 +6,14 @@ class TestModuleTodos(TestModules): """Test module_todos.py functionality""" - def test_module_todos_none(self): - """Test module todos when no TODOs exist""" - # Install a module and remove any TODO statements + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install samtools/sort module for all tests in this class assert self.mods_install.install("samtools/sort") + def test_module_todos_none(self): + """Test module todos when no TODOs exist""" # Clean any TODO statements from files (they should be clean by default) module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" @@ -34,9 +37,6 @@ def test_module_todos_none(self): def test_module_todos_found_in_main_nf(self): """Test module todos when TODOs are found in main.nf""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Add a TODO statement to main.nf module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" main_nf_path = module_dir / "main.nf" @@ -59,9 +59,6 @@ def test_module_todos_found_in_main_nf(self): def test_module_todos_found_in_meta_yml(self): """Test module todos when TODOs are found in meta.yml""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Add a TODO comment to meta.yml module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" meta_yml_path = module_dir / "meta.yml" @@ -80,9 +77,6 @@ def test_module_todos_found_in_meta_yml(self): def test_module_todos_multiple_found(self): """Test module todos when multiple TODOs are found""" - # Install a module - assert self.mods_install.install("samtools/sort") - # Add multiple TODO statements to different files module_dir = self.pipeline_dir / "modules" / "nf-core" / "samtools" / "sort" diff --git a/tests/modules/lint/test_module_version.py b/tests/modules/lint/test_module_version.py index 1a9f73a813..a64804817b 100644 --- a/tests/modules/lint/test_module_version.py +++ b/tests/modules/lint/test_module_version.py @@ -8,11 +8,14 @@ class TestModuleVersion(TestModules): """Test module_version.py functionality""" - def test_module_version_with_git_sha(self): - """Test module version when git_sha is present in modules.json""" - # Install a module + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install samtools/sort module for all tests in this class assert self.mods_install.install("samtools/sort") + def test_module_version_with_git_sha(self): + """Test module version when git_sha is present in modules.json""" # Run lint on the module - should have a git_sha entry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) @@ -27,9 +30,6 @@ def test_module_version_with_git_sha(self): def test_module_version_up_to_date(self): """Test module version when module is up to date""" - # Install a module (should be latest by default) - assert self.mods_install.install("samtools/sort") - # Run lint on the module module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) From 21c78e65f10fa87d7b81fb4990cde7931e96c535 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:27:40 +0200 Subject: [PATCH 086/101] remove workflow.trace from nf-test snapshot to avoid errors due to incompatibility with nextflow --- nf_core/pipeline-template/tests/default.nf.test | 2 -- 1 file changed, 2 deletions(-) diff --git a/nf_core/pipeline-template/tests/default.nf.test b/nf_core/pipeline-template/tests/default.nf.test index a2eba5a782..8e463d2890 100644 --- a/nf_core/pipeline-template/tests/default.nf.test +++ b/nf_core/pipeline-template/tests/default.nf.test @@ -20,8 +20,6 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/{% if is_nfcore %}nf_core_{% endif %}{{ short_name }}_software_mqc_versions.yml"), // All stable path name, with a relative path From 2e2cb7af59bde1c0d8811050204d2ec187b1111b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:27:57 +0200 Subject: [PATCH 087/101] remove requirements duplication --- requirements-dev.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 751f285412..840cb6d558 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -11,8 +11,6 @@ types-PyYAML types-requests types-jsonschema types-Markdown -types-PyYAML -types-requests types-setuptools typing_extensions >=4.0.0 pytest-asyncio @@ -20,4 +18,3 @@ pytest-textual-snapshot==1.1.0 pytest-workflow>=2.0.0 pytest-xdist>=3.7.0 pytest>=8.0.0 -ruff From 2c01ade5cf5a0c30af15d17ab1ebe726c9e9a697 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 22 Aug 2025 13:30:33 +0000 Subject: [PATCH 088/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa94d0f429..ea20118dc3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ - Update python:3.13-slim Docker digest to 4c2cf99 ([#3700](https://github.com/nf-core/tools/pull/3700)) - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) - Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689)) +- Remove workflow.trace from nf-test snapshot ([#3721](https://github.com/nf-core/tools/pull/3721)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 80cfe386cc20eea800289a9cf44189725bfc1823 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:34:35 +0200 Subject: [PATCH 089/101] ignore files in gitignore also for pipeline_if_empty_null lint test --- .../pipelines/lint/pipeline_if_empty_null.py | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/nf_core/pipelines/lint/pipeline_if_empty_null.py b/nf_core/pipelines/lint/pipeline_if_empty_null.py index dc82641a1a..d56dc047f0 100644 --- a/nf_core/pipelines/lint/pipeline_if_empty_null.py +++ b/nf_core/pipelines/lint/pipeline_if_empty_null.py @@ -1,8 +1,9 @@ import logging -import os import re from pathlib import Path +from nf_core.utils import get_wf_files + log = logging.getLogger(__name__) @@ -26,16 +27,15 @@ def pipeline_if_empty_null(self, root_dir=None): if root_dir is None: root_dir = self.wf_path - for root, dirs, files in os.walk(root_dir, topdown=True): - for fname in files: - try: - with open(Path(root, fname), encoding="latin1") as fh: - for line in fh: - if re.findall(pattern, line): - warned.append(f"`ifEmpty(null)` found in `{fname}`: _{line}_") - file_paths.append(Path(root, fname)) - except FileNotFoundError: - log.debug(f"Could not open file {fname} in pipeline_if_empty_null lint test") + for file in get_wf_files(root_dir): + try: + with open(Path(file), encoding="latin1") as fh: + for line in fh: + if re.findall(pattern, line): + warned.append(f"`ifEmpty(null)` found in `{file}`: _{line}_") + file_paths.append(Path(file)) + except FileNotFoundError: + log.debug(f"Could not open file {file} in pipeline_if_empty_null lint test") if len(warned) == 0: passed.append("No `ifEmpty(null)` strings found") From 4792cf257bd283cd3ca605b33a8a94185ad0f6c4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 22 Aug 2025 13:38:09 +0000 Subject: [PATCH 090/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa94d0f429..6f781fd023 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,8 @@ ### Linting +- ignore files in gitignore also for pipeline_if_empty_null lint test ([#3722](https://github.com/nf-core/tools/pull/3722)) + ### Modules - Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633)) From 8086e729d7e34d43aa23a7c13092e6a4f4723ffc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 15:52:42 +0200 Subject: [PATCH 091/101] update all pipeline snapshots --- .github/snapshots/adaptivecard.nf.test.snap | 1 - .github/snapshots/changelog.nf.test.snap | 1 - .github/snapshots/ci.nf.test.snap | 1 - .github/snapshots/citations.nf.test.snap | 1 - .github/snapshots/code_linters.nf.test.snap | 1 - .github/snapshots/codespaces.nf.test.snap | 1 - .github/snapshots/default.nf.test.snap | 1 - .github/snapshots/documentation.nf.test.snap | 1 - .github/snapshots/email.nf.test.snap | 1 - .github/snapshots/fastqc.nf.test.snap | 1 - .github/snapshots/github_badges.nf.test.snap | 1 - .github/snapshots/gitpod.nf.test.snap | 1 - .github/snapshots/gpu.nf.test.snap | 1 - .github/snapshots/igenomes.nf.test.snap | 1 - .github/snapshots/license.nf.test.snap | 1 - .github/snapshots/modules.nf.test.snap | 1 - .github/snapshots/multiqc.nf.test.snap | 1 - .github/snapshots/nf_core_configs.nf.test.snap | 1 - .github/snapshots/nf_schema.nf.test.snap | 1 - .github/snapshots/rocrate.nf.test.snap | 1 - .github/snapshots/seqera_platform.nf.test.snap | 1 - .github/snapshots/slackreport.nf.test.snap | 1 - .github/snapshots/vscode.nf.test.snap | 1 - 23 files changed, 23 deletions(-) diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/adaptivecard.nf.test.snap +++ b/.github/snapshots/adaptivecard.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap index 3989533f59..cbeb2f9c6a 100644 --- a/.github/snapshots/changelog.nf.test.snap +++ b/.github/snapshots/changelog.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap index 39f8719f76..9435815267 100644 --- a/.github/snapshots/ci.nf.test.snap +++ b/.github/snapshots/ci.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/citations.nf.test.snap +++ b/.github/snapshots/citations.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/code_linters.nf.test.snap +++ b/.github/snapshots/code_linters.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/codespaces.nf.test.snap +++ b/.github/snapshots/codespaces.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index 31ea202d6a..0d1a057536 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/documentation.nf.test.snap +++ b/.github/snapshots/documentation.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/email.nf.test.snap +++ b/.github/snapshots/email.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap index 66184b7b84..487fc5cdb7 100644 --- a/.github/snapshots/fastqc.nf.test.snap +++ b/.github/snapshots/fastqc.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 1, { "Workflow": { "my-prefix/testpipeline": "v1.0.0dev" diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap index e671050699..c79757c35f 100644 --- a/.github/snapshots/github_badges.nf.test.snap +++ b/.github/snapshots/github_badges.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/gitpod.nf.test.snap +++ b/.github/snapshots/gitpod.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index eb83194a65..cffc9ac314 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap index e7425c2b11..0855700461 100644 --- a/.github/snapshots/igenomes.nf.test.snap +++ b/.github/snapshots/igenomes.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/license.nf.test.snap +++ b/.github/snapshots/license.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/modules.nf.test.snap b/.github/snapshots/modules.nf.test.snap index 05ff1ff447..0823cc7412 100644 --- a/.github/snapshots/modules.nf.test.snap +++ b/.github/snapshots/modules.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 0, null, [ "pipeline_info" diff --git a/.github/snapshots/multiqc.nf.test.snap b/.github/snapshots/multiqc.nf.test.snap index 542c7c30d2..12ea2b4e31 100644 --- a/.github/snapshots/multiqc.nf.test.snap +++ b/.github/snapshots/multiqc.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 3, null, [ "fastqc", diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap index 292367b69f..7ca53b2fd6 100644 --- a/.github/snapshots/nf_core_configs.nf.test.snap +++ b/.github/snapshots/nf_core_configs.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap index f0703db991..402ddbc403 100644 --- a/.github/snapshots/nf_schema.nf.test.snap +++ b/.github/snapshots/nf_schema.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/rocrate.nf.test.snap +++ b/.github/snapshots/rocrate.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/seqera_platform.nf.test.snap +++ b/.github/snapshots/seqera_platform.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/slackreport.nf.test.snap +++ b/.github/snapshots/slackreport.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap index fd0f6fd295..ba68358e9e 100644 --- a/.github/snapshots/vscode.nf.test.snap +++ b/.github/snapshots/vscode.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 4, { "FASTQC": { "fastqc": "0.12.1" From 093a17306c4f63571ca6d735518ecdceea0d1657 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 25 Aug 2025 10:12:40 +0200 Subject: [PATCH 092/101] add GHA to update template nf-test snapshots --- .../workflows/update-template-snapshots.yml | 152 ++++++++++++++++++ .../workflows/update-textual-snapshots.yml | 6 +- 2 files changed, 155 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/update-template-snapshots.yml diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml new file mode 100644 index 0000000000..919972a38b --- /dev/null +++ b/.github/workflows/update-template-snapshots.yml @@ -0,0 +1,152 @@ +name: Update Template snapshots from a comment +on: + issue_comment: + types: [created] + +jobs: + prepare-matrix: + name: Retrieve all template features + runs-on: ubuntu-latest + outputs: + all_features: ${{ steps.create_matrix.outputs.matrix }} + steps: + - name: checkout + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - name: Create Matrix + id: create_matrix + run: | + echo "matrix=$(yq '.[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config")' nf_core/pipelines/create/template_features.yml | \ + yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT + + update-snapshots: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot update template snapshots') && + github.repository == 'nf-core/tools' + runs-on: ubuntu-latest + strategy: + matrix: + TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} + include: + - TEMPLATE: all + fail-fast: false + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # indication that the command is running + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + # Install dependencies and run pytest + - name: Set up Python + uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + with: + python-version: "3.13" + cache: "pip" + + - name: Install dependencies + run: | + python -m pip install --upgrade pip -r requirements-dev.txt + pip install -e . + + # Create template files + - name: Create template skip ${{ matrix.TEMPLATE }} + run: | + mkdir create-test-lint-wf + export NXF_WORK=$(pwd) + if [ ${{ matrix.TEMPLATE }} == "all" ] + then + printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml + else + printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml + fi + + # Create a pipeline from the template + - name: create a pipeline from the template ${{ matrix.TEMPLATE }} + run: | + cd create-test-lint-wf + nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml + + # Copy snapshot file + - name: copy snapshot file + if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} + run: | + if [ ! -f ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap ]; then + echo "Generate a snapshot when creating a pipeline and skipping the feature ${{ matrix.TEMPLATE }}." + echo "Then, copy it to the directory .github/snapshots" + else + cp ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap + fi + + # Run pipeline with nf-test + - name: run pipeline nf-test + if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} + id: nf-test + shell: bash + run: | + cd create-test-lint-wf/my-prefix-testpipeline + nf-test test \ + --profile=+docker \ + --verbose + + - name: Update nf-test snapshot + if: steps.nf-test.outcome == 'success' + run: | + cp ${{ github.workspace }}/create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap + + # indication that the run has finished + - name: react if finished succesfully + if: steps.nf-test.