UCSD 2023 UC Carpentries Fall Workshop

General Information

The Carpentries aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This workshop is designed for researchers and enables non-experts to develop computing skills for research analysis. We will cover basic concepts and tools, such as - working with libraries and data frames; reading and plotting data; creating and using functions; the shell using command-line applications; cleaning and transforming data; and more. Participants will be encouraged to help one another and to apply what they This is a free workshop and is open to all University of California students, staff, and faculty. 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: This workshop is open to University of California students, staff, postdocs, and faculty. You don't need to have any previous knowledge of programming or the tools presented in the workshop to attend. A laptop is required for each session.

Requirements: Participants must have a laptop or desktop with a few specific software packages installed (listed below).

Contact: Please email carpentries@ucsd.edu for more information.

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

Date	Day	Topics
Sept 11	Day 1	The Unix Shell: Introduction, Navigating the file system, & working with files & directories
Sept 12	Day 2	Version Control with Git: Introduction, Creating a Repository, Tracking Changes, and Collaborating
Sept 13	Day 3	Intro to R & RStudio: basics, data structures, data import/export, dylyr
Sept 14	Day 4	Intro to R & RStudio: dplyr (cont.), tidyverse, plotting with ggplot2 and knitr
Sept 18	Day 5	Intro to Python: Running/writing, variables/assignment, data types/type conversions, built-in functions/help, libraries, reading/writing data in Dataframes, and Pandas Dataframes
Sept 19	Day 6	Intro to Python: plotting, lists, for loops, conditionals, looping over datasets, and writing functions
Sept 20	Day 7	Tidy Data: learn how to use this tool to clean, transform, and track changes made to data
Sept 21	Day 8	SQL:Introduction, Creating a Repository, Tracking Changes, and Collaborating

Curriculum

For this workshop we will be referencing the The UNIX Shell, Version Control with Git, R for Reproducible Scientific Analysis, Plotting and Programming in Python, Tidy Data, and SQL Carpentries curricula.

Data

We will be using the specific software downloads and data for each lesson. Please refer to the listing of downloads needed for each session you'll be attending as provided at this link.

Collaborative Notes

We will use HackMD collaborative notes for taking notes, and sharing URLs and bits of code. The links to each session are listed at this link.

Zoom Installation

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:

Two monitors: If you have two monitors, plan to have your terminal up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with Make commands.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

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

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: SWC R Install Windows

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

Video Tutorial: SWC R Install Mac

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at . 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

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).

Open https://www.anaconda.com/products/individual#download-section with your web browser.
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)
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: SWC Install Python on Windows

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

Video Tutorial: SWC Install Python on Mac

Open https://www.anaconda.com/products/individual#download-section with your web browser.
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.)
Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
Type
```
bash Anaconda3-
```
and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
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).
Close the terminal window.

The Bash Shell

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

Download the Git for Windows installer.
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" and click on "Next".
3. 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.)
4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
6. Ensure that "Use Windows' default console window" is selected and click on "Next".
7. Ensure that "Default (fast-forward or merge) is selected and click "Next"
8. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
9. Click on "Install".
10. Click on "Finish" or "Next".
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: Windows Installation

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 MacOS Installation

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.

Git should be installed on your computer as part of your Bash install (see the Shell installation instructions).

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: SWC Install Shell, Git, and Nano on Mac

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.

SQLite

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

Windows

The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.