Fix squidpy.pl.extract on views (#663)

* Fix `squidpy.pl.extract` on views

* Fix docs linter

docs/source/conf.py

@@ -136,7 +136,13 @@
     "enchant.tokenize.MentionFilter",
 ]
 # see the solution from: https://github.com/sphinx-doc/sphinx/issues/7369
-user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"
+linkcheck_ignore = [
+    # 403 Client Error
+    "https://doi.org/10.1126/science.aar7042",
+    "https://doi.org/10.1126/science.aau5324",
+    "https://doi.org/10.1093/bioinformatics/btab164",
+    "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716260/",
+]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

squidpy/pl/_graph.py

@@ -87,7 +87,7 @@ def centrality_scores(
     df[cluster_key] = df.index.values
 
     clusters = adata.obs[cluster_key].cat.categories
-    palette = _get_palette(adata, cluster_key=cluster_key, categories=clusters)
+    palette = _get_palette(adata, cluster_key=cluster_key, categories=clusters, palette=palette)
 
     score = scores if score is None else score
     score = _assert_non_empty_sequence(score, name="centrality scores")
@@ -292,7 +292,7 @@ def ripley(
         legend_kwargs.setdefault("bbox_to_anchor", (1, 0.5))
 
     categories = adata.obs[cluster_key].cat.categories
-    palette = _get_palette(adata, cluster_key=cluster_key, categories=categories) if palette is None else palette
+    palette = _get_palette(adata, cluster_key=cluster_key, categories=categories, palette=palette)
     if ax is None:
         fig, ax = plt.subplots(figsize=figsize, dpi=dpi)
     else:

squidpy/pl/_utils.py

@@ -167,13 +167,14 @@ def _warn_if_exists_obs(adata: AnnData, obs_key: str) -> None:
             for col in obsm.columns:
                 obs_key = f"{prefix[i]}{col}"
                 _warn_if_exists_obs(tmp_adata, obs_key)
-                tmp_adata.obs[obs_key] = obsm.loc[:, col]
+                tmp_adata.obs[obs_key] = obsm[col]
         else:
             # names will be integer indices
             for j in range(obsm.shape[1]):
                 obs_key = f"{prefix[i]}{j}"
                 _warn_if_exists_obs(tmp_adata, obs_key)
-                tmp_adata.obs[obs_key] = obsm[:, j]
+                # https://github.com/scverse/squidpy/issues/646
+                tmp_adata.obs[obs_key] = pd.Series(obsm[:, j], index=tmp_adata.obs_names)
 
     return tmp_adata
 

tests/plotting/test_image.py

@@ -1,5 +1,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
 import pytest
 import scanpy as sc
 from anndata import AnnData
@@ -67,15 +68,12 @@ def test_transpose_channelwise(self, small_cont_4d: ImageContainer, transpose: b
         assert res is None, res
 
 
-def test_extract(adata: AnnData, cont: ImageContainer, caplog):
-    """
-    Calculate features and extract columns to obs
-    """
-    # get obsm
+@pytest.mark.parametrize("is_view", [False, True])
+def test_extract(adata: AnnData, cont: ImageContainer, caplog, is_view: bool):
     sq.im.calculate_image_features(adata, cont, features=["summary"])
 
     # extract columns (default values)
-    extr_adata = sq.pl.extract(adata)
+    extr_adata = sq.pl.extract(adata[:10] if is_view else adata)
     # Test that expected columns exist
     for col in [
         "summary_ch-0_quantile-0.9",
@@ -88,15 +86,15 @@ def test_extract(adata: AnnData, cont: ImageContainer, caplog):
         "summary_ch-2_quantile-0.5",
         "summary_ch-2_quantile-0.1",
     ]:
-        assert col in extr_adata.obs.columns
+        np.testing.assert_array_equal(np.isfinite(extr_adata.obs[col]), True)
 
     # get obsm that is a numpy array
     adata.obsm["pca_features"] = sc.pp.pca(np.asarray(adata.obsm["img_features"]), n_comps=3)
     # extract columns
-    extr_adata = sq.pl.extract(adata, obsm_key="pca_features", prefix="pca_features")
+    extr_adata = sq.pl.extract(adata[3:10] if is_view else adata, obsm_key="pca_features", prefix="pca_features")
     # Test that expected columns exist
     for col in ["pca_features_0", "pca_features_1", "pca_features_2"]:
-        assert col in extr_adata.obs.columns
+        np.testing.assert_array_equal(np.isfinite(extr_adata.obs[col]), True)
 
     # extract multiple obsm at once (no prefix)
     extr_adata = sq.pl.extract(adata, obsm_key=["img_features", "pca_features"])
@@ -115,12 +113,4 @@ def test_extract(adata: AnnData, cont: ImageContainer, caplog):
         "1",
         "2",
     ]:
-        assert col in extr_adata.obs.columns
-
-    # TODO: test similarly to ligrec
-    # currently logging to stderr, and not captured by caplog
-    # extract obsm twice and make sure that warnings are issued
-    # with caplog.at_level(logging.WARNING):
-    #    extr2_adata = sq.pl.extract(extr_adata, obsm_key=['pca_features'])
-    #    log = caplog.text
-    #    assert "will be overwritten by extract" in log
+        np.testing.assert_array_equal(np.isfinite(extr_adata.obs[col]), True)

tox.ini

@@ -186,7 +186,7 @@ basepython = python3.9
 deps = -r{toxinidir}/docs/requirements.txt
 skip_install = true
 allowlist_externals = sphinx-build
-passenv = SQUIDPY_DOWNLOAD_NOTEBOOKS
+passenv = SQUIDPY_DOWNLOAD_NOTEBOOKS,PYENCHANT_LIBRARY_PATH
 commands =
     sphinx-build -W --keep-going -b spelling {toxinidir}/docs/source {toxinidir}/docs/build/spellcheck
     sphinx-build -q -W --keep-going -b linkcheck {toxinidir}/docs/source {toxinidir}/docs/build/linkcheck