Instructors:
Maximilian Dolling, Tobias Schlauch, Bezaye Tesfaye, Christian Meeßen
Helpers:
Stefan Lüdtke
General Information
This workshop is the practical part of the lecture series prepared for researchers at GFZ. It aims to teach researchers how to publish a reproducible software covering the basic principles of software development and best practices.
The workshop includes topics on:
Who:
The course is aimed at graduate students and other researchers, that want do publish their research software.
You need to have basic knowledge on Python and the Linux Bash.
Knowledge of git and GitLab are recommended.
Where: This training will take place online.
The instructors will provide you with the information you will need to connect to this meeting.
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.
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 the software 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 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.)
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 Core" 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 some versions of macOS is Bash, and
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 and you can run Bash by typing bash
If you want to change your default shell, see
this Apple Support article and follow the instructions on "How to change your default shell".
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
a terminal and press the Enter key. If the message printed
does not end with '/bash' then your default is something else and you
can run Bash by typing bash.
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 or gitlab. You will need a
supported
web browser.
For this workshop we will be using GFZ gitlab instance.
Please login atleast once using your GFZ account or through Helmholtz AAI before the workshop.
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.
Python
Python is a popular language for
research computing, and great for general-purpose programming as
well. We will use plain Python for the workshop.
Please make sure you install Python version 3.x
(e.g., 3.6 is fine).
If you encounter problems, please contact us (see above).
On Windows 10 open up the Powershell (open the start menu and start typing 'Powershell' to find it)
In the opened window type 'python --version' and hit enter
The Windows App Store opens and and provides you with the Python setup. If instead the Powershell gives you an output like 'Python 3.x.x', you already have installed it.
After the installation is done, close and reopen the Powershell and again type 'python --version'.
Python should be installed by default on you system.
Verify the installation by opening the Terminal app and type 'python3 --version'.
The output should be something like 'Python 3.x.x'
Python might be installed by default on your system.
Verify the installation by opening the Terminal app and type 'python3 --version'.
The output should be something like 'Python 3.x.x'
If it is not installed, open a terminal
Depending on your operating system, install python with on of these:
sudo apt install python
sudo apt-get install python
sudo pacman -S python
sudo dfn install python
Pipenv
You will find further Pipenv installation instructions for different OS HERE
or HERE