Bug#910686: Pymol 2.2.0 sources available from github

Discussion:

(too old to reply)

Alois Schloegl

2018-10-09 20:40:01 UTC

Package: pymolÂ Â Â

Version: 2.2.0

Severity: wishlist

The open source version of Pymol 2.2.0 is available from here now:

Â Â https://github.com/schrodinger/pymol-open-source

Â Â https://github.com/schrodinger/pymol-open-source/releases

It seems, debian/watch file is not aware of this new release, attached
is a revised watch file .

May I also suggest to package pymol 2.2.0 ?

Best regards,

Â Alois

Michael Banck

2018-10-20 08:10:01 UTC

Permalink

Hi Alois,

Package: pymol
Version: 2.2.0
Severity: wishlist
   https://github.com/schrodinger/pymol-open-source
   https://github.com/schrodinger/pymol-open-source/releases
It seems, debian/watch file is not aware of this new release, attached
is a revised watch file .
May I also suggest to package pymol 2.2.0 ?

I actually started looking at it locally a while ago and forgot to push
the changes, they are now on salsa, including a new watch file. I'll
see whether yours is a better fix and will merge if so.

Not sure I'll get to uploading it soonish though :-/

Michael

Michael Banck

2018-10-20 08:50:01 UTC

Permalink

Hi,

Post by Michael Banck
I actually started looking at it locally a while ago and forgot to push
the changes, they are now on salsa, including a new watch file. I'll
see whether yours is a better fix and will merge if so.
Not sure I'll get to uploading it soonish though :-/

I've updated the debian packaging in git now and pymol-2.2.0 builds, but
(i) the upstream git files need updating (Andreas did that in the
past?) and (ii) the autopkgtests fail in a somewhat weird way for me:

|autopkgtest [10:38:14]: testing package pymol version 2.2.0-1
|autopkgtest [10:38:14]: build not needed
|autopkgtest [10:38:15]: test command1: preparing testbed
|Get:1 file:/tmp/autopkgtest.yS77Sj/binaries InRelease
|Ign:1 file:/tmp/autopkgtest.yS77Sj/binaries InRelease
|Get:2 file:/tmp/autopkgtest.yS77Sj/binaries Release [816 B]
|Get:2 file:/tmp/autopkgtest.yS77Sj/binaries Release [816 B]
|Get:3 file:/tmp/autopkgtest.yS77Sj/binaries Release.gpg
|Ign:3 file:/tmp/autopkgtest.yS77Sj/binaries Release.gpg
|Get:4 file:/tmp/autopkgtest.yS77Sj/binaries Packages [2258 B]
|Reading package lists...
|Reading package lists...
|Building dependency tree...
|Reading state information...
|Correcting dependencies...Starting pkgProblemResolver with broken count: 1
|Starting 2 pkgProblemResolver with broken count: 1
|Investigating (0) autopkgtest-satdep:amd64 < 0 @iU mK Nb Ib >
|Broken autopkgtest-satdep:amd64 Depends on pymol:amd64 < none | 2.2.0-1 @un uH > (>= 0~)
| Considering pymol:amd64 0 as a solution to autopkgtest-satdep:amd64 -2
| Removing autopkgtest-satdep:amd64 rather than change pymol:amd64
|Done
| Done
|Starting pkgProblemResolver with broken count: 0
|Starting 2 pkgProblemResolver with broken count: 0
|Done
|The following packages will be REMOVED:
| autopkgtest-satdep
|0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
|1 not fully installed or removed.
|After this operation, 0 B of additional disk space will be used.
|(Reading database ... 11766 files and directories currently installed.)
|Removing autopkgtest-satdep (0) ...

Andreas, can you take a look?

Michael

Stuart Prescott

2018-10-21 01:00:01 UTC

Permalink

Hi Michael,

Post by Michael Banck
I've updated the debian packaging in git now and pymol-2.2.0 builds, but
(i) the upstream git files need updating (Andreas did that in the
past?)

Having downloaded the upstream source (with uscan) and ensuring that you have
no uncommitted changes:

$ gbp import-orig ../pymol_2.2.0.orig.tar.gz

(I've done this locally, do you want me to push that change?)

