From 3c27bee91ac1a329a53cce9a33f92992fb1ef849 Mon Sep 17 00:00:00 2001
From: Jean-Christophe Lachance <jclachan@ip29.m>
Date: Sat, 30 May 2020 12:14:56 -0400
Subject: [PATCH 1/2] Step3 fixes

---
 docs/BOFdat_step3.ipynb | 248 ++++++++--------------------------------
 1 file changed, 50 insertions(+), 198 deletions(-)

diff --git a/docs/BOFdat_step3.ipynb b/docs/BOFdat_step3.ipynb
index f03715a..4a6355a 100644
--- a/docs/BOFdat_step3.ipynb
+++ b/docs/BOFdat_step3.ipynb
@@ -12,9 +12,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "from BOFdat import step3\n",
@@ -89,9 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "#Inputs to generate the initial population\n",
@@ -298,13 +294,7 @@
       "(<Metabolite pe140_p at 0x7f3b15a9bdd0>, True)\n",
       "(<Metabolite 2agpg120_c at 0x7f3b07ea6210>, True)\n",
       "(<Metabolite 2tdecg3p_p at 0x7f3b15aadb90>, True)\n",
-      "(<Metabolite 2odecg3p_c at 0x7f3b15a9bcd0>, True)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite 2odecg3p_c at 0x7f3b15a9bcd0>, True)\n",
       "(<Metabolite hdcoa_c at 0x7f3b15a7f450>, True)\n",
       "(<Metabolite o16a4colipa_e at 0x7f3b15aadc90>, False)\n",
       "(<Metabolite udcpgl_c at 0x7f3b141421d0>, True)\n",
@@ -476,13 +466,7 @@
       "(<Metabolite pydxn_c at 0x7f3b15a283d0>, True)\n",
       "(<Metabolite sucorn_c at 0x7f3b15a32e50>, True)\n",
       "(<Metabolite dhcinnm_c at 0x7f3b15a32d50>, False)\n",
-      "(<Metabolite idon__L_c at 0x7f3b15a32f50>, True)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite idon__L_c at 0x7f3b15a32f50>, True)\n",
       "(<Metabolite pac_c at 0x7f3b15a32150>, False)\n",
       "(<Metabolite 3hpppn_e at 0x7f3b15a04b10>, False)\n",
       "(<Metabolite ctbt_c at 0x7f3b15a36490>, False)\n",
@@ -654,13 +638,7 @@
       "(<Metabolite aacald_c at 0x7f3b15a94e10>, False)\n",
       "(<Metabolite gbbtn_p at 0x7f3b15a4aad0>, False)\n",
       "(<Metabolite 4abut_p at 0x7f3b15bd6d10>, True)\n",
-      "(<Metabolite mnl_p at 0x7f3b15a3fc90>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite mnl_p at 0x7f3b15a3fc90>, False)\n",
       "(<Metabolite 12ppd__R_c at 0x7f3b15a4add0>, True)\n",
       "(<Metabolite dad_5_c at 0x7f3b15bf6350>, True)\n",
       "(<Metabolite LalaDgluMdap_p at 0x7f3b15a3f190>, True)\n",
@@ -831,13 +809,7 @@
       "(<Metabolite acmana_c at 0x7f3b15b5e3d0>, False)\n",
       "(<Metabolite fcl__L_c at 0x7f3b15b5ebd0>, False)\n",
       "(<Metabolite h2_e at 0x7f3b15b5eed0>, False)\n",
-      "(<Metabolite nmn_e at 0x7f3b07a946d0>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite nmn_e at 0x7f3b07a946d0>, False)\n",
       "(<Metabolite man6p_e at 0x7f3b15b39d90>, False)\n",
       "(<Metabolite csn_p at 0x7f3b15b5e9d0>, False)\n",
       "(<Metabolite cytd_p at 0x7f3b15b77f50>, True)\n",
@@ -1010,13 +982,7 @@
       "(<Metabolite gal1p_c at 0x7f3b140d6790>, True)\n",
       "(<Metabolite dann_c at 0x7f3b140d6490>, True)\n",
       "(<Metabolite gdpmann_c at 0x7f3b140d6a90>, True)\n",
-      "(<Metabolite 2h3oppan_c at 0x7f3b140d6b90>, True)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite 2h3oppan_c at 0x7f3b140d6b90>, True)\n",
       "(<Metabolite hpyr_c at 0x7f3b1568ce10>, True)\n",
       "(<Metabolite tartr__L_e at 0x7f3b07a94690>, False)\n",
       "(<Metabolite cbi_c at 0x7f3b140d6d90>, False)\n",
@@ -1187,13 +1153,7 @@
       "(<Metabolite glcr_p at 0x7f3b15844190>, False)\n",
       "(<Metabolite tre_p at 0x7f3b14200a50>, False)\n",
       "(<Metabolite imp_e at 0x7f3b14200250>, False)\n",
-      "(<Metabolite feoxam_un_p at 0x7f3b15978610>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite feoxam_un_p at 0x7f3b15978610>, False)\n",
       "(<Metabolite gal1p_e at 0x7f3b14200950>, False)\n",
       "(<Metabolite LalaDglu_c at 0x7f3b15978510>, True)\n",
       "(<Metabolite acglc__D_c at 0x7f3b14200c50>, True)\n",
@@ -1364,13 +1324,7 @@
       "(<Metabolite orot_c at 0x7f3b07f818d0>, True)\n",
       "(<Metabolite damp_c at 0x7f3b07effed0>, True)\n",
       "(<Metabolite fmn_c at 0x7f3b07ed7710>, True)\n",
-      "(<Metabolite 3oddcoa_c at 0x7f3b07ed7510>, True)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite 3oddcoa_c at 0x7f3b07ed7510>, True)\n",
       "(<Metabolite trnaglu_c at 0x7f3b07ed7d10>, False)\n",
       "(<Metabolite ins_e at 0x7f3b141a3690>, True)\n",
       "(<Metabolite q8_c at 0x7f3b07ed7810>, True)\n",
@@ -1542,13 +1496,7 @@
       "(<Metabolite 2agpe161_c at 0x7f3b15551190>, True)\n",
       "(<Metabolite forcoa_c at 0x7f3b142535d0>, True)\n",
       "(<Metabolite moadcosh_c at 0x7f3b142538d0>, False)\n",
-      "(<Metabolite ttrcyc_e at 0x7f3b142534d0>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite ttrcyc_e at 0x7f3b142534d0>, False)\n",
       "(<Metabolite ribflv_c at 0x7f3b07f81b90>, True)\n",
       "(<Metabolite lac__L_e at 0x7f3b142531d0>, True)\n",
