University of British Columbia - EOAS

Sep 20-21, 2016

9:00 am - 5:00 pm

Instructors: Doug Latornell, Nancy Soontiens, Karina Ramos Musalem

Helpers: Tereza Jarnikova, Idalia Machuca, Anna Mittelholz, Keelin Scully, Cindy Yu

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Specific focuses of the workshop will be:

  1. Version Control — software tools to maintain and make accessible previous versions of code, data files, etc.
  2. Automation — techniques to take the repetitive, error-prone drudgery out of a whole range of computer analyses
  3. Introduction to computer shell/command-line and programming tools that make 1 & 2 possible

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The workshop is aimed at graduate students and other researchers who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate that knowledge into practical tools to help them work more productively. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: ESB-5104, 2207 Main Mall, Vancouver. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

Contact: Please mail Susan Allen for more information.



Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 The Unix shell
10:30 Break
12:30 Lunch break
13:30 Version Control with Mercurial
15:00 Break
16:50 Wrap-up

Day 2

09:00 Building Programs with Python
10:30 Break
12:30 Lunch break
13:30 Building Programs with Python (cont'd)
15:00 Break
16:50 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Coffee, Tea and Snacks

Coffee, tea, and snacks will be provided during the mid-morning and mid-afternoon breaks each day of the workshop.


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things

Other Resources

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Loops and conditionals
  • Creating and using functions
  • Assertions and testing
  • Debugging
  • Using Python from the command line
  • Reference...

Other Resources

Version Control with Mercurial

  • Automated Version Control
  • Configuring Mercurial
  • Creating a repository
  • Tracking Files
  • Recording Changes
  • Exploring History
  • Recovering Old Versions
  • Ignoring Things
  • Remote Repositories
  • Working with Clone Repositories
  • Collaboration
  • Merging Changes from Difference Clones
  • Merge Conflicts
  • Open Science
  • Licenses
  • Repository Hosting

Other Resources


To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.


The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.


Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.


nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.


Mercurial is a version control system that lets you track what changes were made when to files. It has options for easily updating a shared or public version of your code on You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer).

You will need an account at for parts of the Mercurial lesson. Basic Bitbucket accounts are free. We encourage you to create a Bitbucket account if you don't have one already.


Install Mercurial and KDiff3 by downloading and running the TortoiseHg installer.

Mac OS X

Install Mercurial by downloading and running the installer for your version of OS X from the downloads page. Also, please install the KDiff3 diff and merge tool. Be aware that you must add the KDiff3 installation directory to your system path. The workshop etherpad has some tips for doing that. If you need help with this, please ask one of the instructors before the workshop.

If you use the homebrew package manager, you can install Mercurial with brew install mercurial, and KDiff3 with brew install kdiff3.


If Mercurial is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install mercurial and for Fedora run sudo yum install mercurial. Also, please install the KDiff3 diff and merge tool. It should also be available via your package manager.


Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).


Video Tutorial
  1. Open with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial
  1. Open with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.


  1. Open with your web browser.
  2. Download the Python 3 installer for Linux.
  3. Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  4. Open a terminal window.
  5. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear.
  6. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).