pirl-unc / tcrsift / 25705813745

Build # 25705813745

Build Type

push

github

Committed by web-flow

Commit Message

Add CXCL13/ENTPD1 enrichment selection branch (#1)

* Add CXCL13/ENTPD1 enrichment selection branch for tumor-reactive TILs

CXCL13 and ENTPD1 (CD39) were added to MARKER_GENES_DEFAULT but not used
in any selection branch. These exhaustion markers are known to enrich for
neoantigen-reactive TILs. This adds a dedicated enrichment_markers branch
using the same percentile-based panel score logic as cytolytic/antigen
response branches.

- Add ENRICHMENT_GENES_DEFAULT constant and enrichment_genes_preferred param
- Wire is_branch_enrichment_markers into is_branch_any union
- Add --enrichment-genes CLI flag (default: CXCL13,ENTPD1)
- Update tests with CXCL13/ENTPD1 mock data and enrichment assertions
- Run lint.sh before pytest in test.sh

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* Make ruff the default linter; pylint opt-in via env var

test.sh runs lint.sh as a pre-step (added in this branch). Default to
ruff so the test gate is fast and robust on shared dev envs — pylint's
astroid dependency has lagged Python language features in the past
(e.g. PEP 695 type aliases broke in older releases), which we hit
during the 0.2.7 deploy. Opt into pylint via
TCRSIFT_LINT_INCLUDE_PYLINT=1 (CI / pre-release).

* Bump version to 0.8.0

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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