Consolidate project config under pyproject

[ravwojdyla]

See the latest docs at: https://packaging.python.org/en/latest/ and a sample project at: https://github.com/pypa/sampleproject

Summary of changes:

• consolidate project setup/config under pyproject.toml
  • this makes setup.cfg and more importantly setup.py no more
    • some doc: https://packaging.python.org/en/latest/discussions/setup-py-deprecated/
• git-ignore bio2zarr/_version.py
  • scm was configured to write this file, I'm not entire sure we need it, but to keep this consistent I have copied it over, but that also means we probably want to gitignore it?
• configure build-system
• include readme in the project config
• urls include links to both documentation and repo
• zip-safe is deprecated, and include-package-data is true by default
  • see: https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
• update tool.ruff target version to the minimal specified supported python - py3.9
  • this also forces to use list vs typing.List etc
• use ruff's isort support
  • some setting are not available in ruff - do we need them?
• remove obsolete flake8 config
• git-ignore IDE directories including .idea and .vscode
• update pre-commit ruff version from 0.3.7 to 0.4.2

[ravwojdyla]

I have tested this setup using:

python3 -m build --wheel

The resulting package:

unzip -l dist/bio2zarr-0.0.7.dev6+gc03b708-py3-none-any.whl

Archive:  dist/bio2zarr-0.0.7.dev6+gc03b708-py3-none-any.whl
  Length      Date    Time    Name
---------  ---------- -----   ----
       49  04-29-2024 08:11   bio2zarr/__init__.py
      527  04-29-2024 08:11   bio2zarr/__main__.py
      445  04-29-2024 10:01   bio2zarr/_version.py
    14397  04-29-2024 08:11   bio2zarr/cli.py
     9006  04-29-2024 08:11   bio2zarr/core.py
     6768  04-29-2024 08:11   bio2zarr/plink.py
      142  04-29-2024 08:11   bio2zarr/provenance.py
       79  04-29-2024 08:11   bio2zarr/typing.py
    83310  04-29-2024 09:56   bio2zarr/vcf.py
    17328  04-29-2024 09:56   bio2zarr/vcf_utils.py
    11357  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/LICENSE
    16931  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/METADATA
       92  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/WHEEL
      131  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/entry_points.txt
        9  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/top_level.txt
     1323  04-29-2024 10:01   bio2zarr-0.0.7.dev6+gc03b708.dist-info/RECORD
---------                     -------
   161894                     16 files

You can see the files included in the dist-info in a gist here.

Test install/run was successful:

pip install projects/bio2zarr/dist/bio2zarr-0.0.7.dev6+gc03b708-py3-none-any.whl

Follow by:

vcf2zarr explode sample.vcf.gz sample.exploded