Software Carpentry at UNH: The backstory

I first heard of Software Carpentry in a YouTube video of its founder Greg Wilson’s talk at the SciPy 2014 conference:

The talk really impressed me. I was convinced that their work was absolutely crucial for an open and more productive research community to exist. This was a mostly selfish thought, by the way. I was tired of reading papers with seemingly awesome results, but not having access to the source code to reproduce (and maybe build upon) those results. I was also fed up with emailed Word documents and the resulting lost changes and half-baked version-control-via-file-name. I was never taught any better though, which is exactly why we need groups like Software Carpentry!

Shortly after watching the talk, I submitted a form on the Software Carpentry website requesting more information regarding hosting a workshop at UNH, where I am currently wrapping up a PhD in mechanical engineering. I ended up getting some information, but decided I had enough on my plate with research and put the idea back on the shelf.

Fast-forward six months or so. I received an email from the man himself, Greg Wilson, asking what I thought about hosting a workshop at UNH. Almost star-struck, I was reinvigorated and decided to try to get the ball rolling. Besides, graduating is overrated anyway.

I had some emails sent around my department and the School of Marine Science and Engineering (SMSOE) to gauge interest. To my surprise, more than 20 people responded, which was enough to move forward. The next task was to find funding for the administrative fee and travel and accommodations for the volunteer instructors. A couple proposals later, the SMSOE and ME department agreed to fund the workshop at an approximate 80/20 ratio.

The workshop was to take place during the summer, which made finding instructors within close proximity (to save on travel costs) a little tricky. A few rounds of prospective candidates later, Byron Smith, a PhD candidate in Ecology and Evolutionary Biology at the University of Michigan, and Ivan Gonzalez, a physicist and programmer at the Martinos Center for Biomedical Imaging in Boston agreed to teach our workshop. Software Carpentry also found us another helper, Daniel Hocking, who is a UNH PhD alum in Natural Resources and Environmental Studies currently working at the USGS Conte Anadromous Fish Research Center. Being volunteers for such a great organization, there was no question that these guys were going to do an awesome job.

I was excited. We had the funding, the room, the instructors, and the dates set. The only thing left was to get some learners registered and make it happen!

From WordPress to Jekyll

After reading many articles and comments extolling the virtues of static HTML (speed, efficiency, simplicity, etc.) and being a very happy GitHub user for a while now, I decided to migrate my personal website from WordPress to Jekyll and use GitHub Pages for hosting.

After an unsuccessful attempt to use jekyll-import with my old database credentials, I used the export tool built into WordPress to generate an XML version of the site and ran that through jekyll-import, but didn’t like that posts didn’t translate to Markdown. I finally ended up using Exitwp, which generated Markdown with YAML front matter. Exitwp did a reasonable job, though the amount of tweaking I had to do would have been prohibitive for anything above ~20 posts. I manually downloaded and replaced all images, tweaked YAML metadata, had to reformat all tables (originally generated with a WordPress plugin), and had to change some LaTeX syntax, but got it done in a few hours.

One unexpected snag was that Kramdown, the default Markdown renderer, would not allow for GitHub-flavored syntax highlighting in fenced code blocks, e.g.,

```python
print("hello world")
```

This was remedied by switching over to Redcarpet, which was as simple as editing the markdown entry in _config.yml.

I’ve only made a couple visual tweaks to the default Jekyll theme so far and I’m actually quite pleased with it. So far Jekyll seems like a winner, allowing me to easily work offline in Markdown, ditch my old web host, and hopefully write more frequently!