My twitter feed currently is ablaze with discussions about sexism in tech and science. As a member of the social group that goes through life with difficulty set to "easy", of course none of this has happened to me. I don't know what it feels like to go to a …

Recently I was faced with an external program that I wanted to call from my script that only writes its output to a file, not to stdout. Faced with having to call this program a lot of times in parallel, I decided to fake up its output files via POSIX …

I'm currently writing a Python parser for GenBank files. I know BioPython has one, and it doesn't even suck, but BioPython requires a bunch of C extensions, so I can't go and just ship it with my Python application.

So I'm creating a BioPython-compatible API for the classes that I …

Another day, another piece of testing mayhem. I've completed the 0.1 version of my Flask-Downloader helper class. With this, I could complete my web app. Now, the downloader itself has a bunch of tests to make sure it's working as expected, but I was also going to test the …

Today, I decided to go for the downloader component that can download files on the behalf of the users. While looking at how to test this, I actually noticed that the mm_unit functionality has been merged into the minimock package. Sweet. I wanted to keep this modular, a downloader sounds …

Today, I decided to go and restructure my webapp into a package as recommended by the Flask "Larger Applications" pattern. Thanks to my existing test suite, the move was quick and pain-free. I had to fix imports in one of the tests, but apart from that, the only thing I …

Looks like my system strikes back. A fitting thing to happen for an episode 2, I guess. Turns out that nosetests and virtualenv need some extra care and feeding when kept together. Installing another copy of nosetests into my virtualenv fixed the test failures I was seeing. Thanks to the …

I've decided to start the campaign by ditching the existing PHP web app. I lost all confidence in it last Friday, when I found that it only worked by accident, due to a well-placed typo. As I'm rewriting the web app anyway, I thought I could also ditch PHP altogether …

Following the hallowed US American tradition of declaring war on whatever things you don't like, I've decided to declare war on legacy code this week.

By legacy code, I mostly mean untested code, following the definition of Michael Feathers' book Working with Legacy Code. That's a great read, by the …

I just had to package up a python package to make installation of a software we use at work easier. The systems we run here are Suse- and Ubuntu-based, so I got to package RPMs and debs.

I did package the odd perl package and some bioinformatics tool before, but …