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Added scanpy adaptors#13

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remydubois merged 3 commits into
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feat/scanpy-adaptors
Mar 25, 2026
Merged

Added scanpy adaptors#13
remydubois merged 3 commits into
mainfrom
feat/scanpy-adaptors

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  1. This PR adds the possibility to use illico.asymptotic_wilcoxon(…, return_as_scanpy=True) as a drop-in-replacement for scanpy.tl.rank_genes_groups(…, method="wilcoxon"). This requires:
    1. Exponentiating post-aggregation in fold-change calculation
    2. Outputting the z-score
    3. Formatting the output as a dictionary of recordarrays where genes are ordered by z-score
  2. This PR re-establishes the correct convention of U-statistic. Previous versions returned U-stat of the control group (rest, in the OVR setup), instead of the perturbed group.
  3. This PR finally adds test to compare output of illico and output of scanpy.
  4. This PR optimizes the Rust CSR routine which was suffering from unnecessary data copies.
  5. Updates illico runtimes in the readme.

@remydubois remydubois merged commit 670ca85 into main Mar 25, 2026
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