Institute of Arctic and Alpine Research (INSTAAR), Room 620

3100 Marine Street, Boulder, CO 80309
Jan 7-9, 2015
9:00 am - 5:00 pm

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 three-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.

Instructors: Aron Ahmadia, Chris Kees

Who: This is an internal training workshop for University of Colorado Boulder graduate students.

Where: 3100 Marine Street, Boulder, CO 80309. Get directions with OpenStreetMap or Google Maps.

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

Contact: Please mail for more information.


Day 1

08:00 Setup Help
09:00 Introduction and Overview
09:30 Automating Your Actions with the UNIX shell
10:30 Break
10:45 Build Automation
12:00 Lunch break
13:00 Fundamentals of Python
14:30 Break.
14:45 Fundamentals of Python
16:30 Daily Wrap-up

Day 2

09:00 Introduction to Version Control with Git
10:30 Break
10:45 The Git Developer's Workflow
12:00 Lunch break
13:00 Introduction to the IPython Notebook (Jupyter)
13:30 Scientific Computing with NumPy and SciPy
14:30 Break.
14:45 Visualization with Matplotlib
15:15 Visualizing geospatial data
16:30 Daily Wrap-up

Day 3

09:00 Testing in Python
10:30 Break.
10:45 Working with and developing community codes
12:00 Lunch break
13:00 Group and individual project sprints
16:00 Training Wrap-up


To participate in this workshop 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 workshop.



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.


Git 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.



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

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.


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.


Windows users will need to complete one last step. After installing both Python and Git Bash, download this file, making sure that it has a .py extension on the end when you save it. Next, open Git Bash and type each of these three commands, hitting Return after each one: cd, cd Desktop, python You'll see a blinking underscore for a bit, and then eventually you'll once again see a $ symbol with the blinking underscore after it. You can close Git Bash at this point.

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 Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.


  • Download and install Anaconda CE.
  • 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 Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).


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.

  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).

Testing your setup

To test that your system is configured properly, complete the following four steps. If any of these do not succeed, or if you run into any other trouble, please email Aron Ahmadia immediately.