made sure all production code works properly

iAMB-RWTH-Aachen · Jul 23, 2024 · fed9fa7 · fed9fa7
1 parent 27e05db
commit fed9fa7
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diff --git a/Figures/.ipynb_checkpoints/Figure3_sensitivities_protein-overproduction-checkpoint.ipynb b/Figures/.ipynb_checkpoints/Figure3_sensitivities_protein-overproduction-checkpoint.ipynb
diff --git a/Figures/.ipynb_checkpoints/SuppFigure1_VSC-distributions-checkpoint.ipynb b/Figures/.ipynb_checkpoints/SuppFigure1_VSC-distributions-checkpoint.ipynb
diff --git a/Figures/Figure1_toy-model.png b/Figures/Figure1_toy-model.png
diff --git a/Figures/Figure1_toy_ec_pam.py b/Figures/Figure1_toy_ec_pam.py
diff --git a/Figures/Figure1_toy_model-sensitivities.png b/Figures/Figure1_toy_model-sensitivities.png
diff --git a/Figures/Figure2_sensitivities_gecko_pam.ipynb b/Figures/Figure2_sensitivities_gecko_pam.ipynb
@@ -19,7 +19,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Loading PAModelpy modules version 0.0.3.3\n"
+      "Loading PAModelpy modules version 0.0.3.3\n",
+      "Loading PAModelpy modules version 0.0.3.11\n"
      ]
     }
    ],
@@ -137,7 +138,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 84,
+   "execution_count": 4,
    "id": "cf73a888-2270-4ea9-9cc8-4c9e0f5eceaa",
    "metadata": {},
    "outputs": [],
@@ -296,7 +297,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 85,
+   "execution_count": 5,
    "id": "f1fc7967-5869-4911-8ed4-2cee897adbd7",
    "metadata": {},
    "outputs": [],
@@ -465,7 +466,7 @@
      "text": [
       "Set parameter Username\n",
       "Academic license - for non-commercial use only - expires 2025-03-06\n",
-      "Read LP format model from file /tmp/tmp17g51dve.lp\n",
+      "Read LP format model from file /tmp/tmpe3uw5551.lp\n",
       "Reading time = 0.01 seconds\n",
       ": 1877 rows, 5424 columns, 21150 nonzeros\n",
       "Setting up the proteome allocation model iML1515\n",
@@ -661,7 +662,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Read LP format model from file /tmp/tmplwjs1kgg.lp\n",
+      "Read LP format model from file /tmp/tmpifgb0c5l.lp\n",
       "Reading time = 0.01 seconds\n",
       ": 1877 rows, 5424 columns, 21150 nonzeros\n",
       "Setting up the proteome allocation model iML1515\n",
@@ -820,7 +821,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 18,
    "id": "703cce12",
    "metadata": {},
    "outputs": [],
@@ -834,7 +835,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 19,
    "id": "b893abf9-cc29-470d-85ab-23e575200079",
    "metadata": {},
    "outputs": [],
@@ -864,7 +865,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 20,
    "id": "b11ae446-27b5-4e18-b3bb-9553acbb397c",
    "metadata": {},
    "outputs": [],
@@ -884,7 +885,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 21,
    "id": "7280d7de-3ee7-46ef-aa2c-945f4401db78",
    "metadata": {},
    "outputs": [],
@@ -896,15 +897,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 86,
+   "execution_count": 22,
    "id": "419a3716",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_25011/1583535961.py:24: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n",
+      "/tmp/ipykernel_11219/1583535961.py:24: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n",
       "  fig_pam.subplots_adjust(left=0.3)\n"
      ]
     },
@@ -971,15 +972,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 87,
+   "execution_count": 23,
    "id": "1a2a55bd-67a7-4bda-9dd0-2716e5d0deb6",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_25011/2436902049.py:20: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n",
+      "/tmp/ipykernel_11219/2436902049.py:20: UserWarning: This figure was using constrained_layout, but that is incompatible with subplots_adjust and/or tight_layout; disabling constrained_layout.\n",
       "  fig.subplots_adjust(left=0.3)\n"
      ]
     },

diff --git a/Figures/Figure2_sensitivities_gecko_pam.png b/Figures/Figure2_sensitivities_gecko_pam.png