UoR Carpentries

University of Reading

Online

July 27-30, 2021

9:00 - 15:00

Instructors: Dan Brady, Maria Broadbridge, Paul Heaton, Etienne Roesch

Helpers: Nico Biagi, Carolyn McNabb, Emmanuelle Rodrigues Nunes, Brendan Williams

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. 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: July 27-30, 2021. 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 e.b.roesch@reading.ac.uk for more information.

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

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.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

A few days prior to the workshop, we have organised a "setup clinic" day, during which we will be available on Teams to help you install the relevant pieces of software. Please use this opportunity to test your setup before attending the workshop.

Tuesday 27 July, 2021

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
11:00 Morning break
11:30 Automating Tasks with the Unix Shell (Continued)
12:00 Lunch break
13:00 Version control with Git
14:30 Afternoon break
15:00 Version control with Git (Continued)
16:00 Wrap-up
16:30 END

Wednesday 28 July, 2021

09:00 R for reproducible scientific analysis
10:30 Morning break
11:00 R for reproducible scientific analysis (Continued)
12:30 Lunch break
13:30 R for reproducible scientific analysis
14:45 Afternoon break
15:00 R for reproducible scientific analysis (Continued). Links to Emmanuelle's scripts: cats_dataset_example_to_source.R, script_control_flow.R, script_data_frames.R, and script_subset.R.
16:45 Wrap-up
17:00 END

Friday 30 July, 2021

09:00 R for reproducible scientific analysis
10:00 Morning break
10:30 R for reproducible scientific analysis (Continued). Links to Carolyn's scripts: Functions_explained.R, dplyr_tidyr.R, and plotting_with_ggplot2.R
12:00 Lunch break
13:00 R for reproducible scientific analysis
14:10 Afternoon break
14:40 R for reproducible scientific analysis (Continued)
16:00 Wrap-up
16:30 Post-workshop Survey
16:50 END

Setup

To participate in a Software Carpentry workshop, you will need access to software as 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.

A few days prior to the workshop, we hold a "setup clinic", during which some of us will be available on Teams to help you out with installing the relevant pieces of software. Please use this opportunity to test your setup before you attend the workshop.

Install the videoconferencing client

We use a dedicated team on the University Microsoft Teams. Upon confirmation of your registration to the workshop, you will be added to the team, and event calendar items should show up your Outlook calendar for the workshop. Simply follow the event link to join the workshop.

We will all have a much, much better experience of the workshop if you turn on your camera: we will be a small group, and we aim to all learn from each other, and boost our sense of community on campus. Of course, we will understand if, for a reason or another, you prefer to keep it turned off, but please give it some thought.

Set up your workspace

You can access Microsoft Teams on your computer, your tablet or your phone, from a web browser or the native app. The native app can be resource-intensive, especially on older computers and/or MacOS or Linux. It is advised that you test your system before the workshop, as there won't be time to troubleshoot connections during the workshop. It is totally possible to attend the workshop from one device, e.g. a tablet, and code along the exercises from another, e.g. a laptop. You can also join a meeting on team using the same account and from different devices at the same time; as we may use the chat to share snippets of code, this would allow you to copy-paste onto the device you use to do the exercises.

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.