Winona State University

August 14-16, 2017

9:00 am - 4:30pm

Instructors: Hannah Leverentz, Chris Malone, Nathan Moore

Helpers: Silas Bergen, Todd Iverson, Chris Phan

General Information

Software Carpentry aims to help students, teachers, and 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.

The Software Carpentry and Data Carpentry organizations have a large number of tutorials written and available on the web via a Creative Commons Attribution License. These lessons could be classified as "Open Educational Resources", and we think this material can be relevant and useful to the undergraduate classroom. Further, the best way to get to know the lessons is to work through them, in teams, in a dedicated setting. Attendees should expect to gain proficiency with the shell, programming in python, and implementing revision control with git, all in a supportive setting. There will also be some discussion of how we can use these materials in undergraduate classrooms.

Please note, if you teach, study, or work outside of science you are still very welcome! The practices presented at the workshop are quite general, and have led to the sister organizations of Library Carpentry, https://librarycarpentry.github.io/, and The Programming Historian http://programminghistorian.org/.

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

Who: The course is aimed at faculty members within the Minnesota State system. Depending on registrations there may be space for staff, students, and community members. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Pasteur Hall 129, Winona State University, Winona, MN 55987. Get directions with OpenStreetMap or Google Maps.

When: August 14-16, 2017. Add to your Google Calendar. Note, the workshop is scheduled around several events in the Welcome Week Calendar at Winona State University. The total contact time for the workshop will be about 2 work days, but the meetings will be spread over three days: Monday morning, Tuesday all day, and Wednesday afternoon.

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 organisers 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 and we will attempt to provide them.

Registration: To register, please fill out this google form. The workshop is funded by the Minnesota Legislature, via Minnesota State system. Per the funders' intention, faculty members have first priority in registration. Other staff, students, and community members who fill out this form will be added to a waiting list. If workshop seats are open on August 7 we will contact those on the waiting list.

There is no fee for the 3-day workshop, and coffee will be provided during the breaks. On-campus parking will be available. Meals, transportation, and lodging are not provided. Feel free to contact the organizers for advice on travel and accomodations.

Contact: Please email nmoore@winona.edu or hleverentz@winona.edu for more information.


Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1, Monday August 14

08:30 Soft start, computer setup questions, coffee
09:00 Welcome and Introductions, slides
09:15 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break

Day 2, Tuesday August 15

09:00 Analyzing data with R, part 1 notes
10:30 Coffee
12:00 Lunch break
13:00 Writing programs with R, part 2
14:30 Coffee
16:00 Wrap-up

Day 3, Wednesday August 16

13:00 Version control with Git
14:30 Coffee
16:00 Wrap-up

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 R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R 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 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.

Windows

Video Tutorial
  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. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. 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 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). 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).

Mac OS X

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 yum 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. 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.

Windows

Video Tutorial

nano is a basic 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.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic 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.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

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 Gedit, Kate or Sublime Text.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Mac OS X

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.