Hi Andreas, Yes, /usr/lib/ should be replaced with /usr/bin. Within the scope of my PHD, I will probably modify proteinortho in the future, so a integration to stable in 2 years sounds good to me. The heaviest updates are done for now (~300 commits) but there will be probably some minor or maybe major changes/updates from time to time. In the meanwhile this backports integration seems reasonable to me. If I can help in any way, just let me know. Greetings, Paul
On Fri, Jul 19, 2019 at 9:33 AM Andreas Tille <[email protected]> wrote: > Hi Paul, > > On Fri, Jul 19, 2019 at 08:59:16AM +0200, Paul Klemm wrote: > > I tested it and everything works how i expect it to be.s > > Thanks a lot for testing. > > > But there is one > > problem: please include a link to all the binaries, e.g. > > proteinortho_grab_proteins.pl is often used after a proteinortho call. > > Is this true for all those files currently in > > /usr/lib/proteinortho/ > > Than we can move them right to /usr/bin. (For some reason I assumed > that these would be small helpers only but if users expect all files in > their PATH these should be there.) > > > Also I am just curious: How long does it take for a package to go from > > unstable to stable? > > Debian stable has the name *stable* since there is usually *no* > migration of new code. Thus proteinortho will be released in its than > latest version with the next Debian release which will be Debian 11 - > probably in about two years. Since this is probably not what you want > for your users we provide backports[1] to stable at request. But users > need to include those backports in their souces.list. So what we should > do right now is: > > 1. Fix the location of files (please answer above) > 2. Wait until proteinortho has migrated to testing > 3. Upload to buster-backports > > BTW, I'm always CCing [email protected] and I'd prefer if you > would send your questions to this public list as well since we are a > team and there are chances that I fail to answer private mails. > > > Thank you very much, Paul > > You are welcome > > Andreas. > > [1] https://backports.debian.org/ > > > On Wed, Jul 17, 2019 at 4:26 PM Andreas Tille <[email protected]> wrote: > > > > > Hi Paul, > > > > > > On Wed, Jul 17, 2019 at 03:30:49PM +0200, Paul Klemm wrote: > > > > I would like to test the package but i cannot find proteinortho 6.0.6 > > > > neither with apt-get install nor apt-cache search. Or is it too > early? > > > > > > New packages are uploaded to Debian unstable. You need to add this to > > > your sources.list (but be carefully and set your apt_preferences > > > properly - otherwise the system tries to upgrade your whole system to > > > unstable!) Or you download from here: > > > > > > https://tracker.debian.org/pkg/proteinortho > > > > > > and install it manually. > > > > > > Hope this helps > > > > > > Andreas. > > > > > > > On Tue, Jul 16, 2019 at 10:51 AM Andreas Tille <[email protected]> > wrote: > > > > > > > > > Hi Paul, > > > > > > > > > > On Tue, Jul 16, 2019 at 08:59:14AM +0200, Paul Klemm wrote: > > > > > > Hey Andreas, > > > > > > Sorry for the confusion, I was not aware of any rules. > > > > > > > > > > No problem to sort things out. :-) > > > > > > > > > > > And thank you very > > > > > > much for your time and effort. > > > > > > > > > > You are welcome. It would help if you could test the package and > > > report > > > > > any issue you might face. > > > > > > > > > > Kind regards > > > > > > > > > > Andreas. > > > > > > > > > > > Kind regards, Paul > > > > > > > > > > > > On Mon, Jul 15, 2019 at 8:52 PM Andreas Tille <[email protected]> > > > wrote: > > > > > > > > > > > > > Hi Paul, > > > > > > > > > > > > > > On Sat, Jul 13, 2019 at 05:06:05PM +0200, Andreas Tille wrote: > > > > > > > > If you talk about a PR the source is probably on some Git > > > repository > > > > > > > > (which I'm not aware about). Please let me know the Git > > > repository > > > > > > > > and if there is a release tag it accordingly (we usually do > not > > > > > > > > package random commits or pull requests). > > > > > > > > > > > > > > I've now understood that you created a clone of the packaging > > > > > repository > > > > > > > in salsa and tried to upgrade the packaging. I admit I just > copied > > > > > your > > > > > > > work in the debian/ dir and commited this to the packaging > > > repository. > > > > > > > I really appreciate your intend to help, but there are some > rules > > > > > > > specified in Debian Med team policy[1] which are simplifying > the > > > > > > > maintenance in the team. You are happily invited to be guided > into > > > > > > > these rules. Otherwise it might be easier if you simply ping > here > > > on > > > > > > > the list that some new upstream version is out. Usually its a > > > quite > > > > > > > automatic process to upgrade (but the proteinortho 6.x series > was > > > > > hidden > > > > > > > for our tools since the download location had changed - this > kind > > > of > > > > > > > change is very important to know for the packaging). > > > > > > > > > > > > > > Kind regards and thanks for your effort in any case > > > > > > > > > > > > > > Andreas. > > > > > > > > > > > > > > [1] https://med-team.pages.debian.net/policy/ > > > > > > > > > > > > > > -- > > > > > > > http://fam-tille.de > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Paul Klemm > > > > > > Department of Pharmaceutical Chemistry > > > > > > Philipps-University Marburg > > > > > > Marbacher Weg 6, 35037 Marburg, Germany > > > > > > Phone: +49 (0)6421 28 22870 > > > > > > Mobile: +49 (0)178 1387867 > > > > > > > > > > -- > > > > > http://fam-tille.de > > > > > > > > > > > > > > > > > > -- > > > > Paul Klemm > > > > Department of Pharmaceutical Chemistry > > > > Philipps-University Marburg > > > > Marbacher Weg 6, 35037 Marburg, Germany > > > > Phone: +49 (0)6421 28 22870 > > > > Mobile: +49 (0)178 1387867 > > > > > > -- > > > http://fam-tille.de > > > > > > > > > > -- > > Paul Klemm > > Department of Pharmaceutical Chemistry > > Philipps-University Marburg > > Marbacher Weg 6, 35037 Marburg, Germany > > Phone: +49 (0)6421 28 22870 > > Mobile: +49 (0)178 1387867 > > -- > http://fam-tille.de > > -- Paul Klemm Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35037 Marburg, Germany Phone: +49 (0)6421 28 22870 Mobile: +49 (0)178 1387867
