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Installing Topographica

Topographica is platform-independent, and all instructions below apply to Linux, UNIX, Mac, or Windows, unless otherwise specified. In Windows, to get a command prompt, you can use the Run command from the Start menu and enter cmd; on other systems you can start a Terminal or similar application.

The instructions below explain how to install Topographica using pip (for most users), using virtualenv (if you don’t have pip access or want a separate working environment, e.g. just to try out Topographica), or using git (if you want the latest version, or need to track our files using revision control).

First install Python

Topographica is written in Python, which is available for nearly all operating systems and is usually already installed (try running python --version from the command prompt). If Python version 2.6 or later is not installed, you can download the latest version for your system from python.org. Note that we do not yet support Python3, so if only python3 is installed you will need to install python2 as well (e.g. Python 2.7).

If Python isn’t already installed, it may be convenient to get it from one of the integrated scientific Python distributions like Python(X,Y), EPD, or Anaconda CE. These distributions are particularly useful for Windows and Mac users, who might not otherwise have a C compiler (necessary for good performance in Topographica) and optimized math and matrix libraries. On any system, the integrated distributions also provide a lot of useful related packages, including most of Topographica’s dependencies.

Quick recipe for Ubuntu Linux

If you’re installing on Ubuntu Linux 12.04, all you need to do is:

  1. sudo apt-get update
  2. sudo apt-get install python-pip python-tk python-imaging-tk python-numpy
  3. sudo apt-get install ipython python-gmpy python-matplotlib python-scipy
  4. sudo pip install topographica

Step 3 is optional, but highly recommended. The remaining sections below explain the general cross-platform procedure, but if you have problems on any particular platform, you might consider using an Ubuntu 12.04 virtual machine to try out Topographica so that you can use the simple recipe above. Similar approaches should work on other platforms, but we don’t currently have a list of the precise steps in each case.

Install via pip

The typical way to install the most recently released version of Topographica is via pip from the command prompt:

pip install --user topographica

This will fetch Topographica and its required dependencies (i.e., param, paramtk, imagen, numpy, and PIL, for the 0.9.8 release) from PyPI and install them into your home directory. The files will be stored in a subdirectory called .local on Linux and Mac, and into the user’s %APPDATA% subdirectory on Windows (typically named Application Data).

Beyond these absolutely required packages, you will probably also want to install others necessary for good performance (by at least a factor of 100), to provide some optional types of plotting, and to improve the command-line interface:

pip install --user gmpy matplotlib scipy ipython

Other useful packages are described on our dependencies page, and can usually be installed the same way.

If you have root or adminstrator access to your machine and want these libraries to be available to all users of your system, you can omit --user, or else install the dependencies via your system’s package manager, if any.

If your system does not have pip installed or has an old version lacking the --user option, but you do have root or administrator access, you should first install pip using:

easy_install pip

or the equivalent for your package manager. If you don’t have easy_install, you can install pip by downloading get-pip.py and running python get-pip.py.

Install via virtualenv

If your machine lacks pip and you do not have root or administrator access, then you can obtain a local copy of pip by downloading virtualenv.py. Just run it using Python to create a clean “virtual environment” that includes pip and into which you can install Topographica and its dependencies:

> python virtualenv.py VENV
> VENV/bin/pip install topographica
> VENV/bin/topographica -g

(Not tested under Windows.) You can then install any other dependencies using pip as described above. Of course, instead of VENV you can use any name you like for your virtual environment, and you can have multiple different virtual environments for different purposes.

Many people use virtualenv even if they do have root access, because it allows you to install whatever you like without affecting any other installations. Virtualenv is also an excellent way to try out Topographica, because you can simply delete the generated VENV directory if you decide not to keep the installation, with no effect on your system.

Install via Git

If you want the most current version of Topographica, or if you want to track Topographica development over time, you’ll want the github version of Topographica instead of installing it via pip.

Running Topographica

Because there are many ways a user might install Topographica (or any other Python package), the next step is to figure out where the topographica script (used for launching Topographica) and the example and model files (used as starting points for your modelling) ended up.

If you follow the instructions above, the topographica script is usually ~/.local/bin/topographica or ~/VENV/bin/topographica on Linux, UNIX, and Mac. On Windows pip installations it is usually %APPDATA%\Python\scripts\topographica (where %APPDATA% is something like C:\Users\jbednar\AppData\Roaming; AppData is often hidden in the filesystem so you may need to enable display of hidden files).

Once you’ve located the topographica script, it will save typing if you make sure that the location of that script is in your command prompt path. Instructions for doing so differ by platform, but should be easily obtainable. On Windows one convenient way to put the script on the path is to create a file called topographica.bat containing a single line like:

@C:\Python27\python.exe %APPDATA%\Python\scripts\topographica %*

(where you use the appropriate path to both Python and your topographica script) and put it somewhere in your path (e.g. C:\Windows\System32).

The example files are usually in ~/.local/share/topographica/examples/ on Linux, UNIX, and Mac systems, and in %APPDATA%\Python\Share\Topographica\examples on Windows, or in the corresponding VENV directories.

Once you’ve located the script and the examples, you can start the GUI version of Topographica from the command prompt using something like: topographica -g ~/.local/share/topographica/examples/tiny.ty or python %APPDATA%\Python\scripts\topographica -g %APPDATA%\Python\share\topographica\examples\tiny.ty (on Windows).

Running Topographica interactively is described in detail in the User Manual. If you want to get straight into working with a full network, a good way to begin is by working through the SOM or GCAL tutorials.

Have fun with Topographica, and be sure to subscribe to the topographica-announce mailing list to hear about future updates!