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Re: Debian Med Covid special?



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
>


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