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.
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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.
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:
701 19th Street South, Birmingham, AL 35233 (Room 102).
Get directions with
OpenStreetMap
or
Google Maps.
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).
We will be hosting two helper sessions to assist with package and software installations if you encounter any issues:
Session 1 will be on 7/8/25 from 8a.m. - 10a.m. CST. Zoom link is available here
Session 2 will be on 7/8/25 from 3p.m. - 5p.m. CST. Zoom link is available here
Accessibility:
We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
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.
Workshop Recordings:
Carpentries workshops are designed to be interactive rather than lecture-based, with lessons that build upon one another.
To foster a positive online learning environment, we strongly recommend that participants join in real time.
As a result, workshop recordings are not recommended and may not be available to learners.
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.
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 will use two datasets as part of this lesson over the next two days. Please ensure that
all datasets are downloaded and working before the start of the workshop
For bash, please follow the instructions and download the data located
here.
If the text link is not working, copy and paste the below url into your browser:
https://swcarpentry.github.io/shell-novice/#download-files
For Python, please follow the instructions and download the data located
here.
If the text link is not working, copy and paste the below url into your browser:
https://swcarpentry.github.io/python-novice-gapminder/index.html#getting-the-data
The Bash Shell
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
To install WSL 2, you will need Administrator (“admin”) privileges on your laptop/PC.
If you have a device provided by an institution that does not give you admin rights, please either request that they:
Give you admin rights (temporarily or otherwise) to install WSL 2 yourself OR
Install WSL 2 for you
If you experience any issues, please install Git for Windows using the instructions below.
Click on the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard, and type “System” in the search bar.
Click the “System (Control Panel)” option.
In the window that opens, there will be information about your current Windows system, including the version. Here is an example from Windows 11:
Depending on your version, please go to the relevant instructions below.
Windows XP/Vista/7/8
These versions of Windows are considered End Of Life, and are not recommended for use in modern data science.
Software may experience issues, and security updates are also not available which puts your machine at risk.
Please consider upgrading your Windows version if you are able to do this yourself, or speak with your local IT administrator to discuss options available to you to upgrade.
If you are running any of these Windows versions, please install Git for Windows using the installation instructions below.
Windows 10 (earlier than version #1903)
For older versions of Windows 10 (version 1903/OS build 18362 and below), please follow the Git for Windows installation instructions below.
Windows 10 (version #1903 and later) and Windows 11
WSL 2 is recommended for more modern versions of Windows as it provides an accurate and representative experience of Linux, but provided from within your Windows environment.
We will install Ubuntu via the Microsoft Store.
It is possible to install WSL within the Windows Powershell command prompt, and full instructions are on the Microsoft website.
Note: You will need to restart your computer after installing WSL 2, so make sure you have saved any work.
Why Ubuntu?
Linux comes in many flavours, called “distributions”, and each has its own benefits, features and quirks!
WSL 2 is a fully fledged Linux environment that runs completely within your Windows 10 or 11 operating system.
While there are many Linux distributions available to install (e.g. Ubuntu, Debian, Fedora, Mint, Arch, Gentoo, and hundreds more!), WSL 2 only supports a handful of distributions listed above due to the way it needs to be integrated with Windows itself.
So, we will use the default that WSL 2 recommends, Ubuntu.
Via the Microsoft Store:
Open the Windows Start Menu button in the bottom left corner of your screen (four blue squares), or tap the Win Windows button on your keyboard (between the bottom left CTRL and ALT keys) and search “store”. Open the Microsoft Store.
In the Microsoft Store search bar, type “wsl ubuntu”, and select the Ubuntu 22.04 or 24.04 option (at the time of writing, Ubuntu 22.04.06 LTS, or Ubuntu 24.04.01 LTS):
If a pop-up window appears asking if you want to make changes to your device, select “Yes”
The install should proceed, and this can take a few minutes depending on your PC performance and internet download speed.
Once installed, restart the computer.
Once restarted, reopen the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard. In the search bar, type either:
Ubuntu: selecting Ubuntu 22.04.06 LTS or Ubuntu 24.04.01 LTS from the Start Menu will open the bash prompt directly, or
Terminal: this will open a new Windows Terminal window, which will look like a blank black window with a blinking cursor waiting for input. Note: This terminal might default to Powershell, and not Ubuntu. If this is the case, click the down arrow in the Terminal window menu bar at the top, and then click Ubuntu 22.04 or 24.04, depending on the version you installed. It will also show keyboard shortcuts (e.g. Ctrl+Shift+1) to open the various prompts available within the Terminal application.
Once you have installed WSL 2, you will need to install some software within the Ubuntu operating system in order to use it effectively. Make sure you are using Ubuntu by checking you see the bash prompt:
The first thing to do is to update the list of available Ubuntu software packages, using a tool called apt.
Type the following command into the bash prompt:
sudo apt update
Note: You will be prompted to enter your password. This is the password you set when installing Ubuntu, and will not show up on the screen as you type it in.
This is a security feature of the terminal, and is normal behaviour.
Install updated versions of the base packages required across all our lessons, by typing:
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.
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".
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.
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.)
Select "Use bundled OpenSSH".
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press Enter)
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press Enter, you should see SUCCESS: Specified value was saved.
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.
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.