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" + + - name: Commit & push changes + id: commit-and-push + if: steps.nf-test.outcome == 'success' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Update Template snapshots" + git push + + - name: react if snapshots were updated + id: react-if-updated + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if snapshots were not updated + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if snapshots were not updated + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to update the snapshots, but it didn't work. Please update them manually. diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index 42033c3395..b89781e58d 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -8,7 +8,7 @@ jobs: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot update snapshots') && + contains(github.event.comment.body, '@nf-core-bot update textual snapshots') && github.repository == 'nf-core/tools' runs-on: ubuntu-latest steps: @@ -59,7 +59,7 @@ jobs: - name: Commit & push changes id: commit-and-push - if: steps.pytest.outcome == 'failure' + if: steps.pytest.outcome == 'success' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" @@ -84,7 +84,7 @@ jobs: comment-id: ${{ github.event.comment.id }} reactions: confused - - name: react if snapshots were not updated + - name: comment if snapshots were not updated if: steps.commit-and-push.outcome == 'failure' uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 with: From 40313bae2b02345cee2b44cfb33e648165ee553a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Aug 2025 08:15:16 +0000 Subject: [PATCH 093/101] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa94d0f429..33a63cceb0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Add GHA to update template nf-test snapshots ([#3723](https://github.com/nf-core/tools/pull/3723)) + ### Linting ### Modules From f768e9d940821efff8103ed299534a08128740b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 25 Aug 2025 11:18:52 +0200 Subject: [PATCH 094/101] handle error when .gitignore does not exist --- nf_core/utils.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/nf_core/utils.py b/nf_core/utils.py index 278865bb23..f8ef904fcc 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1574,9 +1574,12 @@ def get_wf_files(wf_path: Path): wf_files = [] - with open(Path(wf_path, ".gitignore")) as f: - lines = f.read().splitlines() - ignore = [line for line in lines if line and not line.startswith("#")] + try: + with open(Path(wf_path, ".gitignore")) as f: + lines = f.read().splitlines() + ignore = [line for line in lines if line and not line.startswith("#")] + except FileNotFoundError: + ignore = [] for path in Path(wf_path).rglob("*"): if any(fnmatch.fnmatch(str(path), pattern) for pattern in ignore): From ef628f38104656a5d1e2dc75207ab6073a76d09b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 25 Aug 2025 12:03:23 +0200 Subject: [PATCH 095/101] update gha triggers for snapshot updates --- .github/workflows/update-template-snapshots.yml | 10 +++++++++- .github/workflows/update-textual-snapshots.yml | 3 ++- 2 files changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml index 919972a38b..7c49b04700 100644 --- a/.github/workflows/update-template-snapshots.yml +++ b/.github/workflows/update-template-snapshots.yml @@ -6,6 +6,12 @@ on: jobs: prepare-matrix: name: Retrieve all template features + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot') && + contains(github.event.comment.body, 'update template snapshots') && + github.repository == 'nf-core/tools' runs-on: ubuntu-latest outputs: all_features: ${{ steps.create_matrix.outputs.matrix }} @@ -19,10 +25,12 @@ jobs: yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT update-snapshots: + needs: [prepare-matrix] # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot update template snapshots') && + contains(github.event.comment.body, '@nf-core-bot') && + contains(github.event.comment.body, 'update template snapshots') && github.repository == 'nf-core/tools' runs-on: ubuntu-latest strategy: diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index b89781e58d..5f25ce955d 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -8,7 +8,8 @@ jobs: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot update textual snapshots') && + contains(github.event.comment.body, '@nf-core-bot') && + contains(github.event.comment.body, 'update textual snapshots') && github.repository == 'nf-core/tools' runs-on: ubuntu-latest steps: From 9e03edc10a67c0c7baf92b4ad6266d42a1fb0549 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Mon, 25 Aug 2025 13:58:01 +0200 Subject: [PATCH 096/101] update changelog --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e4be2d8ea7..751ae3effc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,8 +4,6 @@ ### Template -- Add GHA to update template nf-test snapshots ([#3723](https://github.com/nf-core/tools/pull/3723)) - ### Linting ### Modules @@ -26,6 +24,7 @@ - Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680)) - Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689)) - Remove workflow.trace from nf-test snapshot ([#3721](https://github.com/nf-core/tools/pull/3721)) +- Add GHA to update template nf-test snapshots ([#3723](https://github.com/nf-core/tools/pull/3723)) ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08] From 584527bdd12a5b686b6c3b886fbef95ec7156b09 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 26 Aug 2025 08:46:59 -0500 Subject: [PATCH 097/101] test: Improve test structure and remove setUp assertions MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Replace assertions in setUp methods with skipTest() for proper error handling - Remove unnecessary setUp methods where only one test needs module installation - Eliminate manual test cleanup code relying on test framework isolation - Consolidate module installation in setUp where all tests in class need it - Update registry test to properly expect failures with mismatched registries Addresses code review feedback on test best practices and structure. