Migrate setup configuration to pyproject.toml

[altheaden]

In this PR I migrated the setup configurations that were previously in setup.cfg, setup.py, and MANIFEST.in into a single pyproject.toml file. The only exception is the configurations for flake8, since it does not yet support pyproject.toml configuration, so its config options have been moved into a new file, .flake8.

Checklist

• Testing comment in the PR documents testing used to verify the changes

[altheaden]

Testing

I tested this by running:

conda activate base
conda config --add channels conda-forge 
conda config --set channel_priority strict 
conda create -y -n mache_dev --file spec-file.txt 
conda activate mache_dev 
python -m pip install .

and then testing the installation by running:

mache --help
mache sync --help
mache --version

all of which had the expected output.

[xylar]

Hmm, something isn't quite working right with finding the package and adding the package data. If I run:

$ mache sync diags --help

I see:

Traceback (most recent call last):
  File "/gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/bin/mache", line 5, in <module>
    from mache.__main__ import main
  File "/gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/__main__.py", line 5, in <module>
    from mache import sync
ImportError: cannot import name 'sync' from 'mache' (/gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/__init__.py)

If I look at:

$ ls /gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/
discover.py  machine_info.py  permissions.py  version.py
__init__.py  __main__.py      __pycache__

it seems like only the python files directly in mache are there and not the subdirectories or their contents.

[xylar]

The latest changes all look great! I'll test it one more time tomorrow (today already!) and merge if the tests work out.

[xylar]

Yep, everything worked great for me this time. I installed the package with:

conda create -y -n mache_dev --file spec-file.txt
conda activate mache_dev
python -m pip install .

Then, the following worked as expected:

mache sync diags --help

and each of these directories had the expected non-python files:

ls /gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/cime_machine_config/
ls /gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/machines/
ls /gpfs/fs1/home/ac.xylar/chrysalis/miniforge3/envs/mache_dev/lib/python3.12/site-packages/mache/spack/

[xylar]

@altheaden, very nice work!