Update template to v0.6.0

[scverse-bot]

cookiecutter-scverse released v0.6.0.

Changes

CI updates

We now more consistently embrace hatch and uv in the template. CI now generates the job matrix from that hatch configuration. This means the pyproject.toml file is now the one single point of truth for both local and CI test jobs.

• Get test matrix from hatch by @grst in Get test matrix from hatch cookiecutter-scverse#390
• Enable parallel testing with hatch by @grst in Enable parallel testing with hatch cookiecutter-scverse#430
• chore: update code cov by @ilan-gold in chore: update code cov cookiecutter-scverse#427
• Fix remaining uv cache globs in workflows by @flying-sheep in Fix remaining uv cache globs in workflows cookiecutter-scverse#388
• Switch root tests to uv by @flying-sheep in Switch root tests to uv cookiecutter-scverse#384
• Fix uv cache glob for script tests by @flying-sheep in Fix uv cache glob for script tests cookiecutter-scverse#387
• Test pre-release dependencies by @grst in Test pre-release dependencies cookiecutter-scverse#393
• Use hatch on RTD by @grst in Use hatch on RTD cookiecutter-scverse#402
• Fix ruff-check naming by @Zethson in Fix ruff-check naming cookiecutter-scverse#414
• fix codecov upload (closes Bump min Python version to 3.8; CI update #381) by @ilia-kats in fix codecov upload (closes #381) cookiecutter-scverse#382

Documentation updates

We improved the "contributing guide" that is also synced into the repos using this template to recommend hatch
as the default project manager.

• Fix repo migration commands by @le-ander in Fix repo migration commands cookiecutter-scverse#380
• Delete docs/Makefile by @grst in Delete docs/Makefile cookiecutter-scverse#383
• restore missing links by @Zethson in restore missing links cookiecutter-scverse#411
• Update documentation by @grst in Update documentation cookiecutter-scverse#406

Chore

• Update pre-commit config
• Re-enable dry-run for release by @grst in Re-enable dry-run for release cookiecutter-scverse#394
• Create template sync PRs from versioned branch by @grst in Create template sync PRs from versioned branch cookiecutter-scverse#401

Full Changelog: scverse/cookiecutter-scverse@v0.5.0...v0.6.0

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 19.30%. Comparing base (6abf5ba) to head (410c01d).
⚠️ Report is 21 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #647       +/-   ##
===========================================
- Coverage   79.26%   19.30%   -59.96%     
===========================================
  Files          51       51               
  Lines        4576     4604       +28     
===========================================
- Hits         3627      889     -2738     
- Misses        949     3715     +2766     

Files with missing lines	Coverage Δ
src/scirpy/get/__init__.py	38.46% <100.00%> (-59.66%)	⬇️
src/scirpy/ir_dist/__init__.py	21.21% <100.00%> (-70.95%)	⬇️
src/scirpy/util/__init__.py	37.98% <100.00%> (-54.26%)	⬇️

... and 41 files with indirect coverage changes

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