pirl-unc / tsarina / 24687014274
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coverage: 41.353% (-1.0%) from 42.345%
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v0.10.0: drop local _aggregate_refs, route --format refs through hitlist (#17)

Upstream tsarina.cli_hits._aggregate_refs landed in hitlist 1.12.0 as
hitlist.aggregate.aggregate_per_pmhc_with_refs. Retires the tsarina-local
copy and delegates entirely to hitlist.

Changes

- pyproject.toml: bump hitlist>=1.12.1 (1.12.0 for the aggregator,
  1.12.1 required for the classify_allele_resolution Pair[Gene, Gene]
  fix that unblocks hitlist data build on current IEDB/CEDAR exports).
- cli_hits.py: delete _aggregate_refs (~95 lines); import
  aggregate_per_pmhc_with_refs from hitlist.aggregate and dispatch to it
  on args.format == "refs". --format help text updated.
- tests/test_cli_hits_refs.py: drop duplicated aggregation unit tests,
  keep the CLI _SUPPORTED_FORMATS check, add a contract test asserting
  hitlist's aggregator surfaces the ms_pmhc_* columns the CLI depends on.

Breaking changes

1. Output columns renamed to hitlist's ms_pmhc_* convention
   (ms_pmhc_hit_count, ms_pmhc_ref_count, ms_pmhc_pmids, ms_pmhc_tissues,
   ms_pmhc_diseases, ms_pmhc_cell_lines, ms_pmhc_in_cancer,
   ms_pmhc_in_healthy_tissue, ms_pmhc_mono_hit_count). Aligns tsarina
   with hitlist's other pMHC aggregations.
2. --format refs now filters to mhc_restriction.str.startswith("HLA-")
   rows, matching aggregate_per_pmhc's behavior. v0.9.0's local
   aggregator did not filter. Follow-up hitlist issue will reconsider
   whether the filter should live in the aggregator or be caller-opt-in.

Net -182 lines of aggregation code. 166 passed. Closes #16.

758 of 1833 relevant lines covered (41.35%)

0.41 hits per line

Coverage Regressions

Lines Coverage ∆ File
79
37.5
 -8.18% cli_hits.py
Jobs
ID Job ID Ran Files Coverage
1 24687014274.1 30
41.35
 GitHub Action Run
Source Files on build 24687014274