diff --git a/CHANGELOG.md b/CHANGELOG.md index e107b8bb..f83ddd97 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,8 @@ ## BUG FIXES +* `cellmapper_scvi`: Bump the base image from `openproblems/base_pytorch_nvidia:1.0.0` to `:1`. (PR #53). + * `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). * Fix the component paths, build paths and `rename_keys` separator in the helper scripts, which prevented `scripts/create_datasets/test_resources.sh` and both `run_test.sh` scripts from running at all (PR #22). diff --git a/src/methods/cellmapper_linear/config.vsh.yaml b/src/methods/cellmapper_linear/config.vsh.yaml index 821a846b..e824cd85 100644 --- a/src/methods/cellmapper_linear/config.vsh.yaml +++ b/src/methods/cellmapper_linear/config.vsh.yaml @@ -66,7 +66,7 @@ engines: setup: - type: python packages: - - cellmapper>=0.2.2 + - cellmapper>=0.2.6 runners: - type: executable - type: nextflow diff --git a/src/methods/cellmapper_linear/script.py b/src/methods/cellmapper_linear/script.py index a3635928..194235e2 100644 --- a/src/methods/cellmapper_linear/script.py +++ b/src/methods/cellmapper_linear/script.py @@ -48,8 +48,8 @@ cmap.compute_mapping_matrix(kernel_method=par['kernel_method']) print("Predict on test data", flush=True) -cmap.map_obsm(key="mod2", prediction_postfix="pred") -mod2_pred = csc_matrix(cmap.query.obsm["mod2pred"]) +cmap.map_obsm(key="mod2", prediction_postfix="_pred") +mod2_pred = csc_matrix(cmap.query.obsm["mod2_pred"]) print("Write output AnnData to file", flush=True) output = ad.AnnData( diff --git a/src/methods/cellmapper_scvi/config.vsh.yaml b/src/methods/cellmapper_scvi/config.vsh.yaml index a86f6502..c54b1963 100644 --- a/src/methods/cellmapper_scvi/config.vsh.yaml +++ b/src/methods/cellmapper_scvi/config.vsh.yaml @@ -69,11 +69,11 @@ resources: dest: utils.py engines: - type: docker - image: openproblems/base_pytorch_nvidia:1.0.0 + image: openproblems/base_pytorch_nvidia:1 setup: - type: python packages: - - cellmapper>=0.2.2 + - cellmapper>=0.2.6 - scvi-tools>=1.3.0 - muon>=0.1.6