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merged 2 commits into from
Sep 29, 2023
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[pre-commit.ci] pre-commit autoupdate #50

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a81f49a
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Sep 25, 2023
e4d09f5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 25, 2023
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8 changes: 4 additions & 4 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,11 @@ repos:
- id: nbqa-black
- id: nbqa-isort
- repo: https://github.com/psf/black
rev: 23.7.0
rev: 23.9.1
hooks:
- id: black
- repo: https://github.com/pre-commit/mirrors-prettier
rev: v3.0.2
rev: v3.0.3
hooks:
- id: prettier
- repo: https://github.com/asottile/blacken-docs
Expand Down Expand Up @@ -51,7 +51,7 @@ repos:
- id: trailing-whitespace
- id: check-case-conflict
- repo: https://github.com/PyCQA/autoflake
rev: v2.2.0
rev: v2.2.1
hooks:
- id: autoflake
args:
Expand All @@ -71,7 +71,7 @@ repos:
- flake8-bugbear
- flake8-blind-except
- repo: https://github.com/asottile/pyupgrade
rev: v3.10.1
rev: v3.13.0
hooks:
- id: pyupgrade
args: [--py3-plus, --py38-plus, --keep-runtime-typing]
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26 changes: 13 additions & 13 deletions datasets/README.md
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Expand Up @@ -4,19 +4,19 @@ The example notebooks operate on a set of spatial omics datasets that can be dow

Here you can find the dataset hosted in S3 object storage.

| Dataset | .zarr.zip | S3 (see note below!) |
| :----------------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
| cosmx_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr> |
| mcmicro_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr> |
| merfish | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr> |
| mibitof | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr> |
| steinbock_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr> |
| toy | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr> |
| visium | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr> |
| visium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr> |
| 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> |
| 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> |
| 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> |
| Dataset | .zarr.zip | S3 (see note below!) |
| :------------------------------------------------------------------------------------------------------------------------------------------------------: | :----------------------------------------------------------------------------------: | :-----------------------------------------------------------------------------------: |
| cosmx_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zarr> |
| mcmicro_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr> |
| merfish | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/merfish.zarr> |
| mibitof | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr> |
| steinbock_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr> |
| toy | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/toy.zarr> |
| visium | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zarr> |
| visium_io | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zip> | <https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_io.zarr> |
| 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> |
| 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> |
| 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> |
| [additional resources for methods developers](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/developers_resources/storage_format/) | - | - |

## Note
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