pdb2pqr maintained by DebiChem team but in Debian Med repository?

[Andreas Tille-5]

Hi,

when touching some packages to add Enhances fields I realised
that pdb2pqr is (formally?) maintained by DebiChem team but is
sitting in Debian Med repository.  I admit I do not mind which
actual team is mentioned in the maintainers field but I think
it makes sense to put the packaging in the according repository.

Perhaps this fact is the reason that nobody uploaded the new
version?

Could anybody please comment on this issue?

Kind regards

     Andreas.

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[Michael Banck]

On Fri, Oct 16, 2009 at 11:01:44PM +0200, Andreas Tille wrote:
> when touching some packages to add Enhances fields I realised
> that pdb2pqr is (formally?) maintained by DebiChem team but is
> sitting in Debian Med repository.  I admit I do not mind which
> actual team is mentioned in the maintainers field but I think
> it makes sense to put the packaging in the according repository.
>
> Perhaps this fact is the reason that nobody uploaded the new
> version?

It's not like previous versions got uploaded.
 
> Could anybody please comment on this issue?

There are still copyright/license issues to resolve according to Manuel,
IIRC.


Michael


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[Steffen Moeller-3]

Hello,

Michael Banck wrote:

> On Fri, Oct 16, 2009 at 11:01:44PM +0200, Andreas Tille wrote:
>> when touching some packages to add Enhances fields I realised
>> that pdb2pqr is (formally?) maintained by DebiChem team but is
>> sitting in Debian Med repository.  I admit I do not mind which
>> actual team is mentioned in the maintainers field but I think
>> it makes sense to put the packaging in the according repository.
>>
>> Perhaps this fact is the reason that nobody uploaded the new
>> version?
>
> It's not like previous versions got uploaded.
>  
>> Could anybody please comment on this issue?
>
> There are still copyright/license issues to resolve according to Manuel,
> IIRC.

I agree that the situation is somewhat strange, but I admit to like it. Manuel
(a DD by now) IMHO correctly indicated that the other tools that pdb2pqr
interacts with are all in DebiChem and that as such it would make sense for
pdb2pqr to be showing up there, too. Other candidates to move to DebiChem for
that reason are BALL, the MGLTools and the autodocksuite. We probably all agree
that it is up to the respective maintainer to decide where to officially anchor
some Debian maintenance. I personally would appreciate a dual team maintenance.
As long as the debian/control file indicates where to find the repository,
which could be any, we should not care. Actually, IIRC, I even explicitly asked
Manuel not to move his sources to strengthen our ties. If not, then I should
have done.

I don't know about what the exact status of the copyright issue is. But I know
Manuel to be at it.

Best,

Steffen


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[Manuel Prinz-3]

> Michael Banck wrote:
> > There are still copyright/license issues to resolve according to Manuel,
> > IIRC.

Am Sonntag, den 18.10.2009, 17:14 +0200 schrieb Steffen Moeller:
> I don't know about what the exact status of the copyright issue is. But I know
> Manuel to be at it.

Both of the above is true. There are currently license issues that have
to be sorted out. I'm in contact with upstream about that and I we're
working on it. Due to time constraints on both sides of the line, it's
not progressing as fast as we all like it to be. That's unfortunate but
we'd like to do it right.

About the group issue: We (Steffen and I) did the preliminary packaging
work in Debian Med, as we were both members of that group and I did not
know about Debichem back then. Michael invited me to put the package
under the Debichem umbrella. I think it is the right place for the
package, and agreed with Steffen to move it. I have not done that step
as there is still work going on. When it is ready, I'll do the move of
the repositories. I think it won't heared anyone if it stays in the
Debian Med SVN since this one is referenced in the bug report currently.

I think the package is almost ready, though I fear that it might get
rejected again in the current state. I also have to test it with Python
2.6 to not interfere with the ongoing transition. Once I'm sure it will
not put burdon on others, I will upload and get ftp-master's feedback.
If it won't work out, we will have to wait for a new upstream version.
But I'm quite confident it will be OK.

Best regards
Manuel


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[Andreas Tille-6]

On Sun, Oct 18, 2009 at 07:37:02PM +0200, Manuel Prinz wrote:
> Both of the above is true. There are currently license issues that have
> to be sorted out. I'm in contact with upstream about that and I we're
> working on it. Due to time constraints on both sides of the line, it's
> not progressing as fast as we all like it to be. That's unfortunate but
> we'd like to do it right.

Good luck with this.

> About the group issue: We (Steffen and I) did the preliminary packaging
> work in Debian Med, as we were both members of that group and I did not
> know about Debichem back then. Michael invited me to put the package
> under the Debichem umbrella. I think it is the right place for the
> package, and agreed with Steffen to move it. I have not done that step
> as there is still work going on. When it is ready, I'll do the move of
> the repositories. I think it won't heared anyone if it stays in the
> Debian Med SVN since this one is referenced in the bug report currently.

