add nb + refactor __init__.py + add graphviz to reqs

cadCAD/diagram/__init__.py

@@ -1 +1 @@
-from cadCAD_diagram.config_diagram import diagram, diagram_from_config
+from cadCAD.diagram.config_diagram import diagram, diagram_from_config

documentation/examples/cadCAD_diagram.ipynb

@@ -0,0 +1,257 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def policy_1(p, s, h, v):\n",
+    "    return {\"pi_1\": v[\"var_1\"]}\n",
+    "\n",
+    "\n",
+    "def policy_2(p, s, h, v):\n",
+    "    return {\"pi_1\": v[\"var_1\"], \"pi_2\": v[\"var_1\"] * v[\"var_2\"]}\n",
+    "\n",
+    "\n",
+    "def suf_1(p, s, h, v, pi):\n",
+    "    return (\"var_1\", pi[\"pi_1\"])\n",
+    "\n",
+    "\n",
+    "def suf_2(p, s, h, v, pi):\n",
+    "    return (\"var_2\", pi[\"pi_2\"])\n",
+    "\n",
+    "\n",
+    "psubs = [\n",
+    "    {\n",
+    "        \"label\": \"Test\",\n",
+    "        \"policies\": {\"policy_1\": policy_1, \"policy_2\": policy_2},\n",
+    "        \"variables\": {\"var_1\": suf_1, \"var_2\": suf_2},\n",
+    "    }\n",
+    "]\n",
+    "\n",
+    "initial_state = {\"var_1\": 0, \"var_2\": 1}\n",
+    "\n",
+    "params = {\"param_1\": 0, \"param_2\": 1}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.append('..')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "image/svg+xml": [
+       "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n",
+       "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
+       " \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
+       "<!-- Generated by graphviz version 2.43.0 (0)\n",
+       " -->\n",
+       "<!-- Title: cluster_timestep Pages: 1 -->\n",
+       "<svg width=\"481pt\" height=\"183pt\"\n",
+       " viewBox=\"0.00 0.00 693.14 264.00\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<g id=\"graph0\" class=\"graph\" transform=\"scale(1.44 1.44) rotate(0) translate(4 260)\">\n",
+       "<title>cluster_timestep</title>\n",
+       "<polygon fill=\"pink\" stroke=\"transparent\" points=\"-4,4 -4,-260 689.14,-260 689.14,4 -4,4\"/>\n",
+       "<g id=\"clust1\" class=\"cluster\">\n",
+       "<title>cluster_psub_0</title>\n",
+       "<polygon fill=\"thistle\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"8,-8 8,-248 677.14,-248 677.14,-8 8,-8\"/>\n",
+       "<text text-anchor=\"middle\" x=\"342.57\" y=\"-232.8\" font-family=\"Times,serif\" font-size=\"14.00\">Partial State Update Block</text>\n",
+       "</g>\n",
+       "<g id=\"clust3\" class=\"cluster\">\n",
+       "<title>cluster_variables_0</title>\n",
+       "<polygon fill=\"skyblue\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"16,-88 16,-217 106,-217 106,-88 16,-88\"/>\n",
+       "<text text-anchor=\"middle\" x=\"61\" y=\"-201.8\" font-family=\"Times,serif\" font-size=\"14.00\">State</text>\n",
+       "</g>\n",
+       "<g id=\"clust4\" class=\"cluster\">\n",
+       "<title>cluster_policy_0</title>\n",
+       "<polygon fill=\"thistle\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"126,-16 126,-217 390.64,-217 390.64,-16 126,-16\"/>\n",
+       "<text text-anchor=\"middle\" x=\"258.32\" y=\"-201.8\" font-family=\"Times,serif\" font-size=\"14.00\">Policies</text>\n",
+       "</g>\n",
+       "<g id=\"clust5\" class=\"cluster\">\n",
