removed squidpy as docs dependency; using scanpy instead

raphael-group · Dec 2, 2024 · 314a7e6 · 314a7e6
1 parent de8ae35
commit 314a7e6
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Showing 2 changed files with 5 additions and 15 deletions.
diff --git a/docs/source/notebooks/paste2_tutorial.ipynb b/docs/source/notebooks/paste2_tutorial.ipynb
@@ -11,8 +11,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import scanpy as sc\n",
-    "import seaborn as sns\n",
-    "import squidpy as sq"
+    "import seaborn as sns"
    ]
   },
   {
@@ -133,18 +132,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sq.pl.spatial_scatter(\n",
-    "    sliceA, frameon=False, shape=None, color=\"layer_guess_reordered\", figsize=(10, 10)\n",
-    ")\n",
-    "sq.pl.spatial_scatter(\n",
-    "    sliceB, frameon=False, shape=None, color=\"layer_guess_reordered\", figsize=(10, 10)\n",
-    ")\n",
-    "sq.pl.spatial_scatter(\n",
-    "    sliceC, frameon=False, shape=None, color=\"layer_guess_reordered\", figsize=(10, 10)\n",
-    ")\n",
-    "sq.pl.spatial_scatter(\n",
-    "    sliceD, frameon=False, shape=None, color=\"layer_guess_reordered\", figsize=(10, 10)\n",
-    ")"
+    "sc.pl.spatial(sliceA, color=\"layer_guess_reordered\", spot_size=100, frameon=False)\n",
+    "sc.pl.spatial(sliceB, color=\"layer_guess_reordered\", spot_size=100, frameon=False)\n",
+    "sc.pl.spatial(sliceC, color=\"layer_guess_reordered\", spot_size=100, frameon=False)\n",
+    "sc.pl.spatial(sliceD, color=\"layer_guess_reordered\", spot_size=100, frameon=False)"
    ]
   },
   {

diff --git a/pyproject.toml b/pyproject.toml
@@ -59,7 +59,6 @@ docs = [
     "sphinx-autodoc-annotation",
     "jupyterlab",
     "plotly",
-    "squidpy"
 ]
 
 [project.entry-points."napari.manifest"]