fixes

.github/workflows/examples.yml

@@ -35,5 +35,5 @@ jobs:
     
     - name: Ensure notebooks complete without errors with pytest and nbmake
       run: |
-        pip install '.[tests]'
+        pip install '.[all]'
         pytest --nbmake examples/*ipynb

examples/customized_meteor_diffmap.ipynb

@@ -15,15 +15,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# ruff: noqa: T201\n",
+    "\n",
     "import numpy as np\n",
     "import reciprocalspaceship as rs\n",
+    "from matplotlib import pyplot as plt\n",
     "\n",
+    "from meteor.diffmaps import compute_difference_map, max_negentropy_kweighted_difference_map\n",
     "from meteor.rsmap import Map\n",
-    "from meteor.diffmaps import max_negentropy_kweighted_difference_map, compute_difference_map\n",
     "from meteor.tv import tv_denoise_difference_map\n",
-    "from meteor.validate import map_negentropy\n",
-    "\n",
-    "from matplotlib import pyplot as plt"
+    "from meteor.validate import map_negentropy"
    ]
   },
   {
@@ -132,7 +133,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "optimal k-parameter: 0.01 / negentropy: 0.00127\n"
+      "optimal k-parameter: 0.01, negentropy: 0.00127\n"
      ]
     }
    ],
@@ -142,7 +143,7 @@
     ")\n",
     "kewighted_negentropy = map_negentropy(k_weighted_diffmap)\n",
     "\n",
-    "print(f\"optimal k-parameter: {kweight_parameter} / negentropy: {kewighted_negentropy:.5f}\")"
+    "print(f\"optimal k-parameter: {kweight_parameter}, negentropy: {kewighted_negentropy:.5f}\")"
    ]
   },
   {
@@ -172,7 +173,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -187,7 +188,7 @@
     }
    ],
    "source": [
-    "plt.figure(figsize=(8,3))\n",
+    "plt.figure(figsize=(8, 3))\n",
     "\n",
     "plt.xlabel(\"TV weight\")\n",
     "plt.ylabel(\"map negentropy\")\n",
@@ -196,8 +197,8 @@
     "# points are not sampled in order of increasing TV weight, so we have to order them\n",
     "sort_order = np.argsort(metadata.tv_weights_scanned)\n",
     "plt.plot(\n",
-    "    np.array(metadata.tv_weights_scanned)[sort_order], \n",
-    "    np.array(metadata.negentropy_at_weights)[sort_order]\n",
+    "    np.array(metadata.tv_weights_scanned)[sort_order],\n",
+    "    np.array(metadata.negentropy_at_weights)[sort_order],\n",
     ")\n",
     "\n",
     "plt.scatter(\n",
@@ -228,7 +229,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -34,6 +34,9 @@ tests = [
     "pytest-xdist",
     "nbmake",
 ]
+notebooks = [
+    "matplotlib",
+]
 
 [project.scripts]
 "meteor.diffmap" = "meteor.scripts.compute_difference_map:main"