…s-for-sub-modules

…dling

- 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.

- 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.

…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.

…ent.yml processing"

This reverts commit 34d5b00.

Co-authored-by: mashehu <mashehu@users.noreply.github.com>

…endencies

Co-authored-by: mashehu <mashehu3@gmail.com>

…l 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 <mashehu3@gmail.com>

- 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.

- Updated pytest.ini_options in pyproject.toml to include a new "integration" marker for better test categorization.

…nt_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.

but it is a link to another json file

Remove workflow.trace from nf-test snapshot

ignore files in gitignore also for pipeline_if_empty_null lint test

Add GHA to update template nf-test snapshots

- 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.

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Co-Authored-By: Claude <noreply@anthropic.com>

Refactor module lint tests

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: nf-core/modules#6505

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

…egex and error handling

- 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 <noreply@anthropic.com>

- 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: nf-core/modules#6505
Fixed in: #3676

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>