pirl-unc / tcrsift / 25533157354
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Add per-clone donor/method aggregations (#8 chunk 2) (#14)

Second slice of #8. Builds on the donor/method foundation from 0.3.0
(enrichment_method field, patient_id/enrichment_method propagated to
adata.obs). Adds the clonotype-table aggregations the next chunk's
filter knobs will read.

In aggregate_clonotypes, after the existing per-sample block:

  - donors / n_donors        — present when patient_id is set
  - methods / n_methods      — present when enrichment_method is set
  - methods_per_donor        — JSON dict {donor: sorted methods list},
                               present when both are set. Stored as a
                               JSON string for clean h5ad/CSV
                               serialization.
  - max_methods_per_donor    — derived scalar: max methods seen for any
                               single donor. This is the value the
                               planned --min-methods-per-donor filter
                               will threshold against.

All four are emitted only when the relevant sample-sheet fields were
supplied — consistent with the optional-metadata pattern from #5.

Tests cover:
- donors / n_donors populated correctly across donors
- methods / n_methods populated correctly
- methods_per_donor JSON dict has the right per-donor lists, and
  max_methods_per_donor matches the longest list
- columns absent when neither field is set
- methods_per_donor / max_methods_per_donor only appear when both
  patient_id AND enrichment_method are set

Bumps version to 0.4.0 — meaningful new schema on the clonotype table.

Next chunk: --min-methods-per-donor / --min-donors filter knobs that
read these columns.

4114 of 5810 relevant lines covered (70.81%)

2.83 hits per line

Coverage Regressions

Lines Coverage ∆ File
8
94.85
 0.59% clonotype.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.9 - 25533157354.1 24
70.77
 GitHub Action Run
2 python-3.12 - 25533157354.2 24
70.8
 GitHub Action Run
3 python-3.10 - 25533157354.3 24
70.8
 GitHub Action Run
4 python-3.11 - 25533157354.4 24
70.8
 GitHub Action Run
Source Files on build 25533157354