From d4bb91aa80385bb91d05d083729f797720d8a62b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B8rgen=20S=2E=20Dokken?= <dokken@simula.no>
Date: Wed, 1 Mar 2023 08:34:08 +0000
Subject: [PATCH] Strip more output

---
 examples/example2/example2.ipynb | 42 +++++++++++---------------------
 1 file changed, 14 insertions(+), 28 deletions(-)

diff --git a/examples/example2/example2.ipynb b/examples/example2/example2.ipynb
index 835f53cb..95d6cd70 100644
--- a/examples/example2/example2.ipynb
+++ b/examples/example2/example2.ipynb
@@ -21,19 +21,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "cc398816",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Authorization required, but no authorization protocol specified\n",
-      "Authorization required, but no authorization protocol specified\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "\n",
@@ -56,7 +47,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "4f4023cf",
    "metadata": {},
    "outputs": [],
@@ -85,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "09079b17",
    "metadata": {},
    "outputs": [],
@@ -136,23 +127,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "fe56e162",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "AttributeError",
-     "evalue": "module 'stubs.common' has no attribute 'sbmodel_from_locals'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[4], line 4\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m \u001b[39mrange\u001b[39m(\u001b[39m10\u001b[39m):\n\u001b[1;32m      3\u001b[0m     curRadius \u001b[39m=\u001b[39m radiusVec[i]\n\u001b[0;32m----> 4\u001b[0m     pc, sc, cc, rc \u001b[39m=\u001b[39m make_model(curRadius)\n\u001b[1;32m      6\u001b[0m     \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m      7\u001b[0m     \u001b[39m# Create/load in mesh\u001b[39;00m\n\u001b[1;32m      8\u001b[0m     \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m      9\u001b[0m     \u001b[39m# Base mesh\u001b[39;00m\n\u001b[1;32m     10\u001b[0m     domain, facet_markers, cell_markers \u001b[39m=\u001b[39m common\u001b[39m.\u001b[39mDemoSpheresMesh(curRadius, \u001b[39m0\u001b[39m) \u001b[39m#0 in second argument corresponds to no ER\u001b[39;00m\n",
-      "Cell \u001b[0;32mIn[3], line 33\u001b[0m, in \u001b[0;36mmake_model\u001b[0;34m(curRadius)\u001b[0m\n\u001b[1;32m     27\u001b[0m r2 \u001b[39m=\u001b[39m Reaction(\u001b[39m\"\u001b[39m\u001b[39mr2\u001b[39m\u001b[39m\"\u001b[39m, [\u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m], [], param_map\u001b[39m=\u001b[39m{\u001b[39m\"\u001b[39m\u001b[39mkon\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mkp\u001b[39m\u001b[39m\"\u001b[39m},\n\u001b[1;32m     28\u001b[0m      eqn_f_str\u001b[39m=\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mkon*Aphos\u001b[39m\u001b[39m\"\u001b[39m, species_map\u001b[39m=\u001b[39m{\u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39m\"\u001b[39m\u001b[39mAphos\u001b[39m\u001b[39m\"\u001b[39m})\n\u001b[1;32m     30\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[1;32m     31\u001b[0m \u001b[39m# Gather all parameters, species, compartments and reactions\u001b[39;00m\n\u001b[1;32m     32\u001b[0m \u001b[39m# =============================================================================================\u001b[39;00m\n\u001b[0;32m---> 33\u001b[0m \u001b[39mreturn\u001b[39;00m common\u001b[39m.\u001b[39;49msbmodel_from_locals(\u001b[39mlocals\u001b[39m()\u001b[39m.\u001b[39mvalues())\n",
-      "\u001b[0;31mAttributeError\u001b[0m: module 'stubs.common' has no attribute 'sbmodel_from_locals'"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "radiusVec = np.logspace(0,1,num=10) # currently testing 10 radius values\n",
     "for i in range(10):\n",
@@ -209,6 +187,14 @@
     "        if modelCur.t >= modelCur.final_t:\n",
     "            break"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4fe15da8",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {