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Chore/modernise and cleanup - #19

Merged

LRabuzin merged 9 commits into

mainfrom

chore/modernise-and-cleanup

Aug 17, 2026

Merged

Chore/modernise and cleanup#19
LRabuzin merged 9 commits into
mainfrom
chore/modernise-and-cleanup

Commits on Aug 13, 2026
- Remove dead code, declare hard deps, and enforce the lint rules
  
  LRabuzin
  and
  claude
  committed
  bbea159
- Modernise the CI stack and fix the package on torch>=2.6
  
  LRabuzin
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  claude
  committed
  ae89157
- Replace the smoke notebooks with runnable vignettes, and add predict_dataloader
  
  LRabuzin
  and
  claude
  committed
  8d4e7f9
- Fix spatial-table export: split ShaDow batches by ptr, stop swallowing errors
  
  LRabuzin
  and
  claude
  committed
  4c7fcd0
- Export the root cell type, fix double-converted root ids, save run vignettes
  
  LRabuzin
  and
  claude
  committed
  26c6eb9
- Export cell-level tables, so tier-2 can measure cells rather than summaries
  
  LRabuzin
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  claude
  committed
  d68bcd8
- Add cell-level tier-2 analyses: per-niche cell types, and global niche structure
  
  LRabuzin
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  claude
  committed
  6a0b994
- Drop the instance-level tier-2 plugins; scale min_cluster_size to the cohort
  
  LRabuzin
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  claude
  committed
  202baeb
Commits on Aug 17, 2026
- Show fine-tuning in vignette 2, and fix the same defaults bug in predict.yaml
  
  LRabuzin
  and
  claude
  committed
  198148f