nf-core · ewels · Dec 14, 2020 · Dec 5, 2020 · Dec 5, 2020 · Dec 5, 2020
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -57,7 +57,7 @@ We aim to write function docstrings according to the [Google Python style-guide]
 You can find this documentation here: [https://nf-co.re/tools-docs/](https://nf-co.re/tools-docs/)
 
 If you would like to test the documentation, you can install Sphinx locally by following Sphinx's [installation instruction](https://www.sphinx-doc.org/en/master/usage/installation.html).
-Once done, you can run `make clean` and then `make html` in the root directory of `nf-core tools`.
+Once done, you can run `make clean` and then `make html` in the `docs/api` directory of `nf-core tools`.
 The HTML will then be generated in `docs/api/_build/html`.
 
 ## Tests

diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,7 @@
 
 .coverage
 .pytest_cache
+docs/api/_build
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/docs/api/_src/bump_version.rst → docs/api/_src/api/bump_version.rst b/docs/api/_src/bump_version.rst → docs/api/_src/api/bump_version.rst
diff --git a/docs/api/_src/create.rst → docs/api/_src/api/create.rst b/docs/api/_src/create.rst → docs/api/_src/api/create.rst
diff --git a/docs/api/_src/download.rst → docs/api/_src/api/download.rst b/docs/api/_src/download.rst → docs/api/_src/api/download.rst
diff --git a/docs/api/_src/api/index.rst b/docs/api/_src/api/index.rst
@@ -0,0 +1,9 @@
+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tests:
+   :glob:
+
+   *
diff --git a/docs/api/_src/launch.rst → docs/api/_src/api/launch.rst b/docs/api/_src/launch.rst → docs/api/_src/api/launch.rst
@@ -1,5 +1,5 @@
 nf_core.launch
-============
+==============
 
 .. automodule:: nf_core.launch
     :members:

diff --git a/docs/api/_src/licences.rst → docs/api/_src/api/licences.rst b/docs/api/_src/licences.rst → docs/api/_src/api/licences.rst
diff --git a/docs/api/_src/api/lint.rst b/docs/api/_src/api/lint.rst
@@ -0,0 +1,14 @@
+nf_core.lint
+============
+
+.. seealso:: See the `Lint Tests <../lint_tests/index.html>`_ docs for information about specific linting functions.
+
+.. automodule:: nf_core.lint
+    :members: run_linting
+    :undoc-members:
+    :show-inheritance:
+
+.. autoclass:: nf_core.lint.PipelineLint
+    :members: _lint_pipeline
+    :private-members: _print_results, _get_results_md, _save_json_results, _wrap_quotes, _strip_ansi_codes
+    :show-inheritance:
diff --git a/docs/api/_src/list.rst → docs/api/_src/api/list.rst b/docs/api/_src/list.rst → docs/api/_src/api/list.rst
diff --git a/docs/api/_src/modules.rst → docs/api/_src/api/modules.rst b/docs/api/_src/modules.rst → docs/api/_src/api/modules.rst
@@ -1,5 +1,5 @@
 nf_core.modules
-============
+===============
 
 .. automodule:: nf_core.modules
     :members:

diff --git a/docs/api/_src/schema.rst → docs/api/_src/api/schema.rst b/docs/api/_src/schema.rst → docs/api/_src/api/schema.rst
@@ -1,5 +1,5 @@
 nf_core.schema
-============
+==============
 
 .. automodule:: nf_core.schema
     :members:

diff --git a/docs/api/_src/sync.rst → docs/api/_src/api/sync.rst b/docs/api/_src/sync.rst → docs/api/_src/api/sync.rst
diff --git a/docs/api/_src/utils.rst → docs/api/_src/api/utils.rst b/docs/api/_src/utils.rst → docs/api/_src/api/utils.rst
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
@@ -74,7 +74,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "nature"
+# html_theme = "nature"
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

diff --git a/docs/api/_src/index.rst b/docs/api/_src/index.rst
@@ -7,12 +7,19 @@ Welcome to nf-core tools API documentation!
 ===========================================
 
 .. toctree::
+   :hidden:
    :maxdepth: 2
    :caption: Contents:
    :glob:
 
-   *
+   lint_tests/index.rst
+   api/index.rst
 
+This documentation is for the ``nf-core/tools`` package.
+
+Primarily, it describes the different `code lint tests <lint_tests/index.html>`_
+run by ``nf-core lint`` (typically visited by a developer when their pipeline fails a given
+test), and also reference for the ``nf_core`` `Python package API <api/index.html>`_.
 
