Project description from the Debian Med team for Outreachy and GSoC 2021.
Quality Assurance and Continuous Integration for Applications in Life Sciences and Medicine
Project Description
The Debian Med project has packaged several applications in life sciences and medicine. Continuous integration for these packages is very important to get reproducible results and ensure that all programs are working together smoothly. In the past, students have done a really great job in not only writing tests but fixing the failures that were uncovered by failed tests. As part of this project, the applicant would write autopkgtests for these packages and report and fix the bugs found in the process.
Mentors
Mentor: Andreas Tille
Co-mentors: Nilesh Patra
Deliverables
Continuous integration tests for Debian Med applications (bioinformatics, life sciences, medical imaging, others), Quality Assurance review and bug fixing.
Desirable Skills and Learning Opportunities
Desirable skills: Background in bioinformatics, medical imaging could be an advantage, but interest in scientific software and reading relevant documentation and papers might be sufficient. Debian packaging skills are an extra plus but can be taught in the project run.
What the intern will learn: Detailed insight into the software maintained by the Debian Med team, bug triaging in scientific software, Debian packaging skills, optimizing bioinformatics and other scientific tools
Application Tasks
Pick one of these bugs and try fixing it.
Asking the mentors for help is perfectly fine and actually recommended. This is, on one hand, proof that the student is able to understand Debian packaging and understands the actual topic at a sufficient level.
Recommended Reading
- Pre-Requisite setup
- [MUST] Building in a clean chroot: any one of sbuild, pbuilder, cowbuilder. We recommend "sbuild"
- Setting up and running autopkgtests
- Examples:
- Going through the mailing list archives for communication between previous years' students and mentors may also be helpful.
- Debian New Maintainer's Guide (optional)
Further Reading
Related Projects
- Quality Assurance and Continuous integration for applications in life sciences and medicine
- Packaging and Quality assurance of COVID-19 relevant applications
- Quality assurance for biological applications inside Debian
- Continuous Integration for all biological applications inside Debian
- Continuous Integration for biological applications inside Debian
Getting in Touch
Please subscribe to the mailing list and feel free to ask for help there. Mentors and co-mentors can be contacted at their email addresses mentioned above.