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my-alaska
previously approved these changes
Dec 21, 2025
my-alaska
previously approved these changes
Dec 21, 2025
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Pull request overview
This PR contains various minor fixes primarily focused on docstrings, formatting, and code quality improvements across the scikit-fingerprints codebase.
Key Changes
- Grammar and spelling corrections in docstrings (e.g., "In case of" → "In the case of")
- Parameter documentation standardization (e.g., "optional" → "default=None", "boolean" → "bool")
- Removal of
# noqa: ARG002comments, with ARG002 added to global ruff ignore list - Bug fixes in applicability domain modules (KNN neighbor exclusion logic)
- Configuration updates: mypy settings moved to pyproject.toml, dependency version updates, GitHub Actions version bumps
Reviewed changes
Copilot reviewed 88 out of 89 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/descriptors/charge.py | Added test for precomputed partial charges |
| tests/applicability_domain/utils.py | Changed threshold calculation from median to 25th percentile |
| skfp/utils/validators.py | Grammar fixes and error type corrections in docstrings |
| skfp/utils/parallel.py | Fixed typo "functions" → "lists" in docstring |
| skfp/preprocessing/*.py | Corrected shape documentation from "n_samples_conf_gen" to "n_samples" |
| skfp/metrics/*.py | Standardized parameter names (y_pred → y_score) and type documentation |
| skfp/fingerprints/*.py | Removed ARG002 noqa comments, fixed type hints |
| skfp/filters/*.py | Improved return_type parameter documentation with bullet formatting |
| skfp/distances/*.py | Standardized validation parameters and fixed grammar in docstrings |
| skfp/descriptors/*.py | Changed "optional" to "default=None" in parameter docs |
| skfp/datasets/moleculeace/*.py | Fixed import paths and adjusted doctest output formatting |
| skfp/applicability_domain/*.py | Fixed KNN neighbor exclusion bug, removed ARG002 comments |
| ruff.toml | Added ARG002 to global ignore list |
| pyproject.toml | Updated RDKit version limit, moved mypy config, removed pip-audit/xenon |
| mypy.ini | Deleted (moved to pyproject.toml) |
| .github/workflows/*.yml | Bumped GitHub Actions versions (v4→v6, v5→v7) |
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mjste
reviewed
Dec 22, 2025
my-alaska
approved these changes
Dec 27, 2025
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Changes
A lot of minor fixes, primarily docstrings or formatting.
Checklist before requesting a review
make test-coverage)make docsand seedocs/_build/index.html)