CI (#2)

* Start on CI workflow (incl. binder env)

* fix branches; add schedule (7:07 on Sunday)

* try to fix action

* forgot to make it a list

* correct cron

* Is this midnight sunday?

* cleanup

* Add answer patches

Author: dwhswenson

.github/workflows/answers_1.patch

@@ -0,0 +1,43 @@
+diff --git a/1_tps_sampling_tutorial.ipynb b/1_tps_sampling_tutorial.ipynb
+index 7814be1..555e20a 100644
+--- a/1_tps_sampling_tutorial.ipynb
++++ b/1_tps_sampling_tutorial.ipynb
+@@ -191,6 +191,16 @@
+     "# Figure out which atoms make the dihedral, find their atom indices, then create the CV."
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER\n",
++    "psi = paths.MDTrajFunctionCV(\"psi\", md.compute_dihedrals, engine.topology, indices=[[6,8,14,16]])"
++   ]
++  },
+   {
+    "cell_type": "markdown",
+    "metadata": {},
+@@ -232,6 +242,21 @@
+     "# YOUR TURN: define the `alpha_R` state"
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER\n",
++    "alpha_R = (\n",
++    "    paths.PeriodicCVDefinedVolume(phi, lambda_min=-180/deg, lambda_max=0/deg, \n",
++    "                                  period_min=-np.pi, period_max=np.pi)\n",
++    "    & paths.PeriodicCVDefinedVolume(psi, lambda_min=-100/deg, lambda_max=0/deg,\n",
++    "                                    period_min=-np.pi, period_max=np.pi)\n",
++    ").named(\"alpha_R\")"
++   ]
++  },
+   {
+    "cell_type": "markdown",
+    "metadata": {},

.github/workflows/answers_2.patch

@@ -0,0 +1,96 @@
+diff --git a/2_tps_analysis_tutorial.ipynb b/2_tps_analysis_tutorial.ipynb
+index a6ab056..52b6e52 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
+-   },
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### 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
+-   },
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER (1/3)\n",
++    "step = storage.steps[25]\n",
++    "shooting_pt = step.change.canonical.details.shooting_snapshot\n",
++    "sp_as_traj = paths.Trajectory([shooting_pt])"
++   ]
++  },
++  {
++   "cell_type": "code",
++   "execution_count": null,
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER (2/3)\n",
++    "# visualize using the same approach as above\n",
++    "sp_md_traj = sp_as_traj.to_mdtraj().image_molecules()\n",
++    "sp_view = nv.show_mdtraj(sp_md_traj)\n",
++    "sp_view.add_ball_and_stick(\"ACE ALA NME\")\n",
++    "sp_view.center()\n",
++    "sp_view"
++   ]
++  },
++  {
++   "cell_type": "code",
++   "execution_count": null,
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER (3/3)\n",
++    "# was the step accepted or rejected?\n",
++    "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
+-   },
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER\n",
++    "trajA = flexible.steps[7700].active[0].trajectory\n",
++    "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",

.github/workflows/answers_3.patch

@@ -0,0 +1,37 @@
+diff --git a/3_committor_analysis_tutorial.ipynb b/3_committor_analysis_tutorial.ipynb
+index 449afa4..c7c5b97 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",
+     "# Remember to start by creating a `psi_hash`."
+    ]
+   },
++  {
++   "cell_type": "code",
++   "execution_count": null,
++   "metadata": {},
++   "outputs": [],
++   "source": [
++    "### ANSWER:\n",
++    "psi_hash = lambda x : float(psi(x))\n",
++    "analyzer.to_pandas(label_function=psi_hash)\n",
++    "hist1D, psi_bins = analyzer.committor_histogram(psi_hash, alpha_R, bins=10)\n",
++    "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(\"$p_B$\");"
++   ]
++  },
+   {
+    "cell_type": "markdown",
+    "metadata": {},

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: "Tests"
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  #schedule:
+    #- cron: "0 0 * * 0"
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    name: "Test answer key"
+    strategy:
+      matrix:
+        CONDA_PY: [3.7]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.CONDA_PY }}
+          environment-file: binder/environment.yml
+          activate-environment: ops-tutorial
+      - name: "Install testing tools"
+        run: python -m pip install pytest nbval
+      - name: "Conda info"
+        run: |
+          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
+      - name: "Run tests"
+        run: |
+          pytest --nbval-lax 1_tps_sampling_tutorial.ipynb

binder/environment.yml

@@ -0,0 +1,13 @@
+name: ops-tutorial
+channels:
+  - conda-forge
+  - omnia
+  - defaults
+dependencies:
+  - jupyter
+  - nglview
+  - openmm
+  - tqdm
+  - openpathsampling
+  - openmmtools
+prefix: /Users/dwhs/miniconda3/envs/ops-tutorial