+Vincent, the jalview maintainer Andreas Tille: > On Sat, Dec 10, 2016 at 03:37:00PM +0000, Ximin Luo wrote: >> [..] >> >> That depends on what DebiChem, Debian Med, and the Debian Java Team >> collectively want. >> >> jmol has three reverse dependencies. The new upload, jmol 14, breaks all of >> them. >> >> - biojava3-live can feasibly be dropped from Debian. > > I have asked Olivier about this. > >> - biojava4-live is currently being worked on by the upstream developer. >> We're waiting to hear back from them. > > Olivier has just uploaded a recent BioJava 4 version. I think this one > should be kept in Debian in any case. > >> - jalview's current version doesn't work with jmol 14, but the new version >> does. I started packaging it, but it adds several other dependencies not in >> Debian. Most of them seem bio related: > > From my *personal* and *uneducated* view its better to have a recent > Jmol than an outdated Jalview. While having also an updated Jalview > would be the optimal approach I'm not sure (in other words I doubt) > whether we will manage to package the missing dependencies: > >> https://anonscm.debian.org/cgit/pkg-java/jalview.git/tree/debian/TODO >> >> fr.orsay.lri.varna.* >> htsjdk.samtools.* > > This should be inside the libhtsjdk-java package. > >> org.biodas.jdas.* >> org.jfree.graphics2d.svg.* >>
>From popcon: 600 https://qa.debian.org/popcon.php?package=jmol 300 https://qa.debian.org/popcon.php?package=jalview 70 https://qa.debian.org/popcon.php?package=biojava4-live 90 https://qa.debian.org/popcon.php?package=biojava3-live >> So we have a few options: >> >> 1. Keep everything old in Debian, and SageMath out of Debian stable. > > No. > Thanks for this input, I also feel it doesn't make sense to add software that is already 4 years old to Debian stable, where newer versions exist. They will be 6 years old by the time a new stable comes out, the value to users would be very low. >> 2. Update Jmol in Debian, with a chance of SageMath entering Debian stable, >> but drop biojava4 and jalview from Debian stable. (They can remain broken in >> unstable, with a chance of fixing them later, ofc) >> 3. Update Jmol in Debian, and update biojava4 and jalview as well. > > 4. Update Jmol in Debian, and update biojava4 and drop outdated jalview > (by at least starting the new dependencies and trying to upgrade > jalview) and have the chance of SageMath entering Debian stable. > >> If I work on (3) I don't think I will have any time to properly work on (2), >> but that is where my main personal interest lies. I'm also wondering what >> you all prefer, too. > > May be 4 is a sensible compromise if we could live with backporting > the latest version of Jalview later. > I agree and I'll be happy to move forward on this. Reminding everyone of the release schedule: https://lists.debian.org/debian-devel-announce/2016/11/msg00002.html - The deadline for packages-in-testing to be updated by a newer unstable version is ~Jan 25 - The deadline for new packages to enter testing, is ~Dec 25. - This includes packages that are in unstable, that were/will removed from testing for QA reasons. (e.g. Jmol 12) - This also includes time passing through the NEW queue, for new packages. In summary: - Jmol 14 must be uploaded to unstable by ~Dec 25 - biojava4, jalview must be uploaded to unstable by ~Jan 25 - jalview's extra dependencies must be uploaded to unstable (NEW) by ~Dec 20 or ideally earlier, to give FTP masters a few days to process it. So it's much harder to make this work for jalview. Apologies in advance to any jalview Debian stable users that might be reading this. X -- GPG: ed25519/56034877E1F87C35 GPG: rsa4096/1318EFAC5FBBDBCE https://github.com/infinity0/pubkeys.git
