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Re: New version of proteinortho



Hey Andreas,

thank you for your patch, I did forward this to the PHD student that is responsible for this part of the program. I think this will be done in a week or two, but i cannot promise anything.

Best regards,
Paul

On Mon, Sep 16, 2019 at 1:59 PM Andreas Tille <andreas@an3as.eu> wrote:
Hi again,

ahh, I missed also this mail.  Would you be able to do finalise the port
I've started in a short timeframe?  Its part of the test suite and for
the Debian package we really feel good if we do all tests we can do.

Kind regards

     Andreas.

On Sun, Jul 28, 2019 at 11:48:30AM +0200, Paul Klemm wrote:
> Hi Steffen,
>
> so first of all proteinortho doesnt need python (it just enables synteny
> analysis) but is not required for the usage of the "main"-program.
> Next proteinortho_ffadj_mcs.py only runs with python2 and is not compatible
> with python3 yet. In the future we want to remove the python part entirely
> from this project and rewrite proteinortho_ffadj_mcs.py in perl.
>
> Best regards, Paul
>
>
> Steffen Möller <steffen_moeller@gmx.de> schrieb am Sa. 27. Juli 2019 um
> 13:30:
>
> > Hi Paul, hi Andreas,
> >
> > I just had a look at
> > https://salsa.debian.org/med-team/proteinortho/blob/master/debian/control
> > and found the dependency on plain good ole "python", which the version 2
> > of python and not (as one would rightously assume just any version of
> > python. Should this possibly be "python3", instead? In my understanding
> > this is why the package is not transitioning to testing as Debian
> > currently attempts to remove Python2 from the distribution.
> >
> > Best,
> >
> > Steffen
> >
> > On 17.07.19 16:26, Andreas Tille 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 <andreas@an3as.eu>
> > 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 <tille@debian.org>
> > 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

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