UW October 2021 Software Carpentry (Online)

University of Washington

Online

October 11th - 14th, 2021

9:00 AM - noon

Instructors: Bryna Hazelton, Bernease Herman, Noah Benson, Will Fondrie, Anthony Barente, Timothy Middlekoop, Naomi Alterman

Helpers: Noah Benson, Naomi Alterman, Rob Fatland, Anupama Jha, Anthony Barente

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Eventbrite registration for the Python track:

Eventbrite registration for the R track:

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: October 11th - 14th, 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 nben@uw.edu or janekoh1@uw.edu 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.


Collaborative Notes

We will use this collaborative document 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

Note that the Python and R tracks will meet together on days 1 and 2.

Python Track

Day 1

Lesson Plan

Before starting Pre-workshop survey
09:00 Automating tasks with the Unix shell
10:00 Coffee break
10:15 Unix Shell (continued)

Day 2

Lesson Plan

09:00 Version control with Git
10:00 Coffee break
10:15 Git (continued)

Day 3

Lesson Plan

09:00 Building programs with Python
10:00 Coffee break
10:15 Python (continued)

Day 4

Lesson Plan

09:00 Python (continued)
10:00 Coffee break
10:15 Python (continued)
Before leavingPost-workshop survey

R Track

Day 1

Lesson Plan

Before starting Pre-workshop survey
09:00 Automating tasks with the Unix shell
10:00 Coffee break
10:15 Unix Shell (continued)

Day 2

Lesson Plan

09:00 Version control with Git
10:00 Coffee break
10:15 Git (continued)

Day 3

Lesson Plan

09:00 Building programs with R
10:00 Coffee break
10:15 R (continued)

Day 4

Lesson Plan

09:00 R (continued)
10:00 Coffee break
10:15 R (continued)
Before leavingPost-workshop survey

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.

Participants only need to follow the setup instructions for the modules of the course they are enrolled in. If you are enrolled in the Python track, you should follow the instructions for "The Bash Shell", "Git", "Text Editor", and "Python". If you are enrolled in the R track, you should follow the instructions for "The Bash Shell", "Git", "Text Editor", and "R".

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

Who should follow these instructions: All participants should follow the instructions for setting up the Bash Shell, regardless of whether you are enrolled in the Python or R tracks.

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

Who should follow these instructions: All participants should follow the instructions for setting up Git, regardless of whether you are enrolled in the Python or R tracks.

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

Who should follow these instructions: All participants should follow the instructions for setting up a text editor, regardless of whether you are enrolled in the Python or R tracks.

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.

Python

Who should follow these instructions: You only need to follow the setup instructions for the course in which you have enrolled. You do not need to follow the setup instructions for Python if you are enrolled in the R course and vice versa.

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 (Jupyter Notebook will be installed by Anaconda). 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).

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open https://www.anaconda.com/products/individual#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 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 and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.

R

Who should follow these instructions: You only need to follow the setup instructions for the course in which you have enrolled. You do not need to follow the setup instructions for R if you are enrolled in the Python course and vice versa.

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.