Bump cellmapper_scvi's base image and align both obsm keys

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).

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

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(

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