Re: Debian Med Covid special?
Hi Ben,
On Wed, Mar 25, 2020 at 02:05:34PM +0100, Ben Tris wrote:
>
> This way I direct from FSD to Debian Med, (and maybe other) consider it
> a FSD special.
>
> It also acts as a tasklist for people (like myself) to add and update
> entries.
>
> That is where my focus will be.
I fully accept your focus. But you could automatically generate your
page by accessing the publicly available UDD[1] mirror[2]. So you can
get all the data in you manual page (with exception of the FSD id)
automatically updated. It would simply be a shame if you would waste
your time on manual updates.
Hope this helps
Andreas.
[1] https://wiki.debian.org/UltimateDebianDatabase/
[2] https://udd-mirror.debian.net/
> On 25-03-20 12:31, Andreas Tille wrote:
> > 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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