Quality assurance for biological and medical applications and their preconditions inside Debian

Description of the project: In the last 20 years the Debian Med project has packaged about 1000 applications used in medicine and biology. In previous Outreachy projects starting in 2016 until last year several packages got Continuous Integration tests. It turned out that these tests are extremely helpful to ensure the quality of the software in the focus of the Debian Med team. Besides testing single packages it needs to be verified that related sets of packages are playing well together and are packaged in a way that the user can expect the maximum performance out of the packages (for instance by ensuring that MPI features are used if available and the hardware features are used as best as possible). In the SOC term 2023 we like to extend the CI tests also to preconditions of the Debian Med maintained packages also reaching out to other teams to have a complete CI verified tool chain.

• Confirmed Mentor: AndreasTille

• How to contact the mentor: tille@debian.org

• Confirmed co-mentors: Nilesh Patra <nilesh@debian.org>

• Project size: 175 hour

• Deliverables of the project: Continuous integration tests for all Debian Med applications (life sciences, medical imaging, others) and their preconditions, Quality Assurance review and bug fixing

• Desirable skills: Ability to read scientific documentation, fixing bugs and checking/hacking around code-bases would be needed. Debian packaging skills are an extra plus. Background in bioinformatics could be good, but not a hard requirement.

• What the intern will learn: Detailed insight into the software maintained by the Debian Med team and some language teams (Python, Java, R, etc.), bug triaging in scientific software, Debian packaging skills, optimising bioinformatics and other scientific tools.

• Application tasks: Pick bugs like 986193, 986194, 1009158, 1009159 and 1010653 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.

• 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: freebayes, dazzdb, snap-aligner, ncbi-seg, bio-rainbow, maffilter

• 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, Quality assurance for biological and medical 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.

Improve support of the Rust coreutils in Debian

Description of the project:

Homepage: https://github.com/uutils/coreutils

An article about it: https://lwn.net/Articles/857599/

This project has two goals:

• propose a better way to replace the GNU Coreutils in Debian by the Rust Coreutils

• Improve the compatibility with GNU by fixing https://uutils.github.io/user/test_coverage.html and install/remove all Debian packages to make sure that all necessary features for Debian are well supported

• Confirmed Mentor: Sylvestre Ledru

• How to contact the mentor: sylvestre@debian.org

• Confirmed co-mentors: Terts Diepraam <terts.diepraam@gmail.com>

• Project size: 250 hours

• Deliverables of the project:

• Desirable skills: Rust, packaging

• What the intern will learn: How the coreutils work, the low level part of the of

• Application tasks: Fix a GNU test listed here https://uutils.github.io/user/test_coverage.html