+       "<title>cluster_suf_0</title>\n",
+       "<polygon fill=\"thistle\" stroke=\"black\" stroke-dasharray=\"5,2\" points=\"418.64,-16 418.64,-217 561.64,-217 561.64,-16 418.64,-16\"/>\n",
+       "<text text-anchor=\"middle\" x=\"490.14\" y=\"-201.8\" font-family=\"Times,serif\" font-size=\"14.00\">State Update Functions</text>\n",
+       "</g>\n",
+       "<!-- state_0 -->\n",
+       "<g id=\"node1\" class=\"node\">\n",
+       "<title>state_0</title>\n",
+       "<path fill=\"honeydew\" stroke=\"black\" d=\"M88,-74.73C88,-76.53 75.9,-78 61,-78 46.1,-78 34,-76.53 34,-74.73 34,-74.73 34,-45.27 34,-45.27 34,-43.47 46.1,-42 61,-42 75.9,-42 88,-43.47 88,-45.27 88,-45.27 88,-74.73 88,-74.73\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M88,-74.73C88,-72.92 75.9,-71.45 61,-71.45 46.1,-71.45 34,-72.92 34,-74.73\"/>\n",
+       "<text text-anchor=\"middle\" x=\"61\" y=\"-56.3\" font-family=\"Times,serif\" font-size=\"14.00\">State 1</text>\n",
+       "</g>\n",
+       "<!-- policy_policy_1_0 -->\n",
+       "<g id=\"node5\" class=\"node\">\n",
+       "<title>policy_policy_1_0</title>\n",
+       "<polygon fill=\"palegreen\" stroke=\"black\" stroke-width=\"2\" points=\"246,-90 134,-90 134,-30 246,-30 258,-60 246,-90\"/>\n",
+       "<text text-anchor=\"middle\" x=\"196\" y=\"-56.3\" font-family=\"Times,serif\" font-size=\"14.00\">policy_1 (policy_1)</text>\n",
+       "</g>\n",
+       "<!-- state_0&#45;&gt;policy_policy_1_0 -->\n",
+       "<g id=\"edge6\" class=\"edge\">\n",
+       "<title>state_0&#45;&gt;policy_policy_1_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M88.28,-60C98.61,-60 111.02,-60 123.67,-60\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"123.82,-63.5 133.82,-60 123.82,-56.5 123.82,-63.5\"/>\n",
+       "</g>\n",
+       "<!-- policy_policy_2_0 -->\n",
+       "<g id=\"node6\" class=\"node\">\n",
+       "<title>policy_policy_2_0</title>\n",
+       "<polygon fill=\"palegreen\" stroke=\"black\" stroke-width=\"2\" points=\"246,-180 134,-180 134,-120 246,-120 258,-150 246,-180\"/>\n",
+       "<text text-anchor=\"middle\" x=\"196\" y=\"-146.3\" font-family=\"Times,serif\" font-size=\"14.00\">policy_2 (policy_2)</text>\n",
+       "</g>\n",
+       "<!-- state_0&#45;&gt;policy_policy_2_0 -->\n",
+       "<g id=\"edge7\" class=\"edge\">\n",
+       "<title>state_0&#45;&gt;policy_policy_2_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M88.43,-72.68C94.43,-76.03 100.62,-79.87 106,-84 116.22,-91.85 116.09,-96.76 126,-105 127.13,-105.94 128.29,-106.88 129.46,-107.82\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"127.34,-110.61 137.4,-113.92 131.61,-105.05 127.34,-110.61\"/>\n",
+       "</g>\n",
+       "<!-- variable_var_2_0 -->\n",
+       "<g id=\"node2\" class=\"node\">\n",
+       "<title>variable_var_2_0</title>\n",
+       "<path fill=\"honeydew\" stroke=\"black\" d=\"M98,-182.73C98,-184.53 81.42,-186 61,-186 40.58,-186 24,-184.53 24,-182.73 24,-182.73 24,-153.27 24,-153.27 24,-151.47 40.58,-150 61,-150 81.42,-150 98,-151.47 98,-153.27 98,-153.27 98,-182.73 98,-182.73\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M98,-182.73C98,-180.92 81.42,-179.45 61,-179.45 40.58,-179.45 24,-180.92 24,-182.73\"/>\n",
