docs: as per agreement remove some cplex

This setting should become default instead. Kept in places where it should be explained.
DD-DeCaF · Jul 28, 2017 · 4637f0c · 4637f0c
1 parent 064afe6
commit 4637f0c
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Showing 5 changed files with 15 additions and 62 deletions.
diff --git a/cameo-01-predict-heterologous-pathways.ipynb b/cameo-01-predict-heterologous-pathways.ipynb
@@ -31,7 +31,9 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "## Making sure you have cplex installed\n",
@@ -41,7 +43,9 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "import re\n",
@@ -52,21 +56,12 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "model = read_sbml_model('data/iMM904.xml.gz')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
    "metadata": {
     "collapsed": true
    },
    "outputs": [],
    "source": [
-    "model.solver = \"cplex\""
+    "model = read_sbml_model('data/iMM904.xml.gz')"
    ]
   },
   {
@@ -1287,7 +1282,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "universal.metanetx_universal_model_bigg_rhea_kegg"
@@ -1323,7 +1320,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.6.0"
   },
   "toc": {
    "colors": {

diff --git a/cameo-02-generating-gene-knockout-strategies.ipynb b/cameo-02-generating-gene-knockout-strategies.ipynb
@@ -37,17 +37,6 @@
     "model = read_sbml_model('data/e_coli_core.xml.gz')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "model.solver = \"cplex\""
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -873,17 +862,6 @@
     "model = read_sbml_model('data/e_coli_core.xml.gz')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "model.solver = \"cplex\""
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 16,
@@ -1985,7 +1963,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.6.0"
   },
   "toc": {
    "colors": {

diff --git a/cameo-03-gene-expression-modulation-targets.ipynb b/cameo-03-gene-expression-modulation-targets.ipynb
@@ -45,17 +45,6 @@
     "model = read_sbml_model('data/e_coli_core.xml.gz')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "model.solver = \"cplex\""
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1286,7 +1275,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.6.0"
   },
   "toc": {
    "colors": {

diff --git a/cobrapy-03-manipulating-the-model.ipynb b/cobrapy-03-manipulating-the-model.ipynb
@@ -631,7 +631,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.6.0"
   },
   "toc": {
    "colors": {

diff --git a/cobrapy-05-advanced-constraints-objectives.ipynb b/cobrapy-05-advanced-constraints-objectives.ipynb
@@ -50,17 +50,6 @@
     "model = read_sbml_model('data/e_coli_core.xml.gz')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": [
-    "model.solver = \"cplex\""
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -412,7 +401,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2+"
+   "version": "3.6.0"
   },
   "toc": {
    "colors": {