From 590042761c816d38aa6f344f034f18ad8796eb8e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 May 2026 20:04:16 +0200 Subject: [PATCH 1/6] Update version constraints --- src/base/setup_spatialdata_partial.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) 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"] From 37c74f1d1cfc47587d20538c5c03e67d1e1727b6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 May 2026 22:28:40 +0200 Subject: [PATCH 2/6] ci force From bf6198200db2fc631ede00ef2971a8df2976ca79 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 May 2026 09:19:05 +0200 Subject: [PATCH 3/6] fix default --- scripts/create_resources/test_resources.sh | 3 ++- src/api/comp_data_processor.yaml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh index 4a9cb10..3f635e1 100755 --- a/scripts/create_resources/test_resources.sh +++ b/scripts/create_resources/test_resources.sh @@ -66,5 +66,6 @@ HERE # only run this if you have access to the openproblems-data bucket aws s3 sync --profile op \ - "$DATASET_DIR" s3://openproblems-data/resources_test/task_spatial_segmentation/mouse_brain_combined/ \ + resources_test/task_spatial_segmentation/mouse_brain_combined/ \ + s3://openproblems-data/resources_test/task_spatial_segmentation/mouse_brain_combined/ \ --delete --dryrun diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml index 69deecc..c778417 100644 --- a/src/api/comp_data_processor.yaml +++ b/src/api/comp_data_processor.yaml @@ -58,7 +58,7 @@ argument_groups: required: true multiple: true info: - test_default: ["https://example.com/mouse_brain_combined_paper", "10.1234/example.doi"] + test_default: "10.1234/example.doi" - name: --dataset_summary type: string description: Short description of the dataset. From aac207ceb5d87da4bfd38312a96c41225bd122a0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 May 2026 09:22:26 +0200 Subject: [PATCH 4/6] ci force From 270547a3f453b094ad758feb9fb530567c76ec78 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 May 2026 09:30:07 +0200 Subject: [PATCH 5/6] Make sure uns field is scalar --- scripts/create_resources/test_resources.sh | 5 ++++- src/api/comp_data_processor.yaml | 1 - 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh index 3f635e1..ed9c54e 100755 --- a/scripts/create_resources/test_resources.sh +++ b/scripts/create_resources/test_resources.sh @@ -18,7 +18,10 @@ DATASET_ID=mouse_brain_combined RAW_DATA=resources_test/common DATASET_DIR=resources_test/task_spatial_segmentation/$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 -- \ diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml index c778417..c6cf598 100644 --- a/src/api/comp_data_processor.yaml +++ b/src/api/comp_data_processor.yaml @@ -56,7 +56,6 @@ argument_groups: type: string description: Bibtex reference of the paper in which the dataset was published. required: true - multiple: true info: test_default: "10.1234/example.doi" - name: --dataset_summary From b1ca6daaf640c5d476a236df4b3ce52cf0e79cf4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 May 2026 09:30:40 +0200 Subject: [PATCH 6/6] ci force