test: make pre-release tests work (#1071)

summary: changed the test setup to use uv add to install dependencies with a single solve. This causes anndata-git and pandas >=3 to actually be used and therefore tested.

Fixed all tests affected by this
* ci: change to uv add to install dependencies with single solve
tests: partial fix of tests failing due to anndata-git and pandas >=3

* test: fix remainder tests failing due to anndata-git, pandas>=3 and dask 2025.2.0.

* test: add array_api marker to be ignored.

* docs_build: use uv instead of make for docs build


---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: flying-sheep

.github/workflows/release.yaml

@@ -9,9 +9,9 @@ jobs:
         runs-on: ubuntu-latest
         if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v6
             - name: Set up Python 3.12
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v6
               with:
                   python-version: "3.12"
                   cache: pip

.github/workflows/test.yaml

@@ -13,7 +13,7 @@ jobs:
         runs-on: ${{ matrix.os }}
         defaults:
             run:
-                shell: bash -e {0}
+                shell: bash  # bash also on windows
 
         strategy:
             fail-fast: false
@@ -32,29 +32,27 @@ jobs:
             PRERELEASE: ${{ matrix.prerelease }}
 
         steps:
-            - uses: actions/checkout@v2
-            - uses: astral-sh/setup-uv@v5
+            - uses: actions/checkout@v6
+            - uses: astral-sh/setup-uv@v7
               id: setup-uv
               with:
                   version: "latest"
                   python-version: ${{ matrix.python }}
             - name: Install dependencies
               run: |
                   if [[ "${PRERELEASE}" == "allow" ]]; then
-                    uv sync --extra test
-                    : # uv sync --extra test --prerelease ${PRERELEASE}
-                    uv pip install git+https://github.com/scverse/anndata.git
-                    uv pip install --prerelease allow pandas
-                  else
-                    uv sync --extra test
+                    sed -i '' 's/requires-python.*//' pyproject.toml # otherwise uv complains that anndata requires python>=3.12 and we only do >=3.11 😱
+                    uv add git+https://github.com/scverse/anndata.git
+                    uv add pandas>=3.dev0
                   fi
                   if [[ -n "${DASK_VERSION}" ]]; then
                     if [[ "${DASK_VERSION}" == "latest" ]]; then
-                      uv pip install --upgrade dask
+                      uv add dask
                     else
-                      uv pip install dask==${DASK_VERSION}
+                      uv add dask==${DASK_VERSION}
                     fi
                   fi
+                  uv sync --group=test
             - name: Test
               env:
                   MPLBACKEND: agg
@@ -63,7 +61,7 @@ jobs:
               run: |
                   uv run pytest --cov --color=yes --cov-report=xml
             - name: Upload coverage to Codecov
-              uses: codecov/codecov-action@v4
+              uses: codecov/codecov-action@v5
               with:
                   name: coverage
                   verbose: true

.readthedocs.yaml

@@ -1,19 +1,22 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
+    os: ubuntu-24.04
     tools:
-        python: "3.11"
-sphinx:
-    configuration: docs/conf.py
-    fail_on_warning: true
-python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - docs
-              - torch
+        python: "3.13"
+    jobs:
+        post_checkout:
+            # unshallow so version can be derived from tag
+            - git fetch --unshallow || true
+        create_environment:
+            - asdf plugin add uv
+            - asdf install uv latest
+            - asdf global uv latest
+        build:
+            html:
+                - uv sync --group=docs --extra=torch
+                - uv run make --directory=docs html
+                - mv docs/_build $READTHEDOCS_OUTPUT
 submodules:
     include:
         - "docs/tutorials/notebooks"

pyproject.toml

@@ -51,8 +51,17 @@ dependencies = [
     "xarray-spatial>=0.3.5",
     "zarr>=3.0.0",
 ]
-
 [project.optional-dependencies]
+torch = [
+    "torch"
+]
+extra  = [
+    "napari-spatialdata[all]",
+    "spatialdata-plot",
+    "spatialdata-io",
+]
+
+[dependency-groups]
 dev = [
     "bump2version",
     "sentry-prevent-cli",
@@ -80,38 +89,31 @@ benchmark = [
     "asv",
     "memray",
 ]
-torch = [
-    "torch"
-]
-extra  = [
-    "napari-spatialdata[all]",
-    "spatialdata-plot",
-    "spatialdata-io",
-]
 
