Date: June 6-9, 2022
Time: 1:00-4:00pm PT
Venue: UC San Diego
Instructors: Kimberly Thomas, Saulo Muller Soares, David Palmquist
Helpers: Kimberly Thomas, David Palmquist, Reid Otsuji, Christina Agu
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 used with the Python programming language and version control with Git. 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: This workshop is open to UCSD students, staff, 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.
Where: Virtual (via Zoom).
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail kkt008@ucsd.edu or rotsuji@ucsd.edu for more information.
Assessment: A Co-Curricular of Record activity recognition will be given to the student who:
For more information on the UC San Diego Co-Curricular of Record (CCR), please visit the UCSD Engaged Learning Tools Co-Curricular Record page.
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.
Please be sure to complete these surveys before and after the workshop.
Date | Session | Topics |
---|---|---|
June 6 | Introduction to Python - Session 1 | Jupyter Notebook - Running/Wuitting, Variables and Assignment, Data Types/Type Conversions, Built-in Functions, and Help |
June 7 | Introduction to Python - Session 2 | Libraries, Writing Functions, Reading/Writing data in Dataframes, and Pandas Dataframes |
June 8 | Introduction to Python - Session 3 | Plotting, Lists, For Loops, Looping over Datasets, and Conditionals |
Quiz | Due next session; posted on Canvas | |
June 8 | Version Control with Git | Introduction to Git, Creating a Repository, Tracking Changes, and Collaborating |
For this workshop we will be referencing the Plotting and Programming in Python and Version Control with Git Carpentries curricula.
We will be using the 5 year gapminder data and inflammation data. Please download the both data prior to start of first session.
We will use HackMD collaborative notes for taking notes, and sharing URLs and bits of code.
To participate in this workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.
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).
Video Tutorial: SWC Install Python on Windows
Video Tutorial: SWC Install Python on Mac
bash Anaconda3-and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
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).
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
.