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Ran 08 May 2026 02:18AM UTC

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Committed 08 May 2026 02:16AM UTC coverage: 70.569% (+0.02%) from 70.554%

Job # 25532869609.3

Build Type

push

github

Committed by

web-flow

Commit Message

Cast CDR3 columns to object before fillna in aggregate_clonotypes (#12)

Closes #11. When the AnnData has been round-tripped through h5ad — or
even kept in memory after anndata's auto-categoricalization runs on
obs — `CDR3_alpha` and `CDR3_beta` come back as Categorical. The
existing `.fillna("")` then raises:

  TypeError: Cannot setitem on a Categorical with a new category (),
  set the categories first

because "" isn't in the existing categories. Cast each column to
object first; the post-cast fillna works regardless of how anndata
serialized the dtype.

Same shape as the recurring h5ad-roundtrip class of bugs (#3 / #5 /
#7). The reporter suggests a defensive rehydrate helper to prevent
the next instance — that's tracked as a follow-up improvement.

Adds three regression tests:
- both CDR3 columns Categorical (no NaN)
- alpha Categorical with NaN — exact failure mode from #11
- CDR3b_only mode with Categorical beta (covers clonotype.py:148)

Bumps version to 0.3.1.

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