Merge pull request #24 from metaspace2020/fix-dependencies

Fix dependencies

Author: aeisenbarth

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v4
               with:
-                  python-version: "3.9"
+                  python-version: "3.11"
             - name: Install dependencies
               run: |
                   python -m pip install --upgrade pip wheel

.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Install dependencies
       run: |

.github/workflows/tests.yml

@@ -21,7 +21,7 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python-version: ["3.9", "3.10", "3.11"]
+                python-version: ["3.11", "3.12", "3.13"]
                 os: [ubuntu-latest]
 
         steps:

docs/conf.py

@@ -66,7 +66,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-# Doctest allows to execute example code with directives "" using "make doctest".
+# Doctest allows to execute example code with directives "testcode" using "make doctest".
 # Compared to the Python standard library module, this extension detects code blocks
 # without requiring ">>> " as prefix.
 # Remove doctest flags within the examples ("#doctest: +SKIP"), not to distract readers.

docs/examples.rst

@@ -31,7 +31,11 @@ Plain AnnData with ScanPy
 SquidPy
 -------
 
+.. note:: Example may not work
+   SquidPy (0.4.1) is not anymore compatible with the dependencies used in this project.
+
 .. testcode::
+   :skipif: True
 
    from metaspace_converter import metaspace_to_anndata
    import squidpy as sq
@@ -92,26 +96,21 @@ Here using a reversed colormap which better represents intense values on bright
 
    # Workaround: spatialdata-plot currently does not use points transformation
    sdata.points["maldi_points"] = sdata.transform_element_to_coordinate_system(
-       sdata.points["maldi_points"], "global"
+       "maldi_points", "global"
    )
 
    (
        sdata.pl.render_images("optical_image")
        .pl.render_points(
            "maldi_points",
-           color=sdata.table.var.index[0],
+           color=sdata.tables["table"].var.index[0],
            alpha=1,
            size=2,
            cmap="viridis_r",
        )
-       .pl.show(title=sdata.table.var.index[0], coordinate_systems="global")
+       .pl.show(title=sdata.tables["table"].var.index[0], coordinate_systems="global")
    )
 
-.. testoutput::
-   :hide:
-
-   ...
-
 .. image:: ./_static/img/example_img_sd.png
    :alt: Visualization with SpatialData
 

metaspace_converter/constants.py

@@ -20,6 +20,7 @@ class COL:
 MICROMETER: Final = "micrometer"
 OPTICAL_IMAGE_KEY: Final = "optical_image"
 POINTS_KEY: Final = "maldi_points"
+TABLE_KEY: Final = "table"
 REGION_KEY: Final = "region"
 INSTANCE_KEY: Final = "instance_id"
 X: Final = "x"

metaspace_converter/tests/to_spatialdata_test.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+import xarray as xr
 from multiscale_spatial_image import MultiscaleSpatialImage
 
 from metaspace_converter.constants import COORD_SYS_GLOBAL, OPTICAL_IMAGE_KEY, POINTS_KEY, X, Y
@@ -48,18 +49,18 @@ def test_metaspace_to_spatialdata(
     )
 
     # Check table
-    assert actual.table is not None
+    assert "table" in actual.tables
     dataset = sm.dataset(id=dataset_id)
-    assert actual.table.n_obs == np.prod(get_ion_image_shape(dataset))
-    assert actual.table.n_vars == len(dataset.annotations(fdr=fdr, database=database))
+    assert actual.tables["table"].n_obs == np.prod(get_ion_image_shape(dataset))
+    assert actual.tables["table"].n_vars == len(dataset.annotations(fdr=fdr, database=database))
     assert {
         COL.ion_image_shape_y,
         COL.ion_image_shape_x,
         COL.ion_image_pixel_y,
         COL.ion_image_pixel_x,
-    }.issubset(actual.table.obs.columns)
-    assert np.all(actual.table.var["fdr"] <= fdr)
-    actual_database = actual.table.uns[METASPACE_KEY]["metaspace_to_anndata_parameters"]["database"]
+    }.issubset(actual.tables["table"].obs.columns)
+    assert np.all(actual.tables["table"].var["fdr"] <= fdr)
+    actual_database = actual.tables["table"].uns[METASPACE_KEY]["metaspace_to_anndata_parameters"]["database"]
     assert actual_database == list(database)
 
