This resource is maintained by the Software Carpentry Organization (SWC), which is part of the The Carpentries Organization.
Software Carpentry aims to empower researchers to get their work done in less time and with less pain by teaching them basic research computing skills.
SWC workshops are hands-on and 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:
Usually, this course targets graduate students and other researchers, incl. professors. This iteration of the course, however, is aimed at high school students planning to become researchers.
You don't need to have any previous knowledge of the tools that you will be introduced to during the workshop.
Where:This training will be delivered in hybrid format. The organizers will provide online participants with the information needed to connect to this workshop.
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. Please
notify the instructors in advance of the workshop if you require any accommodations or if there is
anything we can do to make this workshop more accessible to you
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.
Collaborative Notes
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
Syllabus
(The listing below entails more material than can be taught during the short introductory workshops and can serve as resources to explore the topics in more detail.)
The Command Shell
The command shell (a.k.a. UNIX Shell, Bash Shell, Shell) is a power tool that allows computer users to do complex things with just a few keystrokes. Contrary to graphical user interfaces (GUI) it allows users to direct the computer from a more foundational level, using written commands. Even what happens when you click on items in GUIs is directed by written commands. Working in the 'Shell' helps users combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Shell proficiency is fundamental to using a wide range of other powerful tools and computing resources, including “high-performance computing” supercomputers.
Using the Bash Shell the workshop will introduce these concepts and procedures:
Commercial-grade computers are great tools for daily tasks: note taking, word editing, light computation, web searching, and communication. The research world, however, requires machines with larger computational power such as the University of Arizona’s HPC (High-Performance Computing) system. HPCs are used to simulate, compute, extrapolate and generate data using popular research-grade software or novel tools maintained by scientists all around the world.
This section covers the basics for understanding the structure of the UA HPC, including navigation, storage, and job submission. Additionally, we are going to cover GitHub, a powerful platform that researchers and scientists use to communicate and develop scientific software used for research. The Remote Computing section introduces:
Creating and connecting to the HPC using Secure Shell
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.
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 the tool you are learning 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 the tool you will be learning about.
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.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do
tasks more quickly.
Run the installer by double-clicking it and follow the steps below:
Click on "Next" until you reach the page that says "Choosing the default editor used by Git".
On the page that says "Choosing the default editor used by Git", ensure that "Use the Nano editor by default" is selected 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.
On the page that says "Adjusting your PATH environment", 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.)
On the page that says "Choosing he SSH executable", ensure that "Use bundled OpenSSH" is checked.
On the page that says "Choosing HTTPS transport backend", ensure that nsure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
On the page that says "Configuring the line end conversions", ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
On the page that says "Configuring the terminal emulator to use with GitBash", ensure that "Use Windows' default console window" is selected and click on "Next".
On the page that says "Choose the defaulth behavior of 'git pull'", ensure that "Fast-forward or merge is selected and click "Next"
On the page that says "Choose a credential helper", ensure that "Git Credential Manager" is selected and click on "Next".
On the page that says "Configuring extra options", ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Exit the installation mode by clicking 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.
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. Please register for a GitHub account if you don't have one already.
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 (Git Bash)
installation above (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
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 has been installed with the Git Bash installation above. (See the
Shell installation instructions.)
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.