Changelog

Please refer directly to the Releases section on GitHub, where you can find curated release notes for each release. For developers, please consult the contributing guide, which explains how to keep release notes are up-to-date at each release.

Unreleased

Changed

• SpatialData.read() now only accepts a path or URL (str, Path or UPath) for file_path; passing an already-open zarr.Group raises a TypeError. Use spatialdata.read_zarr() to read from a zarr.Group.

• SpatialData.attrs is now typed as dict[str, JSONValue] instead of dict[Any, Any], making explicit the pre-existing invariant that the attrs must be JSON-serializable (they are stored as Zarr attributes). Accordingly, SpatialData.get_attrs() is now typed as returning JSONValue | pd.DataFrame: the previous annotation did not cover attrs values such as lists, numbers, booleans and None, which have always been valid and are returned as-is when return_as=None. This is a typing-only change, the runtime behaviour is unchanged.

• SpatialData.locate_element() now accepts a table (AnnData) in addition to a SpatialElement; tables were already located correctly, but the annotation did not allow passing them. This is a typing-only change, the runtime behaviour is unchanged.

Fixed

• Querying a SpatialData object with multiple (batched) bounding boxes now raises an explicit NotImplementedError instead of failing with an opaque AssertionError. Batched queries are supported when querying a SpatialElement directly, but not when querying a SpatialData object, since that would require returning one SpatialData object per bounding box.