Update reqs and tests

.github/workflows/test.yml

@@ -58,7 +58,7 @@ jobs:
             - name: Install pip dependencies
               run: |
                   python -m pip install --upgrade pip
-                  pip install tox tox-gh-actions codecov
+                  pip install tox tox-gh-actions
 
             - name: Restore data cache
               id: data-cache

.pre-commit-config.yaml

@@ -69,7 +69,3 @@ repos:
           - id: rst-backticks
           - id: rst-directive-colons
           - id: rst-inline-touching-normal
-    - repo: https://github.com/PyCQA/doc8
-      rev: v1.1.1
-      hooks:
-          - id: doc8

docs/source/tutorials.rst

@@ -9,17 +9,17 @@ to a diverse set of different spatial datasets.
 
 .. nbgallery::
 
-    auto_tutorials/tutorial_imc
-    auto_tutorials/tutorial_seqfish
-    auto_tutorials/tutorial_slideseqv2
-    auto_tutorials/tutorial_visium_fluo
-    auto_tutorials/tutorial_visium_hne
-    auto_tutorials/tutorial_mibitof
-    auto_tutorials/tutorial_fouri
-    external_tutorials/tutorial_nanostring
-    external_tutorials/tutorial_vizgen
-    external_tutorials/tutorial_vizgen_mouse_liver
-    external_tutorials/tutorial_xenium
+    tutorials/tutorial_imc
+    tutorials/tutorial_seqfish
+    tutorials/tutorial_slideseqv2
+    tutorials/tutorial_visium_fluo
+    tutorials/tutorial_visium_hne
+    tutorials/tutorial_mibitof
+    tutorials/tutorial_fouri
+    tutorials/tutorial_nanostring
+    tutorials/tutorial_vizgen
+    tutorials/tutorial_vizgen_mouse_liver
+    tutorials/tutorial_xenium
 
 Advanced Tutorials
 ------------------
@@ -31,19 +31,19 @@ This section contains tutorials showcasing advanced :mod:`squidpy` functionaliti
 
 .. nbgallery::
 
-    auto_tutorials/tutorial_read_spatial
-    auto_tutorials/tutorial_image_container
-    external_tutorials/tutorial_napari
-    auto_tutorials/tutorial_image_container_zstacks
+    tutorials/tutorial_read_spatial
+    tutorials/tutorial_image_container
+    tutorials/tutorial_napari
+    tutorials/tutorial_image_container_zstacks
 
 External tutorials
 ------------------
 This section contains tutorials showcasing how :mod:`squidpy` can interface with external libraries.
 
 .. nbgallery::
 
-    external_tutorials/tutorial_tf
-    external_tutorials/tutorial_tangram
-    external_tutorials/tutorial_cellpose_segmentation
-    external_tutorials/tutorial_stardist
-    external_tutorials/tutorial_cellprofiler
+    tutorials/tutorial_tf
+    tutorials/tutorial_tangram
+    tutorials/tutorial_cellpose_segmentation
+    tutorials/tutorial_stardist
+    tutorials/tutorial_cellprofiler

docs/source/utils.py

@@ -17,7 +17,7 @@ def _fetch_notebooks(repo_url: str) -> None:
     def copy_files(repo_path: Union[str, Path]) -> None:
         repo_path = Path(repo_path)
 
-        for dirname in ["external_tutorials", "auto_examples", "auto_tutorials", "gen_modules"]:
+        for dirname in ["tutorials", "auto_examples", "gen_modules"]:
             rmtree(dirname, ignore_errors=True)  # locally re-cloning
             copytree(repo_path / "docs" / "source" / dirname, dirname)
 

requirements.txt

@@ -1,5 +1,5 @@
 aiohttp>=3.8.1
-anndata>=0.8
+anndata>=0.9
 cycler>=0.11.0
 dask-image>=0.5.0
 dask[array]>=2021.02.0
@@ -11,10 +11,10 @@ matplotlib-scalebar>=0.8.0
 networkx>=2.6.0
 numba>=0.56.4
 numpy>=1.23.0
-omnipath>=1.0.5
+omnipath @ git+https://github.com/saezlab/omnipath@master
 pandas>=1.5.0
 Pillow>=8.0.0
-scanpy>=1.9.2
+scanpy>=1.9.3
 scikit-image>=0.19
 scikit-learn>=0.24.0
 statsmodels>=0.12.0

