Re: Debian Med Covid special?
Hi Tris,
On Wed, Mar 25, 2020 at 12:02:17PM +0100, Ben Tris wrote:
> 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
I'd like to repeat that I consider it more sensible not to check what
we package (which might be basic predependencies) but what we consider
helpful for certain tasks:
https://blends.debian.org/med/tasks/
This gives you a preselection including detailed descriptions. Have you
ever checked these out? Your link is really not that helpful.
> That is my base, only non-free I will not use.
The tasks are listing non-free in a separate section. Just ignore this.
> The packages now listed seem to be updated from source this year. (Have
> 74 more to list)
Sure. We are working a bit. ;-)
> 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.
The task pages are **fully** automated just based on a more or less
simple list. You simply add "Recommends" here:
https://salsa.debian.org/blends-team/med/-/blob/master/tasks/covid-19
everything else is rendered right after pushing.
> Im not a coder etc and not involved with Debian internals.
Help from everybody is perfectly welcome. But I'd recommend to
save your time from maintaining manual html pages. We invented
the automated tasks pages since this is no fruitful work.
> I am not related to work in health care.
Would you mind explaining your background?
> 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.
Simply tell me what binary packag is missing here
https://salsa.debian.org/blends-team/med/-/blob/master/tasks/covid-19
which is rendered here
https://blends.debian.org/med/tasks/covid-19
Thanks a lot for your input
Andreas.
> 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
> >
>
>
--
http://fam-tille.de
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