UC Carpentries 2024

UC

Online

Sept 09-20

8:30 am - 12:30 pm PDT

Instructors: Stephanie Nielsen, Scott Peterson, Reid Otsuji, Tim Dennis, Kim Thomas, Kaija Gahm, Jose Niño Muriel, Geoffrey Boushey, David Palmquist, Kaija Gahm

Helpers: Phredd Groves, David Palmquist, Reid Otsuji, Kristi Liu

Register

General Information

The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.

Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/

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

When: Sept 09-20; 8:30 am - 12:30 pm PDT 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. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your Carpentries experience accessible. To request an accommodation for this workshop, please fill out the accommodation request form. If you have questions or need assistance with the accommodation form please email us.

Contact: Please email smniel@ucsc.edu or datascience+carpentries@ucla.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.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1 (Tidy Data)

8:30 AM - 10:00 AM 1. Using Spreadsheet Programs for Data Organization
2. Formatting Data Tables in Spreadsheets
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Formatting Problems
4. Dates as Data
11:30 AM - 12:20 PM 5. Basic Quality Assurance and Control
6. Exporting Data from Spreadsheets
7. Caveats of Popular Data and File Formats

Day 2 (Unix)

8:30 AM - 10:00 AM 1. Introducing the Shell
2. Navigating Files and Directories
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Working With Files and Directories
4. Pipes and Filters
11:30 AM - 12:20 PM 5. Loops
6. Shell Scripts
7. Finding Things

Day 3 (Git)

8:30 AM - 10:00 AM 1. Navigating Git Repositories
2. Recording Changes to Files
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Viewing the History of Changes
4. Undoing Changes
11:30 AM - 12:20 PM 5. Working with Remotes
6. Collaborating with Others

Day 4 (SQL)

8:30 AM - 10:00 AM 1. Using Databases and SQL
2. Selecting Data
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Filtering Data
4. Calculating New Values
11:30 AM - 12:20 PM 5. Aggregating Data
6. Combining Data
End Post-workshop survey

Day 5 (Python: Part 1)

8:30 AM - 10:00 AM 1. Running and Quitting
2. Variables and Assignment
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Data Types and Type Conversion
4. Built-in Functions and Help
11:30 AM - 12:20 PM 5. Conditionals
6. Loops
End Post-workshop survey

Day 6 (Python: Part 2)

8:30 AM - 10:00 AM 1. Functions
2. Libraries
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Reading Tabular Data into DataFrames
4. Pandas DataFrames
11:30 AM - 12:20 PM 5. Plotting
End Post-workshop survey

Day 7 (R: Part 1)

8:30 AM - 10:00 AM 1. Introduction to R and RStudio
2. Project Management With RStudio
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Seeking Help
4. Data Structures
11:30 AM - 12:20 PM 5. Exploring Data Frames
6. Subsetting Data
End Post-workshop survey

Day 8 (R: Part 2)

8:30 AM - 10:00 AM 1. Vectorization
2. Dataframe Manipulation with dplyr
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Creating Publication-Quality Graphics with ggplot2
4. Producing Reports With knitr
End Post-workshop survey

Day 9 (OpenRefine)

8:30 AM - 10:00 AM 1. Introduction to OpenRefine
2. Working with OpenRefine Projects
10:00 AM - 10:10 AM Break
10:10 AM - 11:30 AM 3. Faceting and Filtering Data
4. Clustering and Transformations
11:30 AM - 12:20 PM 5. Exporting and Saving Data
6. Advanced Data Operations
End Post-workshop survey

Setup

To participate in a UC Carpentries 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.

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.

Unrecognized value for variable curriculum set in _config.yml. Currently the variable is set to: FIXME. Check the values of carpentry and curriculum in the _config.yml file.

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, "Choosing the default editor used by Git", 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. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. 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 Mac OS X Ventura and newer versions is Zsh, but 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, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

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 Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

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.

Please open the Terminal app, type git --version and press Enter/Return. If it's not installed already, follow the instructions to Install the "command line developer tools". Do not click "Get Xcode", because that will take too long and is not necessary for our Git lesson. After installing these tools, there won't be anything in your /Applications folder, as they and Git are command line programs. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here. (Note: this project is no longer maintained.) 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 in the pop-up dialog. You can watch a video tutorial about this case.

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.

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 (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/download/success 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/download/success 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/download/success 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.

OpenRefine

For this lesson you will need OpenRefine and a web browser. Note: this is a Java program that runs on your machine (not in the cloud). It runs inside a web browser, but no web connection is needed.

  1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It will not run correctly in Internet Explorer.
  2. Download software from http://openrefine.org/
  3. Create a new directory called OpenRefine.
  4. Unzip the downloaded file into the OpenRefine directory by right-clicking and selecting "Extract ...".
  5. Go to your newly created OpenRefine directory.
  6. Launch OpenRefine by clicking openrefine.exe (this will launch a command prompt window, but you can ignore that - just wait for OpenRefine to open in the browser).
  7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
  1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser. It may not run correctly in Safari.
  2. Download software from http://openrefine.org/.
  3. Create a new directory called OpenRefine.
  4. Unzip the downloaded file into the OpenRefine directory by double-clicking it.
  5. Go to your newly created OpenRefine directory.
  6. Launch OpenRefine by dragging the icon into the Applications folder.
  7. Use Ctrl-click/Open ... to launch it.
  8. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.
  1. Check that you have either the Firefox or the Chrome browser installed and set as your default browser. OpenRefine runs in your default browser.
  2. Download software from http://openrefine.org/.
  3. Make a directory called OpenRefine.
  4. Unzip the downloaded file into the OpenRefine directory.
  5. Go to your newly created OpenRefine directory.
  6. Launch OpenRefine by entering ./refine into the terminal within the OpenRefine directory.
  7. If you are using a different browser, or if OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to use the program.

SQLite

SQL is a specialized programming language used with databases. We use a database manager called SQLite in our lessons.

  • Run "Git Bash" from the Start menu
  • Copy the following curl -fsSL https://jt14den.github.io/2024-09-09-UC/getsql.sh | bash
  • Paste it into the window that Git Bash opened. If you're unsure, ask an instructor for help
  • You should see something like 3.27.2 2019-02-25 16:06:06 ...

If you want to do this manually, download sqlite3, make a bin directory in the user's home directory, unzip sqlite3, move it into the bin directory, and then add the bin directory to the path.

SQLite comes pre-installed on macOS.

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.