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 is named after 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 has:

  • built in functions
  • modules such as math, os, glob, sys, time, and so many others

• Many external packages available

  • numpy Numerical Python

    In [4]: import numpy

  • scipy Scientific Tools for Python

  • search pipy (The Cheese Shop): Python Package Index

• Python Tutorial

Ipython Tips and Tricks

• Ipython: interactive computing environment

• ? 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>