Software Carpentry Week in Review (2 -8 December 2013)

Note: There will be a Mozilla Science Lab meeting this Thursday, starting at 11 AM EDT. 

GitHub and Lesson Development

Software Carpentry is pleased to announce the release of v2013.11 of the lesson materials repository. This release represents nearly 2 years of collaborative lesson development from 54 contributors, and features web-ready lessons for operating and automating with the command line, modular programming (with introductions to Python and R), personal and collaborative version control with Git, and unit testing. Contributors to this release include:

  • Amanda Charbonneau
  • Amy Brown
  • Anthony Scopatz
  • Ariel Rokem
  • Aron Ahmadia
  • Aronne Merrelli
  • Azalee Bostroem
  • Ben Waugh
  • Bernhard Konrad
  • Cam Macdonell
  • Camille Avestruz
  • Christina Koch
  • Cliburn Chan
  • Damien Irving
  • Doug Latornell
  • Ethan White
  • Fernando Perez
  • Greg Wilson
  • Ivan Gonzalez
  • Jed Brown
  • Jessica Kerr
  • John Blischak
  • Jon Pipitone
  • Joshua Ainsley
  • Joshua Ryan Smith
  • Julian Garcia
  • Katy Huff
  • Konrad Hinsen
  • Lynne Williams
  • Matt Davis
  • Matthew Lightman
  • Michael Droettboom
  • Michael Hansen
  • Mike Jackson
  • Milad Fatenejad
  • Molly Gibson
  • Patrick Fuller
  • Paul Ivanov
  • Paul P.H. Wilson
  • Phil Lies
  • Preston Holmes
  • Radhika Khetani
  • Raniere Silva
  • Richard T. Guy
  • Sasha Wood
  • Sri Hari Krishna Narayanan
  • Stephen J. Eglen
  • Steve Haddock
  • Steven Koenig
  • Tommy Guy
  • Trent Hauck
  • W. Trevor King
  • Will Trimble
  • Yuxi Luo

In the discussion on writing and publishing papers in a webby world, Stefan van der Walt linked to a paper-in-progress on GitHub. Check out the repositoryfor an example of how his paper (and the SciPy Proceedings) are authored, automated, and openly reviewed using ReStructured Text.

There have been 57 commits to the repository by 9 authors this week, with 1,013 new lines across 8 files.


Will Trimble led a large team of instructors at a Software Carpentry bootcamp at the NSF-sponsored National Socio-Environmental Synthesis Center (SESYNC) in Annapolis, Maryland from December 3-6. The bootcamp contained a 2-day sequence of normal bootcamp material, followed by 2 more days for project-based work and extra presentations. Software Carpentry sent Will Trimble, Amanda Whitlock, Bernhard Konrad, R. David Murray, Justin Ely, and Aron Ahmadia to instruct and help. SESYNC provided Ian Munoz, Mike Smorul, and Mary Shelley, who also organized. The official course repository is available here.

Software Carpentry Instructors at the SESYNC bootcamp.  Images courtesy @SESYNC

The second half of the University of Melbourne Software Carpentry Bootcamp, which featured four 3-hour sessions spread over two weeks, wrapped up this week as well. More details are available from the registration page and the course repository.

The EPCC hosted a bootcamp from December 3-4, with support from PRACE and the Software Sustainability Institute. Mike Jackson and Mario Antonioletti instructed the bootcamp with assistance from fellow EPCCers Amy Krause, Alistair Grant, Arno Proeme, Dominic Sloan-Murphy, and David Scott. Martin Jones from Edinburgh’s School of Biological Sciences assisted as well. See Mike’s follow-up blog post here.

Upcoming bootcamps


Aleksandra Pawlik posted an announcement about Software Carpentry events at the upcoming American Geophysical Fall Meeting in San Francisco this week. Four Software Sustainability Institute Fellows will be organizing a “Software and Research” Town Hall Session on Thursday, 12 December 2013, at 12:30 PM in Moscone West Room 2004. There will also be a number of other Software Carpentry-related sessions throughout the week, including a presentation on Software Carpentry by Aron Ahmadia Friday morning as part of a series on Open Source Tools and Techniques for Hydrology. Keep an eye on the @swcarpentry Twitter account for up-to-the-minute updates.

Greg Wilson and Software Carpentry welcomed 32 new instructors from six different countries to the Software Carpentry team. Please welcome:

  • Joshua Ainsley
  • Camille Avestruz
  • Philipp Bayer
  • Nichole Bennett
  • Cliburn Chan
  • Emily Davenport
  • Neal Davis
  • Gabriel A. Devenyi
  • Jonah Duckles
  • Jordan Fish
  • Julian Garcia
  • Molly Gibson
  • Ivan Gonzalez
  • Joshua Herr
  • James Hetherington
  • Chris Holdgraf
  • Damien Irving
  • Ted Kirkpatrick
  • Christina Koch
  • Igor Kozlov
  • Luke Lee
  • Matthew Lightman
  • Yuxi Luo
  • David Perez-Suarez
  • Bill Rowell
  • Martin Schilling
  • Raniere Silva
  • Rachel Slaybaugh
  • Shoaib Sufi
  • Gayathri Swaminathan
  • Amanda Whitlock
  • April Wright

Finally, Martin Jones wrote a thought-provoking post about diving deeper into the technical details of programming as a follow-up to his Python for Biologists online book. Here are some of his thoughts:

So if you’re comfortable with the basics of programming—and maybe you’ve already written a fair few useful programs—I encourage you to seek out the corners of your programming language that you haven’t yet ventured into. With any luck, what you’ll find there is not just new features, but new ways of thinking.

See his post, Advanced Python for Biologists, for more!

How to Get Involved with Software Carpentry this Week

There are two discussion issues open in the repository. Please join in if you have thoughts or would like to participate in the discussion on:

Have a good week!