.. _pyoverview

:Last modified: |today|

Python
======

Availability
------------
We provide python 2.7 and modules from Continuum Analytics (Anaconda)<https://store.continuum.io/cshop/anaconda>`_. 

Python modules
^^^^^^^^^^^^^^
Please email support-neuro@berkeley.edu to install or update modules. If you prefer to install a module in your home directory, you may use pip::

    pip install --user package_name

You may now access the python packages w/o any further modification.


Background
----------

  * `Python <http://python.org/>`_ is named after `Monty Python
    <http://en.wikipedia.org/wiki/Monty_Python>`_ , not the snake.

  * it is an interpreted language::

	In [1]: 1+1
	Out[1]: 2


  * you import modules or libraries::

	In [2]: import os

	In [3]: import glob


  * the `Standard Library <http://docs.python.org/library/>`_ has: 
 
    * built in `functions
      <http://docs.python.org/library/functions.html>`_

    * modules such as *math*, *os*, *glob*, *sys*, *time*, and so many
      others

  * *Many* external packages available

    * **numpy**  `Numerical Python <http://numpy.scipy.org/>`_ ::
 
	In [4]: import numpy
 
    * **scipy**  `Scientific Tools for Python <http://www.scipy.org/>`_

    * search pipy (The Cheese Shop): `Python Package Index <http://pypi.python.org/pypi>`_


  * `Python Tutorial <http://docs.python.org/tutorial/index.html>`_



Ipython Tips and Tricks
-----------------------

  * **Ipython**: `interactive computing environment <http://ipython.scipy.org/moin/>`_

  * **? and ??** : allows you to get information about modules, functions, and even see source code::

	In [1]: import os

	In [2]: os.getcwd?
	Type:		builtin_function_or_method
	Base Class:	<type 'builtin_function_or_method'>
	String Form:	<built-in function getcwd>
	Namespace:	Interactive
	Docstring:
	    getcwd() -> path   
	    Return a string representing the current working directory.

	
    An example of **??** ::

	In [5]: os.path.split??
	Type:		function
	Base Class:	<type 'function'>
	String Form:	<function split at 0x26e9f0>
	Namespace:	Interactive
	File:		/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py
	Definition:	os.path.split(p)
	Source:
	def split(p):
	    """Split a pathname.  Returns tuple "(head, tail)" where "tail" is
	    everything after the final slash.  Either part may be empty."""
	    i = p.rfind('/') + 1
	    head, tail = p[:i], p[i:]
	    if head and head != '/'*len(head):
	        head = head.rstrip('/')
	    return head, tail


  * **run** : allows you to run a script::

	In [4]: run myscript.py


  * **who, whos** : information about variables in workspace::

	In [5]: whos
	Variable     Type        Data/Info
	----------------------------------
	dictionary   dict        {'a': 1, 'b': 2}
	name         str         this is a string
	os           module      <module 'os' from '/Libra<...>.7/lib/python2.7/os.pyc'>
	times_two    function    <function times_two at 0x122d630>
	x            int         1
	y            int         2
	z            int         3

  * **psearch** : Search for object in namespaces by wildcard::

	In [3]: psearch os.w*
	os.wait
	os.wait3
	os.wait4
	os.waitpid
	os.walk
	os.write
	
  * **cpaste** : Allows you to paste & execute a pre-formatted code block from clipboard.  You must terminate the block with '--' (two minus-signs) alone on the line::

	In [6]: cpaste
	Pasting code; enter '--' alone on the line to stop.
	:def times_two(input):
	:    """doubles input and returns result"""
	:    print 'Im in times_two'
	:    return input + 2
	:
	:--
	

  * **hist** : hist -r history of what you have typed::

	In [6]: hist -r
	1: pwd
	2: ls
	3: cd ..
	4: run myscript.py
	5: whos
	6: hist -r

  * **macro** : save lines into macro for reuse::

	In [7]: myname = 'cindee'
	In [8]: myname.upper()
	Out[8]: 'CINDEE'
	In [9]: macro nme 7-8
	Macro `nme` created. To execute, type its name (without quotes).
	Macro contents:
	myname = 'cindee'
	myname.upper()
	In [10]: nme
	-------> nme()
	Out[12]: 'CINDEE'

  * **lsmagic** : shows all ipython magic functions::

	In [13]: lsmagic
	Available magic functions:
	%Exit  %Pprint  %Quit  %alias  %autocall  %autoindent  %automagic  
	%bg  %bookmark  %cd  %clear  %color_info  %colors  %cpaste  %debug  	
	%dhist  %dirs  %doctest_mode  %ed  %edit  %env  %exit  %hist  %history  
	%logoff  %logon  %logstart  %logstate  %logstop  %lsmagic  %macro  %magic  
	%p  %page  %paste  %pdb  %pdef  %pdoc  %pfile  %pinfo  %popd  %profile  
	%prun  %psearch  %psource  %pushd  %pwd  %pycat  %quickref  %quit  %r  
	%rehash  %rehashx  %rep  %reset  %run  %runlog  %save  %sc  %store  %sx  
	%system_verbose  %time  %timeit  %unalias  %upgrade  %who  %who_ls  
	%whos  %xmode

	Automagic is ON, % prefix NOT needed for magic functions.


  * **pdb** : starts the python debugger::

	In [14]: pdb
	Automatic pdb calling has been turned ON

	In [15]: jnk = 'abcdefg'

	In [16]: jnk.sort()
	---------------------------------------------------------------------------
	AttributeError                            Traceback (most recent call last)

	/Users/cindeem/Documents/Research/teaching/myscript.py in <module>()
	----> 1 
	      2 
	      3 
	      4 
	      5 

	AttributeError: 'str' object has no attribute 'sort'
	> <ipython console>(1)<module>()

	ipdb>