Add scikit-image as a required dependency#13
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an-altosian wants to merge 1 commit intoCOMBINE-lab:mainfrom
Open
Add scikit-image as a required dependency#13an-altosian wants to merge 1 commit intoCOMBINE-lab:mainfrom
an-altosian wants to merge 1 commit intoCOMBINE-lab:mainfrom
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`scanpy.pp.scrublet()` requires `scikit-image` for automatic threshold calculation when `--remove_doublets` is used. Without it, the call fails: ValueError: threshold is None and thus scrublet requires skimage, but skimage is not installed. The lower bound of >=0.24 ensures compatibility with numpy>=2.x (required by qcatch). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
scikit-image>=0.24as an explicit dependency inpyproject.tomlscanpy.pp.scrublet()callsskimage.filters.threshold_minimumfor automatic threshold calculation--remove_doubletsfails withValueError: threshold is None and thus scrublet requires skimage, but skimage is not installedVersion constraint rationale
>=0.24: required for numpy 2.x compatibility (QCatch pinsnumpy>=2.1.3)[scrublet]extra which requiresscikit-image>=0.23.1Test plan
--remove_doubletsfails withoutscikit-imageinstalledscikit-image>=0.24resolves correctly with existing dependency constraints--remove_doublets --visualize_doubletsflags