Fix multiple methods (#97)

* Fix multiple methods

* Restrict pyarrow version

Author: LouisK92

src/base/setup_spatialdata_partial.yaml

@@ -1,3 +1,4 @@
 setup:
   - type: python
-    pypi: [spatialdata, "anndata>=0.12.0"]
+    pypi: [spatialdata, "anndata>=0.12.0", "pyarrow<22.0.0"]
+    # remove pyarrow when https://github.com/scverse/spatialdata/issues/1007 is fixed

src/methods_cell_type_annotation/moscot/script.py

@@ -24,6 +24,31 @@
 }
  ## 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
+# CUDA/cuDNN (e.g. 9.1). That can override JAX's bundled libraries and cause
+# errors like:
+#   "Loaded runtime CuDNN library: 9.1.0 but source was compiled with: 9.8.0"
+#
+# To prevent that, we remove LD_LIBRARY_PATH before importing JAX so it uses
+# its own compatible, built-in CUDA/cuDNN stack.
+# -----------------------------------------------------------------------------
+import os
+print("LD_LIBRARY_PATH before unset:", os.environ.get("LD_LIBRARY_PATH"), flush=True)
+os.environ.pop("LD_LIBRARY_PATH", None)
+
+# gpu check
+import jax 
+import jaxlib
+print("GPU check", flush=True)
+print("jax:", jax.__version__, flush=True)
+print("jaxlib:", jaxlib.__version__, flush=True)
+print("backend:", jax.default_backend(), flush=True)
+print("devices:", jax.devices(), flush=True)
+print("LD_LIBRARY_PATH:", os.environ.get("LD_LIBRARY_PATH"), flush=True)
+
+
 # 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.'
 assert par['input_scrnaseq_reference'] is not None, 'Single cell input is required for this annotation method.'

src/methods_transcript_assignment/comseg/config.vsh.yaml

@@ -25,7 +25,7 @@ arguments:
     description: "Coordinate system for the transcripts"
   - name: --patch_width
     type: integer
-    default: 1200
+    default: 2000
     description: "Width of image patches for processing"
   - name: --patch_overlap
     type: integer

src/methods_transcript_assignment/comseg/script.py

@@ -12,7 +12,7 @@
     "coordinate_system": "global",
     "output": "temp/comseg/transcripts.zarr",
 
-    "patch_width": 1200,
+    "patch_width": 2000,
     "patch_overlap": 50,
     "transcript_patch_width": 200,
     "mean_cell_diameter": 15.0,

src/methods_transcript_assignment/pciseq/config.vsh.yaml

@@ -163,4 +163,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [ hightime, midcpu, veryhighmem ]
+      label: [ veryhightime, midcpu, veryhighmem ]

src/methods_transcript_assignment/proseg/script.py

@@ -86,7 +86,7 @@
 )
 
 # Make transcript patches
-sopa.make_transcript_patches(sdata_sopa, patch_width=2000, patch_overlap=50, prior_shapes_key="cell_id")
+sopa.make_transcript_patches(sdata_sopa, patch_width=None, patch_overlap=50, prior_shapes_key="cell_id")
 sdata_sopa['transcripts'].attrs['spatialdata_attrs'] = {}
 sdata_sopa['transcripts'].attrs['spatialdata_attrs']['feature_key'] = 'feature_name'