A few changes - added scipy to requirements

put more steps into __init__ all to ease import syntax
Did more work fitting SI/SIS, etc. models and got SIR model running
Switched transmission.py to exponential distribution for infectious period, to improve match to compartmental models

notebooks/example_SIS_nobirths.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -32,14 +32,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2024-12-06 18:10:18.916065: Creating the generic model…\n",
+      "2024-12-06 18:24:58.435154: Creating the generic model…\n",
       "Initializing the generic model with 1 patches…\n"
      ]
     }
@@ -57,33 +57,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "2024-12-06 18:10:20.316939: Running the generic model for 730 ticks…\n"
+      "2024-12-06 18:24:58.949071: Running the generic model for 730 ticks…\n"
      ]
     },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 730/730 [00:06<00:00, 107.24it/s]\n"
+      "100%|██████████| 730/730 [00:22<00:00, 32.50it/s] \n"
      ]
     },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Completed the generic model at 2024-12-06 18:10:27.132344…\n",
-      "Model        :         5,006 µs\n",
-      "Transmission :     5,780,040 µs\n",
-      "Infection_SIS:       920,323 µs\n",
+      "Completed the generic model at 2024-12-06 18:25:21.424122…\n",
+      "Model        :        25,950 µs\n",
+      "Transmission :    14,722,149 µs\n",
+      "Infection_SIS:     6,900,775 µs\n",
       "===============================\n",
-      "Total:             6,705,369 microseconds\n"
+      "Total:            21,648,874 microseconds\n"
      ]
     }
    ],
@@ -96,16 +96,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 50,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "[<matplotlib.lines.Line2D at 0x76f3e44bd6d0>]"
+       "[<matplotlib.lines.Line2D at 0x7b7f99a09820>]"
       ]
      },
-     "execution_count": 50,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -140,19 +140,15 @@
     {
      "data": {
       "text/plain": [
-       "0.8888888888888888"
+       "0.03333333333333333"
       ]
      },
-     "execution_count": 51,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
-   "source": [
-    "1-1/90/.1\n",
-    "\n",
-    "np.mean(model.patches.cases[-365:])"
-   ]
+   "source": []
   },
   {
    "cell_type": "code",