Let's Make Your Script Ready for Publication


May 26-27, 2021

9:00 AM - 6:00 PM

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:

  1. Version Control
  2. Dedicated Environment
  3. Style Guide
  4. Tests
  5. Documentation
  6. License
  7. Release
  8. Citation

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, 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.

When: May 26-27, 2021. Add to your Google Calendar.

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.

Contact: Please email swc-workshop-org@gfz-potsdam.de for more information.

Registration: Please register here.

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.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

09:00 Introduction & preparations
09:30 Put code under version control
11:00 Morning break
11:30 Set up environment
13:00 Lunch break
14:00 Clean up code
15:30 Afternoon break
15:50 Clean up code (continue)
17:10 Wrap-up
17:30 END

Day 2

09:00 Test the code
10:30 Morning break
11:00 Documentation
12:00 Lunch break
13:00 Licensing
14:00 Afternoon break
14:20 Code Citation
15:20 Create release
16:20 Wrap-up
16:50 END


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.

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 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. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    7. Ensure that "Use Windows' default console window" is selected and click on "Next".
    8. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    9. Ensure that "Git Credential Manager Core" is selected and click on "Next".
    10. Ensure that "Enable file system caching" is selected and click on "Next".
    11. Click on "Install".
    12. 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 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 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 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).

  1. On Windows 10 open up the Powershell (open the start menu and start typing 'Powershell' to find it)
  2. In the opened window type 'python --version' and hit enter
  3. 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.
  4. After the installation is done, close and reopen the Powershell and again type 'python --version'.
  1. 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'
  2. If the version < 3 or 'python3' is not found, please follow The Hitchhiker's Guide to Python
  1. 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'
  2. If it is not installed, open a terminal
  3. Depending on your operating system, install python with on of these:
    1. sudo apt install python
    2. sudo apt-get install python
    3. sudo pacman -S python
    4. sudo dfn install python


You will find further Pipenv installation instructions for different OS HERE or HERE