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Integration dev - #10

Merged

adamfreedman merged 8 commits into

mainfrom

integration_dev

Jul 16, 2026

Merged

Integration dev#10
adamfreedman merged 8 commits into
mainfrom
integration_dev

Commits on Jun 30, 2026
- Integrate downsampling workflow modes
  adamfreedman
  committed
  a03e43a
Commits on Jul 3, 2026
- rename bootstrap_clusters to downsample_clusters and scatter per replicate
  adamfreedman
  committed
  6f8c0c4
- lower downsample_cluster_replicate base runtime from 240 to 30 minutes
  adamfreedman
  committed
  cd0573c
Commits on Jul 13, 2026
- Fix SCTransform hang and consolidate downsampling replicates into one job per target
  
  adamfreedman
  and
  claude
  committed
  519fb72
- Explicitly delete per-cluster marker CSVs in combine_markers
  
  adamfreedman
  and
  claude
  committed
  441d1eb
Commits on Jul 14, 2026
- Add scaling regression test for downsample_clusters; run all R-execution tests in CI automatically
  
  adamfreedman
  and
  claude
  committed
  0bf9aaa
- Remove remaining stale downsample_cluster_replicate assertions in test_config_validation.py
  
  adamfreedman
  and
  claude
  committed
  6876725
Commits on Jul 15, 2026
- Bump GitHub Actions to Node.js 24 runtime versions
  
  adamfreedman
  and
  claude
  committed
  1ac5e18