Dask integration

notebooks/aug_5_mandatory_quarantine_analysis.ipynb

@@ -245,7 +245,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "IPython (Python 3)",
    "language": "python",
    "name": "python3"
   },
@@ -259,7 +259,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,

notebooks/aug_6_evaluate_lockdown_protocols.ipynb

@@ -3,9 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import sys\n",
@@ -34,10 +32,19 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/stevewangen/projects/COVID/uw_reopening/src/simulations_v2/load_params.py:132: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.\n",
+      "  params = yaml.load(f)\n",
+      "/Users/stevewangen/projects/COVID/uw_reopening/src/simulations_v2/load_params.py:46: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.\n",
+      "  age_sev_params = yaml.load(f)\n"
+     ]
+    }
+   ],
    "source": [
     "ug_dorm_params = load_params('../src/simulations_v2/params/baseline_testing/august_5/ug_dorm.yaml')[1]\n",
     "ug_off_campus_params = load_params('../src/simulations_v2/params/baseline_testing/august_5/ug_off_campus.yaml')[1]\n",
@@ -52,9 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "interaction_matrix = np.array([[12.5,4,0.1,0.1,1,0.05,0.05,0.1],\n",
@@ -71,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -80,7 +85,7 @@
        "[1.23]"
       ]
      },
-     "execution_count": 32,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -91,10 +96,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 5,
+   "metadata": {},
    "outputs": [],
    "source": [
     "lockdown_matrix_str = \\\n",
@@ -112,10 +115,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 6,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def get_cum_hosp(df):\n",
@@ -154,10 +155,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 7,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def run_multigroup_sim(sim, T):\n",
@@ -188,10 +187,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 8,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def evaluate_testing_policy(params_list, interaction_matrix, group_names, test_frac, T, n,\n",
@@ -215,10 +212,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 9,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def get_params_list_copy():\n",
@@ -234,10 +229,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 10,
+   "metadata": {},
    "outputs": [],
    "source": [
     "def simulate_lockdown(contact_multiplier, infections_thresh, infections_window, nreps=10):\n",
@@ -258,14 +251,43 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "elapsed time 72.88\n"
+     "ename": "TypeError",
+     "evalue": "configure_lockdown() missing 5 required positional arguments: 'self', 'post_lockdown_interaction_matrix', 'new_case_sims_list', 'new_cases_threshold', and 'new_cases_time_window'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-17-894c8e60d180>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mMultiGroupSimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfigure_lockdown\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m: configure_lockdown() missing 5 required positional arguments: 'self', 'post_lockdown_interaction_matrix', 'new_case_sims_list', 'new_cases_threshold', and 'new_cases_time_window'"
+     ]
+    }
+   ],
+   "source": [
+    "dir(MultiGroupSimulation.configure_lockdown())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "ename": "TypeError",
+     "evalue": "configure_lockdown() missing 1 required positional argument: 'new_cases_time_window'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-11-1be1c1e80f6c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mstart\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mlockdowns\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfinal_infections\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msimulate_lockdown\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1000\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m7\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"elapsed time {:.2f}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mend\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mstart\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m<ipython-input-10-9d85281ee980>\u001b[0m in \u001b[0;36msimulate_lockdown\u001b[0;34m(contact_multiplier, infections_thresh, infections_window, nreps)\u001b[0m\n\u001b[1;32m     12\u001b[0m                                       \u001b[0mlockdown_matrix\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     13\u001b[0m                                        \u001b[0mnew_cases_thresh\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 14\u001b[0;31m                                        infections_window)\n\u001b[0m",
+      "\u001b[0;32m<ipython-input-8-9395c849a930>\u001b[0m in \u001b[0;36mevaluate_testing_policy\u001b[0;34m(params_list, interaction_matrix, group_names, test_frac, T, n, post_lockdown_matrix, new_cases_threshold, new_cases_time_window)\u001b[0m\n\u001b[1;32m      4\u001b[0m     \u001b[0msim\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mMultiGroupSimulation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mparams_list\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minteraction_matrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgroup_names\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m     \u001b[0msim\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfigure_lockdown\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpost_lockdown_matrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew_cases_threshold\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnew_cases_time_window\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      7\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      8\u001b[0m     \u001b[0minf_matrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhosp_matrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlockdown_trajectories\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minfection_trajectories\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrun_multiple_trajectories\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msim\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mT\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mTypeError\u001b[0m: configure_lockdown() missing 1 required positional argument: 'new_cases_time_window'"
      ]
     }
    ],
@@ -548,7 +570,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "IPython (Python 3)",
    "language": "python",
    "name": "python3"
   },
@@ -562,7 +584,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.3"
+   "version": "3.6.2"
   }
  },
  "nbformat": 4,