diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh index 4a9cb10..ed9c54e 100755 --- a/scripts/create_resources/test_resources.sh +++ b/scripts/create_resources/test_resources.sh @@ -18,7 +18,10 @@ DATASET_ID=mouse_brain_combined RAW_DATA=resources_test/common DATASET_DIR=resources_test/task_spatial_segmentation/$DATASET_ID -mkdir -p $DATASET_DIR +if [ -d "$DATASET_DIR" ]; then + rm -rf "$DATASET_DIR" +fi +mkdir -p "$DATASET_DIR" # process dataset viash run src/data_processors/process_dataset/config.vsh.yaml -- \ @@ -66,5 +69,6 @@ HERE # only run this if you have access to the openproblems-data bucket aws s3 sync --profile op \ - "$DATASET_DIR" s3://openproblems-data/resources_test/task_spatial_segmentation/mouse_brain_combined/ \ + resources_test/task_spatial_segmentation/mouse_brain_combined/ \ + s3://openproblems-data/resources_test/task_spatial_segmentation/mouse_brain_combined/ \ --delete --dryrun diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml index 69deecc..c6cf598 100644 --- a/src/api/comp_data_processor.yaml +++ b/src/api/comp_data_processor.yaml @@ -56,9 +56,8 @@ argument_groups: type: string description: Bibtex reference of the paper in which the dataset was published. required: true - multiple: true info: - test_default: ["https://example.com/mouse_brain_combined_paper", "10.1234/example.doi"] + test_default: "10.1234/example.doi" - name: --dataset_summary type: string description: Short description of the dataset. diff --git a/src/base/setup_spatialdata_partial.yaml b/src/base/setup_spatialdata_partial.yaml index a552792..7e3f4be 100644 --- a/src/base/setup_spatialdata_partial.yaml +++ b/src/base/setup_spatialdata_partial.yaml @@ -1,5 +1,3 @@ setup: - type: python - # spatialdata>=0.7.3a1 is required as a workaround for a bug in spatialdata<=0.7.2 - # See: https://github.com/scverse/spatialdata/issues/1090 - pypi: ["spatialdata>=0.7.3a1", "anndata>=0.12.0", "zarr>=3.0.0"] + pypi: ["spatialdata>=0.7.3", "anndata>=0.12.0", "zarr>=3.0.0"]