Merge branch 'main' into fix/warning

Author: Zethson

.github/workflows/prepare_test_data.yaml

@@ -1,6 +1,8 @@
 name: Prepare test data
 
 on:
+    schedule:
+        - cron: "0 0 1 * *" # run once a month to prevent artifact expiration
     workflow_dispatch:
 # uncomment and adjust the branch name if you need to add new datasets to the artifact
 #    push:
@@ -44,7 +46,7 @@ jobs:
                   done
 
             - name: Upload artifacts
-              uses: actions/upload-artifact@v3
+              uses: actions/upload-artifact@v4
               with:
                   name: data
                   path: ./data

.github/workflows/test.yaml

@@ -53,18 +53,12 @@ jobs:
 
             - name: Download artifact of test data
               if: matrix.python == '3.12'
-              uses: dawidd6/action-download-artifact@v2
+              uses: dawidd6/action-download-artifact@v9
               with:
                   workflow: prepare_test_data.yaml
                   name: data
                   path: ./data
 
-            - name: List the data directory
-              if: matrix.python == '3.12'
-              run: |
-                  ls -l ./data
-                  pwd
-
             - name: Test
               env:
                   MPLBACKEND: agg

README.md

@@ -5,10 +5,14 @@
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 [![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/spatialdata-io/badges/version.svg)](https://anaconda.org/conda-forge/spatialdata-io)
 
 [badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
 [link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
+[badge-pypi]: https://badge.fury.io/py/spatialdata-io.svg
+[link-pypi]: https://pypi.org/project/spatialdata-io/
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 
@@ -107,10 +111,10 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/scverse/spatialdata-io/issues
-[changelog]: https://spatialdata.scverse.org/projects/io/en/latest/changelog.html
-[link-docs]: https://spatialdata.scverse.org/projects/io/en/latest/
-[link-api]: https://spatialdata.scverse.org/projects/io/en/latest/api.html
-[link-cli]: https://spatialdata.scverse.org/projects/io/en/latest/cli.html
+[changelog]: https://spatialdata.scverse.org/projects/io/en/stable/changelog.html
+[link-docs]: https://spatialdata.scverse.org/projects/io/en/stable/
+[link-api]: https://spatialdata.scverse.org/projects/io/en/stable/api.html
+[link-cli]: https://spatialdata.scverse.org/projects/io/en/stable/cli.html
 [//]: # "numfocus-fiscal-sponsor-attribution"
 
 spatialdata-io is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).

src/spatialdata_io/__main__.py

@@ -620,8 +620,8 @@ def macsima_wrapper(
 @click.option("--name", "-n", type=str, help="name of the element to be stored")
 @click.option(
     "--data-axes",
-    type=click.Choice(["cyx", "czyx"], case_sensitive=False),
-    help="Axes of the data for image files. Valid values are 'cyx' and 'czyx'.",
+    type=str,
+    help="Axes of the data for image files. Valid values are permutations of 'cyx' and 'czyx'.",
 )
 @click.option(
     "--coordinate-system",
@@ -636,7 +636,9 @@ def read_generic_wrapper(
     data_axes: str | None = None,
     coordinate_system: str | None = None,
 ) -> None:
-    """Read generic data to SpatialData."""
+    """Read generic data to SpatialData"""
+    if data_axes is not None and "".join(sorted(data_axes)) not in ["cxy", "cxyz"]:
+        raise ValueError("data_axes must be a permutation of 'cyx' or 'czyx'.")
     generic_to_zarr(input=input, output=output, name=name, data_axes=data_axes, coordinate_system=coordinate_system)
 
 

src/spatialdata_io/converters/generic_to_zarr.py

@@ -68,14 +68,14 @@ def generic_to_zarr(
     )
 
     if output.exists():
-        sdata = SpatialData.read_zarr(output)
+        sdata = SpatialData.read(output)
         if name in sdata:
             raise ValueError(
                 f"Name {name} already exists in {output}; please provide a different name or delete the "
                 f"existing element."
             )
         sdata[name] = element
-        sdata.write_element(name, element_name=name)
+        sdata.write_element(element_name=name)
         print(f"Element {name} written to {output}")
     else:
         sdata = SpatialData.init_from_elements(elements={name: element})

src/spatialdata_io/readers/generic.py

@@ -52,6 +52,8 @@ def generic(
     -------
     Parsed spatial element.
     """
+    if isinstance(input, str):
+        input = Path(input)
     if coordinate_system is None:
         coordinate_system = DEFAULT_COORDINATE_SYSTEM
     if input.suffix in VALID_SHAPE_TYPES:

src/spatialdata_io/readers/visium_hd.py

@@ -381,7 +381,7 @@ def _get_bins(path_bins: Path) -> list[str]:
             affine = Affine(affine_matrix, input_axes=("x", "y"), output_axes=("x", "y"))
 
             # determine the size of the transformed image
-            bounding_box = get_extent(image)
+            bounding_box = get_extent(image, coordinate_system=dataset_id)
             x0, x1 = bounding_box["x"]
             y0, y1 = bounding_box["y"]
             x1 -= 1
@@ -412,7 +412,7 @@ def _get_bins(path_bins: Path) -> list[str]:
                 numpy_data, ProjectiveTransform(projective_shift).inverse, output_shape=transformed_shape, order=1
             )
             warped = np.round(warped * 255).astype(np.uint8)
-            warped = Image2DModel.parse(warped, dims=("y", "x", "c"), transformations={"global": affine}, rgb=True)
+            warped = Image2DModel.parse(warped, dims=("y", "x", "c"), transformations={dataset_id: affine}, rgb=True)
 
             # we replace the cytassist image with the warped image
             images[dataset_id + "_cytassist_image"] = warped
@@ -466,7 +466,7 @@ def _load_image(
 ) -> None:
     if path.exists():
         if path.suffix != ".btf":
-            data = imread(path, **imread_kwargs)
+            data = imread(path)
             if len(data.shape) == 4:
                 # this happens for the cytassist, hires and lowres images; the umi image doesn't need processing
                 data = data.squeeze()
@@ -486,7 +486,13 @@ def _load_image(
             )
 
         image = DataArray(data, dims=("c", "y", "x"))
-        parsed = Image2DModel.parse(image, scale_factors=scale_factors, rgb=None, **image_models_kwargs)
+        parsed = Image2DModel.parse(
+            image,
+            scale_factors=scale_factors,
+            rgb=None,
+            transformations={dataset_id: Identity()},
+            **image_models_kwargs,
+        )
         images[dataset_id + suffix] = parsed
     else:
         warnings.warn(f"File {path} does not exist, skipping it.", UserWarning, stacklevel=2)

tests/test_generic.py

@@ -87,7 +87,7 @@ def test_cli_read_generic_image_invalid_data_axes(runner: CliRunner) -> None:
             ],
         )
         assert result.exit_code != 0, result.output
-        assert "'invalid_axes' is not one of 'cyx', 'czyx'." in result.output
+        assert "data_axes must be a permutation of 'cyx' or 'czyx'." in result.exc_info[1].args[0]
 
 
 @pytest.mark.parametrize("cli", [True, False])