Sparse2D version 3

[sfarrens]

Summary

• Updated Sparse2D version to 3.0.0, which now handles building of Python bindings and supports Apple Silicon (M1/M2 chips)
• Removed redundant binding files
• Deprecated use of PyQT, pyqtgraph needs to be installed manually otherwise show methods will raise an error, methods to be removed in follow-up release
• Updated default Python version in Conda environment to 3.10
• Switched testing framework to PyTest and dropped testing for Python 3.6
• Added develop.txt with development dependencies
• Other minor clean up changes

Issues

• The latest version of Sparse2D breaks the MR 2D1D tests, these have been skipped and an issue has been opened to resolve this in a future patch
• There is also an issue with mr_deconv in the latest version of Sparse2D, which raises a segementation fault in some cases, the corresponding test has been skipped and an issue has been opened to investigate

[codecov-commenter]

Codecov Report

Merging #183 (d3a0781) into develop (ae34ae4) will increase coverage by 1.57%.
The diff coverage is 45.33%.

@@             Coverage Diff             @@
##           develop     #183      +/-   ##
===========================================
+ Coverage    61.88%   63.46%   +1.57%     
===========================================
  Files           30       36       +6     
  Lines         1658     2184     +526     
===========================================
+ Hits          1026     1386     +360     
- Misses         632      798     +166     

Flag	Coverage Δ
unittests	63.46% <45.33%> (+1.57%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
examples/pysap/structure.py	100.00% <ø> (ø)
pysap/base/loaders/mat.py	50.00% <ø> (ø)
pysap/base/observable.py	45.00% <ø> (ø)
pysap/base/plugins.py	0.00% <0.00%> (-37.15%)	⬇️
pysap/base/utils.py	35.00% <ø> (ø)
pysap/configure.py	27.77% <0.00%> (ø)
pysap/data.py	68.84% <0.00%> (-0.28%)	⬇️
pysap/extensions/formating.py	19.63% <0.00%> (ø)
pysap/extensions/sparse2d.py	100.00% <ø> (ø)
pysap/extensions/tools.py	52.20% <ø> (-0.74%)	⬇️
... and 23 more

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[paquiteau]

Great work, this put PySAP on better tracks for its installation and usage.

As a more general reflexion I think this PR could also be the occasion to move to a standart pyproject.toml file (which will combine develop.txt, requirements.txt, setup.cfg etc...)

For the CI i recommend to switch to the more general setup-python ¹ action, to be more close to the user experience.

Footnotes

1. as recommended by github: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python ↩

[paquiteau]

LGTM !

[sfarrens]

Thanks a lot @paquiteau! 🙏

I will need to update the git tag for Sparse2D once I make release over there, but I can do that in a separate PR, before we make a new PySAP release.