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pirl-unc / tcrsift / 25532685520
84%

Build:
DEFAULT BRANCH: main
Ran 08 May 2026 02:11AM UTC
Jobs 4
Files 23
Run time 1min
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08 May 2026 02:10AM UTC coverage: 70.566% (+0.005%) from 70.561%
25532685520

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Add enrichment_method field; propagate donor/method to obs (#8 chunk 1) (#10)

First slice of #8. Lays the metadata foundation for donor/method-aware
analysis without yet adding aggregations, filters, or reports.

- sample_sheet.Sample gains a free-form `enrichment_method` field, kept
  distinct from the fixed-enum `source` so users can label arbitrary
  selection strategies (AIMpos, IFNpos, tetpos, AIMpos_CTYneg, ...).
- to_dataframe() now includes both `patient_id` (previously dead
  metadata, accepted but never serialized) and `enrichment_method`.
- loader.load_sample propagates `patient_id` and `enrichment_method`
  into adata.obs alongside source/expected_tcell_type. Uses the same
  conditional-skip pattern as #5 so unset fields don't create all-None
  object columns that break h5ad write.
- CSV and YAML loaders pass the new field through unchanged because
  Sample(**row_dict) absorbs it.

Tests cover: propagation when set, absence when unset, sample-sheet
DataFrame round-trip, free-form value acceptance, and CSV/YAML loader
ingestion.

Bumps version to 0.3.0 — first minor on the donor/method work.

Foundation only; per-clone aggregations (n_methods_per_donor, n_donors,
methods_per_donor) and filter knobs land in subsequent chunks.

4066 of 5762 relevant lines covered (70.57%)

2.82 hits per line

Coverage Regressions

Lines Coverage ∆ File
20
84.77
0.08% sample_sheet.py
15
86.3
0.0% loader.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.12 - 25532685520.1 08 May 2026 02:11AM UTC 23
70.55
GitHub Action Run
2 python-3.10 - 25532685520.2 08 May 2026 02:11AM UTC 23
70.55
GitHub Action Run
3 python-3.11 - 25532685520.3 08 May 2026 02:11AM UTC 23
70.55
GitHub Action Run
4 python-3.9 - 25532685520.4 08 May 2026 02:11AM UTC 23
70.53
GitHub Action Run
Source Files on build 25532685520
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Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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