improve softwareVersionsToYAML() #24
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Can we split these into two PRs? 😬 |
maxulysse
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maxulysse
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Oct 22, 2025
maxulysse
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Oct 22, 2025
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Done, and even better, made 3 +1 in the end |
nvnieuwk
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Oct 22, 2025
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Love it! can this also be documented?
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Also, can you create some tests? |
nvnieuwk
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Oct 22, 2025
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* docs: fix typo in softwareVersionsToYAML documentation Fix typo in JavaDoc example code where 'versions_yamllet'' was incorrectly written instead of 'versions_yaml'. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> * refactor: simplify softwareVersionsToYAML with focused helper methods Refactored the complex 166-line softwareVersionsToYAML() method by extracting only essential helper methods that provide real value: Core improvements: - Main method now ~100 lines with visible, straightforward logic - Extracted 4 focused helper methods (down from original over-engineered 13): * processYamlContent(): Eliminates duplicate YAML parsing (used 5+ times) * mergeParsedYaml(): Handles complex nested/flat YAML detection logic * mergeProcessMap(): Reusable process map merging with key cleaning * hasToFileMethod(): Safety-critical reflection for Path detection - Type routing, simple string operations, and sorting kept inline - Uses small recursive closure for nested list handling - Eliminates deeply nested closures from original implementation Benefits: - Better balance between simplicity and maintainability - Main logic flow visible and easy to follow - Real complexity extracted to testable helpers - No thin wrapper methods adding unnecessary indirection - All tests pass without modification This approach keeps both Nextflow usage AND the code simple while improving on the original deeply-nested 166-line implementation. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]> --------- Co-authored-by: Claude <[email protected]>
edmundmiller
approved these changes
Oct 29, 2025
This was referenced Oct 29, 2025
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Initial PR split into: