aeisenbarth

When transforming a MultiscaleSpatialImage, a KeyError is raised. See https://github.com/scverse/spatialdata/issues/378 So far, I've modified the test case to cover both SpatialImage and MultiscaleSpatialImage and reproduce the problem. I have no...

[Proposal] Rename Sequence transformation to avoid clashes

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When type-hinting my code, I frequently need `Sequence` from `collections.abc`. In order to avoid name clashes, one can do for either of the two: ```python from spatialdata.transformations import Sequence as...

The [implementation of `transform`](https://github.com/scverse/spatialdata/blob/cf1c1f74c9aaa1f99eca3ebc363cc990e381fb7d/src/spatialdata/_core/operations/transform.py#L262C9-L262C10) for `MultiscaleSpatialImage` is not covered by tests. This is a problem because (Multiscale)SpatialImage are structurally and implementationwise significantly different. For scale1 and greater, the key is...

`get_masks` interface changed from cellpose 1.x to 2.x

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When clicking "recompute last masks with new cellprob + model match", I get the error: ``` File …/lib/python3.8/site-packages/cellpose_napari/_dock_widget.py:116, in widget_wrapper..compute_masks(masks_orig= (1000, 1000) uint16, flows_orig=[ (1560, 1560, 3) uint8, (2, 1560,...

SkipValidation does not ignore ForwardReference

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### Initial Checks - [X] I confirm that I'm using Pydantic V2 ### Description Although a forward reference type-hint is marked with SkipValidation, Pydantic insists on importing it and rebuilding...

Filter nested commands

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## Summary The `commands` option currently allows to filter commands only at the first nesting level. When CLIs have deeper level of subcommands there is no way to filter or...

Support setup.cfg

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Setup.py has been replaced by setup.cfg and is now moving towards pyproject.toml. Probably there aren't many projects on setup.py anymore. While I was cleaning up an old setup.py & miniver...

Partial data update to existing YAML file (preserving comments, whitespace)

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By principal, and in the current scope of pydantic-yaml, a file saved back from a Pydantic object only contains features stored in the Pydantic object. This affects flexible syntax (quoting...

Instantiating the `SMInstance` class in the Python client with wrong login details leads to an unusable instance. Actual behavior: In contrast to the deprecated `login` method (which raises `BadRequestException`), the...

Subject: Create autosummary template variables dynamically based on `objtype` from documenters, enabling custom object types like `pydantic_model` to be selectable in templates (https://github.com/sphinx-doc/sphinx/issues/12021, https://github.com/mansenfranzen/autodoc_pydantic/issues/33). ### Feature or Bugfix - [x]...