Re: Debian Med Covid special?
Hello Andreas,
I contribute(d) to the FSD FSF GNU etc. Some bugs outside.
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.
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
>>>
>>
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