25520083609
77%

Ran 07 May 2026 09:19PM UTC

Jobs 4

Files 23

Run time 1min

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Committed 07 May 2026 08:24PM UTC coverage: 70.596% (+0.06%) from 70.539%

Build # 25520083609

Build Type

push

github

Committed by

web-flow

Commit Message

Fix h5ad write failure on missing VDJ barcodes; misc bug cleanup (#4)

- loader.combine_gex_and_vdj: preserve bool/int dtypes after reindex so
  GEX cells without a VDJ contig get False / 0 instead of NaN. Fixes
  TypeError raised by anndata when writing has_TRA / TRA_count etc. to
  /obs (issue #3).
- loader: count productive contigs correctly when CellRanger exports the
  column as a string instead of bool.
- annotate.match_clonotypes: initialize db_match_partial=False so rows
  that never hit the partial-match fallback are False rather than NaN.
- model._fit_logistic_newton: log a warning when bailing on a
  near-singular Hessian, so callers can tell an unconverged fit from a
  clean one.
- Bump version to 0.2.7.

Coverage Stats

4072 of 5768 relevant lines covered (70.6%)

2.82 hits per line

Coverage Regressions

Lines	Coverage	∆	File
31	86.64	0.33%	loader.py
12	84.78	-0.61%	model.py
1	95.29	0.03%	annotate.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.9 - 25520083609.1	07 May 2026 09:30PM UTC	23	70.56	GitHub Action Run
2	python-3.10 - 25520083609.2	07 May 2026 09:19PM UTC	23	70.58	GitHub Action Run
3	python-3.11 - 25520083609.3	07 May 2026 09:29PM UTC	23	70.58	GitHub Action Run
4	python-3.12 - 25520083609.4	07 May 2026 09:31PM UTC	23	70.58	GitHub Action Run

pirl-unc / tcrsift / 25520083609
77%

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pirl-unc / tcrsift / 25520083609 77%

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