pirl-unc / tcrsift / 21916519681

Builds Branch Commit Type Ran Committer Via Coverage
21916519681 main Add til-select v2 CSV compatibility and bump version push iskandr github
70.37
21873489947 main Add til-select workflow for TIL-only prioritization push iskandr github
72.88
21766868105 main Align TIL workflows, optional annotation, and docs/CLI consistency push iskandr github
70.56
21716777488 main Add tests for GEX augmentation push iskandr github
70.48
21386154377 main Fix pipeline issues and add tests push iskandr github
68.45
21264988424 main Update develop.sh to activate venv and use uv Checks for active venv, local .venv, or local venv directory. Creates a new .venv with uv if none found. Uses uv pip for editable install when available. Co-Authored-By: Claude Opus 4.5 <noreply@anth... push iskandr github
64.52
21262765240 main Add safe calculation utilities and improve input validation - Add safe_divide, safe_percentage, safe_mode utilities to validation.py to prevent division-by-zero errors across the codebase - Add validate_cdr3_dataframe for bulk CDR3 sequence val... push iskandr github
64.52
21220620640 main Add tests for load_cellranger_gex and load_sample functions - TestLoadCellrangerGex: Basic loading, QC metrics, filter flags, error handling - TestLoadSample: Combined GEX+VDJ loading, VDJ-only loading, metadata propagation - Created mock 10x mat... push iskandr github
64.05
21217739954 main Fix loader tests to match actual function behavior - _extract_tcell_markers adds all marker columns with 0 for missing genes - combine_gex_and_vdj returns all GEX cells with VDJ columns merged (left join) - Loader coverage improved from 19% to 49... push iskandr github
62.34
21194649738 main Fix import: use _pivot_vdj_by_barcode instead of non-existent pivot_vdj_to_cells Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> push iskandr github
60.27
21194117485 main Add future annotations import for Python 3.9 compatibility Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> push iskandr github
60.29
21181237675 main Add mnemonic command to README Document the `tcrsift mnemonic` command that generates pronounceable names from CDR3 sequences (e.g., CASSLGQAYEQYF → "Dr. Loguq Aye, MD"). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> push iskandr github
59.72
21158910483 main Improve test data for logistic regression and add end-to-end tests - Add clonotypes_for_logistic fixture to conftest.py with 200 realistic clones that avoid perfect separation warnings in statsmodels - Update logistic regression tests to use sh... push iskandr github
59.72
21152761811 main Suppress expected warnings in tests with small synthetic data Add pytest.mark.filterwarnings decorators to tests that use small synthetic data with statsmodels logistic regression and empty AnnData objects. These warnings are expected behavior an... push iskandr github
59.72
21149391068 main Add multi-format TIL input support and multi-sample matching - Add til_csv and til_h5ad fields to Sample model for flexible TIL data input - Add load_til_data() with support for h5ad, CSV, and VDJ directory formats - Auto-detect CDR3 column namin... push iskandr github
59.72