A possible solution to the problem

notebooks/sympy_bug_hunt.ipynb

@@ -93,7 +93,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{t, N, S, I, beta}\n"
+      "{S, t, I, beta, N}\n"
      ]
     }
    ],
@@ -188,11 +188,108 @@
     "print(state in eqn.free_symbols)\n",
     "print(sympy.diff(eqn, state))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "True\n"
+     ]
+    }
+   ],
+   "source": [
+    "# So I think this is because the t used in eqn is new (created in the check equantion function)\n",
+    "# but the t we want is model._t which gets into _pramDict in line 97 of base_ode_model.py\n",
+    "print(model._paramDict['t'] == model._t)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "False\n"
+     ]
+    }
+   ],
+   "source": [
+    "# which as before is _not_ in the equation\n",
+    "print(model._t in eqn.free_symbols)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/latex": [
+       "$\\displaystyle t$"
+      ],
+      "text/plain": [
+       "t"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# So lets get the t in the equation and replace it with model_t\n",
+    "\n",
+    "# can't index sets\n",
+    "eqn_t = [symb for symb in eqn.free_symbols if str(symb)=='t'][0]\n",
+    "eqn_t"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# A little bit of light substitution\n",
+    "new_eqn =  eqn.subs(eqn_t, model._t)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "t\n",
+      "True\n",
+      "-0.62172*I*S*beta*sin(0.628*t)/N\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Lets try that again\n",
+    "state=model._paramDict['t']\n",
+    "print(state)\n",
+    "print(state in new_eqn.free_symbols)\n",
+    "print(sympy.diff(new_eqn, state))"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pygom_19",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -206,9 +303,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }