Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi, we are in preparation of the next stable release and thus we should verify that our metapackages are up to date. I admit I'm regularly checking med-bio and med-bio-dev to contain everything it needs but we have those three subsets that need some more detailed knowledge about the packages. Specifically med-cloud will be released as metapackage (bio-ngs and bio-phylo are just rendered as tasks pages - no metapackages with dependencies and thus not effectively affecting the release). It would be great if those who feel competent would check the according tasks files and edit them if necessary. (Please raise your hand if you have no idea what I'm talking about and you do not know what to do.) Kind regards Andreas. -- http://fam-tille.de
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi, Andreas, على الخميس 5 كانون الثاني 2017 08:39، كتب Andreas Tille: > Hi, > > we are in preparation of the next stable release and thus we should > verify that our metapackages are up to date. I admit I'm regularly > checking med-bio and med-bio-dev to contain everything it needs but we > have those three subsets that need some more detailed knowledge about > the packages. Specifically med-cloud will be released as metapackage > (bio-ngs and bio-phylo are just rendered as tasks pages - no > metapackages with dependencies and thus not effectively affecting the > release). It would be great if those who feel competent would check > the according tasks files and edit them if necessary. > I did express an interest in this before and started working on that, but it's a little difficult to keep track of progress in distributing from bio to the more specific ones without removing them from bio. The problem here is making the leap to actually releasing a bio-ngs metapackage (which is too late now anyway). Is there a way to make subgroups without having them be subtasks? For example, if on bio-ngs, we want to group aligners, how would we do that? Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
على السبت 7 كانون الثاني 2017 00:45، كتب Afif Elghraoui: > The > problem here is making the leap to actually releasing a bio-ngs > metapackage (which is too late now anyway). Maybe it's not too late [1]. I think new binary packages are still allowed into testing--just not new source packages. If that's the case, can we make bio-ngs and others into real packages and have med-bio depend on them? Then I can start reorganizing things more enthusiastically. regards Afif 1. https://lists.debian.org/debian-devel-announce/2016/12/msg0.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi Afif, On Sat, Jan 07, 2017 at 12:51:26AM -0800, Afif Elghraoui wrote: > > The > > problem here is making the leap to actually releasing a bio-ngs > > metapackage (which is too late now anyway). > > Maybe it's not too late [1]. I think new binary packages are still > allowed into testing--just not new source packages. Metapackages are an exception here anyway. While we should not try to move too much around the Blends metapackages are re-uploaded short before the final release. The rationale is that dependencies might have been removed in the freeze process. But for sure the release team wants *small* changes at that time so we should really hurry up in changing things. > If that's the case, can we make bio-ngs and others into real packages > and have med-bio depend on them? Then I can start reorganizing things > more enthusiastically. I'm fine with this. In the past I made several attempts to make med-bio more fine grained but it was not actively supported by others and I'm personally lacking the required detailed knowledge. Kind regards Andreas. > 1. https://lists.debian.org/debian-devel-announce/2016/12/msg0.html -- http://fam-tille.de
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
On السبت 7 كانون الثاني 2017 03:48, Andreas Tille wrote: Hi Afif, On Sat, Jan 07, 2017 at 12:51:26AM -0800, Afif Elghraoui wrote: Metapackages are an exception here anyway. While we should not try to move too much around the Blends metapackages are re-uploaded short before the final release. The rationale is that dependencies might have been removed in the freeze process. But for sure the release team wants *small* changes at that time so we should really hurry up in changing things. Ok If that's the case, can we make bio-ngs and others into real packages and have med-bio depend on them? Then I can start reorganizing things more enthusiastically. I'm fine with this. In the past I made several attempts to make med-bio more fine grained but it was not actively supported by others and I'm personally lacking the required detailed knowledge. Ok, so I will plan to move things out of med-bio into the more specific ones in the next few days. Is there a way to group things within tasks? For example, in bio-ngs, I think it would be appropriate to have some sections, like "aligners" and "genome assemblers". Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi Afif, On Sat, Jan 07, 2017 at 02:38:32PM -0800, Afif Elghraoui wrote: > > Ok, so I will plan to move things out of med-bio into the more specific ones > in the next few days. I think it is a bit late now but I do not see any harm done. Today I will upload the current status to make a "legal" upload to unstable that will reach testing automatically. I'm perfectly fine if we do the restructuration in Stretch+1. Kind regards Andreas. -- http://fam-tille.de
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi, Andreas, على الثلاثاء 24 كانون الثاني 2017 00:59، كتب Andreas Tille: > Hi Afif, > > On Sat, Jan 07, 2017 at 02:38:32PM -0800, Afif Elghraoui wrote: >> >> Ok, so I will plan to move things out of med-bio into the more specific ones >> in the next few days. > > I think it is a bit late now but I do not see any harm done. Yes, I'm sorry about that. When I looked at this, I started getting distracted by why we are maintaining med-bio-* separately instead of directly adding to science-bio-*. Even though we as Debian Med are maintaining it, I don't think that presenting this sort of "implementation detail" to users/administrators is worth any confusion. Right now we have science-bio depending on med-bio. If I moved on, we would have had science-bio > med-bio > med-bio-ngs, med-bio-phylo. When I saw previous discussions of this science-bio/med-bio situation on list archives, it was that it doesn't matter because the dependency resolver considers them all the same. Since all these tasks packages are part of the Blends group anyway, is there any advantage for us to put all these scientific packages into med-bio-* vs science-bio-*? There are technically differences between biological software and biomedical software which I think get blurred and might cause confusion. > Today I > will upload the current status to make a "legal" upload to unstable that > will reach testing automatically. I'm perfectly fine if we do the > restructuration in Stretch+1. > Sure. Reads like a plan. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Please check med-bio-ngs, med-bio-phylo and med-cloud
Hi Afif, On Wed, Jan 25, 2017 at 12:51:31AM -0800, Afif Elghraoui wrote: > > Right now we have science-bio depending on med-bio. If I moved on, we > would have had science-bio > med-bio > med-bio-ngs, med-bio-phylo. When > I saw previous discussions of this science-bio/med-bio situation on list > archives, it was that it doesn't matter because the dependency resolver > considers them all the same. > > Since all these tasks packages are part of the Blends group anyway, is > there any advantage for us to put all these scientific packages into > med-bio-* vs science-bio-*? There are technically differences between > biological software and biomedical software which I think get blurred > and might cause confusion. I think the main point why we should care about the med-* name space inside the Debian Med team is that we have a dedicated team with competence in this field. I consider the science-* packages as not as fine grained metapackages that are less probable to be installed but rather as information for the users on the tasks page (we might consider even "Metapackage: false" here). > > Today I > > will upload the current status to make a "legal" upload to unstable that > > will reach testing automatically. I'm perfectly fine if we do the > > restructuration in Stretch+1. > > Sure. Reads like a plan. Fine. Kind regards Andreas. -- http://fam-tille.de
