Merge branch 'release-0.10'

.travis.yml

@@ -0,0 +1,5 @@
+language: python
+python:
+  - "2.7"
+install: 'pip install .'
+script: './setup.py test'

NEWS.md

@@ -1,4 +1,13 @@
 
+v0.10.2 (2015-05-22)
+--------------------
+
+- Various minor documentation and packaging updates. PSAMM is now available
+  through [PyPI](https://pypi.python.org/pypi/psamm) and the documentation has
+  been updated to reflect this. The documentation is available through
+  [Read the Docs](https://psamm.readthedocs.org/). Lastly, the test suite is
+  automatically run by [Travis CI](https://travis-ci.org/zhanglab/psamm).
+
 v0.10.1 (2015-05-21)
 --------------------
 

README.md → README.rst

@@ -1,46 +1,51 @@
 PSAMM metabolic modeling tools
 ==============================
 
+.. image:: https://travis-ci.org/zhanglab/psamm.svg?branch=develop
+   :alt: Build Status
+   :target: https://travis-ci.org/zhanglab/psamm
+.. image:: https://readthedocs.org/projects/psamm/badge/?version=latest
+   :alt: Documentation Status
+   :target: https://readthedocs.org/projects/psamm/?badge=latest
+.. image:: https://badge.fury.io/py/psamm.svg
+   :alt: Package Status
+   :target: https://pypi.python.org/pypi/psamm
+
 Tools related to metabolic modeling, reconstruction, data parsing and
 formatting, consistency checking, automatic gap filling, and model simulations.
 
-See [NEWS](NEWS.md) for information on recent changes. The `master` branch
+See NEWS_ for information on recent changes. The `master` branch
 tracks the latest release while the `develop` branch is the latest version in
 development. Please apply any pull requests to the `develop` branch when
 creating the pull request.
 
+.. _NEWS: NEWS.md
+
 Install
 -------
 
-Use `pip` to install (it is recommended to use a
-[Virtualenv](https://virtualenv.pypa.io/)):
+Use `pip` to install (it is recommended to use a Virtualenv_):
 
-``` shell
-$ pip install git+https://github.com/zhanglab/psamm.git
-```
+.. code:: shell
 
-The `psamm-import` tool is developed in
-[a separate repository](https://github.com/zhanglab/psamm-import). After
+    $ pip install psamm
+
+The `psamm-import` tool is developed in `a separate repository`_. After
 installing PSAMM the `psamm-import` tool can be installed using:
 
-``` shell
-$ pip install git+https://github.com/zhanglab/psamm-import.git
-```
+.. code:: shell
+
+    $ pip install git+https://github.com/zhanglab/psamm-import.git
+
+.. _Virtualenv: https://virtualenv.pypa.io/
+.. _a separate repository: https://github.com/zhanglab/psamm-import
 
 Documentation
 -------------
 
-See the bundled documentation for more information. The documentation can be
-generated using [Sphinx](http://sphinx-doc.org/):
-
-``` shell
-$ git clone git@github.com:zhanglab/psamm.git
-$ pip install -e psamm[docs]
-$ cd psamm/docs/
-$ make html
-```
+The documentation for PSAMM is available at `Read the Docs`_.
 
-Then open `psamm/docs/_build/html/index.html`.
+.. _Read the Docs: https://psamm.readthedocs.org/
 
 Software license
 ----------------
@@ -58,4 +63,6 @@ GNU General Public License for more details.
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-See [LICENCE](LICENSE).
+See LICENSE_.
+
+.. _LICENSE: LICENSE

docs/index.rst

@@ -7,6 +7,7 @@ Contents:
 .. toctree::
    :maxdepth: 2
 
+   overview
    install
    file_format
    commands

docs/install.rst

@@ -7,7 +7,7 @@ The Python module can be installed using ``pip``. This will typically require
 
 .. code-block:: shell
 
-    $ pip install git+https://github.com/zhanglab/psamm.git
+    $ pip install psamm
 
