fix: update argument name (#639)

opencobra · Dec 7, 2017 · 98d5eca · 98d5eca
1 parent f85b164
commit 98d5eca
Showing 1 changed file with 13 additions and 49 deletions.
diff --git a/documentation_builder/phenotype_phase_plane.ipynb b/documentation_builder/phenotype_phase_plane.ipynb
@@ -9,10 +9,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "source": [
     "Production envelopes (aka phenotype phase planes) will show distinct phases of optimal growth with different use of two different substrates. For more information, see [Edwards et al.](http://dx.doi.org/10.1002/bit.10047)\n",
     "\n",
@@ -22,11 +19,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import cobra.test\n",
@@ -37,22 +30,15 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "source": [
     "We want to make a phenotype phase plane to evaluate uptakes of Glucose and Oxygen."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "prod_env = production_envelope(model, [\"EX_glc__D_e\", \"EX_o2_e\"])"
@@ -61,11 +47,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -141,36 +123,25 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "source": [
     "If we specify the carbon source, we can also get the carbon and mass yield. For example, temporarily setting the objective to produce acetate instead we could get production envelope as follows and pandas to quickly plot the results."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 4,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "prod_env = production_envelope(\n",
-    "    model, [\"EX_o2_e\"], objective=\"EX_ac_e\", c_source=\"EX_glc__D_e\")"
+    "    model, [\"EX_o2_e\"], objective=\"EX_ac_e\", carbon_source=\"EX_glc__D_e\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -270,11 +241,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "metadata": {
-    "collapsed": false,
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -304,10 +271,7 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {
-    "deletable": true,
-    "editable": true
-   },
+   "metadata": {},
    "source": [
     "Previous versions of cobrapy included more tailored plots for phase planes which have now been dropped in order to improve maintainability and enhance the focus of cobrapy. Plotting for cobra models is intended for another package."
    ]
@@ -329,9 +293,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.2"
+   "version": "3.6.3"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }