Quality assurance and continuous integration for biological and medical applications inside Debian
Description of the project: The Debian Med Blend has packaged a lot of applications used in medicine and biology for Debian. To enhance and continuously ensure the quality of the packaged software we try to implement Continuous Integration tests for all our packages. This was accomplished thanks to several past interns. These tests are of specific importance since only a very small share of the developers inside the Debian Med project are actual users of the software and thus automated testing is required to provide our users with the quality we like to approach. Interns are also not necessarily comfortable with the topic of medicine and biology - reading documentation or publications or directly contact the authors of the software frequently gives sensible ideas how to write a test for the software.
Confirmed Mentor: Andreas Tille
How to contact the mentor: tille@debian.org
Confirmed co-mentors: Emmanuel Arias <eamanu@debian.org>, Étienne Mollier <emollier@debian.org>
Difficulty level: medium
Project size: Depending from students availability this project can be medium or large. The advantage of the project is it can be split into small pieces
Deliverables of the project:Continuous integration tests for Debian Med applications lacking a test, Quality Assurance review and bug fixing if issues might be uncovered
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, optimising bioinformatics and other scientific tools
Application tasks: Pick bugs like 1035121, 1035175, 1035178, 1035182, 1035188, 1035200, 1035277, 1036500, 1036506 and try fixing it - asking the mentor 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.
Related projects: SummerOfCode2016/Projects/BioToolsTesting, SummerOfCode2017/Projects/QA_BiologyApps, ?Continuous_Integration_for_biological_applications_inside_Debian, SummerOfCode2019/ApprovedProjects/CIforDebianMed SummerOfCode2020/ApprovedProjects/DebianMedQAGSoC and Outreachy Project Proposal: Quality Assurance and Continuous integration for applications in life sciences and medicine