Thanks, Andreas, This is the title now: COronaVIrus Disease 2019 (COVID-19) Special: Free Software Directory
https://qa.debian.org/developer.php?email=debian-med-packaging%40lists.alioth.debian.org That is my base, only non-free I will not use. The packages now listed seem to be updated from source this year. (Have 74 more to list) Now Im going to insert an extra column with COVID-19 YES/NO (something like that) Then Im going to insert 74 more packages. Eventually I want to expand it and list every package from that page. Everything I do is not automated, it takes some time. Im not a coder etc and not involved with Debian internals. I am not related to work in health care. Thank you for reviewing, It takes more time for me to invest this correspondings. For the next couple of days I will only inform If Im sure a package is COVID-19 related. On 25-03-20 10:49, Andreas Tille wrote: > Hi Ben, > > On Tue, Mar 24, 2020 at 10:51:07PM +0100, Ben Tris wrote: >> I have put up a list with recent updated Debian Med packages. > Could you please explain on what basis you assembled this list. > > To give only two examples that make me wondering about this: > > kleborate - tool to screen Klebsiella genome assemblies > > Well, I injected this package since it helps my colleagues and its a > useful package, thought. However, I fail to see the connection between > Klebsiella and COVID-19. > > libspdlog-dev - Very fast, header only or compiled, C++ logging library > (source: spdlog mentioned in your list) > > Well, sure this is used in some of our Debian Med packages. But adding > this to such a list opens the question why you leave out libc and linux > kernel. IMHO we need to track issues inside these packages via > dependencies. I plan to enhance our Blends QA tools by a page which > lists testing migration issues that are showing issues inside dependant > packages. Similarly with libopencv-dev (source opencv). > > We have lots of packages that might be more relevant currently on our > med-bio list[1] (which you hopefully consulted when you assembled your > list). > >> Also inviting to update or add entries to the Free Software Directory. >> >> https://www.gezapig.nl/debianmedcovid.html > In your list you are naming source packages. The Blends framework is > based on binary packages so I will translate this to the probably most > relevant binary package. Regarding debian-science I admit I do not > really know what exactly you might have in mind. Debian-Science > contains *a huge amount* of packages. Do you consider some specific > metapackage more relevant? > > In any case I have added the extract of your list[2] to the covid-19 > task. I admit if you want changes here I'd really appreciate merge > requests (or simply send me a diff to the list I attached to this mail: > sourcepkg.list is basically column three of your web page above and > pkg.list is my translation to binary packages). > >> Debian Meds r-cran-surveillance relates to predicting outbreaks? . > Well, probably I could cut-n-paste the whole med-epi task. So I did in > my latest commit[3]. Rendering the web pages will take say one hour > after pushing the new data. > > As a first work item: I remember that I failed to solve bug #813821 > (of source package pynn - see my bug log). > >> May be interesting: >> >> https://www.eff.org/deeplinks/2020/03/embracing-open-science-medical-crisis-0 >> >> With these mentioned links >> >> https://nextstrain.org/ https://www.gisaid.org/ https://openpcr.org/ > I just inspected nextstrain.org. All those tools are requiring > > https://blends.debian.org/med/tasks/covid-19#auspice > > This in turn needs about 20 nodejs packages. Do we want to tackle > these in a COVID-19 web tools effort? > > Looking at gisaid.org I think that's just a data exchange. If you > find some software tool we could package it would be great if we > could help. > > Openpcr.org does not really look like Open Source: > > OpenPCR Software > The OpenPCR application runs on both Windows > and Mac OS X platforms using Adobe Air. > > For sure we could use the COVID-19 crisis as a chance to ask software > authors to free their code - but we have other work to do now IMHO. > > Thanks a lot for all your input > > Andreas. > > [1] >>>> https://blends.debian.org/med/tasks/bio >>>> https://blends.debian.org/med/tasks/bio-dev >>>> https://blends.debian.org/med/tasks/epi >>>> ??? > [2] > https://salsa.debian.org/blends-team/med/-/commit/3e8075e331a90c494fbf1dfaa4bb6acc2cdd1815 > [3] > https://salsa.debian.org/blends-team/med/-/commit/b0229eafc61f9a32fa892fc2847b0a818dfb9aa3 >