       "(<Metabolite so4_c at 0x7f3b07f81d50>, True)\n",
@@ -1718,13 +1666,7 @@
       "(<Metabolite 3amp_e at 0x7f3b07f50650>, False)\n",
       "(<Metabolite 14glucan_e at 0x7f3b07f50950>, False)\n",
       "(<Metabolite athr__L_c at 0x7f3b07f57c10>, True)\n",
-      "(<Metabolite 3opalmACP_c at 0x7f3b07f50050>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite 3opalmACP_c at 0x7f3b07f50050>, False)\n",
       "(<Metabolite 3hcvac11eACP_c at 0x7f3b07f50a50>, False)\n",
       "(<Metabolite sq_p at 0x7f3b14281590>, False)\n",
       "(<Metabolite acampnt_c at 0x7f3b079f4150>, False)\n",
@@ -1895,13 +1837,7 @@
       "(<Metabolite 1agpe141_p at 0x7f3b14044d10>, True)\n",
       "(<Metabolite 1agpg161_p at 0x7f3b14044f10>, True)\n",
       "(<Metabolite LalaDglu_e at 0x7f3b1403b250>, False)\n",
-      "(<Metabolite sufbcd_2fe2s2_c at 0x7f3b1403b350>, False)\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "(<Metabolite sufbcd_2fe2s2_c at 0x7f3b1403b350>, False)\n",
       "(<Metabolite cm_e at 0x7f3b14134e50>, False)\n",
       "(<Metabolite fe3dhbzs3_p at 0x7f3b079f42d0>, False)\n",
       "(<Metabolite dxylnt_c at 0x7f3b14063bd0>, False)\n",
@@ -2076,13 +2012,6 @@
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
-      "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
@@ -2138,13 +2067,8 @@
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
-      "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
+      "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
+      "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
       "/usr/local/lib/python2.7/dist-packages/sklearn/metrics/classification.py:516 \u001b[1;31mRuntimeWarning\u001b[0m: invalid value encountered in double_scalars\n",
@@ -2260,13 +2184,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44624680>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445a0a28>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44624b00>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b44625ef0>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b44625ef0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1421f488>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44556560>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44556a70>\n",
@@ -2385,13 +2303,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445ad950>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1403e050>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1403e170>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b1479ec20>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b1479ec20>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1403e440>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b3f80>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14774dd0>\n",
@@ -2856,13 +2768,7 @@
       "\n",
       "[186 rows x 117 columns]\n",
       "Im in loop 1 and I have 0 valid individuals\n",
-      "4\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "4\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1a06c680>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b4128>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44590ab8>\n",
@@ -2979,13 +2885,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445ab200>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445abdd0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1476eb00>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445ab1b8>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445ab1b8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07e8e2d8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07e8e200>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1473d7a0>\n",
@@ -3102,13 +3002,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14767200>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44562908>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44562680>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b07f88998>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b07f88998>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07f88f38>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445624d0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14761440>\n",
@@ -3538,13 +3432,7 @@
       "\n",
       "[186 rows x 115 columns]\n",
       "Im in loop 1 and I have 0 valid individuals\n",
-      "4\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "4\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07a7e488>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445954d0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44590950>\n",
