diff --git a/_viash.yaml b/_viash.yaml index 51acb10..17b6093 100644 --- a/_viash.yaml +++ b/_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: diff --git a/scripts/create_test_resources/README.md b/scripts/create_test_resources/README.md new file mode 100644 index 0000000..46bb116 --- /dev/null +++ b/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` diff --git a/scripts/create_test_resources/mouse_brain_combined.sh b/scripts/create_test_resources/mouse_brain_combined.sh new file mode 100755 index 0000000..fdc4e37 --- /dev/null +++ b/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 diff --git a/src/base/setup_spatialdata_partial.yaml b/src/base/setup_spatialdata_partial.yaml new file mode 100644 index 0000000..d2b72a2 --- /dev/null +++ b/src/base/setup_spatialdata_partial.yaml @@ -0,0 +1,3 @@ +setup: + - type: python + pypi: ["spatialdata", "anndata>=0.12.0", "zarr>=3.0.0"] diff --git a/src/base/setup_txsim_partial.yaml b/src/base/setup_txsim_partial.yaml new file mode 100644 index 0000000..5646a46 --- /dev/null +++ b/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)