Post by Michael Banck
|autopkgtest [10:38:14]: testing package pymol version 2.2.0-1
|autopkgtest [10:38:14]: build not needed
|autopkgtest [10:38:15]: test command1: preparing testbed
|Get:1 file:/tmp/autopkgtest.yS77Sj/binaries InRelease
|Ign:1 file:/tmp/autopkgtest.yS77Sj/binaries InRelease
|Get:2 file:/tmp/autopkgtest.yS77Sj/binaries Release [816 B]
|Get:2 file:/tmp/autopkgtest.yS77Sj/binaries Release [816 B]
|Get:3 file:/tmp/autopkgtest.yS77Sj/binaries Release.gpg
|Ign:3 file:/tmp/autopkgtest.yS77Sj/binaries Release.gpg
|Get:4 file:/tmp/autopkgtest.yS77Sj/binaries Packages [2258 B]
|Reading package lists...
|Reading package lists...
|Building dependency tree...
|Reading state information...
|Correcting dependencies...Starting pkgProblemResolver with broken count: 1
|Starting 2 pkgProblemResolver with broken count: 1

How are you running the tests? It looks like you've not given autopkgtest the
precompiled debs and haven't let it redo the compilation. The following works
fine:

$ autopkgtest -B pymol_2.2.0-1_amd64.changes \
--- adt-virt-schroot unstable-amd64-sbuild

The test scripts succeed although there are actually some errors in the test
output:

Error: unknown Setting: 'cull_spheres'.

(I can't see any documentation about that no longer being a command -- the
test does otherwise run just fine though)

There was also speculation a while back about this being the right time to
switch from Python 2 to Python 3 and from tk to Qt.

Any thoughts?

Cheers
Stuart

--
Stuart Prescott http://www.nanonanonano.net/ ***@nanonanonano.net
Debian Developer http://www.debian.org/ ***@debian.org
GPG fingerprint 90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7

Michael Banck

2018-10-21 14:50:02 UTC

Permalink

Hi,

Post by Stuart Prescott
Hi Michael,

Post by Michael Banck
I've updated the debian packaging in git now and pymol-2.2.0 builds, but
(i) the upstream git files need updating (Andreas did that in the
past?)

Having downloaded the upstream source (with uscan) and ensuring that you have
$ gbp import-orig ../pymol_2.2.0.orig.tar.gz
(I've done this locally, do you want me to push that change?)

Sure!

Post by Stuart Prescott

How are you running the tests?

I run them along sbuild, using its --run-autopkgtest option. That is
usually not a problem.

I'll take a second look if it works fine for you.

Michael

Michael Banck

2018-10-21 15:00:01 UTC

Permalink

Hi,

Post by Stuart Prescott
There was also speculation a while back about this being the right time to
switch from Python 2 to Python 3 and from tk to Qt.

I'd be fine with that, but I have to say I haven't tested the Qt
interface a lot and I won't be of much help in case of regressions.

Michael

Stuart Prescott

2018-10-28 13:00:01 UTC

Permalink

Further to our recent discussions of pymol

* I've pushed a couple of changes to git for version 2.2.0+dfsg-1 which I
think is ready to upload to unstable.

Post by Michael Banck

Post by Stuart Prescott
There was also speculation a while back about this being the right time to
switch from Python 2 to Python 3 and from tk to Qt.

I'd be fine with that, but I have to say I haven't tested the Qt
interface a lot and I won't be of much help in case of regressions.

* I've also pushed a debian/experimental branch that uses Python 3 and Qt. I
think it's ready to get uploaded to experimental at least -- it will go
through NEW on the way.

I'll make these two uploads in a few days unless anyone spots problems.

Looking through the build-time and autopkgtest tests, I found a few Python 2→3
problems that I've patched (already merged upstream).

I'm not convinced that the tests we've got actually test the package properly
-- if individual tests fail, the tests are still reported as passed. In
discussing testing with upstream, it seems there is a separate repository of
tests that can be used. Do we add that as an extra tarball for a multi-tarball
source package? Or try to upload it as an extra source package?

https://github.com/schrodinger/pymol-testing

Cheers
Stuart

--
Stuart Prescott http://www.nanonanonano.net/ ***@nanonanonano.net
Debian Developer http://www.debian.org/ ***@debian.org
GPG fingerprint 90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7