update

Author: sthiele

MANIFEST.in

@@ -1,3 +1,3 @@
 include src/encodings/*.lp
-include CHANGES.txt
-include README.rst
+include CHANGELOG.md
+include README.md

README.md

@@ -1,44 +1,42 @@
 # Installation
 
-
 You can install meneco by running:
 
     > pip install --user meneco
 
-On Linux the executable script can then be found in ``~/.local/bin``
+On Linux the executable script can then be found in `~/.local/bin`
 
-and on MacOS the script is under ``/Users/YOURUSERNAME/Library/Python/3.2/bin``.
+and on MacOS the script is under `/Users/YOURUSERNAME/Library/Python/3.2/bin`.
 
 
 # Usage Command line interface
 
 Typical usage is:
 
-    > meneco.py -d draftnetwork.sbml -s seeds.sbml -t targets.sbml -r repairnetwork.sbml 
+    > meneco.py -d draftnetwork.sbml -s seeds.sbml -t targets.sbml -r repairnetwork.sbml
 
 For more options you can ask for help as follows:
 
-     > meneco.py --h
-     usage: meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
-                      [--enumerate]
+    > meneco.py --h
+    usage: meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
+                     [--enumerate]
 
-     optional arguments:
-       -h, --help            show this help message and exit
-       -d DRAFTNET, --draftnet DRAFTNET
-                             metabolic network in SBML format
-       -s SEEDS, --seeds SEEDS
-                             seeds in SBML format
-       -t TARGETS, --targets TARGETS
-                             targets in SBML format
-       -r REPAIRNET, --repairnet REPAIRNET
-                             perform network completion using REPAIRNET a metabolic
-                             network in SBML format
-       --enumerate           enumerate all minimal completions
+    optional arguments:
+      -h, --help            show this help message and exit
+      -d DRAFTNET, --draftnet DRAFTNET
+                            metabolic network in SBML format
+      -s SEEDS, --seeds SEEDS
+                            seeds in SBML format
+      -t TARGETS, --targets TARGETS
+                            targets in SBML format
+      -r REPAIRNET, --repairnet REPAIRNET
+                            perform network completion using REPAIRNET a metabolic
+                            network in SBML format
+      --enumerate           enumerate all minimal completions
 
 
 # Usage Library
 
-
 For a guided example, see a demonstration IPython [Notebook](http://nbviewer.jupyter.org/github/bioasp/meneco/blob/master/meneco.ipynb).
 
 

meneco.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This notebook is a preview demo of [meneco](https://pypi.python.org/pypi/meneco/) combined with the [IPython](http://ipython.org/) interactive environment. This demo assumes you have meneco 1.5.2 already installed.  "
+    "This notebook is a preview demo of [meneco](https://pypi.python.org/pypi/meneco/) combined with the [IPython](http://ipython.org/) interactive environment. This demo assumes you have meneco 1.5.3 already installed.  "
    ]
   },
   {

setup.py

@@ -16,15 +16,16 @@
 # along with meneco.  If not, see <http://www.gnu.org/licenses/>.
 # -*- coding: utf-8 -*-
 from setuptools import setup
-                         
+
 setup(
   name             = 'meneco',
   version          = '1.5.3',
   url              = 'http://bioasp.github.io/meneco/',
   license          = 'GPLv3+',
   description      = 'Metabolic Network Completion. Compute minimal completions '
                      'to your draft network with reactions from a repair network.',
-  long_description = open('README.rst').read(),
+  long_description = open('README.md').read(),
+  long_description_content_type="text/markdown",
   author           = 'Sven Thiele',
   author_email     = '[email protected]',
   packages         = ['__meneco__'],