BLD: deprecation warnings from setuptools (auto-included packages)

[neutrinoceros]

Building a wheel with --verbose

python -m pip wheel --verbose --progress-bar off --no-deps --wheel-dir build .

Yields the following warnings

SetuptoolsDeprecationWarning:     Installing 'yt.frontends.amrvac.tests.sample_parfiles' as data is deprecated, please list it in `packages`.
      !!


      ############################
      # Package would be ignored #
      ############################
      Python recognizes 'yt.frontends.amrvac.tests.sample_parfiles' as an importable package,
      but it is not listed in the `packages` configuration of setuptools.

      'yt.frontends.amrvac.tests.sample_parfiles' has been automatically added to the distribution only
      because it may contain data files, but this behavior is likely to change
      in future versions of setuptools (and therefore is considered deprecated).

      Please make sure that 'yt.frontends.amrvac.tests.sample_parfiles' is included as a package by using
      the `packages` configuration field or the proper discovery methods
      (for example by using `find_namespace_packages(...)`/`find_namespace:`
      instead of `find_packages(...)`/`find:`).

      You can read more about "package discovery" and "data files" on setuptools
      documentation page.

7 directories are affected

• yt.frontends.amrvac.tests.sample_parfiles
• yt.frontends.artio.artio_headers
• yt.geometry._selection_routines
• yt.utilities.grid_data_format.docs
• yt.utilities.grid_data_format.scripts
• yt.utilities.lib.cykdtree.windows
• yt.utilities.lib.ewahboolarray (soon to be removed in BLD: Split EWAH bool array code #2711)

It should be easily fixable, but it's likely that we don't actually want to include everything there (I suspect some of these files are actually not used anymore)

[neutrinoceros]

Actually it seems to me that only yt.frontends.amrvac.tests.sample_parfiles should be included in wheels because it can be used to run some tests, the rest is all source files and internal docs that serve no purpose in a wheel AFAICT.

[neutrinoceros]

Working on a patch. I'll open a PR once I see builds passing on my fork: https://github.com/neutrinoceros/yt/actions/workflows/wheels.yaml

[neutrinoceros]

Related discussion upstream: pypa/setuptools#3340

[matthewturk]

I'd rather the fix be to make sure we include the files rather than exclude them, unless they are very large or detrimental in some way.

[neutrinoceros]

Fine with me. For now I'm actually struggling to do anything with them because the recommandation is to include them via pyproject.toml but we actually use MANIFEST.in for that and I am not sure I understand how they interact.

[neutrinoceros]

I'll give a try to combining pyproject.toml with MANIFEST.in and use wheel-inspect to check that we don't miss anything