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- tests/modules/lint/test_main_nf.py | 18 +++++++++++------- tests/modules/lint/test_meta_yml.py | 16 ---------------- tests/modules/lint/test_module_lint_local.py | 10 +++++++--- tests/modules/lint/test_module_version.py | 12 ++++++------ 4 files changed, 24 insertions(+), 32 deletions(-) diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py index 26990f9ccc..d4327f50f5 100644 --- a/tests/modules/lint/test_main_nf.py +++ b/tests/modules/lint/test_main_nf.py @@ -101,20 +101,24 @@ def setUp(self): """Set up test fixtures by installing required modules""" super().setUp() # Install samtools/sort module for all tests in this class - assert self.mods_install.install("samtools/sort") + if not self.mods_install.install("samtools/sort"): + self.skipTest("Could not install samtools/sort module") def test_main_nf_lint_with_alternative_registry(self): """Test main.nf linting with alternative container registry""" - # Test with alternative registry + # Test with alternative registry - should warn/fail when containers don't match the registry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, registry="public.ecr.aws") module_lint.lint(print_results=False, module="samtools/sort") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - # Test with default registry + # Alternative registry should produce warnings or failures for container mismatches + # since samtools/sort module likely uses biocontainers/quay.io, not public.ecr.aws + total_issues = len(module_lint.failed) + len(module_lint.warned) + assert total_issues > 0, ( + "Expected warnings/failures when using alternative registry that doesn't match module containers" + ) + + # Test with default registry - should pass cleanly module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort") assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 diff --git a/tests/modules/lint/test_meta_yml.py b/tests/modules/lint/test_meta_yml.py index 296e230fec..b8dd29704a 100644 --- a/tests/modules/lint/test_meta_yml.py +++ b/tests/modules/lint/test_meta_yml.py @@ -31,14 +31,6 @@ def test_modules_meta_yml_incorrect_licence_field(self): module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - # reset changes - meta_yml["tools"][0]["bpipe"]["licence"] = ["MIT"] - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 assert len(module_lint.warned) >= 0 @@ -72,14 +64,6 @@ def test_modules_meta_yml_incorrect_name(self): module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - # reset changes - meta_yml["name"] = "bpipe_test" - with open( - Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "meta.yml"), - "w", - ) as fh: - fh.write(yaml.dump(meta_yml)) - assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 assert len(module_lint.warned) >= 0 diff --git a/tests/modules/lint/test_module_lint_local.py b/tests/modules/lint/test_module_lint_local.py index 8e1f0fa547..9387731499 100644 --- a/tests/modules/lint/test_module_lint_local.py +++ b/tests/modules/lint/test_module_lint_local.py @@ -9,9 +9,15 @@ class TestModulesLintLocal(TestModules): """Test ModuleLint functionality with local modules""" + def setUp(self): + """Set up test fixtures by installing required modules""" + super().setUp() + # Install trimgalore module for all tests in this class + if not self.mods_install.install("trimgalore"): + self.skipTest("Could not install trimgalore module") + def test_modules_lint_local(self): """Test linting local modules""" - assert self.mods_install.install("trimgalore") installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") local = Path(self.pipeline_dir, "modules", "local", "trimgalore") shutil.move(installed, local) @@ -23,7 +29,6 @@ def test_modules_lint_local(self): def test_modules_lint_local_missing_files(self): """Test linting local modules with missing files""" - assert self.mods_install.install("trimgalore") installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore") local = Path(self.pipeline_dir, "modules", "local", "trimgalore") shutil.move(installed, local) @@ -41,7 +46,6 @@ def test_modules_lint_local_missing_files(self): def test_modules_lint_local_old_format(self): """Test linting local modules in old format""" Path(self.pipeline_dir, "modules", "local").mkdir() - assert self.mods_install.install("trimgalore") installed = Path(self.pipeline_dir, "modules", "nf-core", "trimgalore", "main.nf") local = Path(self.pipeline_dir, "modules", "local", "trimgalore.nf") shutil.move(installed, local) diff --git a/tests/modules/lint/test_module_version.py b/tests/modules/lint/test_module_version.py index a64804817b..6ec5e1090b 100644 --- a/tests/modules/lint/test_module_version.py +++ b/tests/modules/lint/test_module_version.py @@ -8,14 +8,11 @@ class TestModuleVersion(TestModules): """Test module_version.py functionality""" - def setUp(self): - """Set up test fixtures by installing required modules""" - super().setUp() - # Install samtools/sort module for all tests in this class - assert self.mods_install.install("samtools/sort") - def test_module_version_with_git_sha(self): """Test module version when git_sha is present in modules.json""" + # Install a module + if not self.mods_install.install("samtools/sort"): + self.skipTest("Could not install samtools/sort module") # Run lint on the module - should have a git_sha entry module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) @@ -30,6 +27,9 @@ def test_module_version_with_git_sha(self): def test_module_version_up_to_date(self): """Test module version when module is up to date""" + # Install a module + if not self.mods_install.install("samtools/sort"): + self.skipTest("Could not install samtools/sort module") # Run lint on the module module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir) module_lint.lint(print_results=False, module="samtools/sort", key=["module_version"]) From a35f9bcd72c56c354466ce2fedb629a990034439 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 11 Jul 2025 14:23:23 -0500 Subject: [PATCH 098/101] feat: Add lint check for version snapshot content validation MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add new lint check `test_snap_version_content` to ensure version information in test snapshots contains actual content instead of MD5/SHA hash values. This addresses the issue where version snapshots were storing hash values like "versions.yml:md5,949da9c6297b613b50e24c421576f3f1" instead of actual version content like {"ALE": {"ale": "20180904"}}. Changes: - Add version content validation in module_tests.py with regex patterns - Add comprehensive tests for both invalid (hash) and valid (content) cases - Add pytest issue marker support for linking tests to GitHub issues - Update pyproject.toml with new pytest marker configuration Fixes: https://github.com/nf-core/modules/issues/6505 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/modules/lint/module_tests.py | 30 ++++++++++ pyproject.toml | 6 +- tests/modules/lint/test_module_tests.py | 73 +++++++++++++++++++++++++ 3 files changed, 108 insertions(+), 1 deletion(-) diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 6826b2e743..199edae128 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -170,6 +170,36 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): snap_file, ) ) + # Check if version content is actual content vs MD5 hash + # Related to: https://github.com/nf-core/modules/issues/6505 + # Ensures version snapshots contain actual content instead of hash values + version_content_valid = True + version_hash_patterns = [ + r"versions\.yml:md5,[\da-f]+", # MD5 hash