Pyproject code refactor

[sfarrens]

Summary

This PR refactors the codebase to simplify maintenance and development.

• Removed setup.py and setup.cfg and added pyproject.toml
• Removed redundant files/directories: .pylintrc, .pyup.yml, develop.txt, docs/requirements.txt, notebooks
• Ran Black on modopt (i.e. only style changes, no changes to code or tests)
• Updated docs: removed redundant notebook tools, cleaned up
• Updated manifest
• Simplified CI tests: several tests can now be run manually rather that being triggered for each commit, only the latest version of Python will run automatically

To Do

• Update README.md and installation instructions
• Check that new CI/CD works correctly
• Additional checks

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[paquiteau]

Great work !
We might want to push it further by using a src layout to tidy things up further and avoiding distributing test, examples and other files with the python package (see https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/ for more info)

Also, the signals for the CI needs to be update I guess in the github settings (to avoid the Expected — Waiting for status to be reported )

[paquiteau]

I am not so sure we need a MANIFEST.in (which is for source distribution) anymore. Everything should be handled by pyproject.toml.

[sfarrens]

I was trying to find some concrete information on this, if you have any references for this point I will check them out.

[paquiteau]

Looking at this issue again for another project of mine I found the following references:

• https://stackoverflow.com/a/57437660
• https://setuptools.pypa.io/en/latest/userguide/datafiles.html

TLDR: As we are in a python-only codebase, with no extra data files, there is no need for the MANIFEST.in everything is handled by setuptools.

[paquiteau]

Instead of hardcoding the version, use setuptools-scm plugin and the following

Suggested change

	__version__ = "1.6.1"
	try:
	# -- Distribution mode --
	# import from _version.py generated by setuptools_scm during release
	from ._version import version as __version__
	except ImportError:
	# -- Source mode --
	# use setuptools_scm to get the current version from src using git
	from setuptools_scm import get_version as _gv
	from os import path as _path
	__version__ = _gv(_path.join(_path.dirname(__file__), _path.pardir))

[sfarrens]

Yeah, this was always just temporary, but nice implementation! I will quick look at what the current consensus is on this point before committing, but I like this.

[paquiteau]

Should'nt be more people in the list 😇 ?

[sfarrens]

Yes, of course! I am still playing around with the formatting and metadata. I was think for the authors section we could put something like "The CEA-COSMIC Team" or "The ModOpt Team" to be a more inclusive term for everyone who has contributed. Any thoughts/suggestions are certainly welcome.

I will explicitly add you as a maintainer before I finalise this PR.

[paquiteau]

I would rather declare the dependencies directly in the pyproject.toml file.
And use setuptools-scm to track the version (see my other comment on modopt/__init__.py

Suggested change

	[tool.setuptools.dynamic]
	dependencies = {file = ["requirements.txt"]}
	version = {attr = "modopt.__version__"}
	[tool.setuptools_scm]
	write_to = "modopt/_version.py"
	version_scheme = "python-simplified-semver"
	local_scheme="no-local-version"

[sfarrens]

OK, I will look into this.

[sfarrens]

Thanks for the feedback @paquiteau, I am still playing around with this PR, but I like these suggestions. I will play around some more this week and ping you when the PR is ready for final review.