 [tool.coverage.run]
 source = ["spatialdata"]
 omit = [
     "**/test_*.py",
 ]
 
-[tool.pytest.ini_options]
+[tool.pytest]
 testpaths = ["tests"]
-xfail_strict = true
+strict = true
 addopts = [
-#    "-Werror",  # if 3rd party libs raise DeprecationWarnings, just use filterwarnings below
     "--import-mode=importlib",  # allow using test files with same name
     "-s",  # print output from tests
 ]
 # These are all markers coming from xarray, dask or anndata. Added here to silence warnings.
 markers = [
     "slow: marks tests as slow (deselect with '-m \"not slow\"')",
     "gpu: run test on GPU using CuPY.",
+    "array_api: used by anndata.tests.helpers, not us",
     "skip_with_pyarrow_strings: skipwhen pyarrow string conversion is turned on",
 ]
 # info on how to use this https://stackoverflow.com/questions/57925071/how-do-i-avoid-getting-deprecationwarning-from-inside-dependencies-with-pytest
 filterwarnings = [
-    #     "ignore:.*U.*mode is deprecated:DeprecationWarning",
+    # "error",  # if 3rd party libs raise DeprecationWarnings, TODO: filter them individually below
+    # "ignore:.*U.*mode is deprecated:DeprecationWarning",
 ]
 
 [tool.jupytext]

tests/core/test_centroids.py

@@ -183,7 +183,7 @@ def test_get_centroids_invalid_element(images):
         region_key="region",
         instance_key="instance_id",
     )
-    with pytest.raises(ValueError, match="The object type <class 'anndata._core.anndata.AnnData'> is not supported."):
+    with pytest.raises(ValueError, match=r"The object type <class 'anndata.*AnnData'> is not supported"):
         get_centroids(adata)
 
 

tests/io/test_pyramids_performance.py

@@ -88,4 +88,8 @@ def test_write_image_multiscale_performance(sdata_with_image: SpatialData, tmp_p
         num_chunks_all_scales.item(),
         num_chunks_all_scales.item() + 1,
     }
-    assert actual_num_chunk_reads == num_chunks_scale0.item()
+    # We set a range here as with certain dask versions more reads occur. This checks whether the range is still
+    # acceptable, if not then we can check whether it is due to SpatialData or Dask and act accordingly.
+    # In addition, we could do use a mock side effect to check that the entry points from within spatialdata are within
+    # the expected range.
+    assert actual_num_chunk_reads in range(0, num_chunks_scale0.item() * 2 + 1)

tests/io/test_readwrite.py

@@ -13,6 +13,7 @@
 import zarr
 from anndata import AnnData
 from numpy.random import default_rng
+from packaging.version import Version
 from shapely import MultiPolygon, Polygon
 from upath import UPath
 from zarr.errors import GroupNotFoundError
@@ -1067,7 +1068,7 @@ def test_read_sdata(tmp_path: Path, points: SpatialData) -> None:
     assert_spatial_data_objects_are_identical(sdata_from_path, sdata_from_zarr_group)
 
 
-def test_sdata_with_nan_in_obs() -> None:
+def test_sdata_with_nan_in_obs(tmp_path: Path) -> None:
     """Test writing SpatialData with mixed string/NaN values in obs works correctly.
 
