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Improve types and docstrings #109

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Improve types and docstrings #109

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Zethson
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@Zethson Zethson commented Nov 14, 2024

  • Switches to uv for faster builds (cache slows it down)
  • Adds and refactors lots of types and docstrings.
  • Changed a few stdout messages. Happy to revert them. There's a bit of Claude in here.

There's many more but I'll do this in passes. Easier to review and omg this takes time.

Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
@Zethson Zethson changed the title Improve some docstrings Improve types and docstrings Nov 14, 2024
@Zethson Zethson marked this pull request as ready for review November 14, 2024 22:00
.github/workflows/unit_test.yml Outdated Show resolved Hide resolved
src/scportrait/io/daskmmap.py Show resolved Hide resolved
src/scportrait/io/daskmmap.py Outdated Show resolved Hide resolved
src/scportrait/pipeline/_utils/spatialdata_helper.py Outdated Show resolved Hide resolved
src/scportrait/tools/ml/pretrained_models.py Outdated Show resolved Hide resolved
src/scportrait/pipeline/_utils/sdata_io.py Outdated Show resolved Hide resolved
src/scportrait/pipeline/_utils/sdata_io.py Outdated Show resolved Hide resolved
if self.cache is not None:
path = os.path.join(self.config["cache"], f"{self.__class__.__name__}_")
path = os.path.join(self.directory["cache"], f"{self.__class__.__name__}_") # type: ignore
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self.directory should raise an error I think because it doesn't exist. Was there a specific reason you changed it?

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Yes, self.config does not exist. What should it be?

Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
Signed-off-by: zethson <lukas.heumos@posteo.net>
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