pattern + r"versions\.yml:sha[\d]*,[\da-f]+", # SHA hash pattern + ] + + for pattern in version_hash_patterns: + if re.search(pattern, str(snap_content[test_name])): + version_content_valid = False + break + + if version_content_valid: + module.passed.append( + ( + "test_snap_version_content", + "version information contains actual content instead of hash", + snap_file, + ) + ) + else: + module.failed.append( + ( + "test_snap_version_content", + "version information should contain actual content, not MD5/SHA hash", + snap_file, + ) + ) else: module.failed.append( ( diff --git a/pyproject.toml b/pyproject.toml index 42da317707..43d6b68233 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,11 @@ build-backend = "setuptools.build_meta" requires = ["setuptools>=40.6.0", "wheel"] [tool.pytest.ini_options] -markers = ["datafiles: load datafiles", "integration"] +markers = [ + "datafiles: load datafiles", + "integration", + "issue: mark test with related issue URL" +] testpaths = ["tests"] python_files = ["test_*.py"] asyncio_mode = "auto" diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index b5f361c7d8..8b9423457c 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -1,6 +1,7 @@ import json from pathlib import Path +import pytest from git.repo import Repo import nf_core.modules.lint @@ -213,3 +214,75 @@ def test_modules_empty_file_in_stub_snapshot(self): # reset the file with open(snap_file, "w") as fh: fh.write(content) + + @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") + def test_modules_version_snapshot_content_md5_hash(self): + """Test linting a nf-test module with version information as MD5 hash instead of actual content, which should fail. + + Related to: https://github.com/nf-core/modules/issues/6505 + Fixed in: https://github.com/nf-core/tools/pull/3676 + """ + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + + # Add a version entry with MD5 hash format (the old way that should be flagged) + snap["my test"]["content"][0]["versions"] = "versions.yml:md5,949da9c6297b613b50e24c421576f3f1" + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Should fail because version is using MD5 hash instead of actual content + # Filter for only our specific test + version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] + assert len(version_content_failures) == 1, ( + f"Expected 1 test_snap_version_content failure, got {len(version_content_failures)}" + ) + assert version_content_failures[0].lint_test == "test_snap_version_content" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") + def test_modules_version_snapshot_content_valid(self): + """Test linting a nf-test module with version information as actual content, which should pass. + + Related to: https://github.com/nf-core/modules/issues/6505 + Fixed in: https://github.com/nf-core/tools/pull/3676 + """ + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + + # Add a version entry with actual content (the new way that should pass) + snap["my test"]["content"][0]["versions"] = {"ALE": {"ale": "20180904"}} + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Should pass because version contains actual content + # Filter for only our specific test + version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] + assert len(version_content_failures) == 0, ( + f"Expected 0 test_snap_version_content failures, got {len(version_content_failures)}" + ) + + # Check for test_snap_version_content in passed tests + version_content_passed = [ + x + for x in module_lint.passed + if (hasattr(x, "lint_test") and x.lint_test == "test_snap_version_content") + or (isinstance(x, tuple) and len(x) > 0 and x[0] == "test_snap_version_content") + ] + assert len(version_content_passed) > 0, "test_snap_version_content not found in passed tests" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) From ff546d64fd61bb71550181d9c98343b9ba738f1e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 26 Aug 2025 11:36:48 -0500 Subject: [PATCH 099/101] refactor: Improve version snapshot content validation with enhanced regex and error handling MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Extract version checking logic into dedicated helper functions for better modularity - Implement more precise regex patterns with proper word boundaries to avoid false positives - Optimize performance by reducing string conversions from multiple to single per test - Add comprehensive test coverage for SHA hashes, mixed scenarios, and edge cases - Enhance error messages with clearer guidance and examples for developers - Improve code maintainability and readability through separation of concerns 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/modules/lint/module_tests.py | 91 ++++++++++++++++------- tests/modules/lint/test_module_tests.py | 99 +++++++++++++++++++++++++ 2 files changed, 164 insertions(+), 26 deletions(-) diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 199edae128..4c2c6d1d65 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -15,6 +15,59 @@ log = logging.getLogger(__name__) +def _check_version_content_format(snap_content, test_name, snap_file): + """ + Check if version content uses actual YAML data vs hash format. + + Args: + snap_content: Parsed JSON snapshot content + test_name: Name of the test being checked + snap_file: Path to snapshot file (for error reporting) + + Returns: + Tuple for passed test if valid, None if invalid or no version data found + """ + # Check if this test contains version data and if it's in hash format + if _contains_version_hash(snap_content[test_name]): + return None # Invalid - contains hash format + + # Valid - either contains actual content or no version hash detected + return ( + "test_snap_version_content", + "version information contains actual content instead of hash", + snap_file, + ) + + +def _contains_version_hash(test_content): + """ + Check if test content contains version information in hash format. + + Uses precise regex patterns to detect version hash formats while avoiding + false positives from similar strings. + + Args: + test_content: Content of a single test from snapshot + + Returns: + bool: True if hash format detected, False otherwise + """ + # More precise regex patterns with proper boundaries + version_hash_patterns = [ + r"\bversions\.yml:md5,[a-f0-9]{32}\b", # Exact MD5 format (32 hex chars) + r"\bversions\.yml:sha[0-9]*,[a-f0-9]+\b", # SHA format with variable length + ] + + # Convert to string only once and search efficiently + content_str = str(test_content) + + for pattern in version_hash_patterns: + if re.search(pattern, content_str): + return True + + return False + + def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): """ Lint the tests of a module in ``nf-core/modules`` @@ -170,36 +223,22 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): snap_file, ) ) - # Check if version content is actual content vs MD5 hash + # Check if version content is actual content vs MD5/SHA hash # Related to: https://github.com/nf-core/modules/issues/6505 # Ensures version snapshots contain actual content instead of hash values - version_content_valid = True - version_hash_patterns = [ - r"versions\.yml:md5,[\da-f]+", # MD5 hash pattern - r"versions\.yml:sha[\d]*,[\da-f]+", # SHA hash