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Merged
merged 184 commits into from
Mar 20, 2025
Merged

Develop v0.13.2~~> main #1247

merged 184 commits into from
Mar 20, 2025

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@garrettwrong
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@garrettwrong garrettwrong commented Mar 17, 2025 •
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Draft notes below. Started experimental gallery run on caf. Still possible to include LUD.

Plan to continue on to testing after (or if punting LUD). 10028 recon testing complete, 10073 in progress (last attempt was cancelled due to an unannounced server reboot). Final testing can begin after I push the tag.

(edit20240320, corrected some typos)

ASPIRE v0.13.2 is a patch release, adding multiple fixes, updates, and new supporting features.

This release provides the following features:

  • legacy_whitening isotropic noise estimator
  • sph_harm updates/optimizations
  • grid and Filter caching
  • Batched (GPU) class average BFR alignment

Bug fixes and cleanup:

  • Large scale image stacking OOM
  • nearest_rotation patch
  • CTFFilter correction
  • SymmetryGroup warnings
  • more dtype cleanup
  • Remove all remaining legacy m_ usage
  • Support mrcs file extension
  • IndexedSource filter mapping

Systems/CI Updates:

  • Numpy 2 support
  • Scipy 1.15 support
  • Remove deprecated cufinufft workaround
  • Migrate gallery loggers toward print
  • CI downloader caching

garrettwrong and others added 30 commits November 20, 2024 08:38
@garrettwrong
Remove Numpy 1 limitation
adb02d0
@garrettwrong
latest np2, Inf to inf
c60d8f2
@garrettwrong
row_stack to vstack
23b88c3
@garrettwrong
np2 copy False -> None
6235411
@garrettwrong
np2 breaks np.sign for complex
eecb8d1
@garrettwrong
np2 multiply xform dtype cast
6ecda62
@garrettwrong
sk pca copy False
f23d36e
@garrettwrong
sk pca copy False
ebaeb04
@garrettwrong
another great np2 improvement
d9ccdef
@garrettwrong
sqrt(weight) dtype not same as weight
e975604
@garrettwrong
looks like np2 impacted mrcfile as well
7fe6b87
@garrettwrong
Tox wants explicit stack level
202f76f
@garrettwrong
missing space in warning message
7bcfd1c
@garrettwrong
misc cleanup, reducing pr delta from draft work
f36f51b
@j-c-c
Remove sklearn workaround
d24bca9
@j-c-c
Min version for sklearn.
71b3002
@j-c-c
Convert gallery logging to print;
74ce51b 
Sphinx Gallery logging is broken.
@j-c-c
typo
e341699
@j-c-c
tox.ini and formatting
d830a3d
@garrettwrong @j-c-c
revert experiment prints back to logging
bf2348e
@j-c-c
remove redundant ignores
24c150d
@j-c-c
remove conflicting ignores
6c59064
@j-c-c
Remove m_reshape from ffb2d.
05dccc6
@j-c-c
remove m_funcs from fb2d evaluate_t
ea7c114
@j-c-c
remove m_funcs imports from fb2d
89ae284
@j-c-c
remove m_reshape from covar2d.py
25fc5bb
@j-c-c
remove temp test variable
ac25c3c
@j-c-c
remove m_reshape from fb_3d
30fabb8
@j-c-c
Reorder pf in ffb_2d to favor speed over images
6aa36a0
@j-c-c
fix shapes in FB_3D
0eede17
j-c-c and others added 24 commits March 14, 2025 13:51
@j-c-c
revert to export but use correct directory
79ddf95
@j-c-c
use workspace
224b6c3
@j-c-c
remove debug
c63670d
@garrettwrong
Bump version: 0.13.1 → 0.13.2
65353d3
@j-c-c
Change sym_group dtype logger warning to actual warning. Cleanup all …
ae52011 
…warnings associated with this.
@j-c-c
remove added blank lines
6825579
@j-c-c
directly create class in astype
e509eb6
@j-c-c
handle IdentityGroup which has order as an attribbute but not as an a…
41aa9d7 
…rgument.
@j-c-c
dtype weights in parent class. Test with both weights dtypes
bd93bb4
@j-c-c
remove dtype from SymmetryGroup
5d6e95e
@j-c-c
remove dtyping from SymmetryGroup. Fix tests
424f608
@j-c-c
remove unsused import
a950cea
@j-c-c
missed astype
1dbaeab
@j-c-c
about_axis handle floats
2bab895
@j-c-c
revert to self.dtype, but set to doubles
d755689
@j-c-c
copy False
46d6e39
@j-c-c
use np.full in place of np.ones
b4c980f
@j-c-c
fix dtype logic in about_axis
4972243
@j-c-c
more copy False
01ebaa5
@j-c-c
couple more
d090281
@j-c-c
copy True for test fixtures
7147ae3
@j-c-c
use sqrt default type
9052bf2
@j-c-c
linspace
90f2758
@j-c-c
compute in double then cast
c8a9756
@garrettwrong garrettwrong self-assigned this Mar 17, 2025
@garrettwrong garrettwrong marked this pull request as ready for review March 20, 2025 17:51
@garrettwrong garrettwrong requested a review from janden as a code owner March 20, 2025 17:51
@garrettwrong garrettwrong requested a review from amitsinger March 20, 2025 18:34
@garrettwrong garrettwrong merged commit d0f3d09 into main Mar 20, 2025
42 checks passed
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@amitsinger amitsinger amitsinger approved these changes

@janden janden Awaiting requested review from janden janden is a code owner

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