doc notebooks directly added with nbsphinx

This is done instead of converting them to rst first with nbconvert. The notebooks also needed to be run in IPython 3 to work around spatialaudio/nbsphinx#27
aebrahim · Mar 15, 2016 · b641b09 · b641b09
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commit b641b09
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diff --git a/documentation_builder/autodoc.sh b/documentation_builder/autodoc.sh
@@ -3,5 +3,3 @@ sphinx-apidoc -o . ../cobra ../cobra/oven ../cobra/external \
     ../cobra/test ../cobra/solvers/ ../cobra/test_all.py \
     ../cobra/version.py ../cobra/solvers/legacy.py
 rm modules.rst
-
-ipython nbconvert --to=rst *.ipynb
diff --git a/documentation_builder/building_model.ipynb b/documentation_builder/building_model.ipynb
@@ -99,7 +99,7 @@
     {
      "data": {
       "text/plain": [
-       "'malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c'"
+       "'ddcaACP_c + h_c + malACP_c --> 3omrsACP_c + ACP_c + co2_c'"
       ]
      },
      "execution_count": 3,
@@ -136,7 +136,7 @@
     {
      "data": {
       "text/plain": [
-       "frozenset({<Gene STM2378 at 0x7ff664f45490>, <Gene STM1197 at 0x7ff664f45950>})"
+       "frozenset({<Gene STM2378 at 0x7fada4592908>, <Gene STM1197 at 0x7fada45927f0>})"
       ]
      },
      "execution_count": 4,
@@ -232,16 +232,16 @@
      "text": [
       "Reactions\n",
       "---------\n",
-      "3OAS140 : malACP_c + h_c + ddcaACP_c --> co2_c + 3omrsACP_c + ACP_c\n",
+      "3OAS140 : ddcaACP_c + h_c + malACP_c --> 3omrsACP_c + ACP_c + co2_c\n",
       "\n",
       "Metabolites\n",
       "-----------\n",
+      "3omrsACP_c : C25H45N2O9PRS\n",
+      "ddcaACP_c : C23H43N2O8PRS\n",
+      "    ACP_c : C11H21N2O7PRS\n",
       "    co2_c : CO2\n",
       " malACP_c : C14H22N2O10PRS\n",
       "      h_c : H\n",
-      "ddcaACP_c : C23H43N2O8PRS\n",
-      "3omrsACP_c : C25H45N2O9PRS\n",
-      "    ACP_c : C11H21N2O7PRS\n",
       "\n",
       "Genes\n",
       "-----\n",
@@ -275,21 +275,21 @@
  ],
  "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": "2.7.6"
+   "pygments_lexer": "ipython3",
+   "version": "3.4.3"
   }
  },
  "nbformat": 4,

diff --git a/documentation_builder/building_model.rst b/documentation_builder/building_model.rst
diff --git a/documentation_builder/cobra.design.rst b/documentation_builder/cobra.design.rst
@@ -0,0 +1,22 @@
+cobra.design package
+====================
+
+Submodules
+----------
+
+cobra.design.design_algorithms module
+-------------------------------------
+
+.. automodule:: cobra.design.design_algorithms
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: cobra.design
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/documentation_builder/cobra.flux_analysis.rst b/documentation_builder/cobra.flux_analysis.rst
@@ -84,6 +84,14 @@ cobra.flux_analysis.single_deletion module
     :undoc-members:
     :show-inheritance:
 
+cobra.flux_analysis.summary module
+----------------------------------
+
+.. automodule:: cobra.flux_analysis.summary
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 cobra.flux_analysis.variability module
 --------------------------------------
 

diff --git a/documentation_builder/cobra.manipulation.rst b/documentation_builder/cobra.manipulation.rst
@@ -4,6 +4,14 @@ cobra.manipulation package
 Submodules
 ----------
 
+cobra.manipulation.annotate module
+----------------------------------
+
+.. automodule:: cobra.manipulation.annotate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 cobra.manipulation.delete module
 --------------------------------
 
@@ -20,6 +28,14 @@ cobra.manipulation.modify module
     :undoc-members:
     :show-inheritance:
 
+cobra.manipulation.validate module
+----------------------------------
+
+.. automodule:: cobra.manipulation.validate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

diff --git a/documentation_builder/cobra.rst b/documentation_builder/cobra.rst
@@ -7,6 +7,7 @@ Subpackages
 .. toctree::
 
     cobra.core
+    cobra.design
     cobra.flux_analysis
     cobra.io
     cobra.manipulation