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Merged
merged 433 commits into from
Oct 9, 2024
Merged

Develop ~~> Main v0.13.0 #1188

merged 433 commits into from
Oct 9, 2024

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@garrettwrong
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@garrettwrong garrettwrong commented Oct 7, 2024

Draft release notes below

ASPIRE v0.13.0 is minor release, adding new scientific features, GPU basis acceleration, updates and bug fixes.

This release provides the following features:

  • CLSync3N Common Lines algorithm
  • CLSymmetryD2 Common Lines algorithm
  • GPU Acceleration of FFBBasis2D and FLEBasis2D
  • GPU Acceleration of FFBBasis3D
  • Pixel size attributes for Image, Volume, and ImageSource
  • Optimized spherical harmonic computations
  • Adds Sinogram GPU accelerated line projection class

Bug fixes:

  • Reconcile rotation estimation with legacy MATLAB
  • Reconcile shift estimation with legacy MATLAB
  • Fix fuzzy_mask defaults and adds low pixel patch
  • Relion/ASPIRE image offset conventions
  • whiten filter thresholds
  • Remove FINUFFT workarounds for old releases
  • SymmetryGroup pass-through
  • wemd centering patch
  • MeanEstimator defaults
  • Minor 10081 gallery udpates

Testing:

  • Long running workflow speedups (fixture reuse)
  • Reduced batched covar2D test variability
  • Warnings cleanup (Linux 3.8-3.11, M1 3.9)
  • Adds initial tests for common line algorithms with shifts

Systems/CI Updates:

  • Native Apple Silicon support
  • Remove pyshtools dependency
  • Adds OSX ARM CI platform
  • FINUFFT/cuFINUFFT major release updates
  • Update CodeCov Auth

garrettwrong and others added 30 commits August 27, 2024 09:15
@garrettwrong
cleaned up tox syntax remarks
c8484a8
@garrettwrong
fixed docs
d58d6ff
@garrettwrong
fixed minor errors and created tests for str, repr methods
700468b
@garrettwrong
Back Project ~> Backproject
ffd43c8
@garrettwrong
replace _data in test_sinagram
dfa708c
@garrettwrong
init add
8af26fa
@garrettwrong
fix typos
08238c4
@garrettwrong
cleanup S init and usage, func names, etc
e67d871
@garrettwrong
stub in W
1bbeefc
@garrettwrong
stub in W
ca881b2
@garrettwrong
begin stubbing in actual S weight computation
56a51c4
@garrettwrong
fix typo bug
fa708df
@garrettwrong
fix rot reshape bug and stub in probability_scores
8b27e65
@garrettwrong
stub in triangle scores and pair probabilities
138ece9
@garrettwrong
tox checks
58fbbe7 
[skip ci]
@garrettwrong
light cleanup
5856562
@garrettwrong
J weighting
dbedd95
@garrettwrong
add note about possible ij jk bug
d4774c2 
[skip ci]
@garrettwrong
hack in cupy kernel
f33ddf7
@garrettwrong
quick test file
03019c0
@garrettwrong
stashing
6c639bc
@garrettwrong
black
e70fe73
@garrettwrong
debug
a1b2c95
@garrettwrong
stashing, cupy code mostly works
d0ce1d8
@garrettwrong
still debating that bug, but stashing here
88e6d5d
@garrettwrong
autoconf gpu
b7a9a64 
[skip ci]
@garrettwrong
rm debug comments after checking matmul
1166fbb
@garrettwrong
fixup Rijk_lmnop muls
0043330 
[skip ci]
@garrettwrong
re-implement matmul
2e598cf 
[skip ci]
@garrettwrong
add pairs prob kernel
ca8d7b1 
[skip ci]
@garrettwrong garrettwrong self-assigned this Oct 7, 2024
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garrettwrong commented Oct 7, 2024

@j-c-c , time to begin testing :) 🚀

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codecov bot commented Oct 7, 2024 •
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Codecov Report

Attention: Patch coverage is 80.37825% with 249 lines in your changes missing coverage. Please review.

Project coverage is 87.37%. Comparing base (dcedb21) to head (a01d211).
Report is 908 commits behind head on main.

Files with missing lines Patch % Lines
src/aspire/abinitio/commonline_sync3n.py 38.46% 240 Missing ⚠️
src/aspire/abinitio/commonline_d2.py 99.36% 5 Missing ⚠️
src/aspire/abinitio/sync_voting.py 94.11% 2 Missing ⚠️
src/aspire/nufft/cufinufft.py 0.00% 1 Missing ⚠️
src/aspire/sinogram/sinogram.py 90.90% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #1188      +/-   ##
==========================================
- Coverage   88.93%   87.37%   -1.56%     
==========================================
  Files         127      131       +4     
  Lines       11471    13603    +2132     
==========================================
+ Hits        10202    11886    +1684     
- Misses       1269     1717     +448

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@garrettwrong garrettwrong marked this pull request as ready for review October 8, 2024 15:28
@garrettwrong garrettwrong requested a review from janden as a code owner October 8, 2024 15:28
@garrettwrong garrettwrong requested a review from j-c-c October 8, 2024 15:29
j-c-c
j-c-c approved these changes Oct 8, 2024
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🚀

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garrettwrong commented Oct 9, 2024

Merging.

@garrettwrong garrettwrong merged commit 01fdc11 into main Oct 9, 2024
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@amitsinger amitsinger amitsinger approved these changes

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

@j-c-c j-c-c Awaiting requested review from j-c-c

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