Software Carpentry @ UW-Madison

June 6-7, 2018

8:30 am - 4:30 pm

Instructors: Kalin Kiesling, Matthew Garcia, Taylor Scott, Patrick Shriwise

Helpers: Stephen Meyer, Dorothea Salo, Brian Cornille, Christina Koch, Lauren Michael

Registration is required and will be available here starting May 9, 2018 at 5 pm. Make sure to read all details below before registering and to choose appropriately between UW-Madison’s Data Carpentry and Software Carpentry workshops.

General Information

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 researchers who have no prior experience with programming and just want to get started in some basic skills for organizing, combining, and visualizing data, our UW-Madison Data Carpentry workshop (June 4-5) will likely be more appropriate. These two workshops are NOT intended to be taken back-to-back, and you can learn about future workshops at UW-Madison by joining the mailing list of UW-Madison's Advanced Computing Initiative.

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

Who: The course is aimed at UW-Madison graduate students and other UW-Madison researchers. Some prior experience with programming is strongly recommended. However, you don't need to have any previous knowledge of the specific tools that will be presented at the workshop.

Where: Sterling Hall, room 2425. Get directions with OpenStreetMap or Google Maps.

When: June 6-7, 2018. 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:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email megarcia@wisc.edu for more information.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

08:30 Setup
09:00 Automating tasks with the Unix shell
10:30 Break
12:00 Lunch
13:00 Building programs with Python
14:30 Break
16:00 Wrap-up

Day 2

09:00 Version control with Git
10:30 Break
12:00 Lunch
13:00 Building Programs with Python
14:30 Break
16:00 Wrap-up: Additional Resources
16:30 Post-workshop Survey

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

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...

Setup

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 will use both terminal ("shell" or "command-line" interface) and GUI text editors at different times in the workshop, so pay careful attention to the text editors that are available for your system (several are listed below) and make sure that you are using at least one terminal and one GUI editor with which you are comfortable. Above all else, your GUI text editor must save documents as plain text (UTF-8 encoding).

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the SWC 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.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps. Be sure to look for the following options:
    • Keep "Use Git from the Windows Command Prompt" selected. If you forgot 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.
    • Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    • Keep "Use Windows' default console window" selected.
    • Click on "Install".
  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 Git and Bash in the Git Bash program.

macOS

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.

Linux

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

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).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. 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 provided at GitHub.

Windows

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

macOS

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. 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.

Linux

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.

Text Editor

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. These are often GUI editors that save documents in plain text format, with several listed below for each platform. In the terminal window, the default text editor on macOS and Linux is usually set to Vim ("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. Instructors will often use the nano editor in the terminal window, which is a little easier to use when just starting out.

Windows

Video Tutorial

nano is a basic terminal-based text editor and the default that instructors use in the workshop. 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.

A number of GUI editors are available for Windows including Notepad++, Komodo Edit, and Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

nano is a basic terminal-based text editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed in the Linux distribution that underlies the macOS.

A number of GUI editors are available for macOS including Text Wrangler (formerly BBEdit), Sublime Text, Atom, and Geany.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed as a part of your Linux distribution.

A number of GUI editors are available for Linux including Gedit, Kate, Geany, Sublime Text, and Atom.

Python

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).

Windows

Video Tutorial
  1. Open https://www.anaconda.com/download/#windows with your web browser.
  2. Download the Python 3 installer for Windows.
  3. During installation for Python 3 check the box Add Anaconda to my PATH environment variable.
  4. Anaconda does not require administrative priviliges on your computer. A recent update to the Anaconda installer may include the option to install one or more components of Microsoft Visual Studio, which will require administrative privileges if yours is a shared computer. If you do have such access, Visual Studio offers an integrated development environment for your programming activities, but we will not be using it in the SWC workshop time.

macOS

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.

Linux

  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.