Merge branch 'devel' of github.com:biosustain/cameo into devel

biosustain · May 18, 2015 · 3a446ef · 3a446ef
2 parents a33dba5 + 11fc41b
commit 3a446ef
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diff --git a/cameo/strain_design/heuristic/objective_functions.py b/cameo/strain_design/heuristic/objective_functions.py
@@ -121,7 +121,11 @@ class product_yield(ObjectiveFunction):
     """
     def __init__(self, product, substrate, *args, **kwargs):
         super(product_yield, self).__init__(*args, **kwargs)
+        if isinstance(product, Reaction):
+            product = product.id
         self.product = product
+        if isinstance(substrate, Reaction):
+            substrate = substrate.id
         self.substrate = substrate
 
     def __call__(self, model, solution, decoded_representation):

diff --git a/examples/DifferentialFVA.ipynb b/examples/DifferentialFVA.ipynb
diff --git a/examples/Gene Knockout Multiobjective.ipynb b/examples/Gene Knockout Multiobjective.ipynb
diff --git a/examples/Pathway Visualizations with Escher.ipynb b/examples/Pathway Visualizations with Escher.ipynb
diff --git a/examples/Reaction Knockout Multiobjective.ipynb b/examples/Reaction Knockout Multiobjective.ipynb
diff --git a/examples/Reaction Knockout Single Objective.ipynb b/examples/Reaction Knockout Single Objective.ipynb
diff --git a/examples/Simulation Methods.ipynb b/examples/Simulation Methods.ipynb
@@ -6,23 +6,7 @@
    "metadata": {
     "collapsed": false
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/joao/.virtualenvs/cameo-env/lib/python2.7/site-packages/IPython/parallel/client/client.py:452: RuntimeWarning: \n",
-      "            Controller appears to be listening on localhost, but not on this machine.\n",
-      "            If this is true, you should specify Client(...,sshserver='you@10.32.0.166')\n",
-      "            or instruct your controller to listen on an external IP.\n",
-      "  RuntimeWarning)\n",
-      "/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'processing (0.52-pathos)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.\n",
-      "/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'cameo (v0.2.0-51-gd721048-dirty)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.\n",
-      "/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'matlabengineforpython (R2014b)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.\n",
-      "/Users/joao/.venvburrito/lib/python2.7/site-packages/setuptools-8.2-py2.7.egg/pkg_resources.py:2443: PEP440Warning: 'pyre (0.8-pathos)' is being parsed as a legacy, non PEP 440, version. You may find odd behavior and sort order. In particular it will be sorted as less than 0.0. It is recommend to migrate to PEP 440 compatible versions.\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from cameo import load_model"
    ]
@@ -552,7 +536,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.9"
   }
  },
  "nbformat": 4,