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USGS Flagstaff Science Campus

Feb 4-5, 2016

9:00 am - 5:00 pm

Instructors: Mariela Perignon, Rachel Schwartz

Helpers: Daniel Buscombe, Kristin Berry

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".

Who: The course is aimed scientists and engineers affiliated with the USGS. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 2255 N. Gemini Dr., Flagstaff, Arizona. Get directions with OpenStreetMap or Google Maps.

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.


Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Building programs with Python
14:30 Coffee
16:30 Wrap-up

Day 2

09:00 Version control with Git
10:30 Coffee
12:00 Lunch break
13:00 Managing data with SQL
14:30 Coffee
16:30 Wrap-up

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code. Keep the etherpad open in your browser during the workshop so you can quickly access it.


The Unix Shell

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

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
  • Reference...

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
  • Reference...

Managing Data with SQL

  • Reading and sorting data
  • Filtering with where
  • Calculating new values on the fly
  • Handling missing values
  • Combining values using aggregation
  • Combining information from multiple tables using join
  • Creating, modifying, and deleting data
  • Programming with databases
  • Reference...


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.

Please install the software below even if you already have a working version of Python in your computer. A common set of software assures that everyone is working in the same environment as the instructors and minimizes time lost to troubleshooting.

Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.

Contact the instructors if you run into trouble during installation. We also 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.


These instructions will install both Git and Bash (as the application Git Bash).

  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. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you do not select this option, the programs that you need for the workshop will not work properly. If this happens, rerun the installer and select the appropriate option.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

Mac OS X

All versions of Mac OS X use bash as the default shell, so no installation is necessary. 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 in Linux is usually bash. If your machine is set up differently, you can run bash by opening a terminal and typing bash. There is no need to install anything.


Git is a version control system that allows you to track changes made to documents, the author of those changes, and when they were made. It is most often used for coding projects, but almost any type of file can be tracked using git. It is also a powerful collaboration tool and can be used to easily share documents with the public through You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above, are supported browsers).


Git should have 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. Git is a command line program, so this installation won't create any new files in the /Applications folder.
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 should 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 Editors

The text editors most of us regularly use are not optimized for writing code. An editor with features like automatic color-coding of key words and language-specific commenting make code much easier to read and edit, greatly increasing your productivity as a programmer and reducing frustration. We suggest you install one of several code-friendly text editors, but any simple text editor (that can save as plain text) will work.

There are also many situations where you might need to use a text editor within the command line. These programs don't have a GUI (Graphical User Interface) -- you interact with them exclusively by typing into the terminal. The text editor nano is easy to use and the one that instructors will use in the workshop.

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.


To install nano, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

If you want to install a text editor optimized for code, you can use Notepad++ or Sublime Text.

Mac OS X

The text editor nano should be pre-installed in Mac OS X.

If you want to install a text editor optimized for code, you can use Text Wrangler or Sublime Text.


The text editor nano should be pre-installed in Mac OS X.

If you want to install a text editor optimized for code, you can use Gedit, Kate or Sublime Text.


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 use Anaconda, an all-in-one installer. Make sure you install Python version 2.7.

Please install Anaconda even if you already have a working version of Python on your computer. Using a common environment helps workshops run smoothly and facilitate learning. It is easy to uninstall Anaconda after the workshop if you choose to not use it.

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. 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).


  1. Open with your web browser.
  2. Download the Python 2.7 installer for Windows.
  3. Install Python 2.7 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  1. Open with your web browser.
  2. Download the Python 2.7 installer for OS X.
  3. Install Python 2.7 using all of the defaults for installation.


  1. Open with your web browser.
  2. Download the Python 2.7 installer for Linux.
  3. Install Python 2.7 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 from the instructors, preferably before the workshop!).
  4. Open a terminal window.
  5. Type
    bash Anaconda-
    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).


SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.


The Software Carpentry Windows Installer installs SQLite for Windows. You don't need to run the installer again if you used it to install nano.

Mac OS X

SQLite comes pre-installed on Mac OS X.


SQLite comes pre-installed on Linux.