Fix NB 2 for OpenMM 8.1

Also, bump CI versions.

Author: dwhswenson

.github/workflows/ci.yml

@@ -21,9 +21,10 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - 3.7
           - 3.8
           - 3.9
+          - 3.10
+          - 3.11
 
     steps:
       - uses: actions/checkout@v2

2_tps_analysis_tutorial.ipynb

@@ -327,10 +327,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# with OpenMM 8.0 or earlier: timestep = engine.snapshot_timestep\n",
+    "# (also should work for data generated with OpenMM 8.1 or later)\n",
+    "timestep = 2.0 * openmm.unit.femtosecond\n",
     "path_lengths = [len(step.active[0].trajectory) for step in flexible.steps]\n",
     "plt.hist(path_lengths, bins=40, alpha=0.5);\n",
-    "print(\"Maximum:\", max(path_lengths), \"(\"+str(max(path_lengths)*engine.snapshot_timestep)+\")\")\n",
-    "print(\"Average:\", \"{0:.2f}\".format(np.mean(path_lengths)), \"(\"+(np.mean(path_lengths)*engine.snapshot_timestep).format(\"%.3f\")+\")\")\n",
+    "print(\"Maximum:\", max(path_lengths), \"(\"+str(max(path_lengths)*timestep)+\")\")\n",
+    "print(\"Average:\", \"{0:.2f}\".format(np.mean(path_lengths)), \"(\"+(np.mean(path_lengths)*timestep).format(\"%.3f\")+\")\")\n",
     "plt.ylabel(\"Count\")\n",
     "plt.xlabel(\"Path length (Frames)\");"
    ]
@@ -468,7 +471,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -482,7 +485,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.9.13"
   },
   "toc": {
    "base_numbering": 1,