Remove pkg_resources and fix numpy 2.x / RDKit 2025.09 compat#56
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matteoferla wants to merge 2 commits intomasterfrom
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Remove pkg_resources and fix numpy 2.x / RDKit 2025.09 compat#56matteoferla wants to merge 2 commits intomasterfrom
matteoferla wants to merge 2 commits intomasterfrom
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- Replace `pkg_resources` with `pathlib.Path` (branding.py) and `importlib.metadata` (version.py) — setuptools 80+ dropped it - Modernise `_base_dataset_holder.py` from legacy `importlib.resources` API to `files()` API, eliminating DeprecationWarnings - Fix `_collapse_ring.py` numpy 2.x crash: `int(np.where(...)[0])` fails when multiple indices match; use `[0][0]` to pick the first - Fix `test_real_merger` SMILES assertion: round-trip through MolFromSmiles to normalise aromaticity perception across RDKit versions
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Pull request overview
This PR modernizes the codebase's dependency management and resource access patterns to ensure compatibility with Python 3.13+, setuptools 80+, numpy 2.x, and RDKit 2025.09. The changes eliminate deprecation warnings and fix crashes caused by API changes in these newer versions.
Changes:
- Replace deprecated
pkg_resourceswithimportlib.metadata.versionandpathlib.Pathfor package metadata and resource access - Modernize
importlib.resourcesAPI from legacy methods (contents(),read_text(), etc.) to the modernfiles()API - Fix numpy 2.x crash when multiple bonds have equal scores by properly indexing the first match
- Normalize RDKit aromaticity perception differences across versions in test assertions
Reviewed changes
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Show a summary per file
| File | Description |
|---|---|
| fragmenstein/version.py | Replaced pkg_resources.get_distribution() with importlib.metadata.version() for package version retrieval |
| fragmenstein/branding.py | Replaced pkg_resources.resource_string() with pathlib.Path for reading JSON resource file |
| fragmenstein/demo/_base_dataset_holder.py | Modernized from legacy importlib.resources API to files() API for Python 3.13+ compatibility |
| fragmenstein/monster/_collapse_ring.py | Fixed numpy 2.x crash by taking first element when multiple bonds tie for max score |
| tests/monster_combine.py | Added SMILES round-trip normalization to handle RDKit version differences in aromaticity perception |
| .github/ISSUE_TEMPLATE/custom.md | Updated issue template to use importlib.metadata instead of pkg_resources |
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Summary
pkg_resources(dropped in setuptools 80+): replaced withpathlib.Pathandimportlib.metadatainbranding.py,version.py, and the issue template_base_dataset_holder.py: legacyimportlib.resourcesAPI (contents(),read_text(),read_binary(),is_resource()) replaced with modernfiles()API — eliminates allDeprecationWarnings and ensures compatibility with Python 3.13+_collapse_ring.py:1102:int(np.where(scores == d)[0])fails when multiple bonds tie for max score; now takes[0][0]to pick the firsttest_real_merger: round-trip SMILES throughMolFromSmilesto normalise aromaticity perception across RDKit versionsTest results
Remaining 2 errors (
test_incorrect,test_pentachromatic) are algorithmicMProVictor.place()failures likely due to RDKit 2025.09 MCS/substructure changes — unrelated to this PR.