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 >>> >>
