Develop~~>Main v0.14.1

[garrettwrong]

Tentative release notes below.

@j-c-c , I went off the project board, let me know if I've missed any other changes.

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ASPIRE v0.14.1 is patch release focused on reproducing MATLAB results and bringing in some bug fixes.

This release provides the following features:

• legacy_ preprocessing methods, (deprecates legacy=True flags)
• Reproduce MATLAB CTF Filter
• Reproduce MATLAB Crop
• Reproduce MATLAB Phaseflip
• Reproduce MATLAB Normalize Background
• Reproduce MATLAB Whitening
• Default to DiracBasis3D for recons
• Migrate pixel_size out of filter init
• Migrate towards Relion _rlnOriginX(Y)Angst offsets convention
• Add pixel_size to Coef class

Bug fixes:

• Polar cross corr FFT axis fix
• pixel_size passthrough for ClassAvgSource and DenoisedSource
• Downsample pixel_size bug fix

Documentation:

• Ribosome Legacy Preprocess Example
  • Reproduces MATLAB preprocessing to single precision

[j-c-c]

Looks good. A couple things to add:

• Add pixel_size to Coef class (Pixel Size Pass-through #1290)
• pixel_size passthrough for ClassAvgSource and DenoisedSource (Pixel Size Pass-through #1290)
• Downsample pixel_size bug fix (Downsample pixel_size bug #1318)

[codecov]

Codecov Report

❌ Patch coverage is 94.36620% with 16 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.65%. Comparing base (f8f26ee) to head (f26be41).
⚠️ Report is 137 commits behind head on main.

Files with missing lines	Patch %	Lines
src/aspire/noise/noise.py	50.00%	3 Missing ⚠️
src/aspire/operators/filters.py	93.02%	3 Missing ⚠️
src/aspire/source/image.py	94.82%	3 Missing ⚠️
src/aspire/basis/basis.py	92.85%	2 Missing ⚠️
src/aspire/downloader/data_fetcher.py	0.00%	2 Missing ⚠️
src/aspire/reconstruction/estimator.py	50.00%	2 Missing ⚠️
src/aspire/basis/fspca.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1330      +/-   ##
==========================================
+ Coverage   90.60%   90.65%   +0.04%     
==========================================
  Files         133      133              
  Lines       14346    14433      +87     
==========================================
+ Hits        12998    13084      +86     
- Misses       1348     1349       +1     

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[garrettwrong]

Oh, I see, it looks like we had two different 0.14.1 project boards. That's strange. I'll merge them. Thanks

[j-c-c]

LGTM!

[garrettwrong]

We'll do the final checks on the resulting merged code before tagging and pushing the package/release.

[garrettwrong]

Noting the 10028 legacy preprocessing test results had a relative L2 error of 5.55E-07 across the entire dataset as compared to MATLAB at the 179 pixels defined in the example.

Ribosome and Yeast recons are running.

[garrettwrong]

The gallery examples completed.

Ribosome 10028 179px was [email protected]
Yeast 10073 129px was [email protected]