Good Practices in Research Software Development (CodeRefinery)

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General Information

The eScience Center offers a range of free workshops and training courses, open to all researchers affiliated with Dutch research organizations. We organize workshops covering digital skills needed to put reproducible research into practice. These include online collaboration, reproducible code and good programming practices. We also offer more advanced workshops such as GPU Programming, Parallel Programming and Deep Learning.

The key objective of this workshop is to grow researchers’ software skills necessary to apply good practices that enable open and reproducible research. The workshop focuses on building modular, reusable, maintainable, sustainable, reproducible, testable, and robust software. This will allow you to more easily organize, maintain and share your data. The participants should be familiar with programming and regularly write code for their research, but no extensive expertise or knowledge of specific tools are required.

This workshop is inspired by and based on CodeRefinery training materials.

Optional “Introduction to Git” on day one. To ensure all participants are familiar with the basics of version control and Git, we offer an optional “Introduction to version control with Git” session on day one of the workshop. Please take this 1-minute Quiz to self-assess your git knowledge. If you answered all questions correctly, you can join the workshop from day two onwards. Otherwise, you should join the “Introduction to Git” session on day one.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: June 19 - 22, 2023, 9:00 - 13:00 CEST.

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 or training@esciencecenter.nl for more information.

Code of Conduct

Participants are expected to follow these guidelines:

• Use welcoming and inclusive language
• Be respectful of different viewpoints and experiences
• Gracefully accept constructive criticism
• Focus on what is best for the community
• Show courtesy and respect towards other community members

Syllabus

Introduction to version control with Git

• Tracking changes: git add & git commit
• Exploring history, checking out older versions
• Ignoring things with .gitignore files
• Github remotes

Collaboration with Git and Github

• Creating pull requests
• Review process
• Good practices for collaboration
• Contributing to repositories with forks

Code Documentation

• In-code documentation
• Readme files
• Writing documentation with sphinx and ReadTheDocs or Github pages

Modular Code Development

• How can you create blocks of code that can be reused?

Testing

• Introduction to testing: motivation, unit testing, integration testing
• Writing tests with pytest

Continuous Integration

• Introducton to Continuous Integration
• Setting up Continuous Integration with Github Workflows
• Linting and automated testing

Schedule

All times in the schedule are in the CET timezone.

Setup

To participate in this workshop, you will need access to software as 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.

Software setup

Computer

Participants must work on a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) on which they have administrative privileges.

Software

To participate in this workshop, you will need to prepare the following (if you haven’t already):

• Install Shell and Git. Please refer to this page for installation instructions.
• Create a GitHub account. Please refer to this page for instructions.
• Set up an SSH connection to GitHub. Please refer to this page for instructions.
• Install Miniconda. Please refer to this page for instructions.
• Create a Conda environment for the workshop. Please refer to this page for instructions.

To confirm that everything works

You should now be able to open a terminal window and execute the following commands:

Git

git --version

returning (something similar to):

git version 2.37.1 (Apple Git-137.1)

Github account & SSH connection

ssh git@github.com

returning (something similar to):

Hi [username]! You've successfully authenticated, but GitHub does not provide shell access.
Connection to github.com closed.

Conda

conda --version

returning (something similar to):

conda 22.9.0

Conda environment for the workshop

conda activate coderefinery
python -c "import sys; assert sys.version_info.major>=3"
jupyter-lab --version
pytest --version
sphinx-build --version
snakemake --version
conda deactivate

returning (something similar to):

3.9.10
pytest 7.0.1
sphinx-build 4.4.0
7.1.1

If something does not work:

Follow the corresponding setup instructions. If you still need help, come to our dedicated setup session.

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:

• Two monitors: If you have two monitors, plan to have the tool you are learing 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.