Codex/modernize baseline#20
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Pull request overview
Modernizes sbmlcore’s baseline by reducing import-time heaviness, making MDAnalysis-based functionality optional via extras, strengthening CI installation of external tools (DSSP/stride), and adding targeted tests to lock in the new import/version behavior.
Changes:
- Introduces lazy top-level exports in
sbmlcore/__init__.pyand switches version resolution to prefer the localVERSIONfile with metadata fallback. - Makes MDAnalysis an optional dependency via extras and updates MDAnalysis-dependent modules/tests to import/skip more gracefully.
- Updates CI workflows to build/install DSSP/stride reliably and improves subprocess test diagnostics.
Reviewed changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_trajectorydistances.py | Relaxes DataFrame equality tolerances for trajectory distance outputs. |
| tests/test_trajectorydihedrals.py | Skips dihedrals tests when MDAnalysis is unavailable (module-level). |
| tests/test_modernization.py | Adds tests for lightweight top-level import and ResidueDepth offset behavior. |
| tests/test_dssp.py | Improves DSSP/stride failure diagnostics by capturing stdout/stderr. |
| setup.cfg | Raises minimum Python version and reorganizes dependencies into extras. |
| sbmlcore/TrajectoryDistances.py | Defers MDAnalysis import and adds a guard when no frames match time range. |
| sbmlcore/TrajectoryDihedrals.py | Defers MDAnalysis import in multiple code paths. |
| sbmlcore/TempFactors.py | Defers MDAnalysis import behind a helper. |
| sbmlcore/StructuralDistances.py | Defers MDAnalysis import behind a helper. |
| sbmlcore/ResidueDepth.py | Ensures segids is derived from offsets when offsets are provided. |
| sbmlcore/AminoAcidProperties.py | Replaces pkg_resources usage with importlib.resources. |
| sbmlcore/init.py | Implements lazy attribute exports and version resolution logic. |
| .github/workflows/tests.yaml | Updates DSSP/stride install steps and uses .[dev] for test deps. |
| .github/workflows/pypi.yaml | Mirrors workflow updates for release pipeline build/test steps. |
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| filename = files("sbmlcore").joinpath("data/rogov.csv") | ||
| self.lookup = pandas.read_csv(filename) |
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| sbmlcore = importlib.import_module("sbmlcore") | ||
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| assert sbmlcore.__version__ == "0.2.8" |
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| md = | ||
| MDAnalysis | ||
| freesasa |
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| bio = | ||
| biopython | ||
| dev = |
| else: | ||
| distance_array = numpy.concatenate([distance_array, distances]) | ||
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| assert not first_pass, "No trajectory frames matched the requested time range." |
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DylanAdlard
approved these changes
Jun 3, 2026
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Some valid suggestions by copilot to do lazy loading of freesasa and biopython (as now doing for mda)
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