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Add Harmony to scanpy#3953

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Intron7 wants to merge 10 commits intomainfrom
add-harmony
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Add Harmony to scanpy#3953
Intron7 wants to merge 10 commits intomainfrom
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@Intron7 Intron7 commented Jan 26, 2026

After recent changes from Harmonypy its necessary to move HarmonyBatchcorrection to scanpy. This function is based on harmony-pytorch and rapids-singlecell

@Intron7 Intron7 requested a review from flying-sheep January 26, 2026 09:50
@Intron7 Intron7 added this to the 1.12.1 milestone Jan 26, 2026
@Intron7 Intron7 marked this pull request as draft January 26, 2026 09:51
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codecov bot commented Jan 26, 2026

❌ 4 Tests Failed:

Tests completed Failed Passed Skipped
2401 4 2397 357
View the top 3 failed test(s) by shortest run time
tests/test_harmony.py::test_harmony_integrate_reference[fast-float32]
Stack Traces | 1.68s run time
contains 1 failed subtest
tests/test_harmony.py::test_harmony_integrate_reference[original-float64]
Stack Traces | 1.83s run time
contains 1 failed subtest
tests/test_harmony.py::test_harmony_integrate_reference[fast-float64]
Stack Traces | 1.84s run time
contains 1 failed subtest
tests/test_harmony.py::test_harmony_integrate_reference[original-float32]
Stack Traces | 3.18s run time
contains 1 failed subtest

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Looks good! I fixed the docs and made the code a bit nicer, but the reference tests have been failing from the start. Any idea why? You said they work locally for you?

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scanpy.external.pp.harmony_integrate incompatible with newly updated harmonypy>=0.1.0

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