Bringing Modopt to 2024's standards.

[paquiteau]

This PR goals is to:

• move the packaging side to a pyproject toml file.
• setup black and ruff for linting and style
• Move the package to a src layout
• Fixes the erros ruff gives.
• Use a slicker, more efficient CI setup, more close to what is done in MRI-NUFFT.

This is going to be a big one...

Maybe the best is to merge previous PR (#338, #339) and fix the CI here. This supersed what @sfarrens started in #289.

[sfarrens]

@paquiteau do you want me to review what you have done so far in this PR or wait till all the boxed are ticked?

[paquiteau]

I would advise to start the review now, because the changelog is going to be very messy very fast.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 81.15942% with 52 lines in your changes are missing coverage. Please review.

Project coverage is 85.92%. Comparing base (64d6f85) to head (8e277aa).
Report is 15 commits behind head on master.

Files	Patch %	Lines
src/modopt/interface/errors.py	14.28%	12 Missing ⚠️
src/modopt/base/backend.py	56.25%	7 Missing ⚠️
src/modopt/interface/log.py	0.00%	6 Missing ⚠️
src/modopt/opt/algorithms/forward_backward.py	86.48%	5 Missing ⚠️
src/modopt/opt/linear/wavelet.py	61.53%	5 Missing ⚠️
src/modopt/opt/algorithms/gradient_descent.py	50.00%	3 Missing ⚠️
src/modopt/opt/proximity.py	93.02%	3 Missing ⚠️
src/modopt/signal/wavelet.py	50.00%	3 Missing ⚠️
src/modopt/opt/algorithms/base.py	77.77%	2 Missing ⚠️
src/modopt/base/observable.py	75.00%	1 Missing ⚠️
... and 5 more

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Additional details and impacted files

@@            Coverage Diff             @@
##           master     #340      +/-   ##
==========================================
- Coverage   90.58%   85.92%   -4.67%     
==========================================
  Files          36       37       +1     
  Lines        2454     2010     -444     
==========================================
- Hits         2223     1727     -496     
- Misses        231      283      +52     

Flag	Coverage Δ
unittests	85.92% <81.15%> (-4.67%)	⬇️

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[paquiteau]

@sfarrens The CI is now in a pretty good state, apart from the documentation setup. Could you have a look ? I am not mastering what you set up ^^

I think we should drop the MacOs test suite, it takes time, and does not bring that much of value to do the unit test in it. Maybe we still want to at least check if Modopt is installable in MacOs (with M1 chip notably). It remains out of my scope of competence though.

[sfarrens]

@paquiteau amazing work (as always)! I will go through everything next week (I am at a meeting this week). For the macOS test suite we can simply make it manually triggered rather than automatically to reduce the per commit overhead. 🙂

[paquiteau]

@sfarrens any update on the review ?

[sfarrens]

@paquiteau apologies for the delay. I will start going through it ASAP!

[sfarrens]

I only spotted a couple of very minor points. Once these threads are resolved I think we can merge. Nice work! 👏

[sfarrens]

I only spotted a couple of very minor points. Once these threads are resolved I think we can merge. Nice work! 👏

Unless you have further changes planned of course.