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dwhswensondwhswenson
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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
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‎.github/workflows/answers_1.patch‎

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

‎.github/workflows/answers_2.patch‎

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diff --git a/2_tps_analysis_tutorial.ipynb b/2_tps_analysis_tutorial.ipynb
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index a6ab056..52b6e52 100644
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--- a/2_tps_analysis_tutorial.ipynb
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+++ b/2_tps_analysis_tutorial.ipynb
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@@ -137,9 +127,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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- "metadata": {
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- "collapsed": true
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- },
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER \n",
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+ "traj = storage.steps[25].active[0].trajectory"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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"outputs": [],
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"source": [
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"md_traj = traj.to_mdtraj().image_molecules()\n",
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@@ -182,9 +178,45 @@
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{
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"cell_type": "code",
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"execution_count": null,
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- "metadata": {
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- "collapsed": true
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- },
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER (1/3)\n",
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+ "step = storage.steps[25]\n",
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+ "shooting_pt = step.change.canonical.details.shooting_snapshot\n",
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+ "sp_as_traj = paths.Trajectory([shooting_pt])"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER (2/3)\n",
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+ "# visualize using the same approach as above\n",
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+ "sp_md_traj = sp_as_traj.to_mdtraj().image_molecules()\n",
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+ "sp_view = nv.show_mdtraj(sp_md_traj)\n",
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+ "sp_view.add_ball_and_stick(\"ACE ALA NME\")\n",
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+ "sp_view.center()\n",
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+ "sp_view"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER (3/3)\n",
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+ "# was the step accepted or rejected?\n",
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+ "print(step.change.accepted)"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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"outputs": [],
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"source": [
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"storage.close()"
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@@ -464,9 +474,18 @@
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{
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"cell_type": "code",
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"execution_count": null,
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- "metadata": {
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- "collapsed": true
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- },
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER\n",
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+ "trajA = flexible.steps[7700].active[0].trajectory\n",
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+ "trajB = flexible.steps[8000].active[0].trajectory"
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+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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"outputs": [],
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"source": [
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"ax = plotter.plot(xlim=(-np.pi, 0), ylim=(-np.pi/2, np.pi), cmap=\"Blues\")\n",

‎.github/workflows/answers_3.patch‎

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diff --git a/3_committor_analysis_tutorial.ipynb b/3_committor_analysis_tutorial.ipynb
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index 449afa4..c7c5b97 100644
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--- a/3_committor_analysis_tutorial.ipynb
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+++ b/3_committor_analysis_tutorial.ipynb
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@@ -174,15 +161,29 @@
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{
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"cell_type": "code",
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"execution_count": null,
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- "metadata": {
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- "collapsed": true
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- },
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+ "metadata": {},
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"outputs": [],
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"source": [
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"# YOUR TURN: Do the same for the psi variable.\n",
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"# Remember to start by creating a `psi_hash`."
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]
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},
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+ {
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+ "cell_type": "code",
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+ "execution_count": null,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "### ANSWER:\n",
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+ "psi_hash = lambda x : float(psi(x))\n",
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+ "analyzer.to_pandas(label_function=psi_hash)\n",
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+ "hist1D, psi_bins = analyzer.committor_histogram(psi_hash, alpha_R, bins=10)\n",
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+ "bin_widths = [psi_bins[i+1]-psi_bins[i] for i in range(len(psi_bins)-1)]\n",
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+ "plt.bar(x=psi_bins[:-1], height=hist1D, width=bin_widths)\n",
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+ "plt.xlabel(\"$\\psi$\")\n",
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+ "plt.ylabel(\"$p_B$\");"
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+ ]
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+ },
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{
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"cell_type": "markdown",
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"metadata": {},

‎.github/workflows/ci.yml‎

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name: "Tests"
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on:
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pull_request:
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branches:
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- main
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push:
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branches:
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- main
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#schedule:
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#- cron: "0 0 * * 0"
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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tests:
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runs-on: ubuntu-latest
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name: "Test answer key"
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strategy:
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matrix:
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CONDA_PY: [3.7]
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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auto-update-conda: true
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python-version: ${{ matrix.CONDA_PY }}
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environment-file: binder/environment.yml
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activate-environment: ops-tutorial
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- name: "Install testing tools"
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run: python -m pip install pytest nbval
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- name: "Conda info"
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run: |
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conda info
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conda list
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- name: "Patch answers"
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run: |
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patch < .github/workflows/answers_1.patch
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patch < .github/workflows/answers_2.patch
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patch < .github/workflows/answers_3.patch
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- name: "Run tests"
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run: |
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pytest --nbval-lax 1_tps_sampling_tutorial.ipynb

‎binder/environment.yml‎

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name: ops-tutorial
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channels:
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- conda-forge
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- omnia
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- defaults
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dependencies:
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- jupyter
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- nglview
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- openmm
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- tqdm
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- openpathsampling
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- openmmtools
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prefix: /Users/dwhs/miniconda3/envs/ops-tutorial

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