Update template to v0.8.0

[scverse-bot]

cookiecutter-scverse released 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-kats in 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-kats in 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

• ci: remove hacks for docs building by @flying-sheep in ci: remove hacks for docs building scverse/cookiecutter-scverse#462
• ci: list all installed packages in CI output by @grst in List all installed packages in CI output scverse/cookiecutter-scverse#469
• ci: bump codecov-action to v6 to fix signature verification by @timtreis in ci: bump codecov-action to v6 to fix signature verification scverse/cookiecutter-scverse#510
• feat: remove version cargo cult by @flying-sheep in feat: remove __version__ cargo cult scverse/cookiecutter-scverse#495
• docs: update instructions on hatch/VScode integration by @grst in Update instructions on hatch/VScode integration scverse/cookiecutter-scverse#525
• docs: sphinx 9 compatibility, sphinx-tabs→sphinx-design by @flying-sheep in docs: sphinx 9 compatibility, sphinx-tabs→sphinx-design scverse/cookiecutter-scverse#467
• docs: use the official readthedocs badge in README by @ilia-kats in README: use the official readthedocs badge scverse/cookiecutter-scverse#513
• docs: robust links by @flying-sheep in docs: robust links scverse/cookiecutter-scverse#514
• docs: recommend prek over pre-commit by @ilia-kats in support prek in addition to pre-commit scverse/cookiecutter-scverse#485 and by @grst in Recommend prek over pre-commit scverse/cookiecutter-scverse#517
• docs: recommend uv for installation (alternative) by @grst in Recommend uv for installation (alternative) scverse/cookiecutter-scverse#531
• docs: fix typo by @ilan-gold in fix: typo scverse/cookiecutter-scverse#461

Template sync, docs, and initialization (changes do not affect instance repos)

• Fix docs on migrating to the template by @grst in Fix docs on migrating to the template scverse/cookiecutter-scverse#476
• Add docs link to PR comment by @flying-sheep in Add docs link to PR comment scverse/cookiecutter-scverse#478
• Fix cruft changing .git and add info on manual template update by @moinfar in Fix cruft changing .git and add info on manual template update scverse/cookiecutter-scverse#479
• Improve PyPI release instructions in template_usage.md by @grst with @Copilot in Improve PyPI release instructions in template_usage.md scverse/cookiecutter-scverse#490
• Switch to github app for PR creation by @grst in Switch to github app for PR creation scverse/cookiecutter-scverse#488
• Do not trigger cruft workflow on pre-releases by @grst in Do not trigger cruft workflow on pre-releases scverse/cookiecutter-scverse#507
• add contents:read permission to test workflow by @ilia-kats in add contents:read permission to test workflow scverse/cookiecutter-scverse#482
• Take up template sync where it got interrupted by @grst in Take up template sync where it got interrupted scverse/cookiecutter-scverse#487
• Escape GitHub @mentions in template update PR bodies by @grst with @Copilot in Escape GitHub @mentions in template update PR bodies scverse/cookiecutter-scverse#491
• Do not mandate global git config by @grst in Do not mandate global git config scverse/cookiecutter-scverse#518
• fix: template sync no longer breaks from multiple choice options by @grst in fix: template sync no longer breaks from multiple choice options scverse/cookiecutter-scverse#527
• fix: mention casing in publisher docs by @flying-sheep in fix: mention casing in publisher docs scverse/cookiecutter-scverse#470
• Allow user to choose between issue type and labels by @grst in Allow user to choose between issue type and labels scverse/cookiecutter-scverse#511

Additional remarks

• unsubscribe: If you don’t want to receive these PRs in the future,
  add skip: true to template-repos.yml using a PR or,
  if you never want to sync from the template again, delete the .cruft.json file in the root of your repository.
• If there are merge conflicts, you need to resolve them manually.
• The scverse template works best when the pre-commit.ci, readthedocs and codecov services are enabled.
  Make sure to activate those apps if you haven't already.

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📥 Commits

Reviewing files that changed from the base of the PR and between 59e21ae and 8991ec8.

📒 Files selected for processing (20)

• .cruft.json
• .editorconfig
• .github/ISSUE_TEMPLATE/bug_report.yml
• .github/dependabot.yml
• .github/workflows/build.yaml
• .github/workflows/release.yaml
• .github/workflows/test.yaml
• .gitignore
• .pre-commit-config.yaml
• .readthedocs.yaml
• .vscode/extensions.json
• .vscode/launch.json
• .vscode/settings.json
• biome.jsonc
• docs/Makefile
• docs/_templates/autosummary/class.rst
• docs/conf.py
• docs/contributing.md
• docs/extensions/typed_returns.py
• pyproject.toml

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