An Intro to Python

1
An Intro to Python

• Randy Heiland
• heiland_at_indiana.edu
• June 17, 2008

2
An Intro to Python

• How I learned to stop worrying and loved to
  develop software again.

3
Python - a scripting language

• Released in 1991 by Guido van Rossum (at Google
  since Dec 05 where Python is heavily used)
• Python is absolutely free, even for commercial
  use
• Dynamically typed
• Strongly typed
• Auto memory mgt

4
Whats so great about Python?

• High-level lng Syntax (minimal, clean)
• Interpreted Interactive
• (--gt rapid prototyping/development)
• Glue-iness, Wrap-ability (www.swig.org)
• Introspection
• History with science apps (my 1st exposure, LANL)
• Vibrant (community) and evolving (language)
• www.python.org/doc/Humor.html

5
In a nutshell

• Software engineers stay sane while continuing to
  be very productive
• Application scientists arent put off by
  programming complexity
• Creates a short bridge between the two

6
Implementations

• C CPython
• Java Jython
• .NET IronPython

7
So show me some code!
interpreter

• python
• Python 2.5.1
• gtgtgt x 'Euler'
• gtgtgt x
• 'Euler'
• gtgtgt x 2.718
• gtgtgt x 5j
• gtgtgt x
• (2.7185j)
• gtgtgt x.real, x.imag
• (2.718, 5.0)

dynamic typing
8

• gtgtgt x'2'
• gtgtgt y2
• gtgtgt xy
• Traceback (most recent call last)
• File "ltstdingt", line 1, in ltmodulegt
• TypeError cannot concatenate 'str' and 'int'
  objects
• gtgtgt int(x) y
• 4

interpreter

• python
• Python 2.5.1
• gtgtgt x 'Euler'
• gtgtgt x
• 'Euler'
• gtgtgt x 2.718
• gtgtgt x 5j
• gtgtgt x
• (2.7185j)
• gtgtgt x.real, x.imag
• (2.718, 5.0)

strong typing
dynamic typing
9
Python Functions

• gtgtgt def foo(x,y)
• ... z xy
• ... print z
• ...
• gtgtgt foo(3,4)
• 12
• gtgtgt foo(fun',5)
• funfunfunfunfun

Indentation required for statement blocks
10
Python vs. Perl syntaxe.g. hash (dictionary vs.
assoc array)

• for i in range(5)
• x
• for j in range(3)
• xji j
• print x
• --gt outputs
• 0 0, 1 1, 2 2
• 0 1, 1 2, 2 3
• 0 2, 1 3, 2 4
• 0 3, 1 4, 2 5
• 0 4, 1 5, 2 6

• for i (0 .. 6000-1)
• x()
• for j (0 .. 1000-1)
• xji j
• xj

11
Python Modules

• A module is a file containing Python definitions
  and statements
• ltmodule-namegt.py
• import the module to use it
• .pyc byte-compiled, arch-independent file

