Update template to v0.3.0

[scverse-bot]

cookiecutter-scverse released v0.3.0.

Changes

Required actions

The Github release workflow has been updated to use trusted publishing for authentication. You'll need to configure your project on PyPI accordingly. See scverse/cookiecutter-scverse#228 and the PyPI documentation for more details.

Python version update

Python 3.11 now works with numba, so we increased the maximum tested version to Python 3.11.

Enhancements

The automatic template sync is now in regular operation.

Fixes

• Reduce font size in data frames (Saving plots (png, pdf, svg) #250)
• Remove template usage docs from rendered template (now only available in cookiecutter-scverse-instance (Plot overhaul #247)
• Remove sphinx setup function (Cells without alpha chain #246)
• Move the section about how to configure the github release workflow to the template documentation (Settings class #248)
• Use coverage run instead of pytest --cov to compute test coverage (Errors when running ir.pl.clonotype_imbalance and sc.pl.umap of specific clonotypes #244)
• Fix that the LICENSE file wasn't generated for GPL (scirpy to analyze BCR #245)
• Fix socket warning in tests (Integration with dandelion #240)

If there are any questions, feel free to reach out to @grst, e.g. on the scverse zulip.

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 your .cruft file.
• If there are merge conflicts,
  they either show up inline (>>>>>>>) or a .rej file will have been created for the respective files.
  You need to address these conflicts manually. Make sure to enable pre-commit.ci (see below) to detect such files.
• 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 ✅

Comparison is base (d862cf3) 80.22% compared to head (0a6e888) 80.22%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #467   +/-   ##
=======================================
  Coverage   80.22%   80.22%           
=======================================
  Files          49       49           
  Lines        3939     3939           
=======================================
  Hits         3160     3160           
  Misses        779      779           

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