Ship type information (py.typed + mypy CI) and make gpr_to_dnf public#22
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Three related "make the package's contracts real" changes: - Add the PEP 561 py.typed marker so the package's extensive type hints are visible to downstream type checkers (geckopy included). The hatchling wheel ships raven_python/py.typed. - Add mypy to the dev extra, a lenient [tool.mypy] config (ignore_missing_imports for the un-stubbed cobra/optlang/scipy/ruamel), and a mypy CI job. Fix the 36 type errors this surfaced -- all type-only (Path vs str annotations, None-guards that match existing behaviour, optlang Variable typing, isinstance/cast narrowing). No runtime behaviour changes; the full test suite stays green. - Promote manipulation.expand._gpr_to_dnf to a public gpr_to_dnf (re-exported from raven_python.manipulation). geckopy's call sites switch to it in lockstep (separate PR), so no deprecated alias is kept.
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* Use the public gpr_to_dnf from raven-python raven-python promoted manipulation.expand._gpr_to_dnf to a public gpr_to_dnf and keeps no deprecated alias (SysBioChalmers/raven-python#22). Switch geckopy's three references to the public name: - src/geckopy/ec_model/pipeline/populate_ec.py - src/geckopy/utilities/add_new_rxns_to_ec.py - tests/test_expand.py Import-only change; no behaviour change. * tests: align test_doc_top_level_keys with cobra-aligned YAML (id nested under metaData, not top-level)
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What
Tier-1 of the raven-python review — "make the package's existing quality count":
py.typedmarker (PEP 561). The package is already comprehensively typed, but without this marker downstream type checkers (including geckopy) silently ignore every hint. Verified the hatchling wheel shipsraven_python/py.typed.mypyadded to thedevextra, a lenient[tool.mypy]config (ignore_missing_importsfor the un-stubbed cobra/optlang/scipy/ruamel), and amypyCI job. It surfaced 36 real type issues (Path-vs-str slips,None-handling gaps, optlang.primaltyping) — all fixed with type-only changes.mypyis now clean (81 source files); the full suite and ruff stay green.gpr_to_dnfis now public —manipulation.expand._gpr_to_dnfis promoted to a documentedgpr_to_dnf(re-exported fromraven_python.manipulation). No back-compat alias is kept (geckopy isn't in production); geckopy's three call sites switch to it in lockstep — Use the public gpr_to_dnf from raven-python geckopy#26, merge that right after this.Verification
mypy→Success: no issues found in 81 source filespytest→ 618 passed (unchanged from baseline)ruff check→ cleanpython -m build→ wheel containsraven_python/py.typedNo runtime behaviour changes.