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chore: use scverse-misc for data downloading - #4310

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flying-sheep merged 6 commits into
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datasets-misc
Aug 28, 2026
Merged

chore: use scverse-misc for data downloading#4310
flying-sheep merged 6 commits into
mainfrom
datasets-misc

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@flying-sheep

@flying-sheep flying-sheep commented Aug 21, 2026

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Not using the anndata loader here since

  1. we use datasetdir and not a global cache … maybe we should get rid of that.
  2. we use the fallback_urls inspired by SnapATAC2 – maybe that should be added to upstream @timtreis @ilia-kats?

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codecov Bot commented Aug 21, 2026

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Codecov Report

❌ Patch coverage is 91.66667% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.98%. Comparing base (643dff3) to head (fd6cda7).
⚠️ Report is 1 commits behind head on main.
✅ All tests successful. No failed tests found.

Files with missing lines Patch % Lines
src/scanpy/io/_read.py 66.66% 2 Missing ⚠️
src/scanpy/datasets/_datasets.py 90.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4310      +/-   ##
==========================================
- Coverage   82.03%   81.98%   -0.06%     
==========================================
  Files         134      134              
  Lines       13278    13235      -43     
==========================================
- Hits        10893    10851      -42     
+ Misses       2385     2384       -1     
Flag Coverage Δ
hatch-test.low-vers 79.07% <91.66%> (-0.07%) ⬇️
hatch-test.pre 81.85% <91.66%> (-0.06%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
src/scanpy/_utils/__init__.py 75.57% <ø> (-0.23%) ⬇️
src/scanpy/datasets/_utils.py 100.00% <100.00%> (ø)
src/scanpy/io/_download.py 94.73% <100.00%> (-3.45%) ⬇️
src/scanpy/datasets/_datasets.py 92.02% <90.00%> (+0.52%) ⬆️
src/scanpy/io/_read.py 80.59% <66.66%> (-0.52%) ⬇️

@flying-sheep flying-sheep added this to the 1.13.0 milestone Aug 21, 2026
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flying-sheep requested a review from ilia-kats August 21, 2026 09:39

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Looks good to me, but see scverse/scverse-misc#75.

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@flying-sheep
flying-sheep enabled auto-merge (squash) August 28, 2026 10:41
@flying-sheep
flying-sheep merged commit 0779213 into main Aug 28, 2026
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flying-sheep deleted the datasets-misc branch August 28, 2026 10:48
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Use scverse-misc for dataset downloading

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