Make your script ready for publication

Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences

Online

Dec 08-09, 2020

9:00 AM - 6:00 PM

Instructors: Maximilian Dolling, Johannes Petereit, Tobias Schlauch

Helpers: Christian Hüser, Bezaye Tesfaye Belayneh

General Information

This workshop is the practical part of the lecture series which was held in May and June. It aims to teach researchers how to publish a software. While it is not an in-depth lecture of the techniques used, it provides their the basic principles. The workshop provides the participants with an example Python project, which will be used. We will apply together the following things:

  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: Dec 08-09, 2020. 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.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

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 Create release
15:20 Code Citation
16:20 Wrap-up
16:50 END

Setup

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.

Install the videoconferencing client

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:

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.

  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

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.

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 is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

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

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

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).

  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