Update template to v0.8.0 (resolved) - #761
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Resolve the cookiecutter-scverse v0.8.0 sync (#755), adopting upstream tooling/security modernization while preserving repo-specific config. Adopted from the template: - Zizmor + SHA-pinned GitHub Actions, `permissions: contents: read`, `persist-credentials: false` across build/test/release workflows - dependabot; zizmor pre-commit hook; hook rev bumps (biome, pyproject-fmt, ruff); `prek` in the dev group - docs stack: `scverse_misc.sphinx_ext`, scverse.org intersphinx, RTD on Python 3.14, drop the `virtualenv<21` hatch workaround; drop the local autosummary template + `typed_returns` extension (now in scverse-misc) - `.cruft.json` bumped to v0.8.0 Kept (load-bearing divergences the template would regress): - `[project]` real deps/metadata, `hatch-vcs` dynamic version, `matplotlib<3.11` test cap, the entire `[tool.pixi]` block - visual-regression CI plumbing (tests/figures dir + artifact upload) and our hatch-test run/coverage scripts - `docs/notebooks` tutorials submodule + gallery handling (its removal was the RTD build failure) - fuller ruff `lint.select`; mypy pre-commit hook (zizmor audits Actions, not Python types) Rejected the raw cookiecutter scaffold (pp/tl/basic.py, tests/test_basic.py, stub example.ipynb, placeholder version/description).
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #761 +/- ##
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Partials 351 351 🚀 New features to boost your workflow:
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Resolves the cookiecutter-scverse v0.8.0 template sync. Supersedes #755, which is an unmergeable automated PR from the
scverse-botfork (raw placeholders + dropped repo customizations, and maintainers cannot push to that fork's branch). This branch lives in the main repo so CI/RTD actually run..cruft.jsonis bumped to v0.8.0 (6518dfa…), so the next sync diffs against v0.8.0.Adopted from the template
permissions: contents: read,persist-credentials: false(build/test/release)prekin dev groupscverse_misc.sphinx_ext, scverse.org intersphinx, RTD → Python 3.14, dropped thevirtualenv<21workaround; removed the local autosummary template +typed_returnsextension (now provided byscverse-misc)Kept (load-bearing; vanilla would regress)
[project]real deps/metadata,hatch-vcsdynamic version,matplotlib<3.11test cap, the entire[tool.pixi]blocktests/figuresdir + artifact upload) and the hatch-test run/coverage scriptsdocs/notebookstutorials submodule + gallery handling (its removal was Update template to v0.8.0 #755's RTD build failure)lint.select; the mypy pre-commit hook (zizmor audits Actions, not Python types — it does not replace mypy)Rejected
pp/,tl/,basic.py,tests/test_basic.py, stubexample.ipynb, placeholderversion/descriptionCloses #755