+       "<text text-anchor=\"middle\" x=\"61\" y=\"-164.3\" font-family=\"Times,serif\" font-size=\"14.00\">var_2 (int)</text>\n",
+       "</g>\n",
+       "<!-- variable_var_2_0&#45;&gt;policy_policy_2_0 -->\n",
+       "<g id=\"edge4\" class=\"edge\">\n",
+       "<title>variable_var_2_0&#45;&gt;policy_policy_2_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M98.34,-163.08C106.33,-162 115.06,-160.82 123.9,-159.62\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"124.45,-163.08 133.89,-158.27 123.51,-156.14 124.45,-163.08\"/>\n",
+       "</g>\n",
+       "<!-- variable_var_1_0 -->\n",
+       "<g id=\"node3\" class=\"node\">\n",
+       "<title>variable_var_1_0</title>\n",
+       "<path fill=\"honeydew\" stroke=\"black\" d=\"M98,-128.73C98,-130.53 81.42,-132 61,-132 40.58,-132 24,-130.53 24,-128.73 24,-128.73 24,-99.27 24,-99.27 24,-97.47 40.58,-96 61,-96 81.42,-96 98,-97.47 98,-99.27 98,-99.27 98,-128.73 98,-128.73\"/>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M98,-128.73C98,-126.92 81.42,-125.45 61,-125.45 40.58,-125.45 24,-126.92 24,-128.73\"/>\n",
+       "<text text-anchor=\"middle\" x=\"61\" y=\"-110.3\" font-family=\"Times,serif\" font-size=\"14.00\">var_1 (int)</text>\n",
+       "</g>\n",
+       "<!-- variable_var_1_0&#45;&gt;policy_policy_1_0 -->\n",
+       "<g id=\"edge3\" class=\"edge\">\n",
+       "<title>variable_var_1_0&#45;&gt;policy_policy_1_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M98.34,-99.24C106.51,-95.93 115.44,-92.3 124.47,-88.64\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"125.94,-91.82 133.89,-84.81 123.31,-85.33 125.94,-91.82\"/>\n",
+       "</g>\n",
+       "<!-- variable_var_1_0&#45;&gt;policy_policy_2_0 -->\n",
+       "<g id=\"edge5\" class=\"edge\">\n",
+       "<title>variable_var_1_0&#45;&gt;policy_policy_2_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M98.34,-123.84C106.42,-126.02 115.25,-128.41 124.18,-130.83\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"123.32,-134.22 133.89,-133.46 125.15,-127.47 123.32,-134.22\"/>\n",
+       "</g>\n",
+       "<!-- agg_0 -->\n",
+       "<g id=\"node4\" class=\"node\">\n",
+       "<title>agg_0</title>\n",
+       "<ellipse fill=\"greenyellow\" stroke=\"black\" stroke-width=\"2\" cx=\"338.32\" cy=\"-105\" rx=\"44.15\" ry=\"44.15\"/>\n",
+       "<text text-anchor=\"middle\" x=\"338.32\" y=\"-101.3\" font-family=\"Times,serif\" font-size=\"14.00\">Aggregation</text>\n",
+       "</g>\n",
+       "<!-- suf_var_1_0 -->\n",
+       "<g id=\"node7\" class=\"node\">\n",
+       "<title>suf_var_1_0</title>\n",
+       "<polygon fill=\"red\" stroke=\"black\" stroke-width=\"2\" points=\"522.64,-180 444.64,-180 444.64,-120 522.64,-120 534.64,-150 522.64,-180\"/>\n",
+       "<text text-anchor=\"middle\" x=\"489.64\" y=\"-146.3\" font-family=\"Times,serif\" font-size=\"14.00\">var_1 (suf_1)</text>\n",
+       "</g>\n",
+       "<!-- agg_0&#45;&gt;suf_var_1_0 -->\n",
+       "<g id=\"edge8\" class=\"edge\">\n",
+       "<title>agg_0&#45;&gt;suf_var_1_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M380.92,-117.54C397.59,-122.56 417.02,-128.42 434.75,-133.76\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"433.82,-137.13 444.4,-136.67 435.84,-130.43 433.82,-137.13\"/>\n",
+       "</g>\n",
+       "<!-- suf_var_2_0 -->\n",
