Hi Julien, I can put this on my todo list for the Debian Med sprint[1] (if nobody else might beat me in doing this before). For all readers of this mail: You are kindly invited to join our sprint!
Kind regards Andreas. [1] https://wiki.debian.org/Sprints/2026/DebianMedSprint2026 Am Wed, Jan 28, 2026 at 02:58:50PM +0100 schrieb Julien Y. Dutheil: > Dear Andreas and Debmed team, > > We have now released our V3 of the Bio++ libraries (tag v3.0.0 upstream). I > could do a uscan from the salsa repository, but I could not get any > further. It is many years since I packaged the previous version of the > libraries, and my notes are probably completely outdated. May I ask for > your assistance? If someone shows me how to do it for the libbpp-core > library, I can try to do the other ones. > > I sincerely apologize for my helplessness! > > Best regards, > > Julien. > > On Tue, Nov 11, 2025 at 7:59 AM Julien Y. Dutheil <[email protected]> > wrote: > > > Dear Andreas, > > > > thank you very much for the feedback. One more question then: can I keep > > the old package name and still provide libraries named libpp-core3, > > libbpp-seq3, etc, or should I remove the interface version from the library > > names as well (this is possible but rather cumbersome from our side, since > > we have used those new names for several years now, to avoid conflicts > > while the old versions were still in use)? > > > > Best regards, > > > > Julien. > > > > On Mon, Nov 10, 2025 at 10:35 PM Andreas Tille <[email protected]> wrote: > > > >> Hi Julien, > >> > >> Am Mon, Nov 10, 2025 at 08:57:14PM +0100 schrieb Julien Y. Dutheil: > >> > Dear Deb-Med, > >> > > >> > After many years, we are finally ready to release the V3.00 of the Bio++ > >> > libraries (libbpp-core, libbpp-seq, libbpp-phyl, libbpp-popgen, > >> > libbpp-seq-omics, libbpp-phyl-omics, libbpp-qt, libbpp-raa). This new > >> > version introduces a new interface, not backward-compatible (although > >> some > >> > legacy classes have been kept to ease the transition). Therefore, we > >> have > >> > renamed the libraries as libbpp-core3, libbpp-seq3, etc. > >> > It has been a long time since I dived into Debian packaging, but I > >> expect > >> > that releasing this new version by tagging our master branch will > >> trigger > >> > some issues for the Debian packaging, since this should be new Debian > >> > packages, not just updates of the existing ones, right? > >> > >> I admit I would prefer to keep the same source package name and bump > >> SOVERSION of the binary package. The only reason change the source > >> package name would be that both (old an new) versions should be kept > >> both inside Debian. Given the relatively low user base I do not > >> consider it a good idea to tackle the according maintenance burden. > >> > >> > Before we create such a mess, are there any recommendations on how we > >> > should proceed? My gut feeling is that we should get rid of the old ones > >> > and make some brand new packages for this new version, unless there is a > >> > simpler way? (The compilation chain is the same as before, no change > >> from > >> > that side apart from upgrading the various cmake files.) > >> > >> The Debian Med team is fine with wirking on the Dabien packages and I > >> would strongly prefer to keep the old source package names and the > >> Git repository where these are mentioned. > >> > >> Kind regards and thank you for working on the upstream code and for > >> pinging here > >> Andreas. > >> > >> -- > >> https://fam-tille.de > >> > > > > > > -- > Prof. Dr. Julien Y. Dutheil > 0 (+49) 4522 763 484 > Max Planck Institute for Evolutionary Biology > Molecular Systems Evolution > Department of Theoretical Biology > Plön -- GERMANY -- https://fam-tille.de
