Update template to v0.5.0

[scverse-bot]

cookiecutter-scverse released v0.5.0.

Changes

New template sync

We re-implemented template sync from scratch instead on relying on cruft. This allows us to create real merge conflicts that show up as such on GitHub instead of .rej files.

• Generate real merge conflicts on template update by @grst in Generate real merge conflicts on template update scverse/cookiecutter-scverse#364

Enhancements

We committed to using hatch as project and environment manager. By doing so, we simplified the
GitHub actions:

• Hatch envs by @flying-sheep in Hatch envs scverse/cookiecutter-scverse#308
• Upgrade Github actions by @Zethson in Upgrade Github actions scverse/cookiecutter-scverse#324
• Use hatch in github actions by @grst in Use hatch in github actions scverse/cookiecutter-scverse#373

We switched the pre-commit hook from prettier to biome and added a pre-commit hook for autoformatting pyproject.toml files:

• Switch from prettier to Biome by @flying-sheep in Switch from prettier to Biome scverse/cookiecutter-scverse#304
• TOML formatting using pyproject-fmt by @flying-sheep in TOML formatting using pyproject-fmt scverse/cookiecutter-scverse#299

We added (optional) integration with VScode and improved cookiecutter prompts:

• Add VS Code integration by @flying-sheep in Add VS Code integration scverse/cookiecutter-scverse#312
• Add prompts for most variables by @flying-sheep in Add prompts for most variables scverse/cookiecutter-scverse#319

We removed bump2version as recommended way to update versions. Instead, just update the version manually in pyproject.toml or use hatch-vcs

• Remove bump2version by @Zethson in Remove bump2version scverse/cookiecutter-scverse#367

Fixes

• Fix PyPI link in README by @grst in Fix PyPI link in README scverse/cookiecutter-scverse#286
• Fix autosummary template by @flying-sheep in Fix autosummary template scverse/cookiecutter-scverse#297
• Fix string syntax in hook output by @flying-sheep in Fix string syntax in hook output scverse/cookiecutter-scverse#305
• Fix repo metadata by @flying-sheep in Fix repo metadata scverse/cookiecutter-scverse#307
• Fix links by @flying-sheep in Fix links scverse/cookiecutter-scverse#309
• Update post-gen output for hatch by @flying-sheep in Update post-gen output for hatch scverse/cookiecutter-scverse#311
• Fix README links by @flying-sheep in Fix README links scverse/cookiecutter-scverse#321
• Hatch extra-features doesn’t exist by @flying-sheep in Hatch extra-features doesn’t exist scverse/cookiecutter-scverse#326
• Update / fix README template by @le-ander in Update / fix README template scverse/cookiecutter-scverse#356
• Exclude .cruft.json from biome hook by @grst in Exclude .cruft.json from biome hook scverse/cookiecutter-scverse#362
• Switch to session-info2 by @Zethson in Switch to session-info2 scverse/cookiecutter-scverse#366
• Use cruft in github action that creates instance repo by @grst in Use cruft in github action that creates instance repo scverse/cookiecutter-scverse#371
• Even more precautionary bash settings by @grst in Even more precautionary bash settings scverse/cookiecutter-scverse#377

Documentation

• Add instructions on how to migrate an existing project to using the template by @grst in Add instructions on how to migrate an existing project to using the template scverse/cookiecutter-scverse#289
• fix hatch snippets for docs build in contributing.md by @eroell in fix hatch snippets for docs build in contributing.md scverse/cookiecutter-scverse#328
• Add instructions for a pending publisher by @flying-sheep in Add instructions for a pending publisher scverse/cookiecutter-scverse#358
• Add Github Actions documentation and simplify template usage by @Zethson in Add Github Actions documentation and simplify template usage scverse/cookiecutter-scverse#369
• Add more elaborate example by @Zethson in Add more elaborate example scverse/cookiecutter-scverse#365
• Suggest to use uv to run cruft by @grst in Suggest to use uv to run cruft scverse/cookiecutter-scverse#370

Chore

• Remove test reliance on unmaintained pytest-git by @flying-sheep in Remove test reliance on unmaintained pytest-git scverse/cookiecutter-scverse#298
• pre-commit updates

New Contributors

• @eroell made their first contribution in fix hatch snippets for docs build in contributing.md scverse/cookiecutter-scverse#328
• @le-ander made their first contribution in Update / fix README template scverse/cookiecutter-scverse#356
• @scverse-bot made their first contribution in Use cruft in github action that creates instance repo scverse/cookiecutter-scverse#371

Full Changelog: scverse/cookiecutter-scverse@v0.4.0...v0.5.0

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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 62.22%. Comparing base (3b8a5bd) to head (04d6aa2).

❗ There is a different number of reports uploaded between BASE (3b8a5bd) and HEAD (04d6aa2). Click for more details.

HEAD has 1 upload less than BASE

Flag	BASE (3b8a5bd)	HEAD (04d6aa2)
	3	2

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #45       +/-   ##
===========================================
- Coverage   85.85%   62.22%   -23.64%     
===========================================
  Files           9        9               
  Lines         495      495               
===========================================
- Hits          425      308      -117     
- Misses         70      187      +117     

see 4 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Marius1311]

The one test is failing because it's trying to contact OpenAI, but repo secrets like the API key are not exposed to PRs from forks. Should be fine once it's on main.