+       "<g id=\"node8\" class=\"node\">\n",
+       "<title>suf_var_2_0</title>\n",
+       "<polygon fill=\"red\" stroke=\"black\" stroke-width=\"2\" points=\"522.64,-90 444.64,-90 444.64,-30 522.64,-30 534.64,-60 522.64,-90\"/>\n",
+       "<text text-anchor=\"middle\" x=\"489.64\" y=\"-56.3\" font-family=\"Times,serif\" font-size=\"14.00\">var_2 (suf_2)</text>\n",
+       "</g>\n",
+       "<!-- agg_0&#45;&gt;suf_var_2_0 -->\n",
+       "<g id=\"edge9\" class=\"edge\">\n",
+       "<title>agg_0&#45;&gt;suf_var_2_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M380.92,-92.46C397.59,-87.44 417.02,-81.58 434.75,-76.24\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"435.84,-79.57 444.4,-73.33 433.82,-72.87 435.84,-79.57\"/>\n",
+       "</g>\n",
+       "<!-- policy_policy_1_0&#45;&gt;agg_0 -->\n",
+       "<g id=\"edge1\" class=\"edge\">\n",
+       "<title>policy_policy_1_0&#45;&gt;agg_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M258.14,-79.61C267.47,-82.6 277.01,-85.66 286.1,-88.57\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"285.16,-91.95 295.75,-91.67 287.3,-85.28 285.16,-91.95\"/>\n",
+       "</g>\n",
+       "<!-- policy_policy_2_0&#45;&gt;agg_0 -->\n",
+       "<g id=\"edge2\" class=\"edge\">\n",
+       "<title>policy_policy_2_0&#45;&gt;agg_0</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M258.14,-130.39C267.47,-127.4 277.01,-124.34 286.1,-121.43\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"287.3,-124.72 295.75,-118.33 285.16,-118.05 287.3,-124.72\"/>\n",
+       "</g>\n",
+       "<!-- state_1 -->\n",
+       "<g id=\"node9\" class=\"node\">\n",
+       "<title>state_1</title>\n",
+       "<ellipse fill=\"none\" stroke=\"black\" cx=\"633.39\" cy=\"-105\" rx=\"36\" ry=\"18\"/>\n",
+       "<text text-anchor=\"middle\" x=\"633.39\" y=\"-101.3\" font-family=\"Times,serif\" font-size=\"14.00\">state_1</text>\n",
+       "</g>\n",
+       "<!-- suf_var_1_0&#45;&gt;state_1 -->\n",
+       "<g id=\"edge10\" class=\"edge\">\n",
+       "<title>suf_var_1_0&#45;&gt;state_1</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M534.72,-136.01C553.37,-130.09 574.92,-123.24 593.03,-117.5\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"594.23,-120.79 602.7,-114.43 592.11,-114.12 594.23,-120.79\"/>\n",
+       "</g>\n",
+       "<!-- suf_var_2_0&#45;&gt;state_1 -->\n",
+       "<g id=\"edge11\" class=\"edge\">\n",
+       "<title>suf_var_2_0&#45;&gt;state_1</title>\n",
+       "<path fill=\"none\" stroke=\"black\" d=\"M534.72,-73.99C553.37,-79.91 574.92,-86.76 593.03,-92.5\"/>\n",
+       "<polygon fill=\"black\" stroke=\"black\" points=\"592.11,-95.88 602.7,-95.57 594.23,-89.21 592.11,-95.88\"/>\n",
+       "</g>\n",
+       "</g>\n",
+       "</svg>\n"
+      ],
+      "text/plain": [
+       "<graphviz.dot.Digraph at 0x7f28a138d590>"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from cadCAD_diagram.config_diagram import diagram\n",
+    "\n",
+    "diagram(initial_state, params, psubs)"
+   ]
+  },
+  {
+   "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": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

requirements.txt

@@ -11,3 +11,4 @@ pathos>=0.2.8
 numpy>=1.22.0
 pytz>=2021.1
 setuptools>=69.0.2
+graphviz>=0.20.1