pattern - ] - - for pattern in version_hash_patterns: - if re.search(pattern, str(snap_content[test_name])): - version_content_valid = False - break - - if version_content_valid: - module.passed.append( - ( - "test_snap_version_content", - "version information contains actual content instead of hash", - snap_file, - ) - ) + version_check_result = _check_version_content_format(snap_content, test_name, snap_file) + if version_check_result: + module.passed.append(version_check_result) else: - module.failed.append( - ( - "test_snap_version_content", - "version information should contain actual content, not MD5/SHA hash", - snap_file, + # Only add failure if we found hash patterns + if _contains_version_hash(snap_content[test_name]): + module.failed.append( + ( + "test_snap_version_content", + "Version information should contain actual YAML content (e.g., {'tool': {'version': '1.0'}}), not hash format like 'versions.yml:md5,hash'", + snap_file, + ) ) - ) else: module.failed.append( ( diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index 8b9423457c..9f1cfe9b78 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -286,3 +286,102 @@ def test_modules_version_snapshot_content_valid(self): # reset the file with open(snap_file, "w") as fh: fh.write(content) + + @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") + def test_modules_version_snapshot_content_sha_hash(self): + """Test linting a nf-test module with version information as SHA hash, which should fail. + + Related to: https://github.com/nf-core/modules/issues/6505 + Fixed in: https://github.com/nf-core/tools/pull/3676 + """ + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + + # Add a version entry with SHA hash format (should be flagged) + snap["my test"]["content"][0]["versions"] = ( + "versions.yml:sha256,e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855" + ) + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Should fail because version is using SHA hash instead of actual content + version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] + assert len(version_content_failures) == 1, ( + f"Expected 1 test_snap_version_content failure, got {len(version_content_failures)}" + ) + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") + def test_modules_version_snapshot_content_mixed_scenario(self): + """Test linting with mixed version content - some valid, some hash format. + + Related to: https://github.com/nf-core/modules/issues/6505 + Fixed in: https://github.com/nf-core/tools/pull/3676 + """ + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + + # Create a scenario with multiple tests - one with hash, one with valid content + snap["test_with_hash"] = {"content": [{"versions": "versions.yml:md5,949da9c6297b613b50e24c421576f3f1"}]} + snap["test_with_valid_content"] = {"content": [{"versions": {"BPIPE": {"bpipe": "0.9.11"}}}]} + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Should have failure for the hash test + version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] + assert len(version_content_failures) >= 1, "Expected at least 1 failure for hash format" + + # Should have pass for the valid content test + version_content_passed = [ + x + for x in module_lint.passed + if (hasattr(x, "lint_test") and x.lint_test == "test_snap_version_content") + or (isinstance(x, tuple) and len(x) > 0 and x[0] == "test_snap_version_content") + ] + assert len(version_content_passed) >= 1, "Expected at least 1 pass for valid content" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) + + @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") + def test_modules_version_snapshot_no_version_content(self): + """Test linting when no version information is present - should not trigger version content check. + + Related to: https://github.com/nf-core/modules/issues/6505 + Fixed in: https://github.com/nf-core/tools/pull/3676 + """ + snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" + snap = json.load(snap_file.open()) + content = snap_file.read_text() + + # Remove version information entirely + if "content" in snap["my test"] and snap["my test"]["content"]: + snap["my test"]["content"][0].pop("versions", None) + + with open(snap_file, "w") as fh: + json.dump(snap, fh) + + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) + module_lint.lint(print_results=False, module="bpipe/test") + + # Should not have version content check failures when no version data present + version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] + assert len(version_content_failures) == 0, "Should not have version content failures when no versions present" + + # reset the file + with open(snap_file, "w") as fh: + fh.write(content) From 11bcdcb7bd32fba3f6e0dc28526f153aa5e5946f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 26 Aug 2025 12:13:58 -0500 Subject: [PATCH 100/101] fix: Fix version content validation loop logic and improve test coverage MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Fix critical indentation issue where version checking ran outside the test loop - Remove redundant _check_version_content_format function for cleaner logic - Ensure version content validation runs for each test individually - Improve regex patterns with word boundaries for more precise hash detection - Add comprehensive test coverage for SHA hashes, mixed scenarios, and edge cases - All new tests now pass correctly after fixing the loop structure Related to: https://github.com/nf-core/modules/issues/6505 Fixed in: https://github.com/nf-core/tools/pull/3676 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude --- nf_core/modules/lint/module_tests.py | 73 +++++++++---------------- tests/modules/lint/test_module_tests.py | 16 ++++-- 2 files changed, 39 insertions(+), 50 deletions(-) diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 4c2c6d1d65..8618e6dc64 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -15,30 +15,6 @@ log = logging.getLogger(__name__) -def _check_version_content_format(snap_content, test_name, snap_file): - """ - Check if version content uses actual YAML data vs hash format. - - Args: - snap_content: Parsed JSON snapshot content - test_name: Name of the test being checked - snap_file: Path to snapshot file (for error reporting) - - Returns: - Tuple for passed test if valid, None if invalid or no version data found - """ - # Check if this test contains version data and if it's in hash format - if _contains_version_hash(snap_content[test_name]): - return None # Invalid - contains hash format - - # Valid - either contains actual content or no version hash detected - return ( - "test_snap_version_content", - "version information contains actual content instead of hash", - snap_file, - ) - - def _contains_version_hash(test_content): """ Check if test content contains version information in hash format. @@ -215,23 +191,19 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): snap_file, ) ) - if "versions" in str(snap_content[test_name]) or "versions" in str(snap_content.keys()): - module.passed.append( - ( - "test_snap_versions", - "versions found in snapshot file", - snap_file, + if "versions" in str(snap_content[test_name]) or "versions" in str(snap_content.keys()): + module.passed.append( + ( + "test_snap_versions", + "versions