Re: New version of proteinortho

[Andreas Tille <andreas@an3as.eu>]

Hi Paul,

unfortunately this mail hit my inbox in a busy time and became forgotten
for three months now.  Sorry about this.  I now tried to update the package.
The problem is a Python 2 script included into your code.  Python 2 is
End of Live and Debian needs to get rid of all Python 2 code.  I tried my
best by using 2to3 for the port and also did some manual change, but for
this code I'd prefer you having a look:


**Step 2** using blastp+ with : synteny
Running blast analysis: 60% (6/10)Traceback (most recent call last):           
  File "/usr/lib/proteinortho//proteinortho_ffadj_mcs.py", line 861, in <module>
    g1_mod, g2_mod, g1_runs, g2_runs, dists, repMatching, minCsSize, greedy)
  File "/usr/lib/proteinortho//proteinortho_ffadj_mcs.py", line 745, in repeatMatching
    g1_mod_new = sorted(set(g1_mod_res + g1_mod), cmp=chr_srt)
TypeError: 'cmp' is an invalid keyword argument for sort()
 [Error] Failed to run /usr/lib/proteinortho//proteinortho_ffadj_mcs.py for
test/E.faa vs test/M.faa


Here you can find my patch:

    https://salsa.debian.org/med-team/proteinortho/blob/master/debian/patches/2to3.patch

Please fix the remaining things and include the ported script into your
download tarball.

Thank you for your patience and please feel free to ask here if you have
any questions about the Python 3 port

    Andreas.

On Mon, Jul 22, 2019 at 12:48:10PM +0200, Paul Klemm wrote:
> 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 <andreas@an3as.eu> 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 debian-med@lists.debian.org 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 <andreas@an3as.eu> 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
> >
> > --
> > 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