Learn Data Wrangling at the University of Arizona!

Feb. 23-24, 2019


Instructors: Phillip Benoit, Upendra Devisetty, Dawson Fairbanks, Blake Joyce, Chun Ly, Susan Miller, Kristina Riemer

Helpers: Jiali Han, Matt Miller, Noah Nelson, Cristian Palacios, Austen Stewart, Travis Struck, Derrick Yoo, Meghan Balk, Marnee Dearman

General Information

This workshop is taking place during the annual Rodeo Week in Tucson, AZ.

Come for the rodeo, stay to wrangle some data!

Apply for the workshop at https://goo.gl/PA9SSp.

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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 at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Please check your email for the workshop location!. Get directions with OpenStreetMap or Google Maps.

When: Feb. 23-24, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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 organizers have checked that:

Links to workshop materials are being provided below. If we can provide additional resources to help making learning easier for you (e.g. large-font hand-outs, sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email the workshop administrator at hilgert@bio5.org for more information.


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

Pre-workshop Survey

Post-workshop Survey


Saturday February 23

08:30 Access and navigate the command line / Bash Shell
10:30 Break
10:45 Manage data with git/GitHub
12:00 Break
13:00 Automate tasks with shell scripts
14:45 Break
15:00 Automate tasks with shell scripts, cont.
17:00 End of Day

Sunday February 24

08:30 Analyze scientific data with Python and git/GitHub
10:30 Break
11:00 Analyze scientific data with Python and git/GitHub, cont.
12:00 Break
13:00 Analyze scientific data with Python and git/GitHub, cont.
14:45 Break
15:00 Analyze scientific data with Python and git/GitHub, cont.
17:00 End of Day

Schedule subject to change if necessary.

Online Collaboration

We will use the collaborative document at https://pad.carpentries.org/2019-02-23-Tucson for chatting, taking notes, and sharing URLs and bits of code.

Syllabus & Learning Objectives

Take control with the Bash Shell (Command Line/Shell/Unix)

  • Work in vs. work below the GUI
  • Navigate the shell
  • Find, create, copy, move and delete folders and files
  • Shell over GUI: Command history and tab completion
  • Connect commands into workflows: pipes and redirection
  • Automate repetitive tasks: loops
  • Save and run workflows in scripts

Collaborate with git/GitHub

  • Access a repository and pull files
  • Create a repository
  • Record changes: add, commit, ...
  • View changes: status, diff, ...
  • Ignore files
  • Work on the web: clone, pull, push, ...
  • Resolve conflicts

Analyse scientific data with Python

  • Use libraries
  • Work with arrays
  • Read and plot data
  • Create and use functions
  • Use loops and conditionals
  • Use Python from the command line
  • Defensive programming

Syllabus subject to change if necessary.

Prepare Your Computer

To participate in a Software Carpentry workshop, you will need access to the software described below. Unless you prepare your laptop as described below you will be unable to follow along. In addition, you will need an up-to-date web browser, we recommend Firefox, Chrome or Safari as Internet Explorer/Edge can be buggy.

Should you encounter issues while installing the software below, please look for a solution in our Configuration Problems and Solutions wiki page. If even this does not help, please get in touch with us at the contact email listed above and we will attempt to provide a solution.

The Bash Shell

Bash is a commonly-used shell environment that gives you the power to quickly do simple tasks on your computer. Bash stands for 'Bourne Again Shell'; if you are interested in the history of the term and the underlying technological development, please search the Web for 'Bash Shell'.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Ensure “Use the nano editor by default” is selected and click on “Next”.
    3. Ensure "Use Git from Git Bash only" is selected and click on "Next". If you forget 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. Ensure "Use the OpenSSL Library" is selected and click on "Next".
    5. Ensure "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure "Use Windows' default console window" is selected and click on "Next".
    7. Ensure "Enable file system caching" and "Enable Git Credential Manager" is selected and click on "Next".
    8. Click on "Install".
    9. 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 Bash and Git in the Git Bash program.


The default shell in all versions of macOS 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

Writing code is much easier with respectively optimized text editors that include features such as automatic color-coding of key words and syntax-highlighting. We will use the basic editor 'nano' in the workshop; it comes pre-installed with the git-bash download above for Windows, Mac and Linux.


Click the Start button and type 'git bash' into the search window.
Click on the "Git Bash" icon to open the shell.
Type 'nano test.txt' to open a text editor. IF this does not open the nano text editor contact the workshop administrator at the email listed above.
Type 'Test'.
To exit the nano editor press Ctrl and type 'x' (a.k.a. '^X'; additional commands are listed at the bottom of the text edito window.


During the workshop we will be using the basic editor nano. nano should be pre-installed; see the Git installation video tutorial for an example on how to open nano.


During the workshop we will be using the basic editor nano. nano should be pre-installed


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 github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

For the workshop you will need a GitHub account, if you don't have one already please get it at github.com. Basic GitHub accounts are free. However, please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private at GitHub.


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


Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. 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 dnf install git.


Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research 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., 3.6 is fine).

We will teach Python using the Jupyter 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 https://www.anaconda.com/download/#windows 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.


Video Tutorial
  1. Open https://www.anaconda.com/download/#macos 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 https://www.anaconda.com/download/#linux with your web browser.
  2. Download the Python 3 installer for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. 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).
  6. Close the terminal window.

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