     # Check optical image, if requested
@@ -72,7 +73,7 @@ def test_metaspace_to_spatialdata(
     if add_optical_image and add_points:
         # All points should be positioned within the image bounds.
         points_over_image = actual.transform_element_to_coordinate_system(
-            actual.points[points_name_added], target_coordinate_system=COORD_SYS_GLOBAL
+            points_name_added, target_coordinate_system=COORD_SYS_GLOBAL
         )[[Y, X]].compute()
         image_min = (0, 0)
         image_max = _get_image_shape(actual.images[optical_name_added])
@@ -83,7 +84,7 @@ def test_metaspace_to_spatialdata(
 
 
 def _get_image_shape(image: MultiscaleSpatialImage) -> tuple[int, int]:
-    assert isinstance(image, MultiscaleSpatialImage)
+    assert isinstance(image, xr.DataTree)
     sizes = image["scale0"].sizes
     return sizes["y"], sizes["x"]
 

metaspace_converter/to_spatialdata.py

@@ -19,6 +19,7 @@
     OPTICAL_IMAGE_KEY,
     POINTS_KEY,
     REGION_KEY,
+    TABLE_KEY,
     XY,
     YX,
     YXC,
@@ -40,6 +41,7 @@ def metaspace_to_spatialdata(
     optical_name_added: str = OPTICAL_IMAGE_KEY,
     add_points: bool = True,
     points_name_added: str = POINTS_KEY,
+    table_name: str = TABLE_KEY,
     sm: Optional[SMInstance] = None,
     **annotation_filter,
 ) -> SpatialData:
@@ -67,7 +69,8 @@ def metaspace_to_spatialdata(
         add_points: Whether to also add ion image pixel coordinates as SpatialData points. This
             allows to spatially visualize the ion image values. If False, only ion intensities are
             added to the table and coordinates are added to ``obs``.
-        points_name_added: Name of the element where to store the points in the SpatialData object
+        points_name: Name of the element where to store the points in the SpatialData object
+        table_name_added: The name for the SpatialData table to which annotations will be saved.
         sm: Optionally a cached SMInstance
         annotation_filter: Additional keyword arguments passed to the METASPACE API.
 
@@ -101,7 +104,7 @@ def metaspace_to_spatialdata(
         **annotation_filter,
     )
     table = _create_spatialdata_table(adata)
-    sdata = SpatialData(table=table)
+    sdata = SpatialData(tables={table_name: table})
 
     # Create image
     if has_optical_image(dataset) and add_optical_image:

pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "metaspace-converter"
-version = "1.1.1"
+version = "1.1.2"
 authors = [
     {name = "Tim Daniel Rose", email = "tim.rose@embl.de"},
     {name = "Andreas Eisenbarth", email = "andreas.eisenbarth@embl.de"},
 ]
 description = "Convert Metaspace datasets to AnnData"
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 license = {text = "Apache-2.0"}
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
@@ -21,27 +21,29 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
     "anndata>=0.9.2",
     "metaspace2020>=2.0.6",
     "numpy",
     "pandas",
-    "spatial-image>=0.3",
-    "spatialdata>=0.0.15",
+    "spatial-image>=1.1.0",
+    "spatialdata>=0.7.2",
 ]
 dynamic = ["readme"]
 
 [project.optional-dependencies]
 test = [
-    "multiscale-spatial-image>=0.11",
+    "multiscale-spatial-image>=2.0.0",
     "pytest>=7.2",
     "pytest-cov>=4.1",
+    "scikit-image>=0.22", # Avoid binary incompatibility with Numpy 2.0
 ]
 docs = [
+    "anndata~=0.12.10",
     "sphinx~=7.2",
     "sphinx-autodoc-typehints",
     "sphinx-codeautolink",
@@ -51,9 +53,9 @@ docs = [
 #    "myst-nb",
 #    "ipython~=8.6.0",
     # For example code in documentation
-    "scanpy~=1.9.6",
-    "spatialdata-plot~=0.0.6",
-    "squidpy~=1.3.1",
+    "scanpy~=1.11.5",
+    "spatialdata-plot~=0.2.9",
+    #"squidpy~=1.4.1", # Has not been updated to anndata>0.10.9, which is incompatible with SpatialData
 ]
 
 [project.urls]