• E.g. in file foo.py
• def foo(x,y)
• z xy
• print z

12
Large standard library(Python batteries
included)
Just one example module

• gtgtgt import os
• gtgtgt dir(os)
• '_copy_reg', '_execvpe', '_exists', '_exit',
  '_get_exports_list', '_make_stat_result',
  '_make_statvfs_result', '_pickle_stat_result',
  '_pickle_statvfs_result', '_spawnvef', 'abort',
  'access', 'altsep', 'chdir', 'chmod', 'chown',
  'chroot', 'close', 'confstr', 'confstr_names',
  'ctermid', 'curdir', 'defpath', 'devnull', 'dup',
  'dup2', 'environ', 'error', 'execl', 'execle',
  'execlp', 'execlpe', 'execv', 'execve', 'execvp',
  'execvpe', 'extsep', 'fchdir', 'fdopen', 'fork',
  'forkpty', 'fpathconf', 'fstat', 'fstatvfs',
  'fsync', 'ftruncate', 'getcwd', 'getcwdu',
  'getegid', 'getenv', 'geteuid', 'getgid',
  'getgroups', 'getloadavg', 'getlogin', 'getpgid',
  'getpgrp', 'getpid', 'getppid', 'getsid',
  'getuid', 'isatty', 'kill', 'killpg', 'lchown',
  'linesep', 'link', 'listdir', 'lseek', 'lstat',
  'major', 'makedev', 'makedirs', 'minor', 'mkdir',
  'mkfifo', 'mknod', 'name', 'nice', 'open',
  'openpty', 'pardir', 'path', 'pathconf',
  'pathconf_names', 'pathsep', 'pipe', 'popen',
  'popen2', 'popen3', 'popen4', 'putenv', 'read',
  'readlink', 'remove', 'removedirs', 'rename',
  'renames', 'rmdir', 'sep', 'setegid', 'seteuid',
  'setgid', 'setgroups', 'setpgid', 'setpgrp',
  'setregid', 'setreuid', 'setsid', 'setuid',
  'spawnl', 'spawnle', 'spawnlp', 'spawnlpe',
  'spawnv', 'spawnve', 'spawnvp', 'spawnvpe',
  'stat', 'stat_float_times', 'stat_result',
  'statvfs', 'statvfs_result', 'strerror',
  'symlink', 'sys', 'sysconf', 'sysconf_names',
  'system', 'tcgetpgrp', 'tcsetpgrp', 'tempnam',
  'times', 'tmpfile', 'tmpnam', 'ttyname', 'umask',
  'uname', 'unlink', 'unsetenv', 'urandom',
  'utime', 'wait', 'wait3', 'wait4', 'waitpid',
  'walk', 'write'

13
Another standard lib module

• gtgtgt import math
• gtgtgt dir(math)
• '__doc__', '__file__', '__name__', 'acos',
  'asin', 'atan', 'atan2', 'ceil', 'cos', 'cosh',
  'degrees', 'e', 'exp', 'fabs', 'floor', 'fmod',
  'frexp', 'hypot', 'ldexp', 'log', 'log10',
  'modf', 'pi', 'pow', 'radians', 'sin', 'sinh',
  'sqrt', 'tan', 'tanh'
• gtgtgt math.cos(math.pi)
• -1.0

Alternatively gtgtgt from math import gtgtgt cos(pi)
14
Beyond the standard lib - installing community
modules

• There are many freely available community (3rd
  party) modules available. You just need to
  install them - e.g., from a shell
• python setup.py install
• If the installation method is not obvious from
  the modules download site, rf
• http//docs.python.org/inst/inst.html
• http//peak.telecommunity.com/DevCenter/EasyInstal
  l

15
Beyond the standard lib - community packages -
e.g. NumPy

• Google for numpy, download/install it.
• gtgtgt from numpy import arange
• gtgtgt tvals arange(0.,5., 0.1)
• gtgtgt tvals
• array( 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,
  0.7, 0.8, 0.9, 1. ,
• 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7,
  1.8, 1.9, 2. , 2.1,
• 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8,
  2.9, 3. , 3.1, 3.2,
• 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9,
  4. , 4.1, 4.2, 4.3,
• 4.4, 4.5, 4.6, 4.7, 4.8, 4.9)
• gtgtgt tvals1
• 0.10000000000000001

16
MATLAB vs. Python/NumPy

• www.scipy.org/NumPy_for_Matlab_Users
• gtgtgt from numpy import
• gtgtgt b array( (1.5,2,3), (4,5,6) )
• gtgtgt b
• array( 1.5, 2. , 3. ,
• 4. , 5. , 6. )
• gtgtgt b.shape
• (2, 3)
• gtgtgt dir(linalg)
• 'LinAlgError', '__builtins__', '__doc__',
  '__file__', '__name__', '__path__', 'cholesky',
  'det', 'eig', 'eigh', 'eigvals', 'eigvalsh',
  'info', 'inv', 'lapack_lite', 'linalg', 'lstsq',
  'norm', 'pinv', 'qr', 'solve', 'svd',
  'tensorinv', 'tensorsolve', 'test'

