Re-run all notebooks

p-j-smith · Jul 30, 2023 · b6a46d3 · b6a46d3
1 parent 1ba6fb1
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Showing 11 changed files with 450 additions and 461 deletions.
diff --git a/notebooks/1-Introduction.ipynb b/notebooks/1-Introduction.ipynb
diff --git a/notebooks/10-PMFs.ipynb b/notebooks/10-PMFs.ipynb
diff --git a/notebooks/2-AssignLeaflets.ipynb b/notebooks/2-AssignLeaflets.ipynb
diff --git a/notebooks/3-FlipFlop.ipynb b/notebooks/3-FlipFlop.ipynb
@@ -100,7 +100,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "79ba561abf424bef94fe4050b9edaa90",
+       "model_id": "dfd6f2b1cbde41c781f9f47ecc2e62e3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -114,7 +114,7 @@
     {
      "data": {
       "text/plain": [
-       "<lipyphilic.lib.flip_flop.FlipFlop at 0x7f60d70dd430>"
+       "<lipyphilic.lib.flip_flop.FlipFlop at 0x11189b5d0>"
       ]
      },
      "execution_count": 5,
@@ -261,7 +261,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6d323250dd2443609f1910cc58db5bdb",
+       "model_id": "5db4dd90e1de4543bfbae73677fe16fd",
        "version_major": 2,
        "version_minor": 0
       },
@@ -275,7 +275,7 @@
     {
      "data": {
       "text/plain": [
-       "<lipyphilic.lib.flip_flop.FlipFlop at 0x7f6077dcd6a0>"
+       "<lipyphilic.lib.flip_flop.FlipFlop at 0x111986b10>"
       ]
      },
      "execution_count": 10,
@@ -518,9 +518,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:lpp]",
+   "display_name": "Python [conda env:lpp-tutorials]",
    "language": "python",
-   "name": "conda-env-lpp-py"
+   "name": "conda-env-lpp-tutorials-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -532,7 +532,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.11.4"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/notebooks/4-NeighbourCounts.ipynb b/notebooks/4-NeighbourCounts.ipynb
diff --git a/notebooks/5-NeighbourClusters.ipynb b/notebooks/5-NeighbourClusters.ipynb
@@ -44,15 +44,15 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A\n",
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A\n",
       "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D\n",
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D\n",
       "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G\n",
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G\n",
       "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R\n",
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R\n",
       "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n",
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: T\n",
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: T\n",
       "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n"
      ]
     }
@@ -148,7 +148,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "564e422341314a5bb7c253778f7e4e45",
+       "model_id": "440ab038f63e481e8008628df9cb767b",
        "version_major": 2,
        "version_minor": 0
       },
@@ -163,14 +163,14 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/paul/git-repos/mdanalysis/package/MDAnalysis/coordinates/base.py:887: UserWarning: Reader has no dt information, set to 1.0 ps\n",
-      "  warnings.warn(\"Reader has no dt information, set to 1.0 ps\")\n"
+      "/Users/paul/mambaforge/envs/lpp-tutorials/lib/python3.11/site-packages/lipyphilic/lib/base.py:192: UserWarning: Reader has no dt information, set to 1.0 ps\n",
+      "  self.times[i] = ts.time\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<lipyphilic.lib.neighbours.Neighbours at 0x7f65c6ea40a0>"
+       "<lipyphilic.lib.neighbours.Neighbours at 0x16652ded0>"
       ]
      },
      "execution_count": 6,
@@ -210,7 +210,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a3646528952141488e30a69f09f1bf4c",
+       "model_id": "18b45e2416564f87adb4076cab87b24d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -300,7 +300,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a698c0e574b2467d9d8aead1874832b6",
+       "model_id": "20e6e27764704eacad483103f6d22268",
        "version_major": 2,
        "version_minor": 0
       },
@@ -433,7 +433,7 @@
     {
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-       "model_id": "79ad16c9bf9e44628feeee2c6d9ab1a7",
+       "model_id": "91c2e855b650488f9911c6add8c23c10",
        "version_major": 2,
        "version_minor": 0
       },
@@ -447,7 +447,7 @@
     {
      "data": {
       "text/plain": [
-       "<lipyphilic.lib.assign_leaflets.AssignLeaflets at 0x7f65ca610610>"
+       "<lipyphilic.lib.assign_leaflets.AssignLeaflets at 0x166414bd0>"
       ]
      },
      "execution_count": 16,
@@ -502,7 +502,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b6e2a6346ffd4477ac72769e5b65ff01",
+       "model_id": "1cfd3a3d3f8941cbbb71b38c7c18814b",
        "version_major": 2,
        "version_minor": 0
       },
@@ -562,9 +562,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:lpp]",
+   "display_name": "Python [conda env:lpp-tutorials]",
    "language": "python",
-   "name": "conda-env-lpp-py"
+   "name": "conda-env-lpp-tutorials-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -576,7 +576,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.11.4"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/notebooks/6-Registration.ipynb b/notebooks/6-Registration.ipynb
diff --git a/notebooks/7-MSD.ipynb b/notebooks/7-MSD.ipynb