28968419181
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Ran 08 Jul 2026 07:08PM UTC

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Committed 08 Jul 2026 07:04PM UTC coverage: 85.126% (+0.03%) from 85.096%

Build # 28968419181

Build Type

push

github

Committed by

web-flow

Commit Message

3.19.0: refine_cluster recovery-pass primitive (#352) (#354)

Re-embed one compartment on its own Pearson residuals, sub-cluster it, and
relabel each sub-cluster via a caller callback — the shared engine behind
hand-rolled disaggregation passes (γδ/αβ-CD8, DC recovery, tumor sub-states).

annotate_clusters labels over the GLOBAL embedding, whose axes are dominated by
whole-atlas structure; within-compartment biology (rare pDC/cDC1 in myeloid,
genuine γδ vs ambient-αβ CD8 in a cytotoxic cluster, tumor sub-states) does not
resolve there. refine_cluster(adata, mask, relabel_fn=...) isolates a
compartment (label / bool mask / index list / predicate), re-embeds it alone via
embed_cells, and asks relabel_fn(sub_adata) to name each resulting sub-cluster:
return a label, a (label, final_cluster) pair, or None to leave it as-is. The
discriminating logic lives entirely in the callback, so #351 (γδ) and the
DC/tumor passes become thin relabel_fns.

- tcrsift/embed.py: refine_cluster(); exported top-level.
- docs/user-guide/atlas.md: "Recovering sub-structure" section.
- tests/test_refine_cluster.py: split/untouched/mask-forms/final-cluster/
  min-cells-skip/label-col-create coverage (12 tests).

Claude-Session: https://claude.ai/code/session_01Nc9jzi2yp77EVa8yjN1mog

Coverage Stats

12940 of 15201 relevant lines covered (85.13%)

0.85 hits per line

Coverage Regressions

Lines	Coverage	∆	File
7	94.02	0.08%	embed.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.12 - 28968419181.1	08 Jul 2026 07:08PM UTC	48	85.13	GitHub Action Run

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