[GSoC 2022 Final Report] Quality assurance for biological and medical applications inside Debian

[Mohd Bilal]

Hello everyone \o/ ,




** About the project



** Statistics:

Autopkgtests added: 30
Updates : 7
Bugs fixed: 5


Autopkgtests added:

        *python-datacache
        *parallel-fastq-dump
        *nifticlib
        *gifticlib
        *dicomnifti
        *openslide
        *minc-tools
        *dcm2niix
        *atropos
        *python-bioblend
        *python-cobra
        *intake
        *bmtk
        *nifti2dicom
        *biomaj3-cli
        *gdcm
        *megadepth
        *rockhopper
        *emmax
        *zalign
        *plastimatch
        *delly
        *dcmtk
        *nipype
        *emperor
        *python-wdlparse
        *libbigwig
        *libncl
        *gatb-core
        *tvc


Package Updates:

        *q2-dada2
        *q2-feature-classifier
        *q2-fragment-insertion
        *q2-metadata
        *q2-phylogeny
        *delly
        *q2-sample-classifier


RC Bugs fixed

        *dcm2niix (Closes: #1012336)
        *dicomnifti (Closes: #1013364)
        *gdcm (Closes: #1016450)
        *mothur (Closes: #1014104)
        *megadepth (Closes: #1016454)

I'm Mohammed Bilal and I've been the GSoC intern working with the Debian Med Team during 2022.This is my final report for the GSoC project "Quality Assurance and Continuous Integration for Applications in Life Sciences and Medicine". This is an overview of the work done during my GSoC period with Debian Med Team. The Debian Med project has packaged several applications in life sciences and medicine. Continuous integration for these packages is essential to ensure reproducible results and that all components work together. These, tests often uncover bugs in the code and the packaging process that can cause failures on end-user machines. The aim of my project was to write autopkgtests for Debian Med packages, fix existing tests, any pipeline failures and fix the bugs uncovered by these tests. Apart from my gsoc work, I actively contributed to the Debain Ruby Team fixing some omniauth RC bugs[1],helped with some package updates and handled gitlab updates too. I became a Debian Maintainer right before the start of my gsoc journey and I'm thankful to my mentors for giving me access to upload some of my work on my own. Also during gsoc I got the chance to use some of the Debain Project's Infra like I got access to a s390 porterbox for fixing a bug in one of the packages I've worked on I would like to thank my mentors, Andreas Tille and Nilesh Patra for their constant support and encouragement. I had a wonderful experience working with these amazing DDs. They were very quick to respond to my queries, sponsoring uploads and were very supportive. Also I would like to thank other Debian-Med members on the debian-med mailing list and the matrix room who guided me during my GSoC period. Also I'm grateful to Salsa CI Team and Reproducible builds team for their help. I plan to stick around and continue my contributions to Debian in the near feature. A snippet containing the links of all packages I've worked can be found here[2] Finally thanking the Debian Project for giving me this opportunity.I had a fun and productive summer with Debian 😃 [1] - https://bugs.debian.org/cgi-bin/pkgreport.cgi?dist=unstable;include=subject%3AFTBFS+with+ruby-omniauth+2.0.x;maint=pkg-ruby-extras-maintainers%40lists.alioth.debian.org

[2] - https://salsa.debian.org/-/snippets/609

Thanks
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│ Mohammed Bilal                                    │
│ 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F │
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