Create test resources

_viash.yaml

@@ -47,14 +47,10 @@ references:
 
 info:
   image: The name of the image file to use for the component on the website.
-  # Step 5: Replace the task_template to the name of the task.
   test_resources:
     - type: s3
-      path: s3://openproblems-data/resources_test/common/
-      dest: resources_test/common
-    - type: s3
-      path: s3://openproblems-data/resources_test/task_template/
-      dest: resources_test/task_template
+      path: s3://openproblems-data/resources_test/task_spatial_segmentation/
+      dest: resources_test/task_spatial_segmentation
 
 # Step 6: Update the authors of the task.
 authors: 

scripts/create_test_resources/README.md

@@ -0,0 +1,3 @@
+Here we generate a small test dataset, used for `viash test`. Note that the file structure here is a bit simplified compared to `scripts/create_resources` as we only have one dataset.
+
+Copy the data from the `task_ist_preprocessing` test resources: `mouse_brain_combined.sh`

scripts/create_test_resources/mouse_brain_combined.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+set -e
+
+if [ ! -d resources_test/task_spatial_segmentation/mouse_brain_combined ]; then
+  mkdir -p resources_test/task_spatial_segmentation/mouse_brain_combined
+fi
+
+# these files were generated by https://github.com/openproblems-bio/task_ist_preprocessing/tree/main/scripts/create_test_resources
+# we can just copy them for now
+
+aws s3 sync --profile op \
+  s3://openproblems-data/resources_test/task_ist_preprocessing/mouse_brain_combined/raw_ist.zarr \
+  resources_test/task_spatial_segmentation/mouse_brain_combined/raw_ist.zarr
+
+aws s3 cp --profile op \
+  s3://openproblems-data/resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad \
+  resources_test/task_spatial_segmentation/mouse_brain_combined/scrnaseq_reference.h5ad
+
+# ...additional preprocessing if needed ...
+
+# sync to s3
+aws s3 sync --profile op \
+  "resources_test/task_spatial_segmentation/mouse_brain_combined/" \
+  "s3://openproblems-data/resources_test/task_spatial_segmentation/mouse_brain_combined/" \
+  --delete --dryrun

src/base/setup_spatialdata_partial.yaml

@@ -0,0 +1,3 @@
+setup:
+  - type: python
+    pypi: ["spatialdata", "anndata>=0.12.0", "zarr>=3.0.0"]

src/base/setup_txsim_partial.yaml

@@ -0,0 +1,13 @@
+setup:
+  - type: python
+    pypi: ["spatialdata==0.5.0", "anndata>=0.12.0", "pyarrow<22.0.0", "zarr<3.0.0"]
+    # 1. remove pyarrow when https://github.com/scverse/spatialdata/issues/1007 is fixed.
+    #    This is actually fixed now with the spatialdata release 0.6.0. However, the new
+    #    release now comes with zarr 3.0.0. When reading a zarr file that was saved with
+    #    zarr 3.0.0 we can not load it with zarr<3.0.0. (PathNotFoundError: nothing found at path '')
+    # 2. Currently sopa enforces zarr<3.0.0. Therefore we need to save all our data with zarr<3.0.0.
+    #    As soon as this is fixed (https://github.com/gustaveroussy/sopa/issues/347):
+    #    - remove restriction on spatialdata
+    #    - remove zarr<3.0.0
+    #    - remove pyarrow<22.0.0
+    #    - Recreate all the datasets (scripts/create_resources/combine/process_datasets.sh)