     Regression test for https://github.com/scverse/spatialdata/issues/399
@@ -1096,14 +1097,18 @@ def test_sdata_with_nan_in_obs() -> None:
     assert sdata["table"].obs["column_only_region1"].iloc[1] is np.nan
     assert np.isnan(sdata["table"].obs["column_only_region2"].iloc[0])
 
-    with tempfile.TemporaryDirectory() as tmpdir:
-        path = os.path.join(tmpdir, "data.zarr")
-        sdata.write(path)
-
-        sdata2 = SpatialData.read(path)
-        assert "column_only_region1" in sdata2["table"].obs.columns
-        assert sdata2["table"].obs["column_only_region1"].iloc[0] == "string"
-        assert sdata2["table"].obs["column_only_region2"].iloc[1] == 3
-        # After round-trip, NaN in object-dtype column becomes string "nan"
-        assert sdata2["table"].obs["column_only_region1"].iloc[1] == "nan"
-        assert np.isnan(sdata2["table"].obs["column_only_region2"].iloc[0])
+    path = tmp_path / "data.zarr"
+    sdata.write(path)
+
+    sdata2 = SpatialData.read(path)
+    assert "column_only_region1" in sdata2["table"].obs.columns
+    r1 = sdata2["table"].obs["column_only_region1"]
+    r2 = sdata2["table"].obs["column_only_region2"]
+
+    assert r1.iloc[0] == "string"
+    assert r2.iloc[1] == 3
+    if Version(pd.__version__) >= Version("3"):
+        assert pd.isna(r1.iloc[1])
+    else:  # After round-trip, NaN in object-dtype column becomes string "nan" on pandas 2
+        assert r1.iloc[1] == "nan"
+    assert np.isnan(r2.iloc[0])

tests/models/test_models.py

@@ -18,6 +18,7 @@
 from dask.dataframe import DataFrame as DaskDataFrame
 from geopandas import GeoDataFrame
 from numpy.random import default_rng
+from packaging.version import Version
 from shapely.geometry import MultiPolygon, Point, Polygon
 from shapely.io import to_ragged_array
 from spatial_image import to_spatial_image
@@ -311,7 +312,7 @@ def test_shapes_model(self, model: ShapesModel, path: Path) -> None:
     @pytest.mark.parametrize("model", [PointsModel])
     @pytest.mark.parametrize("instance_key", [None, "cell_id"])
     @pytest.mark.parametrize("feature_key", [None, "target"])
-    @pytest.mark.parametrize("typ", [np.ndarray, pd.DataFrame, dd.DataFrame])
+    @pytest.mark.parametrize("typ", [np.ndarray, pd.DataFrame, dd.DataFrame], ids=["numpy", "pandas", "dask"])
     @pytest.mark.parametrize("is_annotation", [True, False])
     @pytest.mark.parametrize("is_3d", [True, False])
     @pytest.mark.parametrize("coordinates", [None, {"x": "A", "y": "B", "z": "C"}])
@@ -937,12 +938,12 @@ def test_categories_on_partitioned_dataframe(sdata_blobs: SpatialData):
     assert np.array_equal(df["genes"].to_numpy(), ddf_parsed["genes"].compute().to_numpy())
     assert set(df["genes"].cat.categories.tolist()) == set(ddf_parsed["genes"].compute().cat.categories.tolist())
 
-    # two behavior to investigate later/report to dask (they originate in dask)
-    # TODO: df['genes'].cat.categories has dtype 'object', while ddf_parsed['genes'].compute().cat.categories has dtype
-    #  'string'
-    # this problem should disappear after pandas 3.0 is released
-    assert df["genes"].cat.categories.dtype == "object"
+    if Version(pd.__version__) >= Version("3"):
+        assert df["genes"].cat.categories.dtype == "string"
+    else:
+        assert df["genes"].cat.categories.dtype == "object"
     assert ddf_parsed["genes"].compute().cat.categories.dtype == "string"
 
+    # behavior to investigate later/report to dask
     # TODO: the list of categories are not preserving the order
     assert df["genes"].cat.categories.tolist() != ddf_parsed["genes"].compute().cat.categories.tolist()