day2.rst

Day 2 -- many miscellaneous topics

You should all start reading XKCD.

Python data structures

See Python data structures

Installing Python packages; useful Python packages

See :doc:`python-packages`

Useful UNIX tools

ssh and screen; BLAST.

SSH instructions here

Installing and using command line BLAST

Testing

When we say "testing" we really mean automated testing. The central problems addressed by testing are correctness and reproducibility. (While these are linked, they are not the same!)

There are two basic kinds of tests that I'd like to briefly discuss. One kind of test is a unit test. The other kind of test is a regression test. (There are also many more.)

Unit tests address small units of code, like functions. They are used to isolate and nail down and prove the functionality of potentially complicated little functions.

Regression tests address the overall function of code, and they are used to make sure that your code is doing the same thing today as it was yesterday.

I'll show you examples of both, but quickly :).

Writing tests

We're going to be using the nose testing framework, which is just a framework that makes it easy to find and execute tests.

Basically, 'nose' creates a command 'nosetests' that finds and runs tests. The idea is that you won't need to register new tests.

A test function looks like this:

def test_something():
   # run some code
   # fail loudly or succeed silently

See testing-with-nose.ipynb.

More reading

For more reading, see:

http://software-carpentry.org/4_0/test/

and

http://ivory.idyll.org/articles/nose-intro.html

and also

http://ivory.idyll.org/blog/software-quality-death-spiral.html

Version Control

(An abbreviated version of: http://ged.msu.edu/angus/git-intro.html)

The purpose of version control is to serve as a method for tacking changes to files, which enables lots of things:

1. track changes (wanted and unwanted) in your files.
2. keep track of an entire history of changes.
3. track multiple independent "branches" of work.
4. collaborate sanely.

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A brief introduction:

1. Web interface and editing files.
2. One-person repositories.
3. One-person repositories with multiple locations.
4. One-person repositories with branches.
5. Collaborations!

Pipelines

Operating on more complex files.

Doing stuff with BLAST output.