Add Cupy as optional dep and as FFTFilter

[PinkShnack]

As described in #10, it would be good to have a gpu implementation built in as an FFTFilter.
A lot of this was done in #8, but we have split that up into #9 and here #16.

Todos

• Add 2d cupy implementation.
• Add 3d (see Move from 2D to 3D array operations: breaking changes #9) cupy implementation. Check to see the difference between the 3D and 2D FFT algorithms with 2D and 3D inputs. write tests to show the diffference and show speed differences. Likely that Cupy3D is NOT required.
  • Cupy3D not needed, this idea was a stayover from when qpretrieve did not by default process FFTs in 3D
• All FFTFilters use axes inputs
• add as optional dep.
• Gracefully handle importing of cupy filter when not in env
• Test: ensure the outputted FFT is identical.
• Examples: show difference between first FFT, warmed up single FFT (pyfftw), and bulk 3D FFT
  • put batch and fft speeds in one graph.
• Add documentation (benchmarking etc)

[paulmueller]

Converted to draft. Please ping me when you need a review 👍

[PinkShnack]

How the tests act with and without optional dependencies using the new test helper method:

• no_pyfftw-no_cupy
  
• with_pyfftw-no_cupy
  
• with-pyfftw-with_cupy
  

[PinkShnack]

@paulmueller please review this, when you have time. :)

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Codecov Report

❌ Patch coverage is 33.33333% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.42%. Comparing base (4446d0d) to head (88fb701).
⚠️ Report is 10 commits behind head on main.

Files with missing lines	Patch %	Lines
qpretrieve/fourier/ff_cupy.py	11.11%	16 Missing ⚠️
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Additional details and impacted files

@@            Coverage Diff             @@
##             main      #16      +/-   ##
==========================================
+ Coverage   85.75%   87.42%   +1.67%     
==========================================
  Files          11       13       +2     
  Lines         400      525     +125     
==========================================
+ Hits          343      459     +116     
- Misses         57       66       +9     

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[PinkShnack]

Hey @paulmueller I made the changes you requested. Check out the new ci matrix. I added a relatively nice way of formatting it. Do you think we need the optional dep to be individually tested also? It baloons the number of jobs.

[paulmueller]

IMO optional dependencies do not need to be tested individually.
The only thing left to do is make the CI tests pass (there are some errors).
If there is no GPU on GHA free plan, you can also remove the corresponding extra.
If there are issues with "Python 3.X" (which is now 3.14), you could also remove that.

[PinkShnack]

IMO optional dependencies do not need to be tested individually.

Great

The only thing left to do is make the CI tests pass (there are some errors). If there are issues with "Python 3.X" (which is now 3.14), you could also remove that.

I assumed that 3.14 would work fine. But you know what they say when you assume...

If there is no GPU on GHA free plan, you can also remove the corresponding extra.

There is none. I will remove the extra with a comment explaining why

@paulmueller looks like this is ready. I removed 3.14, as packages such as cupy and scikit-image do not yet have wheels for it.