NOTE NumPy is written in C and therefore quite
fast
17
Basic Data Structures

• Lists
• Tuples
• Sets
• Dictionaries

• gtgtgt a 2.718, 'fred', 13
• gtgtgt dir(a)
• 'append', 'count', 'extend', 'index', 'insert',
  'pop', 'remove', 'reverse', 'sort'
• gtgtgt a1 56
• gtgtgt a
• 2.718, 56, 13
• gtgtgt a.sort()
• gtgtgt a
• 2.718, 13, 56

(mutable)
18
Basic Data Structures (cont.)

• List comprehensions - concise way to map or
  filter lists

• gtgtgt a
• 2.718, 13, 56
• gtgtgt import math
• gtgtgt math.exp(x) for x in a
• 15.149991940878165, 442413.39200892049,
  2.0916594960129961e24

in the std lib
19
Basic Data Structures (cont.)

• dictionary - 11 reln between key-value pairs
• (hash in Perl Hashtable in Java)

• gtgtgt simParam dict(latticesquare,
  xdim100,ydim100,hex1)
• gtgtgt grids
• square' 0, hex' 1
• gtgtgt dir(IUtoys)
• , 'clear', 'copy', 'fromkeys', 'get',
  'has_key', 'items', 'iteritems', 'iterkeys',
  'itervalues', 'keys', 'pop', 'popitem',
  'setdefault', 'update', 'values'

20
(free) Python shells

• IDLE
• ConTEXT (Windows only)
• IPython (ipython.scipy.org)
• Eclipse w/ pydev

21
Testimonials/Users

• Google
• YouTube
• LLNL, ANL, LBL, LANL
• May/June 2007 issue of Computing in Science
  Engineering (CiSE)

22
Useful Python pkgs

• Data/Analysis
• DBs mysql-python
• Numerics NumPy
• RPy R from Python
• Storage (HDF5) PyTables
• Visualization
• SciVis VTK (Python bindings)
• Plotting matplotlib
• Graphs bgl-python

23
Useful Python pkgs (cont)

• Science
• Chemistry UCSF Chimera, PyMOL, VMD
• Bioinfo BioPython
• Physics PyROOT
• Imaging ITK (Python bindings)
• www.scipy.org/Topical_Software
• www.python.org/about/apps

24
Useful Python pkgs (cont)

• Infrastructure
• Web dev django, TurboGears
• Web Services ZSI, xml
• HPC pyMPI, MYMPI, pp
• 
  (parallelpython.com)
• Grid pyGlobus, pyGridWare
• Star-P Python client
• www.interactivesupercomputing.com/starpexpres
  s/042007/8_Python_Users.html

25
matplotlib

• gtgtgt from pylab import
• gtgtgt def my_func(t)
• s1 cos(2pit)
• e1 exp(-t)
• return s1e1
• gtgtgt tvals arange(0., 5., 0.1)
• gtgtgt plot(tvals, my_func(tvals))
• ltmatplotlib.lines.Line2D object at 0x16ca9d50gt
• gtgtgt show()
• gtgtgt plot(tvals, my_func(tvals), 'bo', tvals,
  my_func(tvals), 'k')
• gtgtgt show()

26
Python-related projects at IU
lifescienceweb.org SDA Lab Mooney Lab
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chembiogrid.org
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CompuCell3D
James Glazier, Physics Simulate cellular
behavior
29
NLOPredict Simpson Lab SDA Lab

• UCSF Chimera (molecular viewer)
• NumPy
• matplotlib

30
VisPort server
ZSI Python-wrapped VTK PyTables pyGlobus