This course aims to teach basic lab skills for research computing. It is a hands-on training that covers the core skills needed to be productive in a small research team. Short tutorials alternate with practical exercises, and all instruction is done via live coding. This workshop is intended for people who have no to little knowledge about the tools that are introduced.
The workshop will cover the following lessons:
Automating tasks with the Unix Shell
Programming with Python
Version Control with Git
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.
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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:
PC-Pool D, Building 20.21, Kollegiengebäude am Zirkel, Teil 2, Zirkel 2, 76131 Karlsruhe.
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).
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.
Roles:
To learn more about the roles at the workshop (who will be doing what),
refer to our Workshop FAQ.
Who can attend?:
This workshop is primarily intended for the members of the Karlsruhe Institute of Technology.
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.
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.
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.
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. Installing all of its research packages individually can be
a bit difficult, so we propose to use the package and environment management system
Conda, that we will install using
Miniforge.
Regardless of how you choose to install it,
please make sure you install a Python version >= 3.9
(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 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).
You can now activate the environment "swc-python" with the following command:
conda activate swc-python
If (swc-python) is displayed at the beginning of the command line prompt instead of (base),
your Python environment has been set up correctly.
You can test that you can open Jupyter Notebooks in your browser by running:
jupyter notebook
After running this command, a Jupyter web page should open in your web browser, showing a list of files and directories. If it is the case, you are all set!
To shut down Jupyter, you can press the keys Ctrl+C in the Miniforge Prompt, then close the Miniforge Prompt window.
Note: if you close and reopen the Miniforge Prompt, you have to reactivate the workshop environment in order to be able to run Jupyter Notebooks again:
conda activate swc-python
Open the application Terminal
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
Download the Miniforge Installer with Python 3 by typing the following command:
Run the Miniforge installer by typing the following command (by running this command, it is assumed that you agree with Miniforge's license):
bash Miniforge3-$(uname)-$(uname -m).sh -b
You can now activate the base environement of Miniforge with the following command:
source ~/miniforge3/bin/activate
This command has to be run each time you want to use Miniforge programs.
If Miniforge has correctly been activated, your terminal should show (base) at the beginning of the command line prompt.
For the workshop, we will create a specific Python environment called "swc-python", using the following command:
You can now activate the environment "swc-python" with the following command:
conda activate swc-python
If (swc-python) is displayed at the beginning of the command line prompt instead of (base),
your Python environment has been set up correctly.
You can test that you can open Jupyter Notebooks in your browser by running:
jupyter notebook
After running this command, a Jupyter web page should open in your web browser, showing a list of files and directories. If it is the case, you are all set!
To shut down Jupyter, you can press the keys Ctrl+C in your terminal, and then Y to accept to shut down the server.
Close the terminal window.
Note: if you close and reopen the Terminal, you have to reactivate Miniforge environments to be able to run Jupyter Notebooks again:
Open a terminal. On most versions of Linux, it is accessible by running
the Gnome Terminal or KDE Konsole or xterm, which can be found
via the applications menu or the search bar.
(The installation requires using the shell. If you aren't
comfortable doing the installation yourself
stop here and request help at the workshop.)
Download the Miniforge Installer with Python 3 by typing the following command:
Run the Miniforge installer by typing the following command (by running this command, it is assumed that you agree with Miniforge's license):
bash Miniforge3-$(uname)-$(uname -m).sh -b
You can now activate the base environement of Miniforge with the following command:
source ~/miniforge3/bin/activate
This command has to be run each time you want to use Miniforge programs.
If Miniforge has correctly been activated, your terminal should show (base) at the beginning of the command line prompt.
For the workshop, we will create a specific Python environment called "swc-python", using the following command:
You can now activate the environment "swc-python" with the following command:
conda activate swc-python
If (swc-python) is displayed at the beginning of the command line prompt instead of (base),
your Python environment has been set up correctly.
You can test that you can open Jupyter Notebooks in your browser by running:
jupyter notebook
After running this command, a Jupyter web page should open in your web browser, showing a list of files and directories. If it is the case, you are all set!
To shut down Jupyter, you can press the keys Ctrl+C in your terminal, and then Y to accept to shut down the server.
Close the terminal window.
Note: if you close and reopen the Terminal, you have to reactivate Miniforge environments to be able to run Jupyter Notebooks again: