re-execute nbs to update numpy types

Author: lilyminium

doc/source/examples/analysis/alignment_and_rms/aligning_structure_to_another.ipynb

@@ -241,7 +241,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(21.712154435976014, 6.817293751703919)\n"
+      "(np.float64(21.712154435976014), 6.817293751703919)\n"
      ]
     }
    ],
@@ -294,7 +294,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(18.991465038265208, 16.603704620787127)\n"
+      "(np.float64(18.991465038265208), 16.603704620787127)\n"
      ]
     }
    ],
@@ -488,7 +488,7 @@
  "metadata": {
   "celltoolbar": "Raw Cell Format",
   "kernelspec": {
-   "display_name": "Python 3.9.15 ('mda-user-guide')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -502,7 +502,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.10.16"
   },
   "toc": {
    "base_numbering": 1,

doc/source/examples/analysis/polymers_and_membranes/hole2.ipynb

@@ -49,7 +49,17 @@
      "shell.execute_reply": "2021-05-19T06:01:12.662787Z"
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/analysis/encore/__init__.py:45: DeprecationWarning: Deprecation in version 2.8.0\n",
+      "MDAnalysis.analysis.encore is deprecated in favour of the MDAKit mdaencore (https://www.mdanalysis.org/mdaencore/) and will be removed in MDAnalysis version 3.0.0.\n",
+      "  warnings.warn(wmsg, category=DeprecationWarning)\n"
+     ]
+    }
+   ],
    "source": [
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -96,7 +106,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/pbarletta/mambaforge/envs/mda-user-guide/lib/python3.9/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behaviour will be changed in 3.0 to be the same as other readers\n",
+      "/Users/lily/micromamba/envs/mda-user-guide-dev/lib/python3.10/site-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.\n",
       "  warnings.warn(\"DCDReader currently makes independent timesteps\"\n"
      ]
     }
@@ -357,7 +367,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.15 ('mda-user-guide')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -371,7 +381,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.10.16"
   },
   "toc": {
    "base_numbering": 1,