Fix moscot script and baysor config (#100)

Author: LouisK92

src/methods_cell_type_annotation/moscot/script.py

@@ -1,29 +1,5 @@
 #!/usr/bin/env python3
 
-import numpy as np
-import anndata as ad
-import scanpy as sc
-
-import moscot as mt
-from moscot.problems.space import MappingProblem
-
-## VIASH START
-par = {
-   'input_spatial_normalized_counts': 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_normalized_counts.h5ad',
-   'input_scrnaseq_reference': 'resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad',
-   'output': 'spatial_with_celltypes.h5ad',
-   'celltype_key': 'cell_type',
-   'alpha': 0.8,
-   'epsilon': 0.01,
-   'tau': 1.0,
-   'rank': 5000,
-   'mapping_mode': 'max',
-}
-meta = {
-   'name': 'moscot',
-}
- ## VIASH END
-
 # --- Fix for CuDNN version mismatch ------------------------------------------
 # JAX wheels (e.g. jax[cuda12]) come with their own CUDA/cuDNN libraries.
 # However, some systems set LD_LIBRARY_PATH to point to an older system-wide
@@ -48,6 +24,30 @@
 print("devices:", jax.devices(), flush=True)
 print("LD_LIBRARY_PATH:", os.environ.get("LD_LIBRARY_PATH"), flush=True)
 
+import numpy as np
+import anndata as ad
+import scanpy as sc
+
+import moscot as mt
+from moscot.problems.space import MappingProblem
+
+## VIASH START
+par = {
+   'input_spatial_normalized_counts': 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_normalized_counts.h5ad',
+   'input_scrnaseq_reference': 'resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad',
+   'output': 'spatial_with_celltypes.h5ad',
+   'celltype_key': 'cell_type',
+   'alpha': 0.8,
+   'epsilon': 0.01,
+   'tau': 1.0,
+   'rank': 5000,
+   'mapping_mode': 'max',
+}
+meta = {
+   'name': 'moscot',
+}
+ ## VIASH END
+
 
 # Optional parameter check: For this specific annotation method the par['input_spatial_normalized_counts'] and par['input_scrnaseq_reference'] are required
 assert par['input_spatial_normalized_counts'] is not None, 'Spatial input is required for this annotation method.'

src/methods_transcript_assignment/baysor/config.vsh.yaml

@@ -76,6 +76,8 @@ engines:
   #      (commands can be retrieved from `viash run src/methods_transcript_assignment/baysor/config.vsh.yaml -- ---dockerfile`)
   - type: docker
     image: python:3.11.13-bookworm
+    __merge__: 
+      - /src/base/setup_spatialdata_partial.yaml
     setup:
       - type: apt
         packages: procps
@@ -84,9 +86,7 @@ engines:
           - openproblems-bio/core#subdirectory=packages/python/openproblems
       - type: python
         packages:
-           #TODO: Add merge with setup_spatialdata_partial.yaml and solve anndata version conflict differently
            - sopa[baysor]
-           - anndata>=0.12.0 
       - type: docker
         run:
           - wget https://github.com/kharchenkolab/Baysor/releases/download/v0.7.1/baysor-x86_x64-linux-v0.7.1_build.zip