Adopt the src layout, VCS versioning and supply chain pinning - #1057
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Moves the package to `src/pertpy` and derives the version from the git tags with hatch-vcs, both as the scverse cookiecutter recommends, and drops the `<3.15` upper bound on `requires-python`. Pins every pre-commit hook to a commit SHA and lets Dependabot update the pre-commit ecosystem alongside the actions, which closes the remaining supply chain gaps that scverse/repo-health flags.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #1057 +/- ##
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Coverage 78.81% 78.81%
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Files 52 52
Lines 7280 7280
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Hits 5738 5738
Misses 1542 1542
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Aligns packaging with the scverse cookiecutter and closes the supply chain gaps that repo-health flags.
Packaging
pertpy/moves tosrc/pertpy/, withtool.hatch.build.targets.wheel.packagespointing at it. The built wheel is unchanged:pertpy/at the top level,py.typedincluded.hatch-vcs, so releases no longer need apyproject.tomledit — just the tag.docs/conf.pyalready read the version from the installed metadata, so it needed no change.requires-pythondrops the<3.15upper bound.tool.coverage.pathsmaps the installed package back ontosrc, so codecov still annotates the repository files.Read the Docs shallow-clones and fetches only the branch being built, which makes VCS versioning report a wrong version. The
post_checkoutjob in.readthedocs.ymlis the remedy RTD documents for exactly this.Supply chain
# frozen:form (security/precommit-pinned).security/dependabot).Actions were already SHA-pinned and every workflow already declares a minimal top-level
permissions:, sosecurity/actions-pinnedand the workflow half ofsecurity/workflow-permissionswere already green.