add test defaults and attempt to use gpu

src/methods/cell2location/config.vsh.yaml

@@ -63,6 +63,8 @@ arguments:
   - name: "--max_epochs_st"
     type: integer
     default: 30000
+    info:
+      test_default: 1000
     description: Maximum number of epochs to train cell2location model for spatial mapping.
 
 resources:
@@ -71,18 +73,16 @@ resources:
 
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_pytorch_nvidia:1.0.0
     setup:
       - type: python
         packages: 
-          - scvi-tools==1.0.4
+          - scvi-tools 
           - cell2location
-          - jax==0.4.23
-          - jaxlib==0.4.23
-          - scipy<1.13 # The scipy.linalg functions tri, triu & tril are deprecated and will be removed in SciPy 1.13.
-
+          - theano
+          - pymc
 runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [hightime, midmem, midcpu]
+      label: [hightime, midmem, midcpu, gpu]

src/methods/cell2location/script.py

@@ -1,5 +1,9 @@
 import anndata as ad
 import numpy as np
+import os 
+
+os.environ["THEANO_FLAGS"] = 'device=cuda,floatX=float32,force_device=True'
+
 from cell2location.cluster_averages.cluster_averages import compute_cluster_averages
 from cell2location.models import Cell2location
 from cell2location.models import RegressionModel
@@ -45,6 +49,7 @@
     batch_key="batch_key",
     # cell type, covariate used for constructing signatures
     labels_key="cell_type",
+    # use_gpu=True
   )
   sc_model = RegressionModel(input_single_cell)
   sc_model.train(max_epochs=par["max_epochs_sc"], batch_size=par["sc_batch_size"])