UM Software Carpentry Workshop: December 8-9, 2022

University of Michigan

Online

Dec 8-9, 2022

9:00am-4:30pm ET

Instructors: Pat Schloss, Grace Kenney, Pariksheet Nanda, Courtney Armour

Helpers: Sarah Arcos, Fred Feng, Sarah Lucas

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 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, but all are welcome to attend. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Dec 8-9, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer 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).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email pschloss@umich.edu for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Click Here to Register


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this Slack channel within the UMCoderspaces Workspace for chatting, taking notes, and sharing URLs and bits of code.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

Before Pre-workshop survey
09:00 Welcome to the workshop
09:15 R for Plotting
10:30 Morning break
10:45 R for Plotting (Continued)
12:00 Lunch break
13:00 The Unix Shell
14:15 Afternoon break
14:30 Intro to git & GitHub
16:30 END

Day 2

09:00 R for Data Analysis
10:30 Morning break
10:45 R for Data Analysis (Continued)
12:00 Lunch break
13:00 Writing Reports with R Markdown
14:30 Afternoon break
14:45 Writing Reports with R Markdown (Continued)
15:30 Conclusions & Wrap-up
16:15 Post-workshop Survey
16:30 END

Setup

To participate in a Software Carpentry workshop, you will need to complete the Pre-workshop setup steps below. In addition, you will need an up-to-date web browser (e.g. Chrome or Firefox). You will not be able to participate in the workshop if you do not complete these steps ahead of time.

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.

If you get stuck, join the CoderSpaces Slack workspace and ask for help in the #install-party channel. We monitor that channel and will help you out as soon as we can!

Pre-workshop setup steps

All installation steps are required prior to receiving workshop Zoom link/meeting ID. Installation will take approximately 20-30 minutes to complete. Help is available in the #install-party channel or email (damki@umich.edu) to set up a time for 1:1 installation troubleshooting.

  1. Install the following software (all instructions are below).
    • Zoom (make sure you have the latest version)
    • A Unix shell (e.g. bash, zsh)
    • git
    • R
    • RStudio, an integrated development environment for R
  2. Create a GitHub account if you do not already have one. You’ll need to know the email associated with your account during the git lesson of the workshop.
  3. After you have installed everything above, download un-report.zip. You’ll need the files included during the workshop.
    1. Move un-report.zip to your Desktop and unzip it (usually double-clicking it will work).
    2. Start up RStudio. In the upper left menu, select File > Open. In the window that opens, go to the un-report/ folder on your Desktop and select the file check_setup.R to open it in RStudio.
    3. Click the Source button to run the script. This script will make sure that everything is installed and setup correctly. You should see output printed to the console window (usually the lower left pane in RStudio).
    4. Take a screenshot of (or copy & paste) the console output and send it via email to the lead instructor (). Be sure to include the line starting with source(" to the end.

If at any point you get stuck or run into problems, please don’t hesitate to ask us for help!

Software Installation Instructions

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

  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. From the dropdown menu select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    7. Ensure that "Use Windows' default console window" is selected and click on "Next".
    8. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    9. Ensure that "Git Credential Manager Core" is selected and click on "Next".
    10. Ensure that "Enable file system caching" is selected and click on "Next".
    11. Click on "Install".
    12. Click on "Finish" or "Next".
  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.

Video Tutorial

The default shell in some versions of macOS is Bash, and Bash is available in all versions, 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.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

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.

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.

For macOS, 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.

Video Tutorial

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. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

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.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

R

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

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.

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.