Add pyproject.toml, with pixi as project management tool. add pixi.lock

[jlnav]

Helps address #1444 and #1403

This adds a pyproject.toml to replace setup.py, which the Python community dramatically encourages.

For project management I chose Pixi (https://pixi.sh/latest/):

• Can install/interact with both conda and PyPI packages. For example, I can specify mpich as a dev dependency without having to say "install pydantic with pip and mpich with conda".
• Can split dependencies/packages into project-inherent "environments". Use pixi install -e dev to use the dev environment. With the lockfile included we're all guaranteed to get a working environment since the lockfile was resolved earlier.
• Very fast rust backend.
• Installing a package documents/adds that install in the pyproject.toml.
• Platform-specific dependencies can be specified to only install on that platform. e.g. us linux people that install the project will get gpcam. As a macOS user I automatically get a different clang from conda-forge I use with mpicc.

This does not mean that users need Pixi, and y'all don't need it either.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.95%. Comparing base (a45928b) to head (61fb6b8).
Report is 215 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff              @@
##           develop    #1459       +/-   ##
============================================
+ Coverage    78.43%   90.95%   +12.52%     
============================================
  Files           76       76               
  Lines         7684     7688        +4     
  Branches      1140     1141        +1     
============================================
+ Hits          6027     6993      +966     
+ Misses        1464      534      -930     
+ Partials       193      161       -32     

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[jmlarson1]

I'd check the instances of setup.py being used/referred. From the root libE directory, run

grep -ir --include=*.* "setup\.py"

[jlnav]

Noting that a very minimal setup.py has been added back. But it'll never need to be updated.

[jlnav]

More information about pixi.lock:

https://pixi.sh/latest/features/lockfile/#how-to-use-a-lock-file

[shuds13]

"pip>=24.3.1,<25", "setuptools>=75.1.0,<76",
should prob be below in build systems so separate build from run deps.

[shuds13]

Thinking lower bounds should be based on what we support. Or if we want to be latest, maybe make a comment to that effect.

[shuds13]

Now support Python 3.13 - make sure any updates to setup.py are put in here.

[shuds13]

I suggest we dont have lock file in here for now.

[shuds13]

And as Jeff points out above:

(libe_general) shudson@shuds:libe_toml$ grep -ir --include=*.* "setup\.py"
libensemble/tests/unit_tests_logger/.coveragerc:    */setup.py/*
libensemble/tests/unit_tests_mpi_import/.coveragerc:    */setup.py/*
libensemble/tests/regression_tests/.coveragerc:    */setup.py/*
libensemble/tests/.coveragerc:    */setup.py
libensemble/tests/unit_tests/.coveragerc:    */setup.py/*
libensemble/tests/functionality_tests/.coveragerc:    */setup.py/*
libensemble/tests/unit_tests_nompi/.coveragerc:    */setup.py/*
MANIFEST.in:include setup.py
docs/xSDK_policy_compatibility.md:|**M1.** Support xSDK community GNU Autoconf or CMake options. |N/A| libEnsemble is a Python package and provides a `setup.py` file for installation. This is compatible with Python's built-in installation feature (`python setup.py install`) and with the ubiquitous `pip` installer. libEnsemble is also in the Spack repository and can be installed with `spack install py-libensemble`. GNU Autoconf or CMake are unsuitable for a Python package.
docs/xSDK_policy_compatibility.md:|**R5.** Provide a mechanism to export ordered list of library dependencies. |Full| The dependencies for libEnsemble are given in `setup.py` and when pip install or pip setup.py egg_info are run, a file is created `libensemble.egg-info/requires.txt` containing the list of required and optional dependencies. If installing through pip, these will automatically be installed if they do not exist (`pip install libensemble` installs req. dependencies, while `pip install libensemble[extras]` installs both required and optional dependencies.|
docs/dev_guide/release_management/release_platforms/rel_pypi.rst:In the package directory on the main branch (the one containing setup.py) do
docs/dev_guide/release_management/release_platforms/rel_pypi.rst:    python setup.py sdist
docs/dev_guide/release_management/release_process.rst:- ``MANIFEST.in`` is checked. Locally, try out ``python setup.py sdist``

Update docs as necessary and other things here. Maybe this is done.

Not sure about changing xSDK_policy_compatibility.md though, it might be duplicate of something in xSDK repo, so maybe leave that for now.