Merge branch 'release-0.10'

NEWS.md

@@ -1,4 +1,10 @@
 
+v0.10.1 (2015-05-21)
+--------------------
+
+- Update README with new repository names and improved install instructions.
+- docs: Add improved install instructions based on README.
+
 v0.10 (2015-05-14)
 ------------------
 

README.md

@@ -16,7 +16,15 @@ Use `pip` to install (it is recommended to use a
 [Virtualenv](https://virtualenv.pypa.io/)):
 
 ``` shell
-$ pip install git+ssh://git@github.com/zhanglab/model_script.git
+$ pip install git+https://github.com/zhanglab/psamm.git
+```
+
+The `psamm-import` tool is developed in
+[a separate repository](https://github.com/zhanglab/psamm-import). After
+installing PSAMM the `psamm-import` tool can be installed using:
+
+``` shell
+$ pip install git+https://github.com/zhanglab/psamm-import.git
 ```
 
 Documentation
@@ -26,13 +34,13 @@ 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/model_script.git
-$ pip install -e model_script[docs]
-$ cd model_script/docs/
+$ git clone git@github.com:zhanglab/psamm.git
+$ pip install -e psamm[docs]
+$ cd psamm/docs/
 $ make html
 ```
 
-Then open `model_script/docs/_build/html/index.html`.
+Then open `psamm/docs/_build/html/index.html`.
 
 Software license
 ----------------

docs/install.rst

@@ -2,27 +2,33 @@
 Install
 =======
 
-The Python module can be installed using ``pip``. It is also possible to
-install a specific tag or branch by appending the name to the Git URL (e.g.
-append ``@v0.1`` to get the tag ``v0.1``). This will typically require ``root``
-permission.
+The Python module can be installed using ``pip``. This will typically require
+*root* permissions.
 
 .. code-block:: shell
 
-    $ pip install git+ssh://git@github.com/zhanglab/model_script.git
+    $ pip install git+https://github.com/zhanglab/psamm.git
 
-Another option is to use ``virtualenv``. First set up a new environment in the
-project directory, and activate it.
+Another option that does not require *root* permissions is to use a
+`Virtualenv`_. First set up a new environment in your project directory and
+activate it:
 
 .. code-block:: shell
 
     $ virtualenv env
     $ . env/bin/activate
 
 Now the Python module can be installed in the virtual environment using the
-``pip`` command without requiring ``root`` permissions. When returning to the
+``pip`` command without requiring *root* permissions. When returning to the
 project, simply reactivate the environment by running the second command.
 
+The *psamm-import* tool is developed in a separate Git repository. After
+installing PSAMM, the *psamm-import* tool can be installed using:
+
+.. code-block:: shell
+
+    $ pip install git+https://github.com/zhanglab/psamm-import.git
+
 Dependencies
 ------------
 
@@ -43,10 +49,10 @@ The Cplex Python bindings will have to be installed manually. If you are using
 a virtual environment (as described above) this should be done after activating
 the virtual environment:
 
-1. Go to the Cplex install directory: ``cd /path/to/Cplex``
-2. Go to the appropriate subdirectory based on your platform:
-   ``cd cplex/python/<platform>``
-3. Run ``pip install .``
+1. Locate the directory where Cplex was installed (e.g. ``/path/to/IBM/ILOG/CPLEX_StudioXXX``).
+2. Locate the appropriate subdirectory based on your platform:
+   ``cplex/python/<platform>`` (e.g. ``cplex/python/x86-64_osx``).
+3. Use ``pip`` to install the package from this directory: ``pip install /path/to/IBM/ILOG/CPLEX_StudioXXX/cplex/python/<platform>``
 
 QSopt_ex
 --------
@@ -59,6 +65,7 @@ can be installed using ``pip``:
 
     $ pip install python-qsoptex
 
+.. _Virtualenv: https://virtualenv.pypa.io/
 .. _python-qsoptex: https://pypi.python.org/pypi/python-qsoptex
 .. _GnuMP: https://gmplib.org/
 .. _QSopt_ex library: https://github.com/jonls/qsopt-ex

setup.py

@@ -20,7 +20,7 @@
 
 setup(
     name='psamm',
-    version='0.10',
+    version='0.10.1',
     description='PSAMM metabolic modeling tools',
     maintainer='Jon Lund Steffensen',
     maintainer_email='jon_steffensen@uri.edu',