====== Python tools for software carpentry ======

Lecturer: Pietro Berkes, <berkes _AT_ brandeis _DOT_ edu>

{{:materials:software_carpentry_cheatsheets_v1_1.pdf|Download the cheat sheets}} for all the tools and methods discussed in the lecture!
===== Course material =====

Slides: {{:materials:software_carpentry_slides_v3.pdf|Download slides}}

Exercises: 

  * {{:materials:day1_exercises_v3.pdf|day1_exercises.pdf (exercise sheet)}}
  * {{:materials:day1_exercises_final.zip|day1_exercises.zip (source code)}}
  * {{:materials:day1_solutions_final.zip|day1_solutions.zip (source code)}}
  * On masterbaboon.com there's {{http://www.masterbaboon.com/2010/09/solving-the-game-set/|an article about writing an efficient solver for Set}}

Outline of the lecture (2h):

  - Unit testing
    * unittest
    * testing with numpy arrays
    * what to test and how for scientific programming
    * code coverage (coverage.py)
  - Debugging
    * pdb
  - Profiling
    * timeit
    * cProfile
  - Other useful tools
    * documenting: pydoc, doctest
    * static checking: pylint

Many live demos, music and dances!


===== Good programming practices =====

==== Software carpentry in general ====

Two comprehensive software carpentry courses:

[[http://software-carpentry.org/|University of Alberta]]

[[http://itb.biologie.hu-berlin.de/~zito/teaching/SC/|Tiziano's course]] at the Bernstein center in Berlin

The classic book about software carpentry: [[http://pragprog.com/titles/tpp/the-pragmatic-programmer | The pragmatic programmer]]

==== Coding standards ====

[[http://www.python.org/dev/peps/pep-0008/|PEP8]], the official Python style guide

[[http://www.logilab.org/857 | pylint ]], tool to check coding standards

===== Test suites =====

[[http://docs.python.org/library/unittest.html|unittest]], the standard Python test framework

[[http://codespeak.net/py/dist/test/test.html|py.test]], an alternative framework that simplifies writing tests and allows for extension and customization of test experience

[[http://somethingaboutorange.com/mrl/projects/nose/0.11.1/|nose]], another popular alternative

[[http://docs.python.org/library/doctest.html | doctest]], write tests inside of docstrings
===== Debugging =====

[[http://docs.python.org/library/pdb.html|pdb]], the standard python debugger

[[http://winpdb.org/download/|winpdb]], a graphical interface for ''pdb''. It's
platform-independent despite its name.

[[http://www.gnu.org/software/ddd/|DDD]] (DataDisplayDebugger), graphical general-purpose debugger.

Python IDEs often have a built-in debugger.

===== Profiling =====

[[http://docs.python.org/library/profile.html|cProfile]], the batteries included
 Python profiler

[[http://docs.python.org/library/timeit.html|timeit]], built-in Python module to
 measure the execution time of small code parts

[[http://www.vrplumber.com/programming/runsnakerun/|RunSnakeRun]], a wxPython-based visualization of profiling results -- very intuitive!