Python/programming

Available online

Feel free to click along!

http://tinyurl.com/slf-python-day1

Python/programming workshop

Advanced programming

Required prior to workshop

• One year of general programming experience
• Basic understanding of Python
• Ability to start a terminal, execute commands
• Installed Python distribution — preferably Enthought or Anaconda

Daily structure

1. Introductionary lecture ~ 1,5 hour
2. Hands-on with lecture material ~ 2-3 hours
3. Support for individual projects ~ 2-3 hours
4. Reserved moments for invidual questsions (see schedule)

Program - day 1

Program - day 2

1. Typical gotchas; references, immutables
2. Best practises
   • Classes, methods and functions; use them!
   • Code formatting; PEP8
   • Don’t repeat yourself; DRY
   • Organizing your code; minimize globals, cleanout imports
   • Comments, Docstrings: documentation
3. Structuring code, working with modules
4. Packaging, creating reusable code

program - day 3

Program - day 1

Inventarisation

Common problems

Program - day 1

Installing Python

A recipe for failure

Installing Python

Available options

System Python

Available on Mac and Linux

Official Python

Available from python.org

Scientific Python distributions

Preferred and suggested

Program - day 1

The Terminal

More or less equivalent:

• Shell
• Command Line Interface (CLI)
• (ba)sh

UNIX shell

Basic principles

• Command ➞ Response
• Input ➞ Output
• Streams and pipes
• Environment variables

UNIX shell

Cygwin: UNIX for Windows

UNIX shell

Common concepts

• Execution search path — $PATH
• Home directory — $HOME, ~
• Current working directory (CWD) — $PWD
• Standard input, error and output (stdin, stderr, stdout)
• Shell scripts (.sh files)

UNIX shell

Common commands

For later reference.

• ls — list directory contents
• cd <dir> — change directory
• pwd — print (show) current working directory
• man <command> — manual for command
• echo "Text $VARIABLE" — print to stdout
• apropos <topic> — search man pages
• export PATH=~/bin:$PATH — set PATH variable
• less <filename> — read and scroll trough file

UNIX shell

Handy tricks

• Hit <TAB> for automatic completion
• Use the ↑ and ↓ keys for command history
• Use <CONTROL-D> to quit a shell (works for Python as well)
• HELP!?
  <command> --help
  e.g.: ls --help

Scripts

“One damn thing after another”

#!/bin/sh
# This first line tells the system it's a shell script.
# Similarly, #!/bin/usr/python would execute Python code.

# Print hello world
echo "Hello world"

# Print $PATH variable
echo "My PATH variable is $PATH"

# Change into some-directory
cd some-directory

# List directory contents
ls

Scripts

Having your script and executing it too

# Set executable permissions
chmod +x myscript.sh

# Executing command outside of $PATH requires explicit path
./myscript.sh

Shell initialization

~/.bash_profile (and ~/.bashrc)

• Executed whenever a terminal is started
• Configures environment variables such as:
  • $PATH
  • $PYTHONPATH
  • $EDITOR
• Sets personal program settings
• Executes arbitrary shell code

Program - day 1

Interactive Python shell

Similar to bash shell: execute command, print output

$ python
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> print 'hello world'
hello world
>>> quit()

IPython

Python shell on steroids

Similar to Mathematica

$ ipython
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
Type "copyright", "credits" or "license" for more information.

IPython 1.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]:

IPython features

Similar to UNIX shell

• Command line completion
• History available
• Syntax coloring
• Much more, read the manual!

ipdb

Interactive debugging

Debugging with IPython-like interface; stop your code anywhere and query variables or execute arbitrary code.

One line to rule them all:

import ipdb; ipdb.set_trace()

ipdb

Important commands

• n — Execute next line of code
• s — Step info function call
• c — Continue execution as normal
• q — Quit debugger

ipdb example

Code:

def addition(one, other):
    import ipdb; ipdb.set_trace()

    print 'Calculating now'

    return one + other

print 'Starting calculation'
addition(2, 5)

print 'Calculation done'

ipdb example

Result:

$ python ipdb-example.py
Starting calculation
> ipdb-example.py(4)addition()
      3
----> 4     print 'Calculating now'
      5

ipdb> n
Calculating now
> ipdb-example.py(6)addition()
      5
----> 6     return one + other
      7

ipdb> n
--Return--
7
> ipdb-example.py(6)addition()
      5
----> 6     return one + other
      7

ipdb> n
> ipdb-example.py(11)<module>()
      9 addition(2, 5)
     10
---> 11 print 'Calculation done'

ipdb> n
Calculation done
--Return--
None
> ipdb-example.py(11)<module>()
      9 addition(2, 5)
     10
---> 11 print 'Calculation done'

ipdb> quit
Exiting Debugger.

Program - day 1

Python packages a.k.a. Eggs

• Whenever you see setup.py, it's an Egg.
• Eggs are self-contained software packages (e.g. libraries, commands)
• Install it through PIP (next slide) or with:
  

  $ python setup.py install

PIP; Python package manager

Search, download, install and upgrade packages

$ pip search <package>

$ pip install <package>

$ pip install --upgrade <package>

$ pip uninstall <package>

requirements.txt

Managing versions of requirements

Textfile with required packages and versions, e.g.:

pkg1
pkg2
pkg3>=1.0,<=2.0
					

Reference: PIP cookbook

requirements.txt

Installing

pip install -r requirements.txt

Creating

pip freeze > requirements.txt

Warning: use only with VirtualEnv (next slide)

VirtualEnv

Keeping things clean

Sets up a 'local' Python distribution allowing you to:

• Install different versions of packages
• Exclude system packages (unless explicitly included)
• Install packages without administrator privileges

VirtualEnv

Usage

Install VirtualEnv (only once):

$ pip install virtualenv

Create an isolated environment:

$ virtualenv [--system-site-packages] <dirname>

Activate the environment:

$ source <dirname>/bin/activate

Deactivate the environment:

$ deactivate

VirtualEnv

Example (1/4)

$ python
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import xmodem
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named xmodem

VirtualEnv

Example (2/4)

$ virtualenv test
New python executable in test/bin/python
Installing Setuptools..............................................................................................................................................................................................................................done.
Installing Pip.....................................................................................................................................................................................................................................................................................................................................done.
$ source test/bin/activate
(test) $ pip install xmodem
Downloading/unpacking xmodem
  Downloading xmodem-0.3.2.tar.gz
  Storing download in cache at ./.pip/download_cache/http%3A%2F%2Fpackages.crate-cdn.com%2F4%2Fe%2F5%2F7%2F4e57f3fadd1f3f043a23f1a87e9d36f944a21b552aabebcdb802154667396567%2Fxmodem-0.3.2.tar.gz
  Running setup.py egg_info for package xmodem

Installing collected packages: xmodem
  Running setup.py install for xmodem

Successfully installed xmodem
Cleaning up...

VirtualEnv

Example (3/4)

(test) $ python
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import xmodem
>>>

VirtualEnv

Example (4/4)

(test) $ deactivate
$ python
Python 2.7.6 (v2.7.6:3a1db0d2747e, Nov 10 2013, 00:42:54)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import xmodem
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named xmodem

Program - day 1

Watch out for:

• Trailing whitespace
• Tabs; use 4 spaces instead
• Trailing newlines

Example

Syntax errors

Use a Linter

Find syntax, style and other errors before running your code: less bugs, more productivity and much more beautiful code.

Thanks!

Any questions?