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Ran 08 May 2026 02:11AM UTC

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Committed 08 May 2026 02:10AM UTC coverage: 70.554% (+0.006%) from 70.548%

Job # 25532685520.1

Build Type

push

github

Committed by

web-flow

Commit Message

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.

Coverage Stats

4066 of 5763 relevant lines covered (70.55%)

0.71 hits per line

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