University of British Columbia

Earth, Ocean and Atmospheric Sciences, ESB-5108
Sep 25-26, 2014
9:00 - 4:00 Thu, 9:00 - 4:30 Fri

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Host: Susan Allen

Instructors: Doug Latornell, Susan Allen

Helpers: Jordan Aaron, Karina Ramos Musalem, Drew Snauffer, Nancy Soontiens, Kathi Unglert, Kang Wang

Who: The course is aimed at graduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Where: Earth, Ocean and Atmospheric Sciences, ESB-5108.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail for more information or to register for the bootcamp.


Coffee and Food

Coffee, tea, and snacks will be provided at morning and afternoon breaks during the bootcamp. Lunch will not be provided, but your are welcome to bring your lunch to eat in the lounge area outside ESB-5108. Magma at the south end of the ground floor of ESB is one option for those who wish to buy lunch.


Thu 25-Sep-2014

09:00 Introduction
09:20 Automating tasks with the Unix shell
10:15 Break
12:00 Lunch
13:00 Version control with Mercurial
14:15 Break
15:45 Wrap-up
16:00 EOAS Department Colloquim
(for those interested - ESB 5104/5106)
Dorrit Jacob, Macquarie University
How to build a carbonate shell - insights from the submicron scale

Fri 26-Sep-2014

09:00 Building programs with Python
10:30 Break
12:00 Lunch
13:00 EOAS Python Examples
14:30 Break
16:00 Wrap-up


The Unix Shell

  • Lessons:
    • Files and directories: pwd, cd, ls, mkdir, ...
    • History and tab completion
    • Pipes and redirection
    • Looping over files
    • Creating and running shell scripts
    • Finding things: grep, find, ...
  • Reference...

Version Control with Mercurial

  • Lessons:
    • Creating a repository
    • Recording changes to files: add, commit, ...
    • Viewing changes: status, diff, ...
    • Ignoring files
    • Working on the web: clone, pull, push, ...
    • Resolving conflicts
    • Open licenses
    • Where to host work, and why
  • Reference...

Programming in Python

  • Lessons:
    • Using libraries
    • Working with arrays
    • Reading and plotting data
    • Creating and using functions
    • Loops and conditionals: for, if, else, ...
    • Using Python from the command line
  • Reference...

EOAS Python Examples

  • Lessons:
    • Weather data with pandas and requests
    • Plotting map data

Reference Guides

These short reference guides cover the basic tools and ideas introduced in our lessons.

  1. The Unix Shell
  2. Version Control with Mercurial
  3. Programming with Python
  4. Recognising prompts and how to exit


To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.



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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.


Mercurial is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on


Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.


  • If you don't already have one, please create a account for yourself. It's free, and if you use your email address you should automatically get the extra perk of unlimited private collaborations.
  • Please follow the setup instructions below (pick the appropriate operating system) to install those tools on the laptop that you will be bringing to the bootcamp.

It is very important that you successfully complete the setup before the bootcamp so that we can start on time, and you can participate fully. If you have difficulty with the setup, or have any questions about the setup instructions, please contact Doug at

  • Also, please ensure that your laptop is able to connect to the ubcsecure wireless network to give you Internet access during the bootcamp.
  • Finally, please take a moment to read the Software Carpentry Bootcamp Code of Conduct.
  • Windows


    • Download and install Anaconda.
    • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

    Git Bash

    Install Git for Windows, which includes a Bash emulator, by download and running the installer.

    Software Carpentry Installer

    This installer requires an active internet connection

    After installing Python and Git Bash:

    • Download the installer.
    • If the file opens directly in the browser select File→Save Page As to download it to your computer.
    • Double click on the file to run it.


    nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

    Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.


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

    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). You may want to keep Terminal in your dock for this workshop.


    We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.


    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.


    • Download and install Anaconda.
    • Use all of the defaults for installation except make sure to check Make Anaconda the default Python.



    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.


    If Mercurial is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get or yum). Also, please install the KDiff3 diff and merge tool.


    Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.


    We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

    1. Download the installer that matches your operating system and save it in your home folder.
    2. Open a terminal window.
    3. Type
      bash Anaconda-
      and then press tab. The name of the file you just downloaded should appear.
    4. 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).