Foundations for Research Computing

Columbia University

January 7-8, 2025

9:00 am - 4:30 pm EST

Instructors: Alan Crosswell, Esther Jackson, Eric Vlach, Dan Woulfin

Helpers: Alan Crosswell, Esther Jackson, Gary Hausman, Axinia Radeva, Eric Vlach

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/

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: Uris Hall. Get directions with OpenStreetMap or Google Maps.

When: January 7-8, 2025; 9:00 am - 4:30 pm EST Add to your Google Calendar.

Requirements: Participants must bring a laptop 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 committed to making this workshop accessible to everybody. The workshop organizers have checked that:

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.

Glosario is a multilingual glossary for computing and data science terms. The glossary helps learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers for their learners.

Contact: Please email dw3105@columbia.edu or rcfoundations@columbia.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

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
10:30 Morning break
11:00 Automating Tasks with the Unix Shell (Continued)
12:00 Lunch break
13:00 Plotting and Programming in Python
14:30 Afternoon break
15:00 Plotting and Programming in Python (Continued)
16:00 Wrap-up
16:30 END

Day 2

09:00 Version Control with Git
10:30 Morning break
11:00 Version Control with Git (Continued)
12:00 Lunch break
13:00 Plotting and Programming in Python
14:30 Afternoon break
15:00 Plotting and Programming in Python (Continued)
16:00 Wrap-up
16:30 Post-workshop Survey
16:40 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.

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.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. We'll be using some standard tools to first install Python and then the packages required for this workshop using pip.

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 Lab notebooks, a programming environment that runs in a web browser (Jupyter Lab will be installed by pip). 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.python.org/downloads/ with your web browser.
  2. Click on Download Python 3.x.y under "Download the latest version for Windows" near the top.
  3. Click on the downloaded installer and run it.
  4. You'll see a popup window from the installer. Check the "Add python.exe to PATH" box near the bottom and then click Install Now.
  5. To confirm that it's installed, open git-bash (installed per the instructions above) and type python --version. This should print something like:"Python 3.12.5".
  6. Next we'll install Jupyter Lab and the various Python packages we'll be using. These will all be installed in a Python "Virtual Environment" (venv). Type these commands in the git-bash shell: 
    	     cd ~/Desktop
	     python -m venv venv
	     source venv/Scripts/activate
	     pip install jupyterlab ipywidgets pandas matplotlib
    That last step will take a while and will print a lot of progress output showing the packages being installed.
  1. Open https://www.python.org/downloads/ with your web browser.
  2. Click on Download Python 3.x.y under "Download the latest version for macOS" near the top.
  3. Click on the downloaded installer and run it, responding to the license agreement prompt, and so on.
  4. To confirm that it's installed, open Terminal and type python --version. This should print something like:"Python 3.12.5".
  5. Next we'll install Jupyter Lab and the various Python packages we'll be using. These will all be installed in a Python "Virtual Environment" (venv). Type these commands in the git-bash shell: 
    	     cd ~/Desktop
	     python -m venv venv
	     source venv/bin/activate
	     pip install jupyterlab ipywidgets pandas matplotlib
    That last step will take a while and will print a lot of progress output showing the packages being installed.
Python is usually already installed on most Linux distributions.
  1. To confirm that it's installed, open a terminal and type python3 --version. This should print something like:"Python 3.12.5".
  2. Next we'll install Jupyter Lab and the various Python packages we'll be using. These will all be installed in a Python "Virtual Environment" (venv). Type these commands in the git-bash shell: 
    	     cd
	     python3 -m venv venv
	     source venv/bin/activate
	     pip install jupyterlab ipywidgets pandas matplotlib
    That last step will take a while and will print a lot of progress output showing the packages being installed.

Data Used in the Lessons

Make sure to download the required data for the Shell and Python lessons: