{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import logging"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "logging.basicConfig(level=\"DEBUG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.io import load_model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from cobra.flux_analysis import geometric_fba"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Scaling...\n",
      " A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00\n",
      "Problem data seem to be well scaled\n"
     ]
    }
   ],
   "source": [
    "model = load_model(\"textbook\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"cplex\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "logging.getLogger().setLevel(logging.DEBUG)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 4e-13; status: optimal.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 481 ms, sys: 0 ns, total: 481 ms\n",
      "Wall time: 480 ms\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<strong><em>Optimal</em> solution with objective value 0.000</strong><br><div>\n",
       "<style scoped>\n",
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       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fluxes</th>\n",
       "      <th>reduced_costs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ACALD</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACALDt</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACKr</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTa</th>\n",
       "      <td>6.007250</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTb</th>\n",
       "      <td>6.007250</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TALA</th>\n",
       "      <td>1.496984</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THD2</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT1</th>\n",
       "      <td>1.496984</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT2</th>\n",
       "      <td>1.181498</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>7.477382</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>95 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "<Solution 0.000 at 0x7f0c62d3f6a0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time geometric_fba(model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"gurobi\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 6.47e-12; status: optimal.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 504 ms, sys: 2.91 ms, total: 507 ms\n",
      "Wall time: 505 ms\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<strong><em>Optimal</em> solution with objective value 0.000</strong><br><div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fluxes</th>\n",
       "      <th>reduced_costs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ACALD</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACALDt</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACKr</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTa</th>\n",
       "      <td>6.007250</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTb</th>\n",
       "      <td>6.007250</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TALA</th>\n",
       "      <td>1.496984</td>\n",
       "      <td>2.220446e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THD2</th>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.220446e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT1</th>\n",
       "      <td>1.496984</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT2</th>\n",
       "      <td>1.181498</td>\n",
       "      <td>-1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>7.477382</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>95 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "<Solution 0.000 at 0x7f0c6288be10>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time geometric_fba(model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "model.solver = \"glpk\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "DEBUG:optlang.glpk_interface:Status undefined. GLPK status code returned by glp_simplex was 1\n",
      "DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 2.96e-13; status: optimal.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 263 ms, sys: 3.46 ms, total: 267 ms\n",
      "Wall time: 263 ms\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<strong><em>Optimal</em> solution with objective value -0.000</strong><br><div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>fluxes</th>\n",
       "      <th>reduced_costs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>ACALD</th>\n",
       "      <td>1.495879e-14</td>\n",
       "      <td>2.914335e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACALDt</th>\n",
       "      <td>1.495879e-14</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACKr</th>\n",
       "      <td>1.554312e-15</td>\n",
       "      <td>1.110223e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTa</th>\n",
       "      <td>6.007250e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ACONTb</th>\n",
       "      <td>6.007250e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TALA</th>\n",
       "      <td>1.496984e+00</td>\n",
       "      <td>-1.665335e-15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>THD2</th>\n",
       "      <td>5.789919e-14</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT1</th>\n",
       "      <td>1.496984e+00</td>\n",
       "      <td>1.665335e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TKT2</th>\n",
       "      <td>1.181498e+00</td>\n",
       "      <td>-2.220446e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TPI</th>\n",
       "      <td>7.477382e+00</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>95 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "<Solution -0.000 at 0x7f0c6283d9b0>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%time geometric_fba(model)"
   ]
  }
 ],
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