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feat: stalign with a fit apply pattern. Also foundation for imputation#1195

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selmanozleyen wants to merge 120 commits into
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selmanozleyen:feat/experimental-fit-core
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feat: stalign with a fit apply pattern. Also foundation for imputation#1195
selmanozleyen wants to merge 120 commits into
scverse:mainfrom
selmanozleyen:feat/experimental-fit-core

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Continuation of #1162

selmanozleyen and others added 30 commits April 2, 2026 13:06
@selmanozleyen selmanozleyen requested a review from timtreis June 8, 2026 09:44
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codecov Bot commented Jun 11, 2026

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Codecov Report

❌ Patch coverage is 45.00000% with 308 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.32%. Comparing base (a9966fd) to head (96bc445).

Files with missing lines Patch % Lines
...ntal/_methods/align_samples/_stalign_impl/_core.py 0.00% 156 Missing ⚠️
...l/_methods/align_samples/_stalign_impl/_helpers.py 0.00% 73 Missing ⚠️
...tal/_methods/align_samples/_stalign_impl/_tools.py 51.94% 37 Missing ⚠️
...experimental/_methods/align_landmarks/_landmark.py 84.12% 6 Missing and 4 partials ⚠️
...py/experimental/_methods/align_samples/_stalign.py 37.50% 9 Missing and 1 partial ⚠️
src/squidpy/experimental/tl/_align/_api.py 72.22% 9 Missing and 1 partial ⚠️
src/squidpy/experimental/_methods/_protocols.py 66.66% 2 Missing and 3 partials ⚠️
src/squidpy/experimental/tl/_align/_io.py 93.90% 3 Missing and 2 partials ⚠️
src/squidpy/experimental/_methods/_registry.py 94.59% 1 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1195      +/-   ##
==========================================
- Coverage   75.32%   73.32%   -2.00%     
==========================================
  Files          56       66      +10     
  Lines        7936     8496     +560     
  Branches     1295     1364      +69     
==========================================
+ Hits         5978     6230     +252     
- Misses       1447     1743     +296     
- Partials      511      523      +12     
Files with missing lines Coverage Δ
src/squidpy/experimental/_methods/_families.py 100.00% <100.00%> (ø)
src/squidpy/experimental/_methods/_registry.py 94.59% <94.59%> (ø)
src/squidpy/experimental/_methods/_protocols.py 66.66% <66.66%> (ø)
src/squidpy/experimental/tl/_align/_io.py 93.90% <93.90%> (ø)
...experimental/_methods/align_landmarks/_landmark.py 84.12% <84.12%> (ø)
...py/experimental/_methods/align_samples/_stalign.py 37.50% <37.50%> (ø)
src/squidpy/experimental/tl/_align/_api.py 72.22% <72.22%> (ø)
...tal/_methods/align_samples/_stalign_impl/_tools.py 51.94% <51.94%> (ø)
...l/_methods/align_samples/_stalign_impl/_helpers.py 0.00% <0.00%> (ø)
...ntal/_methods/align_samples/_stalign_impl/_core.py 0.00% <0.00%> (ø)
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