Good Practices in Research Software Development

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General Information

The eScience Center offers a range of workshops and training courses, aimed at PhD candidates and other researchers or research software engineers. 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, Image Processing 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. The main themes that are addressed are generically applicable, but please note that a lot of the exercises and demonstrations are in Python.

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

Where: Science Park 402, 1098 XH Amsterdam. Get directions with OpenStreetMap or Google Maps.

When: October 22 - 23, 2024, 9:30 - 17:00 CEST.

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.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Workshop files: You will find all slides, notebooks, archived collaborative documents, and other relevant files in the files folder of the workshop website repository after the workshop.

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.