squidpy/pl/_ligrec.py

@@ -267,6 +267,15 @@ def get_dendrogram(adata: AnnData, linkage: str = "complete") -> Mapping[str, An
         target_groups = adata["pvalues"].columns.get_level_values(1)
     if isinstance(target_groups, str):
         target_groups = (target_groups,)
+
+    if not isinstance(adata, AnnData):
+        for s in source_groups:
+            if s not in adata["means"].columns.get_level_values(0):
+                raise ValueError(f"Invalid cluster in source group: {s}.")
+        for t in target_groups:
+            if t not in adata["means"].columns.get_level_values(1):
+                raise ValueError(f"Invalid cluster in target group: {t}.")
+
     if title is None:
         title = "Receptor-ligand test"
 

tests/graph/test_ligrec.py

@@ -33,7 +33,9 @@ def test_adata_no_raw(self, adata: AnnData):
 
     def test_raw_has_different_n_obs(self, adata: AnnData):
         adata.raw = blobs(n_observations=adata.n_obs + 1)
-        with pytest.raises(ValueError, match=rf"Expected `{adata.n_obs}` cells in `.raw`"):
+        # raise below happend with anndata < 0.9
+        # with pytest.raises(ValueError, match=rf"Expected `{adata.n_obs}` cells in `.raw`"):
+        with pytest.raises(ValueError, match=rf"Index length mismatch: {adata.n_obs} vs. {adata.n_obs + 1}"):
             ligrec(adata, _CK)
 
     def test_invalid_cluster_key(self, adata: AnnData, interactions: Interactions_t):

tests/image/test_container.py

@@ -7,12 +7,13 @@
 
 import anndata as ad
 import dask.array as da
-import imageio
+import imageio.v3 as iio
 import numpy as np
 import pytest
 import tifffile
 import xarray as xr
 from anndata import AnnData
+from PIL import Image
 from pytest_mock import MockerFixture
 
 import squidpy as sq
@@ -152,11 +153,16 @@ def test_add_img_invalid_zdim(self, cont: ImageContainer):
     @pytest.mark.parametrize("ext", ["jpg", "png"])
     @pytest.mark.parametrize("shape", [(100, 200, 3), (100, 200, 1)])
     def test_load_ext(self, shape: Tuple[int, ...], ext: str, tmpdir):
-        img_orig = np.random.randint(low=0, high=255, size=shape, dtype=np.uint8)
         fname = tmpdir / f"tmp.{ext}"
-        imageio.imsave(str(fname), img_orig)
 
-        gt = imageio.imread(str(fname))  # because of compression, we load again
+        if shape == (100, 200, 1):
+            img = np.random.randint(256, size=(100, 200), dtype=np.uint8)
+            img_orig = Image.fromarray(img)
+        else:
+            img_orig = np.random.randint(low=0, high=255, size=shape, dtype=np.uint8)
+        iio.imwrite(str(fname), img_orig)
+
+        gt = iio.imread(str(fname))  # because of compression, we load again
         cont = ImageContainer(str(fname))
 
         np.testing.assert_array_equal(cont["image"].values.squeeze(), gt.squeeze())

tests/plotting/test_graph.py

@@ -143,8 +143,10 @@ def test_invalid_means_range_size(self, ligrec_result: Mapping[str, pd.DataFrame
             pl.ligrec(ligrec_result, means_range=[0, 1, 2])
 
     def test_invalid_clusters(self, ligrec_result: Mapping[str, pd.DataFrame]):
-        with pytest.raises(ValueError, match=r"No valid clusters have been selected."):
-            pl.ligrec(ligrec_result, source_groups="foo", target_groups="bar")
+        source_groups = "foo"
+        target_groups = "bar"
+        with pytest.raises(ValueError, match=r"Invalid cluster in .*"):
+            pl.ligrec(ligrec_result, source_groups=source_groups, target_groups=target_groups)
 
     def test_all_interactions_empty(self, ligrec_result: Mapping[str, pd.DataFrame]):
         empty = pd.DataFrame(np.nan, index=ligrec_result["pvalues"].index, columns=ligrec_result["pvalues"].columns)