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Installation

Requirements

Those are Python packages necessary to run cochlea. Currently only Python 2.7 (64-bit) is supported.

  • Numpy
  • Scipy
  • Cython
  • Pandas
  • Matplotlib (optional, for examples)
  • docopt (optional, for the command line scripts)
  • thorns (optional, for examples and stats)
  • matlab_wrapper (optional, for the MAP external model)

Note: We recommend Anaconda Python distribution for Windows users. It comes with all required dependencies in one package.

Installation from PyPI

This is the easiest and recommended way to install cochlea.

On GNU/Linux/BSD, it will download the source package from Python Package Index (PyPI) repository, compile and install it on your system. On Windows, it will download a pre-compiled binary package and install it. Because the package is already compiled, you will not need Cython nor C compiler on Windows. Make sure that you have at least Numpy, Scipy and Pandas on your system, otherwise the installation program (pip) will try (and probably fail) to install them from PyPI.

Type in the console/terminal as root/administrator:

pip install cochlea

or to install for a single user (no root needed):

pip install --user cochlea

Installation from Source Code

First, clone the repository:

git clone https://github.com/mrkrd/cochlea.git

Second, call the installation script inside of the repository:

python setup.py install

The above is the standard way of installing a Python package from a source code. However, if I want follow changes to the source code closely, I prefer to do the following:

python setup.py develop --user

which installs just a link to the cloned repository. In this way, any change in the source code (git repo) is immediately reflected in the installation (no re-installation necessary).

It might be necessary to compile C/Cython code:

make

Installation from Source Code on Windows

Generally, the installation steps are the same as on GNU/Linux/BSD, but you will need to set up a proper environment to compile the Cython/C extensions.

I followed roughly the instructions from CythonExtensionsOnWindows. First of all, you will need Windows SDK (.NET 3.5 SP1). Next, I installed necessary requirements from the Unofficial Windows Binaries for Python Extension Packages repository (I'm not sure, if it would work with Anaconda's Numpy/Scipy/etc). And finally, you can run a script from the repository to compile the binary extensions:

build_windows_dist.bat

Followed by:

python setup.py install

If you get an error about missing _pycat while importing cochlea in Python, most likely the binary sub-modules are not compiled/installed.