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Stop copying train_mod2 into novel's model artifact #47

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Merged
rcannood merged 2 commits into from
Jul 30, 2026
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Stop copying train_mod2 into novel's model artifact #47

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d5ebd53
stop copying train_mod2 into novel's model artifact
rcannood Jul 29, 2026
6eedd48
Merge branch 'main' into perf/novel-model-artifact-size
rcannood Jul 30, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,8 @@

* `lm`: Drop the unused `n_cores` and ask for `lowcpu` rather than `highcpu`. The per-gene loop is `pbapply::pblapply()` without a cluster, so it has always run on one core (PR #42).

* `novel_train`: Store only the metadata `novel_predict` needs in the model artifact, instead of a full copy of `train_mod2` (PR #47).

## BUG FIXES

* `process_dataset`: Fall back to holding out a quarter of the batches when the dataset has no `obs["is_train"]`, rather than silently producing four empty h5ads. `obs["is_train"]` carries the NeurIPS 2021 competition split and stays optional; `obs["cell_type"]` is now declared and required (PR #28).
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3 changes: 2 additions & 1 deletion src/methods/novel/novel_train/script.py
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Expand Up @@ -39,7 +39,8 @@
input_train_mod1 = ad.read_h5ad(par['input_train_mod1'])
input_train_mod2 = ad.read_h5ad(par['input_train_mod2'])

adata = input_train_mod2.copy()
# carries the metadata novel_predict needs; the matrix itself is not used there
adata = ad.AnnData(uns=dict(input_train_mod2.uns))

mod1 = input_train_mod1.uns['modality']
mod2 = input_train_mod2.uns['modality']
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