@@ -3661,13 +3549,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14767710>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b4452d098>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14761c20>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b147b0710>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b147b0710>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1411dd40>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1411c098>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1411c200>\n",
@@ -3784,13 +3666,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1475b950>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445a7908>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445a7320>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b05a8>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b05a8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b0950>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b0830>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b0758>\n",
@@ -4220,13 +4096,7 @@
       "\n",
       "[186 rows x 116 columns]\n",
       "Im in loop 1 and I have 0 valid individuals\n",
-      "4\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "4\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b0791d560>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445abcf8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b0791d128>\n",
@@ -4343,13 +4213,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445abfc8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07b144d0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07a32680>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b4454a290>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b4454a290>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445ab200>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b4454a710>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07a17170>\n",
@@ -4466,13 +4330,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b05a8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44604878>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07951c20>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b44556ab8>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b44556ab8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44556368>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b07979cf8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b4170>\n",
@@ -4902,13 +4760,7 @@
       "\n",
       "[186 rows x 119 columns]\n",
       "Im in loop 1 and I have 0 valid individuals\n",
-      "4\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "4\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b44604878>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b5dd83638>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14708cb0>\n",
@@ -5025,13 +4877,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b073ad368>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b070cfab8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b15d3c200>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445624d0>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b445624d0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14791050>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b1470ec68>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b14755830>\n",
@@ -5148,13 +4994,7 @@
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d84d0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d83b0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d8cb0>\n",
-      "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d85a8>\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d85a8>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d8440>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b077d87a0>\n",
       "<BOFdat.core.initial_population.Individual instance at 0x7f3b445b41b8>\n",
@@ -5609,7 +5449,10 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "outputs": [],
    "source": [
@@ -5824,7 +5667,10 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "outputs": [],
    "source": [
@@ -5980,7 +5826,10 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "outputs": [],
    "source": [
@@ -6041,7 +5890,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": true
+    "collapsed": true,
+    "jupyter": {
+     "outputs_hidden": true
+    }
    },
    "outputs": [],
    "source": []
@@ -6049,23 +5901,23 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.0"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

From f7d3268b8b9f50ddc0a147432e7111e370afb799 Mon Sep 17 00:00:00 2001
From: Jean-Christophe Lachance <jclachan@ip29.m>
Date: Sat, 30 May 2020 12:45:01 -0400
Subject: [PATCH 2/2] Removed multiprocessing from dependencies

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 06d9730..f842d15 100644
--- a/setup.py
+++ b/setup.py
@@ -14,4 +14,4 @@
       install_requires=['cobra>=0.11.0','numpy>=1.13',
 			'BioPython','seaborn',
 			'scikit-learn>=0.18','scipy',
-			'deap','pebble','multiprocessing','matplotlib'])
+			'deap','pebble','matplotlib'])