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Set zarr < 3.0.0 #108

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LouisK92 merged 1 commit into from
Nov 5, 2025
Merged

Set zarr < 3.0.0 #108

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13 changes: 11 additions & 2 deletions src/base/setup_spatialdata_partial.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,13 @@
setup:
- type: python
pypi: [spatialdata, "anndata>=0.12.0", "pyarrow<22.0.0"]
# remove pyarrow when https://github.com/scverse/spatialdata/issues/1007 is fixed
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)