Fix plotting tests for networkx >= 2.6.2 (scverse#1960)

* Update PAGA plots
* Update umap edges plot

scanpy/tests/test_paga.py

@@ -0,0 +1,88 @@
+from functools import partial
+from pathlib import Path
+
+from matplotlib import cm
+
+import scanpy as sc
+
+import pytest
+
+HERE: Path = Path(__file__).parent
+ROOT = HERE / '_images'
+FIGS = HERE / 'figures'
+
+
+@pytest.fixture(scope="module")
+def pbmc():
+    pbmc = sc.datasets.pbmc68k_reduced()
+    sc.tl.paga(pbmc, groups='bulk_labels')
+    pbmc.obs['cool_feature'] = pbmc[:, 'CST3'].X.squeeze()
+    return pbmc
+
+
+@pytest.mark.parametrize(
+    "test_id,func",
+    [
+        ("master_paga", sc.pl.paga),
+        ("master_paga_continuous", partial(sc.pl.paga, color="CST3")),
+        ("master_paga_continuous_obs", partial(sc.pl.paga, color="cool_feature")),
+        (
+            "master_paga_continuous_multiple",
+            partial(sc.pl.paga, color=['CST3', 'GATA2']),
+        ),
+        ("master_paga_compare", partial(sc.pl.paga_compare, legend_fontoutline=2)),
+        (
+            "master_paga_compare_continuous",
+            partial(sc.pl.paga_compare, color='CST3', legend_fontsize=5),
+        ),
+        (
+            "master_paga_compare_pca",
+            partial(sc.pl.paga_compare, basis='X_pca', legend_fontweight='normal'),
+        ),
+    ],
+)
+def test_paga_plots(image_comparer, pbmc, test_id, func):
+    save_and_compare_images = image_comparer(ROOT, FIGS, tol=30)
+    common = dict(threshold=0.5, max_edge_width=1.0, random_state=0, show=False)
+
+    func(pbmc, **common)
+    save_and_compare_images(test_id)
+
+
+def test_paga_pie(image_comparer, pbmc):
+    save_and_compare_images = image_comparer(ROOT, FIGS, tol=30)
+
+    colors = {
+        c: {cm.Set1(_): 0.33 for _ in range(3)}
+        for c in pbmc.obs["bulk_labels"].cat.categories
+    }
+    colors["Dendritic"] = {cm.Set2(_): 0.25 for _ in range(4)}
+
+    sc.pl.paga(pbmc, color=colors, colorbar=False)
+    save_and_compare_images('master_paga_pie')
+
+
+def test_paga_path(image_comparer, pbmc):
+    save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
+
+    pbmc.uns['iroot'] = 0
+    sc.tl.dpt(pbmc)
+    sc.pl.paga_path(
+        pbmc,
+        nodes=['Dendritic'],
+        keys=['HES4', 'SRM', 'CSTB'],
+        show=False,
+    )
+    save_and_compare_images('master_paga_path')
+
+
+def test_paga_compare(image_comparer):
+    # Tests that https://github.com/theislab/scanpy/issues/1887 is fixed
+    save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
+
+    pbmc = sc.datasets.pbmc3k_processed()
+    sc.tl.paga(pbmc, groups="louvain")
+
+    sc.pl.paga_compare(pbmc, basis="umap", show=False)
+
+    save_and_compare_images('master_paga_compare_pbmc3k')

scanpy/tests/test_plotting.py

@@ -1284,79 +1284,6 @@ def test_scatter_rep(tmpdir):
             assert "Error" in comp, f"{s1.outpth}, {s2.outpth} aren't supposed to match"
 
 
-def test_paga(image_comparer):
-    # Sometimes things shift a pixel or so, resulting in diffs up to ~27
-    # The 1px-edges aren’t that good actually as they’re ignored at this tol …
-    save_and_compare_images = image_comparer(ROOT, FIGS, tol=30)
-
-    pbmc = sc.datasets.pbmc68k_reduced()
-    sc.tl.paga(pbmc, groups='bulk_labels')
-
-    common = dict(threshold=0.5, max_edge_width=1.0, random_state=0, show=False)
-
-    # delete bulk_labels_colors to test the creation of color list by paga
-    del pbmc.uns['bulk_labels_colors']
-    sc.pl.paga(pbmc, **common)
-    save_and_compare_images('master_paga')
-
-    sc.pl.paga(pbmc, color='CST3', **common)
-    save_and_compare_images('master_paga_continuous')
-
-    pbmc.obs['cool_feature'] = pbmc[:, 'CST3'].X.squeeze()
-    sc.pl.paga(pbmc, color='cool_feature', **common)
-    save_and_compare_images('master_paga_continuous_obs')
-
-    sc.pl.paga(pbmc, color=['CST3', 'GATA2'], **common)
-    save_and_compare_images('master_paga_continuous_multiple')
-
-    sc.pl.paga_compare(pbmc, legend_fontoutline=2, **common)
-    save_and_compare_images('master_paga_compare')
-
-    sc.pl.paga_compare(pbmc, color='CST3', legend_fontsize=5, **common)
-    save_and_compare_images('master_paga_compare_continuous')
-
-    sc.pl.paga_compare(pbmc, basis='X_pca', legend_fontweight='normal', **common)
-    save_and_compare_images('master_paga_compare_pca')
-
-    colors = {
-        c: {cm.Set1(_): 0.33 for _ in range(3)}
-        for c in pbmc.obs["bulk_labels"].cat.categories
-    }
-    colors["Dendritic"] = {cm.Set2(_): 0.25 for _ in range(4)}
-
-    sc.pl.paga(pbmc, color=colors, colorbar=False)
-    save_and_compare_images('master_paga_pie')
-
-
-def test_paga_path(image_comparer):
-    save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
-
-    pbmc = sc.datasets.pbmc68k_reduced()
-    sc.tl.paga(pbmc, groups='bulk_labels')
-
-    pbmc.uns['iroot'] = 0
-    sc.tl.dpt(pbmc)
-    sc.pl.paga_path(
-        pbmc,
-        nodes=['Dendritic'],
-        keys=['HES4', 'SRM', 'CSTB'],
-        show=False,
-    )
-    save_and_compare_images('master_paga_path')
-
-
-def test_paga_compare(image_comparer):
-    # Tests that https://github.com/theislab/scanpy/issues/1887 is fixed
-    save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
-
-    pbmc = sc.datasets.pbmc3k_processed()
-    sc.tl.paga(pbmc, groups="louvain")
-
-    sc.pl.paga_compare(pbmc, basis="umap", show=False)
-
-    save_and_compare_images('master_paga_compare_pbmc3k')
-
-
 def test_no_copy():
     # https://github.com/theislab/scanpy/issues/1000
     # Tests that plotting functions don't make a copy from a view unless they