Skip to content

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

Open
flying-sheep wants to merge 3 commits into
mainfrom
datasets-misc
Open

chore: use scverse-misc for data downloading#4310
flying-sheep wants to merge 3 commits into
mainfrom
datasets-misc

Conversation

@flying-sheep

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

Copy link
Copy Markdown
Member

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?

@codecov

codecov Bot commented Aug 21, 2026

Copy link
Copy Markdown

Codecov Report

❌ Patch coverage is 91.11111% with 4 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (main@9e259ff). Learn more about missing BASE report.
✅ 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 ⚠️
src/scanpy/datasets/_utils.py 95.83% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #4310   +/-   ##
=======================================
  Coverage        ?   80.01%           
=======================================
  Files           ?      133           
  Lines           ?    13372           
  Branches        ?        0           
=======================================
  Hits            ?    10699           
  Misses          ?     2673           
  Partials        ?        0           
Flag Coverage Δ
hatch-test.low-vers 77.93% <91.11%> (?)
hatch-test.pre 79.88% <91.11%> (?)

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> (ø)
src/scanpy/io/_download.py 94.73% <100.00%> (ø)
src/scanpy/datasets/_datasets.py 92.02% <90.00%> (ø)
src/scanpy/datasets/_utils.py 96.96% <95.83%> (ø)
src/scanpy/io/_read.py 80.59% <66.66%> (ø)

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

@ilia-kats ilia-kats left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Use scverse-misc for dataset downloading

2 participants