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Add CLI for spatialdata_io. #239

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Add CLI for spatialdata_io. #239

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68a0b89
Initial commit for CLI for all readers (not tested yet). Using CLI an…
migueLib Nov 13, 2024
287a9e6
Add list of implemented readers in __readers__ variable.
migueLib Nov 13, 2024
266ba1a
Add list of implemented readers in __readers__ variable.
migueLib Nov 13, 2024
3dfcee9
Add click parser for all available readers.
migueLib Nov 13, 2024
feb6fed
Add cli for converting shapes and images to zarr
LLehner Nov 14, 2024
164b363
pre-commit
LLehner Nov 14, 2024
ddb8680
pre-commit
LLehner Nov 14, 2024
48b25b5
Merge remote-tracking branch 'origin/cli-2spatialdata' into cli-2spat…
migueLib Nov 14, 2024
883a95e
Add reader specific help.
migueLib Nov 14, 2024
628f8e4
Ensure .zarr output and finalize typing in wrapper functions.
migueLib Nov 14, 2024
6925089
Finalize typing in wrapper functions.
migueLib Nov 14, 2024
40fe75b
Finalize typing in wrapper functions.
migueLib Nov 14, 2024
02be05f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 14, 2024
9a5ead4
Fix pre-commit
LLehner Nov 14, 2024
f3933de
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 14, 2024
59ed7f5
Add docstring
LLehner Nov 14, 2024
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1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -23,6 +23,7 @@ urls.Source = "https://github.com/scverse/spatialdata-io"
urls.Home-page = "https://github.com/scverse/spatialdata-io"
dependencies = [
"anndata",
"click",
"numpy",
"scanpy",
"spatialdata>=0.2.3",
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16 changes: 16 additions & 0 deletions src/spatialdata_io/__init__.py
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Expand Up @@ -34,4 +34,20 @@
"visium_hd",
]

__readers__ = [
"codex",
"cosmx",
"curio",
"dbit",
"iss",
"mcmicro",
"merscope",
"seqfish",
"steinbock",
"stereoseq",
"visium",
"visium_hd",
"xenium",
]

__version__ = version("spatialdata-io")
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