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Woods Hole Oceanographic Institution and USGS Woods Hole

Sep 3-4, 2015

9:00 am - 4:30 pm

Instructors: Harriet Alexander, Janet Riley

Helpers: Isabela Le Bras, Kathleen Pitz

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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.

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

This workshop is sponsored by WHOI Ocean Informatics initiative, USGS Woods Hole, and MBLWHOI Library.

Who: The course is aimed at staff and students of the Woods Hole Oceanographic Institution and USGS Woods Hole.

Where: WHOI Quissett Campus, 360 Woods Hole Rd., Woods Hole MA 02543

Building and room: Clark 5-07

Get directions with

See the WHOI visitor page for more information.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail for more information.




Automating tasks with the Unix shell

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


Data files:
10:30 Break
12:00 Lunch

Version Control with Git

  • 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


Our git repo
14:30 Break
16:00 Wrap-up



Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line


For today:

For next steps:
10:30 Break
12:00 Lunch

Advanced Python Topics: Data Analysis with Python

  • Starting with data
  • Index slice subset
  • Data types and format
  • Merging data
  • Data analysis automation: loops and functions
  • Plotting with matplotlib
  • Putting it all together

14:30 Break
16:00 Wrap-up

Coffee provided courtesy of the MBLWHO Library at 8:30 and 1:00.

Bring a bag lunch or grab lunch on campus at The Buttery.

Additional Resources

Etherpad notes

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


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.


Install Git for Windows by downloading and running the installer. 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). 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.


Git is a version control system that lets you track who made changes to what when and 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 version 9 or above).

We'll use GitHub's server to practice collaborating with git during the workshop. Please sign up for a free GitHub account at if you don't already have one. Then add your GitHub username to our list We need to add each person to the GitHub project so they can edit files, and we'd like to do that before the workshop to make best use of everyone's time.


Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.


If Git 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 git and for Fedora run sudo yum install git.

Text Editor

When you're writing code, you need a text editor that will save files as-is without adding proprietary formatting, as Word or other word processors do. It's nice to have an editor optimized for writing code, with features like automatic color-coding of key words.

For this workshop, we'll use Sublime Text. If you already have a favorite plain-text editor you may use it instead.

During the workshop, especially in the git unit, your laptop may launch its default text editor to complete a task The default text editor on Mac OS X and Linux is usually Vi, 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.


We will use Sublime Text 2 for the workshop.

Another editor is Notepad++ Be aware that you must add the installation directory to your system path. Please ask your instructor to help you do this.

nano is another popular basic editor. 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.

Mac OS X

We will use Sublime Text 2 for the workshop.

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 Text Wrangler or nano, which is pre-installed.


We will use Sublime Text 2 for the workshop.

nano is a basic editor that should be pre-installed.

Others editors that you can use are Gedit or Kate.


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 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.

We will teach the advanced Python module 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).


  • Download and install Anaconda.
    Download the Python 2.7 installer (do not follow the link to Python 3). Accept the default configuration options. On the advanced options screen, check both options: add Anaconda to your PATH, and register Anaconda as the default Python.

Mac OS X

  • Download and install Anaconda.
    Download the default Python 2.7 installer (do not follow the link to Python 3). Use all of the defaults for installation.


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 workshop.)

  1. Download the installer that matches your operating system and save it in your home folder. Download the default Python 2.7 installer (do not follow the link to Python 3).
  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).