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Update template to v0.8.0 - #99
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maltekuehl merged 7 commits intoOct 30, 2026
Merged
maltekuehl merged 7 commits into
maltekuehl merged 7 commits into
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The template-sync branch starts from the repository's first commit, so it shares no recent history with main. This merge applies the template changes from v0.6.0 (the version main was on) to v0.8.0 onto main: - CI: actions pinned to commit hashes, least-privilege permissions, persist-credentials: false, codecov-action v7 with OIDC upload, pre-release test job allowed to fail, dependabot for actions. - pre-commit: newer biome, pyproject-fmt and ruff; zizmor hook added. - pyproject: dev/test/doc moved from extras to dependency groups, prek instead of pre-commit, hatch config in the [tool.hatch] table, native [tool.pytest] config with strict = true. - docs: Python 3.14 and Node on Read the Docs, sphinx-design instead of sphinx-tabs, KaTeX instead of MathJax, scverse-misc Sphinx extension replaces the local typed_returns extension and autosummary class template, scverse.org intersphinx URLs; contributing guide updated. - .vscode settings and the template .gitignore restored from the template. Kept from main where the template version would change the package, break the build or drop project data ignores: package version, maintainers and runtime dependencies (including the git dependencies and hatch's allow-direct-references), the tutorial doc dependencies, the extra intersphinx mappings and nitpick exceptions, the CPU-only torch backend in CI and on Read the Docs, and ignores for tutorial data files. .cruft.json points to the template URL instead of the temporary directory written by the sync bot. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Python 3.13 strips the common indentation of docstrings at compile time, so the parameter blocks inserted by _doc_params no longer lined up with the rest of the docstring and the docs build (now on Python 3.14) failed with "Unexpected indentation". Normalise the docstring and the inserted blocks with inspect.cleandoc. Only __doc__ whitespace changes; behaviour is unchanged. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ed in scverse#90 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #99 +/- ##
==========================================
+ Coverage 66.79% 76.69% +9.90%
==========================================
Files 12 15 +3
Lines 524 618 +94
==========================================
+ Hits 350 474 +124
+ Misses 174 144 -30
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cookiecutter-scversereleased v0.8.0.Changes
This release comes with a bunch of smaller fixes and changes to the template, and a lot of under-the-hood changes reducing friction with template sync and initialization.
Changes
The most notable change is the introduction of zizmor as pre-commit hook for hardening github actions against supply-chain attacks. Github actions will be pinned to an immutable hash instead of a version number. Dependabot will take care of updating them (by
@ilan-gold,@grst,@ilia-katsin scverse/cookiecutter-scverse#498).Additionally, we introduced a helper package, scverse-misc, that contains utility code shared across scverse core and ecosystem packages. As an initial step, we moved custom sphinx extensions that were previously part of the template into scverse-misc (by
@ilia-katsin scverse/cookiecutter-scverse#529). Rollout of additional features (shared logging and settings) will follow in the next release.The remaining changes are listed below:
Updates to the template
@flying-sheepin ci: remove hacks for docs building cookiecutter-scverse#462@grstin List all installed packages in CI output cookiecutter-scverse#469@timtreisin ci: bump codecov-action to v6 to fix signature verification cookiecutter-scverse#510@flying-sheepin feat: remove __version__ cargo cult cookiecutter-scverse#495@grstin Update instructions on hatch/VScode integration cookiecutter-scverse#525@flying-sheepin docs: sphinx 9 compatibility, sphinx-tabs→sphinx-design cookiecutter-scverse#467@ilia-katsin README: use the official readthedocs badge cookiecutter-scverse#513@flying-sheepin docs: robust links cookiecutter-scverse#514@ilia-katsin support prek in addition to pre-commit cookiecutter-scverse#485 and by@grstin Recommend prek over pre-commit cookiecutter-scverse#517@grstin Recommend uv for installation (alternative) cookiecutter-scverse#531@ilan-goldin fix: typo cookiecutter-scverse#461Template sync, docs, and initialization (changes do not affect instance repos)
@grstin Fix docs on migrating to the template cookiecutter-scverse#476@flying-sheepin Add docs link to PR comment cookiecutter-scverse#478@moinfarin Fix cruft changing .git and add info on manual template update cookiecutter-scverse#479@grstwith@Copilotin Improve PyPI release instructions in template_usage.md cookiecutter-scverse#490@grstin Switch to github app for PR creation cookiecutter-scverse#488@grstin Do not trigger cruft workflow on pre-releases cookiecutter-scverse#507@ilia-katsin add contents:read permission to test workflow cookiecutter-scverse#482@grstin Take up template sync where it got interrupted cookiecutter-scverse#487@mentionsin template update PR bodies by@grstwith@Copilotin Escape GitHub @mentions in template update PR bodies cookiecutter-scverse#491@grstin Do not mandate global git config cookiecutter-scverse#518@grstin fix: template sync no longer breaks from multiple choice options cookiecutter-scverse#527@flying-sheepin fix: mention casing in publisher docs cookiecutter-scverse#470@grstin Allow user to choose between issue type and labels cookiecutter-scverse#511Additional remarks
add
skip: truetotemplate-repos.ymlusing a PR or,if you never want to sync from the template again, delete the
.cruft.jsonfile in the root of your repository.Make sure to activate those apps if you haven't already.