Uploaded to pip. Fixes #2.

Author: cdiener

README.md

@@ -30,7 +30,13 @@ conda install -c bioconda cobra
 After that you can install CORDA using the pip from conda
 
 ```bash
-pip install https://github.com/cdiener/corda/archive/master.zip
+pip install corda
+```
+
+To install the latest development version use
+
+```bash
+pip install https://github.com/cdiener/corda/archive/devel.zip
 ```
 
 After CORDA for Python comes out of its infancy I will prepare a conda package

docs/index.ipynb

@@ -171,9 +171,9 @@
      "output_type": "stream",
      "text": [
       "build status: reconstruction complete\n",
-      "Inc. reactions: 33/101\n",
+      "Inc. reactions: 20/60\n",
       " - unclear: 0/0\n",
-      " - exclude: 32/100\n",
+      " - exclude: 19/59\n",
       " - low and medium: 0/0\n",
       " - high: 1/1\n",
       "\n"
@@ -192,7 +192,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The metric you see are for irreversible reactions. We can obtain the reversible reconstruction using:"
+    "The metric you see are for reversible reactions. We can obtain the irreversible reconstruction metrics by using:"
    ]
   },
   {
@@ -203,19 +203,21 @@
    },
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "33"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "build status: reconstruction complete\n",
+      "Inc. reactions: 32/101\n",
+      " - unclear: 0/0\n",
+      " - exclude: 31/100\n",
+      " - low and medium: 0/0\n",
+      " - high: 1/1\n",
+      "\n"
+     ]
     }
    ],
    "source": [
-    "rec = opt.cobra_model(name=\"minimum\")\n",
-    "len(rec.reactions)"
+    "print(opt.info(reversible=False))"
    ]
   },
   {
@@ -245,9 +247,9 @@
      "output_type": "stream",
      "text": [
       "build status: reconstruction complete\n",
-      "Inc. reactions: 39/102\n",
+      "Inc. reactions: 24/61\n",
       " - unclear: 0/0\n",
-      " - exclude: 37/100\n",
+      " - exclude: 22/59\n",
       " - low and medium: 0/0\n",
       " - high: 2/2\n",
       "\n"
@@ -278,24 +280,24 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "38\n",
+      "37\n",
       "2pg <=> pep\n",
       "gtp + oaa <=> gdp + pep\n"
      ]
     }
    ],
    "source": [
-    "rec2 = opt.cobra_model(\"plus_pep\")\n",
-    "print(len(rec2.reactions))\n",
-    "use = rec2.metabolites.pep.reactions\n",
+    "rec = opt.cobra_model(\"plus_pep\")\n",
+    "print(len(rec.reactions))\n",
+    "use = rec.metabolites.pep.reactions\n",
     "for r in use: print(r.reaction)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As we can see the algorithm actually included two different ways of producing pep, from 3pg and from oaa and several other reactions. This is due to automatic inclusion of redundant pathways (which is good since it gives your model some robustness). If we do not want that feature we can modify the parameter n in the CORDA initializer."
+    "By default CORDA uses redundancy. This means, in case there are several minimal pathways to reach your objective, CORDA will include several of those (which is good since it gives your model some robustness). If we do not want that feature we can modify the parameter n in the CORDA initializer which denotes the maximum number of redundant pathways to include."
    ]
   },
   {
@@ -309,7 +311,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "33\n",
+      "31\n",
       "gtp + oaa <=> gdp + pep\n"
      ]
     }
@@ -318,9 +320,9 @@
     "opt = CORDA(mod, conf, met_prod=\"pep\", n=1)\n",
     "opt.build()\n",
     "\n",
-    "rec3 = opt.cobra_model(\"plus_pep_nored\")\n",
-    "print(len(rec3.reactions))\n",
-    "use = rec3.metabolites.pep.reactions\n",
+    "rec_min = opt.cobra_model(\"plus_pep_nored\")\n",
+    "print(len(rec_min.reactions))\n",
+    "use = rec_min.metabolites.pep.reactions\n",
     "for r in use: print(r.reaction)"
    ]
   },

setup.py

@@ -13,7 +13,7 @@
 
 setup(
     name='corda',
-    version='0.0.5',
+    version='0.1',
     description='Genome-scale model construction with CORDA',
     long_description=long_description,
     url='https://github.com/cdiener/corda',