More CI (#3)

* Clean up patches

* Add in the rest of the CI

* exclude notebook 3 (for now)

Author: dwhswenson

.github/workflows/ci.yml

@@ -7,8 +7,8 @@ on:
   push:
     branches:
       - main
-  #schedule:
-    #- cron: "0 0 * * 0"
+  schedule:
+    - cron: "0 0 * * 0"
 
 defaults:
   run:
@@ -38,10 +38,12 @@ jobs:
           conda info
           conda list
       - name: "Patch answers"
-        run: |
-          patch < .github/workflows/answers_1.patch
-          patch < .github/workflows/answers_2.patch
-          patch < .github/workflows/answers_3.patch
+        run: source devtools/patch-all
+      - name: "Download data"
+        run: source devtools/download-files
       - name: "Run tests"
         run: |
-          pytest --nbval-lax 1_tps_sampling_tutorial.ipynb
+          pytest --nbval-lax \
+            1_tps_sampling_tutorial.ipynb \
+            2_tps_analysis_tutorial.ipynb \
+            4_mstis_sampling_tutorial.ipynb

.github/workflows/answers_1.patch devtools/a1.patch.github/workflows/answers_1.patch renamed to devtools/a1.patch

@@ -1,35 +1,31 @@
 diff --git a/2_tps_analysis_tutorial.ipynb b/2_tps_analysis_tutorial.ipynb
-index a6ab056..52b6e52 100644
+index 6d25bc4..b335e13 100644
 --- a/2_tps_analysis_tutorial.ipynb
 +++ b/2_tps_analysis_tutorial.ipynb
-@@ -137,9 +127,17 @@
-   {
-    "cell_type": "code",
-    "execution_count": null,
--   "metadata": {
--    "collapsed": true
--   },
+@@ -122,6 +122,16 @@
+     "#traj = storage.steps[####].active[0].trajectory"
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
 +   "metadata": {},
 +   "outputs": [],
 +   "source": [
-+    "### ANSWER \n",
++    "### ANSWER\n",
 +    "traj = storage.steps[25].active[0].trajectory"
 +   ]
 +  },
-+  {
-+   "cell_type": "code",
-+   "execution_count": null,
-+   "metadata": {},
-    "outputs": [],
-    "source": [
-     "md_traj = traj.to_mdtraj().image_molecules()\n",
-@@ -182,9 +178,45 @@
    {
     "cell_type": "code",
     "execution_count": null,
--   "metadata": {
--    "collapsed": true
--   },
+@@ -165,6 +175,44 @@
+     "# Did your selected snapshot come from an accepted or rejected trial?"
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
 +   "metadata": {},
 +   "outputs": [],
 +   "source": [
@@ -65,20 +61,16 @@ index a6ab056..52b6e52 100644
 +    "print(step.change.accepted)"
 +   ]
 +  },
-+  {
-+   "cell_type": "code",
-+   "execution_count": null,
-+   "metadata": {},
-    "outputs": [],
-    "source": [
-     "storage.close()"
-@@ -464,9 +474,18 @@
    {
     "cell_type": "code",
     "execution_count": null,
--   "metadata": {
--    "collapsed": true
--   },
+@@ -422,6 +470,17 @@
+     "# trajB = flexible.steps[####].active[0].trajectory"
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
 +   "metadata": {},
 +   "outputs": [],
 +   "source": [
@@ -87,10 +79,6 @@ index a6ab056..52b6e52 100644
 +    "trajB = flexible.steps[8000].active[0].trajectory"
 +   ]
 +  },
-+  {
-+   "cell_type": "code",
-+   "execution_count": null,
-+   "metadata": {},
-    "outputs": [],
-    "source": [
-     "ax = plotter.plot(xlim=(-np.pi, 0), ylim=(-np.pi/2, np.pi), cmap=\"Blues\")\n",
+   {
+    "cell_type": "code",
+    "execution_count": null,

.github/workflows/answers_2.patch devtools/a2.patch.github/workflows/answers_2.patch renamed to devtools/a2.patch

@@ -1,18 +1,8 @@
 diff --git a/3_committor_analysis_tutorial.ipynb b/3_committor_analysis_tutorial.ipynb
-index 449afa4..c7c5b97 100644
+index 6cbc363..957f0ab 100644
 --- a/3_committor_analysis_tutorial.ipynb
 +++ b/3_committor_analysis_tutorial.ipynb
-@@ -174,15 +161,29 @@
-   {
-    "cell_type": "code",
-    "execution_count": null,
--   "metadata": {
--    "collapsed": true
--   },
-+   "metadata": {},
-    "outputs": [],
-    "source": [
-     "# YOUR TURN: Do the same for the psi variable.\n",
+@@ -168,6 +168,22 @@
      "# Remember to start by creating a `psi_hash`."
     ]
    },
@@ -29,7 +19,7 @@ index 449afa4..c7c5b97 100644
 +    "bin_widths = [psi_bins[i+1]-psi_bins[i] for i in range(len(psi_bins)-1)]\n",
 +    "plt.bar(x=psi_bins[:-1], height=hist1D, width=bin_widths)\n",
 +    "plt.xlabel(\"$\\psi$\")\n",
-+    "plt.ylabel(\"$p_B$\");"
++    "plt.ylabel(\"$p_B$\")"
 +   ]
 +  },
    {

.github/workflows/answers_3.patch devtools/a3.patch.github/workflows/answers_3.patch renamed to devtools/a3.patch

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+figshare_ID=4763686
+version=1
+
+mkdir $figshare_ID
+curl -Lk -o ${figshare_ID}.zip \
+    https://ndownloader.figshare.com/articles/${figshare_ID}/versions/$version
+unzip -d $figshare_ID ${figshare_ID}.zip
+
+mv $figshare_ID/* ./

devtools/download-files

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+patch < ${DIR}/a1.patch
+patch < ${DIR}/a2.patch
+patch < ${DIR}/a3.patch
+#patch < ${DIR}/testing.patch
+