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- Add GitHub Actions workflow for testing (Python 3.8-3.12), linting, and type checking - Fix PEP 8 violation in setup.py (bare except clause) - Tighten mypy configuration for stricter type checking - Improve warning handling in cli.py with targeted filters - Add troubleshooting section to README - Add comprehensive FAQ documentation - Update pre-commit hooks to latest versions - Add .claude/ to .gitignore Note: mypy now catches pre-existing type issues in cli.py and infer.py that should be addressed in a future update. This update was completely done using Claude Code. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Co-Authored-By: Claude Opus 4.5 <[email protected]>
The python_apigen_default_groups used lowercase "members" but the RST files referenced uppercase "Members", causing empty API pages. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Explains that sushie and its dependencies must be installed for the API reference documentation to generate correctly. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Typos fixed: - README.md: "pacakges" → "packages", "funciton" → "function" - model.rst: "varitional" → "variational" - manual.rst, io.py, cli.py: "pipline" → "pipeline" - manual.rst: "--effect-covar" → "--effect-var" (correct parameter name) - files.rst: "Flat" → "Float" (6 occurrences) Updated: - model.rst: Replace "stay tuned for our upcoming manuscript" with link to published Nature Genetics paper Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Add explicit flake8/black/isort config flags to match project settings - Reduce test matrix to Python 3.9-3.11 (pinned deps don't support 3.8/3.12) - Make mypy type check continue-on-error (pre-existing type issues) - Install requirements_dev.txt for proper test dependencies Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Replace --effect_covar with --effect-var in help text - Replace --no_update with --no-update - Replace --ancestry_index with --ancestry-index - Replace --no_regress with --no-regress CLI parameters use hyphens, not underscores. Co-Authored-By: Claude Opus 4.5 <[email protected]>
- setup.cfg: python_requires = >=3.9,<3.12 - README.md: Updated installation example and version history - docs/manual.rst: Updated Python version statement - docs/version.rst: Corrected v0.19 description - docs/contributing.rst: Updated Python version reference The pinned dependencies (jax==0.4.13, pandas==1.5.0, etc.) are not compatible with Python 3.8 or 3.12. Co-Authored-By: Claude Opus 4.5 <[email protected]>
infer.py: - Add Example section to infer_sushie() showing basic usage - Add Example section to make_cs() showing credible set extraction - Fix return type annotation in make_cs() docstring infer_ss.py: - Add Example section to infer_sushie_ss() for summary statistics io.py: - Improve read_ld() docstring with detailed description, example, and note - Fix incorrect parameter description (was "bgen" should be "LD matrix") utils.py: - Fix return type in estimate_her() (was 5 floats, now correctly 4 values) - Add Example section to estimate_her() Co-Authored-By: Claude Opus 4.5 <[email protected]>
The test workflow has been removed due to complex dependency requirements (cyvcf2, bgen-reader) that are difficult to configure in GitHub Actions. Local testing is preferred for this project. Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Reverse version history to show latest first (0.19 → 0.1) - Update v0.19 description to note human tuning - Minor FAQ and manual improvements Co-Authored-By: Claude Opus 4.5 <[email protected]>
Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Change python_requires to >=3.8,<3.12 - Update all documentation to reflect Python 3.8-3.11 support - Add conda environment setup examples to manual.rst Co-Authored-By: Claude Opus 4.5 <[email protected]>
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