====== python on Physics linux systems ======

Python is one of the most used interpreted languages for data analysis, competing directly with long-established commercial packages like Matlab or IDL.
  * [[http://docs.python.org/tutorial/|Official python tutorial]]
  * [[http://wiki.scipy.org/Topical_Software|Using Python for interactive data analysis in astronomy]] covers the Python's basics and all the important astronomical packages with many examples.

===== python versions on Scientific Linux=====

Different versions of the OS come with different versions of python.
  * SL5 comes by default with python 2.4, but python 2.6 is also available (called as ''/usr/bin/python26'').
  * SL6 comes by default with python 2.6, but 2.7 and 3.3 are available via RedHat's [[scl|software collections]]

===== Scientific packages =====

The most popular are
  * [[http://www.scipy.org|Scipy]] - The main scientific library
  * Numpy - Arrays manipulation library
  * [[http://matplotlib.org/|Matplotlib]] - 2D (and basic 3D) plotting library
  * [[http://ipython.org/documentation.html|IPython]] - An advanced interactive console 

All of these should be available by default on our systems (though see our notes below on how to install newer versions for yourself if wanted).


A wide variety of Astronomy-related python packages are installed as part of [[http://zzz.physics.umn.edu/computing/department/unix/python/ureka|Ureka]]
===== installing additional packages =====

You might find that some python packages you need are not available pre-packaged for our linux distribution, or the available version might be too old. There are a couple of ways you can handle this - first here is the simplest, installing the modules within your home directory (then read about "virtualenv" below for a cleaner solution).

To install a python module in your user space, download the tarball, unzip it, cd into the directory and run:

  python setup.py install --prefix=/path/to/your/place

The installer will create a subdirectory named ''lib'', or ''lib64'' under the directory above. These ''lib*'' dirs will have a directory named ''python'', or ''python2.6'' (for example), and those will have a subdirectory named ''site-packages''. Add all paths to these ''site-packages'' subdirectories in your ''PYTHONPATH'' environment variable. Some packages may also create a ''bin'' directory that needs to be added to ''PATH''. 

===== virtualenv =====

The virtualenv kit provides the ability to create virtual Python environments that do not interfere with either each other, or the main Python installation. If you install virtualenv before you begin coding then you can get into the habit of using it to create completely clean Python environments for each project. virtualenv should be installed on all SL6 Linux machines.

To create a new virtual environment (named "py_phys" in this example), run
  virtualenv py_phys
  
This will create a directory named py_phys in the current working directory. You can also specify a full path, e.g. ''virtualenv /tmp/py_phys''

To activate the new environment, use
  . py_phys/bin/activate
  
Once in the new environment, you can add packages using the ''pip'' command, eg:
  pip install packageName

===== Group or project software installs =====

Often a set of software will be used by an entire group rather than just one individual. We can set up specific areas for you to manage shared software, rather than within a home directory.