Infrastructure cleanup

[Darlokt]

Hej evreyone,

I have a project depending on this project and saw there is some cleanup potential in preparation for some bigger refactors/cleanups.

This is a patch series cleaning up the projects infrastructure. Removing/consolidates unnecessary/no longer used files/configs and updating tool configs etc. in preparation for a general cleanup/restructure.

Changes:

• Deleted .bumpversion.cfg as it is not used in the project.
• Deleted .mypy.ini and integrated it into pyproject.toml under the tool.mypy section.
  • Bumped the python version to 3.11 in the mypy configuration to reflect the minimum supported version.
• Updated .pre-commit-config.yaml to remove unused hooks and dependencies.
  • Removed the mirrors-prettier hook as it is conflicting with ruff and .editorconfig settings.
  • Removed the check-ast, end-of-file-fixer, mixed-line-ending and trailing-whitespace hooks as they are redundant with ruff.
  • Removed unsafe fixes from ruff
• Cleaned up the pyproject.toml and updated tool configs
  • Split the tool.ruff configuration into multiple sections to improve readability and maintainability.
  • Updated the ruff to reflect the .editorconfig settings (indentation, line endings, etc.)
  • Set the ruff minimum python version to 3.11 to reflect the minimum supported version.
  • Converted optional dependencies into dependency groups in line with PEP 735, to improve the organization and clarity of the dependencies.
  • Added docstring convention to ruff linting config in line with project standards.
  • Removed pre dependency group as it is not different to the main dependencies and only used for .readthedocs.yaml.
  • Removed bump2version from the dev dependency group as it is not used in the project and abandoned.
• Updated .readthedocs.yaml
  • Removed the pre dependency group from the installation command as it is not different to the main dependencies and only used for .readthedocs.yaml.
  • Updated resolver to use uv instead of pip to install dependencies, as it is faster and works with the implemented dependency groups.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 63.38%. Comparing base (a63ca08) to head (d529aeb).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #400   +/-   ##
=======================================
  Coverage   63.38%   63.38%           
=======================================
  Files          26       26           
  Lines        3217     3217           
=======================================
  Hits         2039     2039           
  Misses       1178     1178           

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[Darlokt]

Fixed CI workflow. Updated it to work with dependency groups and replaced manual caching with actions/setup-python internal caching. Also bumped actions to newer versions.

[Zethson]

Dear @Darlokt ,

this is great! The actual solution that we should aim for is #345 which includes many of the changes & improvements that you're suggesting here. SpatialData itself needs the same treatment.
Would you be interested in tackling it this way?

Let us know if this is unclear, please.