diff --git a/INSTALL.md b/INSTALL.md index e7b21b649..3df850265 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -6,12 +6,11 @@ For usage instructions, please see the -------------------------------------------------------------------------------- -All releases require Python 2.7 to be installed before proceeding. +All releases require Python 2.7+ or 3.4+ to be installed before proceeding. Mac OS X (10.7+) and Ubuntu ship with Python. Windows users without python can download and install python from the [python -website](http://www.python.org/download/releases/2.7.8/). +website](https://www.python.org/ftp/python/2.7.9/python-2.7.9.amd64.msi). -Python 3 support is still considered experimental. #Installation of cobrapy @@ -23,9 +22,9 @@ Python 3 support is still considered experimental. ### GNU/Linux 0. [install pip] (http://pip.readthedocs.org/en/latest/installing.html). -1. Install the python, glpk and gmp libraries. On debian-based +1. Install the python and glpk development libraries. On debian-based systems (including Ubuntu and Mint), this can be done with - ```sudo apt-get install python-dev libglpk-dev libgmp-dev``` + ```sudo apt-get install python-dev libglpk-dev``` 3. In a terminal, run ```sudo pip install cobra``` ### Microsoft Windows @@ -35,10 +34,10 @@ index](https://pypi.python.org/pypi/cobra/). ## Hacking version installation -Use pip to install [Cython](http://cython.org/). Install libglpk and libgmp -using your package manger. This would be ```brew install glpk gmp``` on a Mac -and ```sudo apt-get install libglpk-dev libgmp-dev``` on debian-based systems -(including Ubuntu and Mint). They can obviously also be compiled from the +Use pip to install [Cython](http://cython.org/). Install libglpk +using your package manger. This would be ```brew install glpk``` on a Mac +and ```sudo apt-get install libglpk-dev``` on debian-based systems +(including Ubuntu and Mint). GLPK can also be compiled from the released source. Clone the git repository using your preferred mothod. Cloning from your @@ -52,12 +51,12 @@ command: ## Optional Dependencies On windows, these can downloaded from [this site] (http://www.lfd.uci.edu/~gohlke/pythonlibs/). On Mac/Linux, they can be -installed using pip, from binary installers, or from package managers. +installed using pip, or from the OS package manager (e.g brew, apt, yum). 1. [libsbml](http://sbml.org) >= 5.10 to read/write SBML files * [Windows installer](http://www.lfd.uci.edu/~gohlke/pythonlibs/#libsbml) * Use ```sudo pip install python-libsbml-experimental``` on Mac/Linux -2. [numpy](http://numpy.org) >= 1.6.1 for double_deletion_analysis +2. [numpy](http://numpy.org) >= 1.6.1 for double deletions * [Windows installer](http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy) 3. [scipy](http://scipy.org) >= 0.11 for ArrayBasedModel and saving to *.mat files. * [Windows installer](http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy) @@ -77,7 +76,7 @@ solvers: * [QSopt_ex esolver](http://www.dii.uchile.cl/~daespino/ESolver_doc/main.html) * [MOSEK](http://www.mosek.com/) -ILOG/CPLEX and Gurobi are commercial software packages that, currently, +ILOG/CPLEX, MOSEK, and Gurobi are commercial software packages that currently provide free licenses for academics and support both linear and quadratic programming. GLPK is an opensource linear programming solver; however, it does not support quadratic programming and is not as robust as the