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Merge pull request #50 from scverse/pre-commit-ci-update-config
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‎.pre-commit-config.yaml‎

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- id: nbqa-black
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- id: nbqa-isort
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- repo: https://github.com/psf/black
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rev: 23.7.0
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rev: 23.9.1
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hooks:
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- id: black
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.2
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rev: v3.0.3
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hooks:
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- id: prettier
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- repo: https://github.com/asottile/blacken-docs
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- id: trailing-whitespace
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- id: check-case-conflict
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- repo: https://github.com/PyCQA/autoflake
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rev: v2.2.0
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rev: v2.2.1
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hooks:
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- id: autoflake
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args:
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- flake8-bugbear
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- flake8-blind-except
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.10.1
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rev: v3.13.0
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hooks:
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- id: pyupgrade
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args: [--py3-plus, --py38-plus, --keep-runtime-typing]

‎datasets/README.md‎

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Here you can find the dataset hosted in S3 object storage.
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| Dataset | .zarr.zip | S3 (see note below!) |
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| :----------------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
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| cosmx_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr> |
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| mcmicro_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr> |
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| merfish | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr> |
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| mibitof | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr> |
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| steinbock_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr> |
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| toy | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr> |
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| visium | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr> |
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| visium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr> |
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| visium_associated_xenium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr> |
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| xenium_rep1_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr> |
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| xenium_rep2_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr> |
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| Dataset | .zarr.zip | S3 (see note below!) |
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| :------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
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| cosmx_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr> |
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| mcmicro_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr> |
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| merfish | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr> |
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| mibitof | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr> |
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| steinbock_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr> |
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| toy | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr> |
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| visium | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr> |
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| visium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr> |
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| visium_associated_xenium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zarr> |
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| xenium_rep1_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zarr> |
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| xenium_rep2_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep2_io.zarr> |
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| [additional resources for methods developers](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/developers_resources/storage_format/) | - | - |
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