Environment Cleanup

.gitignore

@@ -1,3 +1,8 @@
-
 .ipynb_checkpoints/*
 .DS_Store
+.idea
+engine/__pycache__
+engine/.ipynb_checkpoints
+notebooks/.ipynb_checkpoints
+ui/__pycache__
+SimCAD.egg-info

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>

engine/.ipynb_checkpoints/run-checkpoint.py

@@ -0,0 +1,21 @@
+from ui.config import state_dict, mechanisms, exogenous_states, env_processes, sim_config
+from engine.configProcessor import generate_config
+from engine.mechanismExecutor import simulation
+from engine.utils import flatten
+
+#from tabulate import tabulate
+import pandas as pd
+
+def main():
+    states_list = [state_dict]
+    configs = generate_config(mechanisms, exogenous_states)
+    # p = pipeline(states_list, configs, env_processes, range(10))
+    N = sim_config['N']
+    r = range(5)
+    # Dimensions: N x r x mechs
+    s = simulation(states_list, configs, env_processes, r, N)
+    result = pd.DataFrame(flatten(s))
+    print('Test')
+#    print(tabulate(result, headers='keys', tablefmt='psql'))
+# remove print and tabulate functions, so it returns a dataframe
+    return result

engine/run.py

@@ -3,7 +3,7 @@ from engine.configProcessor import generate_config
 from engine.mechanismExecutor import simulation
 from engine.utils import flatten
 
-from tabulate import tabulate
+#from tabulate import tabulate
 import pandas as pd
 
 def main():
@@ -12,7 +12,10 @@ def main():
     # p = pipeline(states_list, configs, env_processes, range(10))
     N = sim_config['N']
     r = range(5)
-    # Dimentions: N x r x mechs
+    # Dimensions: N x r x mechs
     s = simulation(states_list, configs, env_processes, r, N)
     result = pd.DataFrame(flatten(s))
-    print(tabulate(result, headers='keys', tablefmt='psql'))
+    print('Test')
+#    print(tabulate(result, headers='keys', tablefmt='psql'))
+# remove print and tabulate functions, so it returns a dataframe
+    return result

notebooks/.ipynb_checkpoints/TestNotebook-checkpoint.ipynb

@@ -0,0 +1,42 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "assert pd.__version__ == '0.23.4'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

notebooks/.ipynb_checkpoints/test-checkpoint.ipynb

@@ -0,0 +1,55 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'ui'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "\u001b[1;32m<ipython-input-1-a6e895c51fc0>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mfrom\u001b[0m \u001b[0mengine\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mrun\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[0mrun\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmain\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;32m~\\AppData\\Local\\Continuum\\anaconda3\\lib\\site-packages\\engine\\run.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mfrom\u001b[0m \u001b[0mui\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mconfig\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mstate_dict\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmechanisms\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mexogenous_states\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0menv_processes\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msim_config\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[0mengine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mconfigProcessor\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mgenerate_config\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[0mengine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmechanismExecutor\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0msimulation\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[0mengine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mutils\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mflatten\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;31mModuleNotFoundError\u001b[0m: No module named 'ui'"
+     ]
+    }
+   ],
+   "source": [
+    "from engine import run\n",
+    "run.main()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}

notebooks/CAD_Engine.ipynb

@@ -1301,13 +1301,13 @@
     {
      "ename": "NameError",
      "evalue": "name 'non_numeric' is not defined",
+     "output_type": "error",
      "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mNameError\u001b[0m                     Traceback (most recent call last)",
+      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-12-9786f8c4c4ba>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mstate_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m's1'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'3323'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m's2'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'2572'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m's3'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'2.657'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m's4'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'7.914'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'timestamp'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'2018-10-01 15:16:26'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'mech_step'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'time_step'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mstate_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mv\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mquantize\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mTWOPLACES\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mROUND_DOWN\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mstate_dict\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mv\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0mstate_dict\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnon_numeric\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      6\u001b[0m \u001b[0mstate_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[1;32m<ipython-input-12-9786f8c4c4ba>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[0mstate_dict\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m{\u001b[0m\u001b[1;34m's1'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'3323'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m's2'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'2572'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m's3'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'2.657'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m's4'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'7.914'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'timestamp'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;34m'2018-10-01 15:16:26'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'mech_step'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m'time_step'\u001b[0m\u001b[1;33m:\u001b[0m \u001b[1;36m2\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[0mstate_dict\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m{\u001b[0m\u001b[0mk\u001b[0m\u001b[1;33m:\u001b[0m \u001b[0mv\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mquantize\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mTWOPLACES\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mROUND_DOWN\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mk\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mv\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mstate_dict\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mtype\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mv\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m==\u001b[0m \u001b[0mDecimal\u001b[0m\u001b[1;33m}\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 5\u001b[1;33m \u001b[0mstate_dict\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mnon_numeric\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      6\u001b[0m \u001b[0mstate_dict\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mNameError\u001b[0m: name 'non_numeric' is not defined"
+      "\u001b[1;31mNameError\u001b[0m: name 'non_numeric' is not defined"
-     ],
+     ]
-     "output_type": "error"
     }
    ],
    "source": [

notebooks/TestNotebook.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,9 +13,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "DiffyQ-SimCAD Env",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "diffyq-simcad"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

notebooks/test.ipynb

@@ -0,0 +1,77 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [
+    {
+     "ename": "ImportError",
+     "evalue": "cannot import name 'run'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mImportError\u001b[0m                               Traceback (most recent call last)",
+      "\u001b[1;32m<ipython-input-5-a6e895c51fc0>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[1;32mfrom\u001b[0m \u001b[0mengine\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mrun\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[0mrun\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mmain\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;31mImportError\u001b[0m: cannot import name 'run'"
+     ]
+    }
+   ],
+   "source": [
+    "from engine import run\n",
+    "run.main()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}