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fix(estimators): accept an AnnData without X - #1383
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The shadow AnnData copied adata.X.dtype, so GPCCA and CFLARE raised AttributeError when X is None (e.g. an AnnData holding only obs, obsm and graphs). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01CEkHnYavwEf7n32j7rNkPv
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Summary
Estimators build their shadow AnnData with
adata.X.dtype, soGPCCA(kernel)raisedAttributeError: 'NoneType' object has no attribute 'dtype'whenadata.XisNone, as in an AnnData that holds onlyobs,obsmand graphs (e.g. a precomputed transition matrix on a large dataset). The shadow AnnData now has noXeither.Testing
TestGPCCASerialization::test_adata_without_x: fits GPCCA through fate probabilities on an AnnData withoutXand checksto_adata(); it fails onmainwith the error above.tests/test_gpcca.py -k "Serialization or test_compute_macrostates or fate": 38 passed, 1 xfailed.🤖 Generated with Claude Code
https://claude.ai/code/session_01CEkHnYavwEf7n32j7rNkPv