Nightly feedstock build failed

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[jp-dark]

SpatialData just did a 0.5.0 release and must have changed their xarray pins. We only use xarray in SOMA for SpatialData, so I'll take a look into loosening our pin.

[jdblischak]

@jp-dark thanks for investigating.

Documenting the error:

+ pip check
spatial-image 1.2.3 has requirement xarray>=2024.10.0, but you have xarray 2024.9.0.
WARNING: Tests failed for tiledbsoma-py-1.17.1.dev20250820-py313hb02ebfe_0.conda - moving package to /home/conda/feedstock_root/build_artifacts/broken

Interesting to note that pip check failed with Python 3.13 for both linux-64 and osx-64. However, the linux-64 build happened to test Python 3.10 first, and pip check passed.

[jdblischak]

SpatialData just did a 0.5.0 release and must have changed their xarray pins. We only use xarray in SOMA for SpatialData, so I'll take a look into loosening our pin.

The problem was the recently released spatial-image 1.2.3. It requires xarray >=2024.10.0, but its conda-forge recipe wasn't updated, which is what allowed it to be installed here in the first place. I have submitted PRs to fix this situation. In other words, you will only need to loosen the xarray pin if you want to be able to install spatial-image 1.2.3 (and anything else that may require this latest version of spatial-image)

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[jdblischak]

My patch for the spatial-image conda binary was merged last night (conda-forge/conda-forge-repodata-patches-feedstock#1066).

However, last night there was a new import error:

Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/tiledbsoma_1755828496265/test_tmp/run_test.py", line 8, in <module>
    import tiledbsoma.io.spatial
  File "$TEST_ENV/lib/python3.11/site-packages/tiledbsoma/io/spatial/__init__.py", line 12, in <module>
    from .outgest import to_spatialdata
  File "$TEST_ENV/lib/python3.11/site-packages/tiledbsoma/io/spatial/outgest.py", line 14, in <module>
    raise err
  File "$TEST_ENV/lib/python3.11/site-packages/tiledbsoma/io/spatial/outgest.py", line 11, in <module>
    import spatialdata as sd
  File "$TEST_ENV/lib/python3.11/site-packages/spatialdata/__init__.py", line 60, in <module>
    from spatialdata import dataloader, datasets, models, transformations
  File "$TEST_ENV/lib/python3.11/site-packages/spatialdata/datasets.py", line 20, in <module>
    from spatialdata._core.operations.aggregate import aggregate
  File "$TEST_ENV/lib/python3.11/site-packages/spatialdata/_core/operations/aggregate.py", line 20, in <module>
    from spatialdata._core.operations.transform import transform
  File "$TEST_ENV/lib/python3.11/site-packages/spatialdata/_core/operations/transform.py", line 17, in <module>
    from spatialdata._core.spatialdata import SpatialData
  File "$TEST_ENV/lib/python3.11/site-packages/spatialdata/_core/spatialdata.py", line 19, in <module>
    from ome_zarr.io import parse_url
  File "$TEST_ENV/lib/python3.11/site-packages/ome_zarr/io.py", line 12, in <module>
    from zarr.storage import FsspecStore, LocalStore, StoreLike
ImportError: cannot import name 'FsspecStore' from 'zarr.storage' ($TEST_ENV/lib/python3.11/site-packages/zarr/storage.py)

[jdblischak]

The restarted builds failed with the same import error. Interestingly it only affects some versions of Python:

• pass: 3.10, 3.13
• fail: 3.11, 3.12

(the py39 build was dropped by conda-forge and will need to be added back similar to conda-forge/tiledb-py-feedstock#270)

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[github-actions]

Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary

[jdblischak]

Last night, the Python 3.12 builds continued to fail with the import error:

ImportError: cannot import name 'FsspecStore' from 'zarr.storage' ($HOST_ENV/lib/python3.12/site-packages/zarr/storage.py)