It is perfectly fine for me in any SVN.  I was just confused by having a
package maintained by DebiChem in our archive.  Nothing more.  I think
there is no sense in competing about package maintenance and the main
maintainer should draw a reasonable decision which repository fits best.
If there is a strong reason to have a package maintained by a different
team in our repository this should be documented in some proper readme
file.  For the moment I would think something like:

   This packaging stuff will be moved to DebiChem SVN with next
   release.

or something like this would clarify things IMHO:
 
> I think the package is almost ready, though I fear that it might get
> rejected again in the current state. I also have to test it with Python
> 2.6 to not interfere with the ongoing transition. Once I'm sure it will
> not put burdon on others, I will upload and get ftp-master's feedback.
> If it won't work out, we will have to wait for a new upstream version.
> But I'm quite confident it will be OK.

Thanks for your work on this

     Andreas.

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http://fam-tille.de


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[Charles Plessy-12]

Le Sun, Oct 18, 2009 at 05:14:26PM +0200, Steffen Moeller a écrit :
> As long as the debian/control file indicates where to find the repository,
> which could be any, we should not care.

Exactly: with ‘debcheckout -a’ it makes little difference if a package is in
reposotory A or B, as long as all the uploaders have commit rights. All DDs can
commit to the debian-med Alioth repositories, and if there are guests who need
acces as well, we can ask the Alioth admins to set up a write ACL for the whole
Debichem project.

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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[Michael Banck]

Hi,

On Sun, Oct 18, 2009 at 07:37:02PM +0200, Manuel Prinz wrote:

> > Michael Banck wrote:
> > > There are still copyright/license issues to resolve according to Manuel,
> > > IIRC.
>
> Am Sonntag, den 18.10.2009, 17:14 +0200 schrieb Steffen Moeller:
> > I don't know about what the exact status of the copyright issue is. But I know
> > Manuel to be at it.
>
> Both of the above is true. There are currently license issues that have
> to be sorted out. I'm in contact with upstream about that and I we're
> working on it. Due to time constraints on both sides of the line, it's
> not progressing as fast as we all like it to be. That's unfortunate but
> we'd like to do it right.

pdb2pqr-1.5 just got released, FYI.  Do you know whether it solves those
issues?


Michael


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[Manuel Prinz-3]

Hi Michael,

On Sun, 2009-11-01 at 20:47 +0100, Michael Banck wrote:
> pdb2pqr-1.5 just got released, FYI.  Do you know whether it solves those
> issues?

I know of the release but did not have time to check yet. But sincerely
hope so! :)

I will have a look at it this evening or the day after.

Best regards
Manuel



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[Michael Banck]

Hi Manuel,

On Mon, Nov 02, 2009 at 10:09:21AM +0100, Manuel Prinz wrote:

> Hi Michael,
>
> On Sun, 2009-11-01 at 20:47 +0100, Michael Banck wrote:
> > pdb2pqr-1.5 just got released, FYI.  Do you know whether it solves those
> > issues?
>
> I know of the release but did not have time to check yet. But sincerely
> hope so! :)
>
> I will have a look at it this evening or the day after.

Did you get around taking a look?  Otherwise, if you could point me to a
public list of issues, I could try to evaluate the new upstream release
myself.


Thanks,

Michael


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[Manuel Prinz-3]

Hi Michael!

Am Samstag, den 05.12.2009, 21:16 +0100 schrieb Michael Banck:
> Did you get around taking a look?  Otherwise, if you could point me to a
> public list of issues, I could try to evaluate the new upstream release
> myself.

I did yesterday and uploaded an updated version a few minutes ago. Most
of the discussion happened privately, so there's no real place to get
yourself informed.

I hope that the package will pass NEW. Copyright is my only concern but
I check with other developers and the things listed should be
sufficient. There is a fallback solution in case it doesn't.

Also, the package needs several changes to improve quality. I'm going to
address them soon. The package is functional as is, though I do not
distribute the webserver part; I also have no motivation to support that
at all, since it is quite hackish and not worth the trouble, IMHO.

PDB2PQR also contains embedded copies of code which are not needed at
all. The size might justify repacking. Any opinions on that?

And what are the feeling towards the new source format? Is it OK with
the group to use 3.0 (whatever) or should I leave it at 1.0?

Best regards
Manuel


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[Andreas Tille-5]

On Sat, Dec 05, 2009 at 11:59:01PM +0100, Manuel Prinz wrote:
> PDB2PQR also contains embedded copies of code which are not needed at
> all. The size might justify repacking. Any opinions on that?

In many cases it is a matter of taste.  I'm personally in favour of
repackaging if it saves certain amount of code for download and
mirroring.
 
> And what are the feeling towards the new source format? Is it OK with
> the group to use 3.0 (whatever) or should I leave it at 1.0?

Why not start using a new format if it is a new package.  There are no
certain numbers about packages using the new format but having some
packages in this format let us gather some experience.

Kind regards

     Andreas.

--
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[Charles Plessy-12]

Le Sun, Dec 06, 2009 at 09:31:55PM +0100, Andreas Tille a écrit :
> On Sat, Dec 05, 2009 at 11:59:01PM +0100, Manuel Prinz wrote:
>  
> > And what are the feeling towards the new source format? Is it OK with
> > the group to use 3.0 (whatever) or should I leave it at 1.0?
>
> Why not start using a new format if it is a new package.  There are no
> certain numbers about packages using the new format but having some
> packages in this format let us gather some experience.

I am systematically converting the packages that have a direct benefit,
for instance the ones distributed as a bzipped tar archive (I like to use
exactly the same original tarball as Upstream). But note however that some
infrastructures like backports.org do not support the new formats yet.

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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