Re: [GSoC Report] [Community Bonding and Week 1] Quality Assurance and Continuous Integration of Packages in Life Sciences and Medicine
Hi Pranav,
thanks for the great work. Just for our understanding: My experience
from former GSoC/Outreachy projects is that I sometimes fail to realise
those mails from GSoC organisation and I have nearly missed some
deadlines for responsed I should give as a mentor. So please watch me
closely and ping me always if your realise that I as a mentor should
do something like fill in some form about your performance or so. Its
perfectly fine to nag me about this.
Its a pleasure to work together with you.
Thanks again
Andreas.
On Mon, Jun 08, 2020 at 03:24:55AM +0530, Pranav Ballaney wrote:
> Hi,
> 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
> <https://salsa.debian.org/med-team/hunspell-en-med/-/commits/master?author=Pranav%20Ballaney>
> 2. ncbi-entrez-direct
> <https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commits/master?author=Pranav%20Ballaney>
> 3. parsnp
> <https://salsa.debian.org/med-team/parsnp/-/commits/master?author=Pranav%20Ballaney>
> 4. fitgcp
> <https://salsa.debian.org/med-team/fitgcp/-/commits/master?author=Pranav%20Ballaney>
> 5. tree-puzzle
> <https://salsa.debian.org/med-team/tree-puzzle/-/commits/master?author=Pranav%20Ballaney>
> 6. filtlong
> <https://salsa.debian.org/med-team/filtlong/-/commits/master?author=Pranav%20Ballaney>
> 7. cgview
> <https://salsa.debian.org/med-team/cgview/-/commits/master?author=Pranav%20Ballaney>
> 8. libsmithwaterman
> <https://salsa.debian.org/med-team/libsmithwaterman/-/commits/master?author=Pranav%20Ballaney>
> 9. transrate-tools
> <https://salsa.debian.org/med-team/transrate-tools/-/commits/master?author=Pranav%20Ballaney>
> 10. biobambam2
> <https://salsa.debian.org/med-team/biobambam2/-/commits/master?author=Pranav%20Ballaney>
> 11. paml
> <https://salsa.debian.org/med-team/paml/-/commits/master?author=Pranav%20Ballaney>
> 12. bandage
> <https://salsa.debian.org/med-team/bandage/-/commits/master?author=Pranav%20Ballaney>
> 13. freebayes
> <https://salsa.debian.org/med-team/freebayes/-/commits/master?author=Pranav%20Ballaney>
> 14. seer
> <https://salsa.debian.org/med-team/seer/-/commits/master?author=Pranav%20Ballaney>
> 15. norsp
> <https://salsa.debian.org/med-team/norsp/-/commits/master?author=Pranav%20Ballaney>
> 16. gasic
> <https://salsa.debian.org/med-team/gasic/-/commits/master?author=Pranav%20Ballaney>
>
> <#bugs-fixed>Bugs fixed:
>
> 1. #954511 <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=954511>:
> Build time tests were fixed in bioperl-run.
> 2. #960368 <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368>:
> Kallisto now shows an error instead of a segmentation fault.
> 3. #806214 <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806214>
> and #890790 <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=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 <https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=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
> <https://github.com/bbuchfink/diamond/issues/351>.
>
> Looking forward to the rest of the GSoC period, especially with another
> CoViD-19 sprint also coming up!
>
> Thanks and regards,
> Pranav
>
> ᐧ
--
http://fam-tille.de
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