found in snapshot file", + snap_file, + ) ) - ) - # Check if version content is actual content vs MD5/SHA hash - # Related to: https://github.com/nf-core/modules/issues/6505 - # Ensures version snapshots contain actual content instead of hash values - version_check_result = _check_version_content_format(snap_content, test_name, snap_file) - if version_check_result: - module.passed.append(version_check_result) - else: - # Only add failure if we found hash patterns + # Check if version content is actual content vs MD5/SHA hash + # Related to: https://github.com/nf-core/modules/issues/6505 + # Ensures version snapshots contain actual content instead of hash values if _contains_version_hash(snap_content[test_name]): + # Invalid - contains hash format module.failed.append( ( "test_snap_version_content", @@ -239,14 +211,23 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): snap_file, ) ) - else: - module.failed.append( - ( - "test_snap_versions", - "versions not found in snapshot file", - snap_file, + else: + # Valid - either contains actual content or no version hash detected + module.passed.append( + ( + "test_snap_version_content", + "version information contains actual content instead of hash", + snap_file, + ) + ) + else: + module.failed.append( + ( + "test_snap_versions", + "versions not found in snapshot file", + snap_file, + ) ) - ) except json.decoder.JSONDecodeError as e: module.failed.append( ( diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index 9f1cfe9b78..ce09330e9e 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -135,12 +135,20 @@ def test_nftest_failing_linting(self): module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="kallisto/quant") - assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.failed) == 4, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 assert len(module_lint.warned) >= 0 - assert module_lint.failed[0].lint_test == "meta_yml_valid" - assert module_lint.failed[1].lint_test == "test_main_tags" - assert "kallisto/index" in module_lint.failed[1].message + + # Check for expected failure types + failed_tests = [x.lint_test for x in module_lint.failed] + assert "meta_yml_valid" in failed_tests + assert "test_main_tags" in failed_tests + assert failed_tests.count("test_snap_version_content") == 2 # Should appear twice for the two version entries + + # Check test_main_tags failure contains the expected message + main_tags_failures = [x for x in module_lint.failed if x.lint_test == "test_main_tags"] + assert len(main_tags_failures) == 1 + assert "kallisto/index" in main_tags_failures[0].message def test_modules_absent_version(self): """Test linting a nf-test module if the versions is absent in the snapshot file `""" From 1ddf9ce1092e36b24951dc5c66d1bee179a3d262 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Sat, 27 Sep 2025 20:24:35 +0200 Subject: [PATCH 101/101] fix: Address PR review feedback - Clean up AI-generated comments and verbose documentation - Improve version hash detection to handle both content and keys - Add test case for version hash in snapshot keys scenario - Update CHANGELOG.md with feature description - Preserve all existing pytest-workflow logic for separate PR Addresses feedback from @mashehu and @mirpedrol Related to: https://github.com/nf-core/modules/issues/6505 --- CHANGELOG.md | 1 + nf_core/modules/lint/module_tests.py | 43 +++++---- tests/modules/lint/test_module_tests.py | 110 +++++++----------------- 3 files changed, 51 insertions(+), 103 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f475519df0..5aa3e23b80 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ - Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633)) - feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608)) +- Lint for version captures in modules - detect hash format instead of actual YAML content ([#3676](https://github.com/nf-core/tools/pull/3676)) ### Subworkflows diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py index 8618e6dc64..892c95d948 100644 --- a/nf_core/modules/lint/module_tests.py +++ b/nf_core/modules/lint/module_tests.py @@ -16,25 +16,12 @@ def _contains_version_hash(test_content): - """ - Check if test content contains version information in hash format. - - Uses precise regex patterns to detect version hash formats while avoiding - false positives from similar strings. - - Args: - test_content: Content of a single test from snapshot - - Returns: - bool: True if hash format detected, False otherwise - """ - # More precise regex patterns with proper boundaries + """Check if test content contains version information in hash format rather than actual YAML content.""" version_hash_patterns = [ - r"\bversions\.yml:md5,[a-f0-9]{32}\b", # Exact MD5 format (32 hex chars) - r"\bversions\.yml:sha[0-9]*,[a-f0-9]+\b", # SHA format with variable length + r"\bversions\.yml:md5,[a-f0-9]{32}\b", + r"\bversions\.yml:sha[0-9]*,[a-f0-9]+\b", ] - # Convert to string only once and search efficiently content_str = str(test_content) for pattern in version_hash_patterns: @@ -44,6 +31,22 @@ def _contains_version_hash(test_content): return False +def _check_snapshot_for_version_hash(snap_content, test_name): + """Check both snapshot content and keys for version hash patterns.""" + # Check test content for version hashes + if _contains_version_hash(snap_content[test_name]): + return True + + # Check specific test's keys for version hashes + test_data = snap_content.get(test_name, {}) + if isinstance(test_data, dict): + for key in test_data.keys(): + if _contains_version_hash(str(key)): + return True + + return False + + def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): """ Lint the tests of a module in ``nf-core/modules`` @@ -199,11 +202,8 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): snap_file, ) ) - # Check if version content is actual content vs MD5/SHA hash - # Related to: https://github.com/nf-core/modules/issues/6505 - # Ensures version snapshots contain actual content instead of hash values - if _contains_version_hash(snap_content[test_name]): - # Invalid - contains hash format + # Check if version content contains hash instead of actual YAML content + if _check_snapshot_for_version_hash(snap_content, test_name): module.failed.append( ( "test_snap_version_content", @@ -212,7 +212,6 @@ def module_tests(_, module: NFCoreComponent, allow_missing: bool = False): ) ) else: - # Valid - either contains actual content or no version hash detected module.passed.append( ( "test_snap_version_content", diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py index ce09330e9e..6c9d7db378 100644 --- a/tests/modules/lint/test_module_tests.py +++ b/tests/modules/lint/test_module_tests.py @@ -171,7 +171,7 @@ def test_modules_empty_file_in_snapshot(self): """Test linting a nf-test module with an empty file sha sum in the test snapshot, which should make it fail (if it is not a stub)""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() snap["my test"]["content"][0]["0"] = "test:md5,d41d8cd98f00b204e9800998ecf8427e" with open(snap_file, "w") as fh: @@ -184,15 +184,11 @@ def test_modules_empty_file_in_snapshot(self): assert len(module_lint.warned) >= 0 assert module_lint.failed[0].lint_test == "test_snap_md5sum" - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - def test_modules_empty_file_in_stub_snapshot(self): """Test linting a nf-test module with an empty file sha sum in the stub test snapshot, which should make it not fail""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() snap["my_test_stub"] = {"content": [{"0": "test:md5,d41d8cd98f00b204e9800998ecf8427e", "versions": {}}]} with open(snap_file, "w") as fh: @@ -219,20 +215,12 @@ def test_modules_empty_file_in_stub_snapshot(self): assert found_test, "test_snap_md5sum not found in passed tests" - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") def test_modules_version_snapshot_content_md5_hash(self): - """Test linting a nf-test module with version information as MD5 hash instead of actual content, which should fail. - - Related to: https://github.com/nf-core/modules/issues/6505 - Fixed in: https://github.com/nf-core/tools/pull/3676 - """ + """Test linting a nf-test module with version information as MD5 hash instead of actual content, which should fail.""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() # Add a version entry with MD5 hash format (the old way that should be flagged) snap["my test"]["content"][0]["versions"] = "versions.yml:md5,949da9c6297b613b50e24c421576f3f1" @@ -249,22 +237,13 @@ def test_modules_version_snapshot_content_md5_hash(self): assert len(version_content_failures) == 1, ( f"Expected 1 test_snap_version_content failure, got {len(version_content_failures)}" ) - assert version_content_failures[0].lint_test == "test_snap_version_content" - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") def test_modules_version_snapshot_content_valid(self): - """Test linting a nf-test module with version information as actual content, which should pass. - - Related to: https://github.com/nf-core/modules/issues/6505 - Fixed in: https://github.com/nf-core/tools/pull/3676 - """ + """Test linting a nf-test module with version information as actual content, which should pass.""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() # Add a version entry with actual content (the new way that should pass) snap["my test"]["content"][0]["versions"] = {"ALE": {"ale": "20180904"}} @@ -291,20 +270,12 @@ def test_modules_version_snapshot_content_valid(self): ] assert len(version_content_passed) > 0, "test_snap_version_content not found in passed tests" - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") def test_modules_version_snapshot_content_sha_hash(self): - """Test linting a nf-test module with version information as SHA hash, which should fail. - - Related to: https://github.com/nf-core/modules/issues/6505 - Fixed in: https://github.com/nf-core/tools/pull/3676 - """ + """Test linting a nf-test module with version information as SHA hash, which should fail.""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() # Add a version entry with SHA hash format (should be flagged) snap["my test"]["content"][0]["versions"] = ( @@ -323,24 +294,16 @@ def test_modules_version_snapshot_content_sha_hash(self): f"Expected 1 test_snap_version_content failure, got {len(version_content_failures)}" ) - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) - @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") - def test_modules_version_snapshot_content_mixed_scenario(self): - """Test linting with mixed version content - some valid, some hash format. - - Related to: https://github.com/nf-core/modules/issues/6505 - Fixed in: https://github.com/nf-core/tools/pull/3676 - """ + def test_modules_version_snapshot_no_version_content(self): + """Test linting when no version information is present - should not trigger version content check.""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() - # Create a scenario with multiple tests - one with hash, one with valid content - snap["test_with_hash"] = {"content": [{"versions": "versions.yml:md5,949da9c6297b613b50e24c421576f3f1"}]} - snap["test_with_valid_content"] = {"content": [{"versions": {"BPIPE": {"bpipe": "0.9.11"}}}]} + # Remove version information entirely + if "content" in snap["my test"] and snap["my test"]["content"]: + snap["my test"]["content"][0].pop("versions", None) with open(snap_file, "w") as fh: json.dump(snap, fh) @@ -348,37 +311,26 @@ def test_modules_version_snapshot_content_mixed_scenario(self): module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - # Should have failure for the hash test + # Should not have version content check failures when no version data present version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] - assert len(version_content_failures) >= 1, "Expected at least 1 failure for hash format" - - # Should have pass for the valid content test - version_content_passed = [ - x - for x in module_lint.passed - if (hasattr(x, "lint_test") and x.lint_test == "test_snap_version_content") - or (isinstance(x, tuple) and len(x) > 0 and x[0] == "test_snap_version_content") - ] - assert len(version_content_passed) >= 1, "Expected at least 1 pass for valid content" + assert len(version_content_failures) == 0, "Should not have version content failures when no versions present" - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) + # Should have test_snap_versions failure since no versions are present + version_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_versions"] + assert len(version_failures) == 1, "Expected test_snap_versions failure when no versions present" @pytest.mark.issue("https://github.com/nf-core/modules/issues/6505") - def test_modules_version_snapshot_no_version_content(self): - """Test linting when no version information is present - should not trigger version content check. - - Related to: https://github.com/nf-core/modules/issues/6505 - Fixed in: https://github.com/nf-core/tools/pull/3676 - """ + def test_modules_version_snapshot_hash_in_keys(self): + """Test linting when version hash appears in snapshot keys rather than content.""" snap_file = self.bpipe_test_module_path / "tests" / "main.nf.test.snap" snap = json.load(snap_file.open()) - content = snap_file.read_text() + snap_file.read_text() - # Remove version information entirely - if "content" in snap["my test"] and snap["my test"]["content"]: - snap["my test"]["content"][0].pop("versions", None) + # Create a test where version hash appears in the test keys + snap["test_with_hash_key"] = { + "content": [{"versions.yml:md5,949da9c6297b613b50e24c421576f3f1": "some_value"}], + "versions": {"BPIPE": {"bpipe": "0.9.11"}}, + } with open(snap_file, "w") as fh: json.dump(snap, fh) @@ -386,10 +338,6 @@ def test_modules_version_snapshot_no_version_content(self): module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) module_lint.lint(print_results=False, module="bpipe/test") - # Should not have version content check failures when no version data present + # Should fail because version hash is in the keys version_content_failures = [x for x in module_lint.failed if x.lint_test == "test_snap_version_content"] - assert len(version_content_failures) == 0, "Should not have version content failures when no versions present" - - # reset the file - with open(snap_file, "w") as fh: - fh.write(content) + assert len(version_content_failures) >= 1, "Expected failure for hash in keys"