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pirl-unc / tcrsift / 28809678586
85%

Build:
DEFAULT BRANCH: main
Ran 06 Jul 2026 05:18PM UTC
Jobs 1
Files 47
Run time 1min
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06 Jul 2026 05:14PM UTC coverage: 84.643% (+0.01%) from 84.632%
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3.1.0: cell embedding module (#321)

Adds tcrsift.embed.embed_cells (Pearson residuals -> PCA -> Harmony -> UMAP -> Leiden) + EmbedConfig, a new 'atlas' deps extra (harmonypy/igraph/leidenalg), and an opt-in embed step in cmd_run (saves atlas.h5ad). Harmony called directly with an orientation guard (the #308 gotcha). Closes #311.

12164 of 14371 relevant lines covered (84.64%)

0.85 hits per line

Coverage Regressions

Lines Coverage ∆ File
188
65.7
-0.3% cli.py
8
96.57
0.2% config.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.12 - 28809678586.1 06 Jul 2026 05:18PM UTC 47
84.64
GitHub Action Run
Source Files on build 28809678586
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  • Changed 3
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  • Coverage Changed 3
Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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