 Indices and tables
 ==================

diff --git a/docs/api/_src/lint.rst b/docs/api/_src/lint.rst
diff --git a/docs/api/_src/lint_tests/actions_awsfulltest.rst b/docs/api/_src/lint_tests/actions_awsfulltest.rst
@@ -0,0 +1,4 @@
+actions_awsfulltest
+===================
+
+.. automethod:: nf_core.lint.PipelineLint.actions_awsfulltest
diff --git a/docs/api/_src/lint_tests/actions_awstest.rst b/docs/api/_src/lint_tests/actions_awstest.rst
@@ -0,0 +1,4 @@
+actions_awstest
+===============
+
+.. automethod:: nf_core.lint.PipelineLint.actions_awstest
diff --git a/docs/api/_src/lint_tests/actions_branch_protection.rst b/docs/api/_src/lint_tests/actions_branch_protection.rst
@@ -0,0 +1,4 @@
+actions_branch_protection
+=========================
+
+.. automethod:: nf_core.lint.PipelineLint.actions_branch_protection
diff --git a/docs/api/_src/lint_tests/actions_ci.rst b/docs/api/_src/lint_tests/actions_ci.rst
@@ -0,0 +1,4 @@
+actions_ci
+==========
+
+.. automethod:: nf_core.lint.PipelineLint.actions_ci
diff --git a/docs/api/_src/lint_tests/actions_lint.rst b/docs/api/_src/lint_tests/actions_lint.rst
@@ -0,0 +1,4 @@
+actions_lint
+============
+
+.. automethod:: nf_core.lint.PipelineLint.actions_lint
diff --git a/docs/api/_src/lint_tests/conda_dockerfile.rst b/docs/api/_src/lint_tests/conda_dockerfile.rst
@@ -0,0 +1,4 @@
+conda_dockerfile
+================
+
+.. automethod:: nf_core.lint.PipelineLint.conda_dockerfile
diff --git a/docs/api/_src/lint_tests/conda_env_yaml.rst b/docs/api/_src/lint_tests/conda_env_yaml.rst
@@ -0,0 +1,6 @@
+conda_env_yaml
+==============
+
+.. automethod:: nf_core.lint.PipelineLint.conda_env_yaml
+.. automethod:: nf_core.lint.PipelineLint._anaconda_package
+.. automethod:: nf_core.lint.PipelineLint._pip_package
diff --git a/docs/api/_src/lint_tests/cookiecutter_strings.rst b/docs/api/_src/lint_tests/cookiecutter_strings.rst
@@ -0,0 +1,4 @@
+cookiecutter_strings
+====================
+
+.. automethod:: nf_core.lint.PipelineLint.cookiecutter_strings
diff --git a/docs/api/_src/lint_tests/files_exist.rst b/docs/api/_src/lint_tests/files_exist.rst
@@ -0,0 +1,4 @@
+files_exist
+===========
+
+.. automethod:: nf_core.lint.PipelineLint.files_exist
diff --git a/docs/api/_src/lint_tests/index.rst b/docs/api/_src/lint_tests/index.rst
@@ -0,0 +1,9 @@
+Lint tests
+============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tests:
+   :glob:
+
+   *
diff --git a/docs/api/_src/lint_tests/licence.rst b/docs/api/_src/lint_tests/licence.rst
@@ -0,0 +1,4 @@
+licence
+=======
+
+.. automethod:: nf_core.lint.PipelineLint.licence
diff --git a/docs/api/_src/lint_tests/nextflow_config.rst b/docs/api/_src/lint_tests/nextflow_config.rst
@@ -0,0 +1,4 @@
+nextflow_config
+===============
+
+.. automethod:: nf_core.lint.PipelineLint.nextflow_config
diff --git a/docs/api/_src/lint_tests/pipeline_name_conventions.rst b/docs/api/_src/lint_tests/pipeline_name_conventions.rst
@@ -0,0 +1,4 @@
+pipeline_name_conventions
+=========================
+
+.. automethod:: nf_core.lint.PipelineLint.pipeline_name_conventions
diff --git a/docs/api/_src/lint_tests/pipeline_todos.rst b/docs/api/_src/lint_tests/pipeline_todos.rst
@@ -0,0 +1,4 @@
+pipeline_todos
+==============
+
+.. automethod:: nf_core.lint.PipelineLint.pipeline_todos
diff --git a/docs/api/_src/lint_tests/readme.rst b/docs/api/_src/lint_tests/readme.rst
@@ -0,0 +1,4 @@
+readme
+======
+
+.. automethod:: nf_core.lint.PipelineLint.readme
diff --git a/docs/api/_src/lint_tests/schema_lint.rst b/docs/api/_src/lint_tests/schema_lint.rst
@@ -0,0 +1,4 @@
+schema_lint
+===========
+
+.. automethod:: nf_core.lint.PipelineLint.schema_lint
diff --git a/docs/api/_src/lint_tests/schema_params.rst b/docs/api/_src/lint_tests/schema_params.rst
@@ -0,0 +1,4 @@
+schema_params
+=============
+
+.. automethod:: nf_core.lint.PipelineLint.schema_params
diff --git a/docs/api/_src/lint_tests/version_consistency.rst b/docs/api/_src/lint_tests/version_consistency.rst
@@ -0,0 +1,4 @@
+version_consistency
+===================
+
+.. automethod:: nf_core.lint.PipelineLint.version_consistency
diff --git a/docs/api/make_lint_rst.py b/docs/api/make_lint_rst.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import fnmatch
+import os
+import nf_core.lint
+
+docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "lint_tests")
+
+# Get list of existing .rst files
+existing_docs = []
+for fn in os.listdir(docs_basedir):
+    if fnmatch.fnmatch(fn, "*.rst") and not fnmatch.fnmatch(fn, "index.rst"):
+        existing_docs.append(os.path.join(docs_basedir, fn))
+
+# Make .rst file for each test name
+lint_obj = nf_core.lint.PipelineLint("", True)
+rst_template = """{0}
+{1}
+
+.. automethod:: nf_core.lint.PipelineLint.{0}
+"""
+
+for test_name in lint_obj.lint_tests:
+    fn = os.path.join(docs_basedir, "{}.rst".format(test_name))
+    if os.path.exists(fn):
+        existing_docs.remove(fn)
+    else:
+        with open(fn, "w") as fh:
+            fh.write(rst_template.format(test_name, len(test_name) * "="))
+
+for fn in existing_docs:
+    os.remove(fn)
diff --git a/docs/api/requirements.txt b/docs/api/requirements.txt
@@ -0,0 +1,2 @@
+Sphinx>=3.3.1
+sphinx_rtd_theme>=0.5.0