Note for Windows Users
If you have used Windows Subsystem for Linux ("WSL2") please open your Ubuntu bash terminal and follow the Linux instructions for each of the software packages below.
If not, please follow the Windows instructions.
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.
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.
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
SSH Token Setup
This is VERY important to do before the workshop in order to complete
the Git workshop. This information can also be found here
Note for Windows Users
If you have used Windows Subsystem for Linux ("WSL2") please open your Ubuntu bash terminal to enter the commands
If not, please use the git-bash.
Open up your terminal (“git-bash” for Windows or “terminal” for Mac
and Linux)
To create an SSH key pair use this command, where the `-t` option
specifies which type of algorithm to use:
$ ssh-keygen -t ed25519
The command will ask for a file name, press Enter to use the default
Generating public/private ed25519 key pair. Enter file in which to
save the key (/c/Users/Alfredo/.ssh/id_ed25519):
You’ll be prompted for a passphrase, be sure to pick something
memorable as there’s no “reset my password” option. You’ll also note
you won’t see any of the letters/numbers/symbols you type, this is
all normal and what you type is recorded even if they don’t show up
Created directory '/c/Users/Alfredo/.ssh'. Enter passphrase (empty for
no passphrase):
You’ll be prompted to enter the passphrase again, enter the same
passphrase you entered in step 3
Enter same passphrase again:
After entering the passphrase, you will see something like below.
(note the specific output will be different for your system, that is
normal). This means the ssh key is created.
Your identification has been saved in /c/Users/Alfredo/.ssh/id_ed25519
Your public key has been saved in /c/Users/Alfredo/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:SMSPIStNyA00KPxuYu94KpZgRAYjgt9g4BA4kFy3g1o a.linguini@ratatouille.fr
The key's randomart image is:
+--[ED25519 256]--+
|^B== o. |
|%*=.*.+ |
|+=.E =.+ |
| .=.+.o.. |
|.... . S |
|.+ o |
|+ = |
|.o.o |
|oo+. |
+----[SHA256]-----+
Run the below command
$ cat ~/.ssh/id_ed25519.pub
Copy what is output to the command line, it should look like the
below:
Click on the profile icon in the top right corner to access the drop
down menu
Click “Settings”
Click “SSH and GPG Keys” on the left side, with the “Access” menu
Click the “New SSH Key” button
Enter a name for the SSH Key (something easy to remember)
Paste your key you copied from step 7 into the large text box
Click “Add SSH key” to complete setup
Go back to the command line, and run this command
$ ssh -T git@github.com
You should receive output like the below, indicating it a success!
Hi Alfredo! You've successfully authenticated, but GitHub does not provide shell access.
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
Conda-forge,
an all-in-one installer.
Regardless of how you choose to install it,
please make sure you install a Python version >= 3.10
(e.g. 3.11 is fine, 3.6 is not).
We will teach Python using the Jupyter Notebook,
a programming environment that runs in a web browser (Jupyter Notebook will be installed by Miniforge). 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).
OneDrive is used by many institutions to sync your user folder (C:\Users\[your-username]\) within an organisation.
It may cause issues with the installation of the Carpentries environment.
If you have OneDrive set up, please ensure that you can access your C:\Users\[your-username]\Downloads folder:
Open File Explorer
Right click on the "Downloads" folder in the left-hand navigation pane
Select "Properties"
In the "Location" tab, ensure that the path is set to C:\Users\[your-username]\Downloads
If you encounter problems, please contact your IT support team and workshop organisers for assistance before the workshop.
Save the file to your C:\Users\[your-username]\Downloads folder.
Make sure that the filename is carpentries_environment.yml and the "Save as type" option is set to YML file (*.yml) The following steps requires using the Miniforge Prompt command line. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.
Open your Start Menu from your taskbar, or use the Win Windows key.
Search for the application "Miniforge Prompt", and click the icon to open it.
Once open, ensure the prompt shows your C:\Users\[your-username] folder. If it does, continue to Step 8 below:
In this case, the prompt shows C:\Users\froggleston. Your username will be different!
If it doesn't:
Find your username by typing whoami and press Enter
Your username will be shown as [machine-name]\[your-username]. You only need the [your-username] part after the slash, i.e. froggleston in this example.
Type cd C:\Users\[your-username] and press Enter
Continue to Step 8 below
If you get stuck, please contact your workshop organisers to get assistance before the workshop starts.
In the Miniforge Prompt window, run the following commands:
Type cd Downloads and press Enter
Type conda env create -f carpentries_environment.yml and press Enter
The installation may take a few minutes depending on your internet connection speed. Once complete, you can close the Miniforge Prompt window.
Download the appropriate Miniforge installer for macOS The following steps require 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 Miniforge3-
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).
Follow the text-only prompts in the terminal. To move through the text, press Spacebar.
Type yes and press Enter (or Return) 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 Miniforge to your PATH (this makes the Miniforge distribution the default Python).
Download the appropriate Miniforge installer for Linux The following steps require 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 Miniforge3-
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).
Follow the text-only prompts in the terminal.
To move through the text, press Spacebar.
Type yes and press Enter (or Return) 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 Miniforge to your PATH (this makes the Miniforge distribution the default Python).
Depending on your version, please go to the relevant instructions below.
![Miniforge Prompt [your-username] as froggleston](assets/img/miniforge_prompt.png)