 Another option that does not require *root* permissions is to use a
 `Virtualenv`_. First set up a new environment in your project directory and

docs/overview.rst

@@ -0,0 +1,30 @@
+
+Overview
+========
+
+PSAMM is a collection of tools related to metabolic modeling, model
+reconstruction, data parsing and formatting, consistency checking,
+automatic gap filling, and model simulations.
+
+PSAMM is developed as an open source project, coordinated through `Github`_.
+The PSAMM software is being developed in the `Zhang Laboratory`_ at the University of Rhode Island and
+is the subject of a research article that has been submitted for
+review. [Steffensen15]_
+
+.. _Github: https://github.com/zhanglab/psamm
+.. _Zhang Laboratory: http://zhanglab.uri.edu/
+
+Software license
+----------------
+
+PSAMM is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program. If not, see http://www.gnu.org/licenses/.

docs/references.rst

@@ -2,21 +2,21 @@
 References
 ==========
 
-.. [Gevorgyan08] Gevorgyan, Albert, Mark G. Poolman, and David a. Fell. 2008.
-    “Detection of Stoichiometric Inconsistencies in Biomolecular Models.”
-    Bioinformatics 24 (19): 2245–51. :doi:`10.1093/bioinformatics/btn425`.
-.. [Kumar07] Satish Kumar, Vinay, Madhukar S Dasika, and Costas D Maranas.
-    2007. “Optimization Based Automated Curation of Metabolic Reconstructions.”
-    BMC Bioinformatics 8 (January): 212. :doi:`10.1186/1471-2105-8-212`.
-.. [Muller13] Müller, Arne C, and Alexander Bockmayr. 2013.
-    “Fast Thermodynamically Constrained Flux Variability Analysis.”
-    Bioinformatics (Oxford, England) 29 (7): 903–9.
+.. [Steffensen15] Steffensen JL, Dufault-Thompson K, Zhang Y. PSAMM: A Portable
+    System for the Analysis of Metabolic Models. Submitted.
+
+.. [Gevorgyan08] Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric
+    inconsistencies in biomolecular models. Bioinformatics. 2008;24: 2245–2251.
+    :doi:`10.1093/bioinformatics/btn425`.
+.. [Kumar07] Satish Kumar V, Dasika MS, Maranas CD. Optimization based
+    automated curation of metabolic reconstructions. BMC Bioinformatics.
+    2007;8: 212. :doi:`10.1186/1471-2105-8-212`.
+.. [Muller13] Müller AC, Bockmayr A. Fast thermodynamically constrained flux
+    variability analysis. Bioinformatics. 2013;29: 903–909.
     :doi:`10.1093/bioinformatics/btt059`.
-.. [Thiele14] Thiele, Ines, Nikos Vlassis, and Ronan M T Fleming. 2014.
-    “FASTGAPFILL : Efficient Gap Filling in Metabolic Networks.”
-    Bioinformatics (Oxford, England) 30 (17): 15–17.
+.. [Thiele14] Thiele I, Vlassis N, Fleming RMT. fastGapFill: efficient gap
+    filling in metabolic networks. Bioinformatics. 2014;30: 2529–31.
     :doi:`10.1093/bioinformatics/btu321`.
-.. [Vlassis14] Vlassis, Nikos, Maria Pires Pacheco, and Thomas Sauter. 2014.
-    “Fast Reconstruction of Compact Context-Specific Metabolic Network Models.”
-    PLoS Computational Biology 10 (1): e1003424.
-    :doi:`10.1371/journal.pcbi.1003424`.
+.. [Vlassis14] Vlassis N, Pacheco MP, Sauter T. Fast Reconstruction of Compact
+    Context-Specific Metabolic Network Models. PLoS Comput Biol. 2014;10:
+    e1003424. :doi:`10.1371/journal.pcbi.1003424`.

setup.py

@@ -18,17 +18,25 @@
 
 from setuptools import setup, find_packages
 
+# Read long description
+with open('README.rst') as f:
+    long_description = f.read()
+
 setup(
     name='psamm',
-    version='0.10.1',
+    version='0.10.2',
     description='PSAMM metabolic modeling tools',
     maintainer='Jon Lund Steffensen',
     maintainer_email='jon_steffensen@uri.edu',
-    url='https://github.com/zhanglab/model_script',
+    url='https://github.com/zhanglab/psamm',
     license='GNU GPLv3+',
 
+    long_description=long_description,
+
     classifiers = [
-        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)'
+        'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
+        'Programming Language :: Python :: 2.7'
     ],
 
     packages=find_packages(),