Origin/dev/refactor code - #19
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Add a comprehensive test suite and coverage output (coverage.json); update pytest.ini and include many new test files under tests/. Update docs components (docs/app/components/ThemeToggle.tsx and docs/app/page.tsx). Modify multiple metbit modules and include regenerated __pycache__ (.pyc) artifacts. Update .gitignore to ignore metbit/__pycache__.
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@copilot resolve the merge conflicts in this pull request |
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Resolved. I merged |
Limit Draft PDF workflow triggers to paper-related files and PRs; update manuscript source (metbit_manuscript.md and paper.md) to expand affiliations, reorganize and flesh out sections (functionality, implementation, results, availability, funding), update date, and replace explicit AI-tool bylines with a generic AI usage disclosure. Remove AI-credit footers from figure-generation scripts and regenerate graphical assets (PNG files) and the .docx; add temporary .docx artifact. Overall cleanup of text, figures, and CI to reflect manuscript revisions and remove named AI assistant credits.
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This pull request introduces several significant changes to the
metbitpackage, focusing on a major reorganization of the codebase into sub-packages, improved API clarity, and new internal utilities for reporting and pairwise analysis. It also includes minor UI improvements in the documentation and the removal of unused or placeholder development scripts.Major codebase reorganization and API improvements:
metbit/__init__.pyto re-export public API from new sub-packages, updated the version to9.0.0-dev, and made Dash app imports optional for environments without heavy dependencies. The__all__list is updated to reflect the new structure.metbit/_compat.py, providing backwards-compatible re-exports from new sub-package paths to ease migration for external users.New internal utilities:
metbit/_internal/pairs.pywith thelazypairclass for generating all pairwise groupings and dataset splits, improving support for group-based analyses.metbit/_internal/report.pywith classes for generating OPLS-DA HTML reports (gen_page,gen_page_legacy) and managing report output paths (oplsda_path).Documentation and UI improvements:
ThemeToggle.tsxto explicitly settype="button"for accessibility and correctness. [1] [2] [3]Linkcomponents inpage.tsxfor improved navigation and SPA behavior.Cleanup and removals:
metbit/dev/auto_report.pyandmetbit/dev/batch_normalisation.pyscripts. [1] [2]