Re: RM pinfish?
Am 14.09.2022 um 22:57 schrieb Nilesh Patra: So I don't think just exchanging names is a very optimal thing to do here. If I don't hear from Steffen, or no-one raises an objection in the next three weeks, I'll proceed to file an RM bug. Steffen??? @Steffen, if you are reading this, a quick reply would be appreciated, really! I just checked on https://github.com/nanoporetech/pinfish and this is now read-only, apparently something is substituting it, just have not yet figured out what that is. So, if it has to go, then it has to go. In general, all on https://github.com/nanoporetech/ would be great to be buildable (and runnable) on Debian. It is basically the sequencing technology that is closest to Debian's principles, with loads of options for the many talents in (and with) Debian to contribute to the research. The spreadsheet typically gives (or should give) the provenance info on why this package was listed, i.e. where it is included in some pipeline (a vertical column) to solve some problem. Pinfish was apparently only listed since nanoporetech provides it, associated with no special column. Hm. With respect to Covid-19, the Nanopore is still state of the art: https://nanoporetech.com/covid-19 , but that art seems to now function also without pinfish. Thank you all, Steffen
Re: [GSoC 2022 Final Report] Quality assurance for biological and medical applications inside Debian
Many, many thanks also from my side. Well done!! I very much hope that you will find your corner of interest in Debian and somehow stay with us. Best wishes, Steffen Am 14.09.2022 um 18:45 schrieb Andreas Tille: Hi Bilal, thanks a lot for all your work! I would be very happy if you would stay in the team and contribute as long as your time permits. Kind regards Andreas. Am Wed, Sep 14, 2022 at 08:31:23PM +0530 schrieb Mohd Bilal: Hello team \o/ , I'm Mohammed Bilal and I've been the GSoC intern working with the Debian Med Team during 2022 and the one who've been bugging this mailing list for the past few months.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 the team. ** About the project 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. ** 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 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 this mailing list and the matrix room who guided me during my GSoC period. You all were super supportive and provided much needed feedback for my work. I plan to stick around and continue my contributions to Debian Med in the near feature. A snippet containing the links of all packages I've worked can be found here[1] Finally thanking the Debian Project for giving me this opportunity.I had a fun and productive summer with Debian đŸ˜ƒ [1] - https://salsa.debian.org/-/snippets/609 Thanks -- Mohammed Bilal 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F
Re: [GSoC 2022 Final Report] Quality assurance for biological and medical applications inside Debian
Hi Bilal, Thank you for all your contributions, that's quite an impressive amount of work that you did in the past year. The autopkgtests you wrote are already of great help today to validate packages for the upcoming Debian release and identify early regressions when introducing newer versions of packages, for themselves and for their dependencies. Looking forward for future contributions, Have a nice day, :) Étienne. Steffen Moeller, on 2022-09-15: > Many, many thanks also from my side. Well done!! > > I very much hope that you will find your corner of interest in Debian > and somehow stay with us. > > Best wishes, > Steffen > > Am 14.09.2022 um 18:45 schrieb Andreas Tille: > > Hi Bilal, > > > > thanks a lot for all your work! I would be very happy if you would stay > > in the team and contribute as long as your time permits. > > > > Kind regards > > > > Andreas. > > > > Am Wed, Sep 14, 2022 at 08:31:23PM +0530 schrieb Mohd Bilal: > > > Hello team \o/ , > > > > > > I'm Mohammed Bilal and I've been the GSoC intern working with the Debian > > > Med > > > Team during 2022 and the one who've been bugging this mailing list for the > > > past few months.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 > > > the team. > > > > > > ** About the project > > > > > > 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. > > > > > > ** 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 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 this mailing list and the matrix room who > > > guided > > > me during my GSoC period. You all were super supportive and provided much > > > needed feedback for my work. I plan to stick around and continue my > > > contributions to Debian Med in the near feature. > > > > > > A snippet containing the links of all packages I've worked can be found > > > here[1] > > > > > > Finally thanking the Debian Project for giving me this opportunity.I had a > > > fun and productive summer with Debian đŸ˜ƒ > > > > > > > > > [1] - https://salsa.debian.org/-/snippets/609 > > > > > > Thanks > > > -- > > > Mohammed Bilal > > > 2D65 BC1E B966 5A6E 97F9 730A B3F5 9452 8521 9E1F > > > > > > > > > > -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/1, please excuse my verbosity. On air: Opeth - A Fair Judgement signature.asc Description: PGP signature
Debian Med video conference on Monday 2022-08-19 18:00 UTC
Hi, this is the call for the next video conference of the Debian Med team that are an established means to organise the tasks inside our team. Please note that we do not meet at 17th as usually but on 19th. Usually it takes us only 15-20min depending what we are talking about and how many people are joining. The next meeting is tomorrow 18:00 UTC https://www.timeanddate.com/worldclock/fixedtime.html?iso=20220919T18 The meeting is on the Debian Social channel https://jitsi.debian.social/DebianMedCovid19 These video meetings were started in the Debian Med Biohackathon. The topic is what contributors have done in the past period and to coordinate the work until the next meeting. For those who are interested in hot topics we want to tackle, here are some items: Preparation of next release by - Pushing latest versions of our software - RC bugs Newcomers are always welcome. Lets keep on the great work and see you tomorrow Andreas. -- http://fam-tille.de
