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[GSoC Report] [Community Bonding and Week 1] Quality Assurance and Continuous Integration of Packages in Life Sciences and Medicine

Here's my report for the duration of community bonding and week 1 for the GSoC project: Quality Assurance and Continuous Integration of Packages in Life Sciences and Medicine.
Since I had already worked on autopkgtests for the last few months, I started working on more packages during the community bonding period itself to avoid delays later. 

Here's all the work that has been accomplished in the GSoC period:

Added/fixed examples, docs and autopkgtests:

  1. hunspell-en-med
  2. ncbi-entrez-direct
  3. parsnp
  4. fitgcp
  5. tree-puzzle
  6. filtlong
  7. cgview
  8. libsmithwaterman
  9. transrate-tools
  10. biobambam2
  11. paml
  12. bandage
  13. freebayes
  14. seer
  15. norsp
  16. gasic

Bugs fixed:

  1. #954511: Build time tests were fixed in bioperl-run.
  2. #960368: Kallisto now shows an error instead of a segmentation fault.
  3. #806214 and #890790: Build time tests had been failing in tree-puzzle for a long time. Upstream was contacted and it was confirmed that failure was only because the output files had not been updated for the last few versions. A patch was written to fix this issue.
  4. #961013 was also investigated for diamond-aligner, with limited success. It was found that the error was not specific to Debian packaging. The issue was narrowed down and a minimal dataset was created to help the upstream authords debug it. Findings were reported at the upstream issue tracker.
Looking forward to the rest of the GSoC period, especially with another CoViD-19 sprint also coming up!

Thanks and regards,

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