Re: [Debichem-devel] updated python-ase / gpaw
Hi Andreas Thanks for the upload! On 24/07/2015 18:14, Andreas Tille wrote: So if you build in an unstable chroot you do not get this error? I have just tried with sbuild now, and I did not get this error. This was with the revision before you commented out the Python 3 changes. Regards Graham -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55b60de9.50...@nerve.org.za
Re: [Debichem-devel] updated python-ase / gpaw
On 24/07/2015 16:53, Andreas Tille wrote: I noticed that ase also should work with Python 3 and thus added a Python 3 package. OK. I had read that Python3 wasn't supported yet [1]: The following packages are required for basic ASE functionality: 1. Python2 version 2.6 or newer. Python3 is not supported yet. 2. NumPy. Unfortunately 1 of 142 fails. Would you mind having a look into this? Weird, I tried building and it passed all the tests (although that was with Python 3.4, not 3.5 as is in unstable). I did get hundreds of Lintian warnings though, e.g. W: python-ase source: binaries-have-file-conflict python-ase python3-ase usr/bin/ase-build Is this normal for packages that produce Python2 and Python3 binaries? What about the recommended packages; python-gtk2, python-matplotlib and python-scipy? Should those become python3-matplotlib and python3-scipy? It seems that there is no python3-gtk2. I must admit I am not comfortable with this change you have made. [1] https://wiki.fysik.dtu.dk/ase/download.html#requirements -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55b25f70.7080...@nerve.org.za
Re: updated python-ase / gpaw
Hi Graham,
On Fri, Jul 24, 2015 at 05:53:20PM +0200, Graham Inggs wrote:
On 24/07/2015 16:53, Andreas Tille wrote:
I noticed that ase also should work with Python 3 and thus added a
Python 3 package.
OK. I had read that Python3 wasn't supported yet [1]:
I simply did:
$ grep 3\.4 * 2/dev/null
PKG-INFO:Classifier: Programming Language :: Python :: 3.4
setup.py: 'Programming Language :: Python :: 3.4',
which seems to be a sign for 3.4 support.
The following packages are required for basic ASE functionality:
1. Python2 version 2.6 or newer. Python3 is not supported yet.
2. NumPy.
Unfortunately 1 of 142 fails. Would you mind having a look into this?
Weird, I tried building and it passed all the tests (although that was with
Python 3.4, not 3.5 as is in unstable).
I was building in an unstable chroot which obviously used Python 3.4
(not 3.5). The log said:
...
tasks/dcdft.py (ScriptTestCase) ... skipped ok
tasks/gbrv.py (ScriptTestCase) ... ERROR
tasks/htb.py (ScriptTestCase) ... ok
tasks/mmbjmp.py (ScriptTestCase) ... ok
turbomole/turbomole_H2.py (ScriptTestCase) ... skipped ok
turbomole/turbomole_h3o2m.py (ScriptTestCase) ... skipped ok
vasp/vasp_Al_volrelax.py (ScriptTestCase) ... skipped ok
vasp/vasp_co.py (ScriptTestCase) ... skipped ok
COCu111.py (ScriptTestCase) ... Test suite failed
ok
==
ERROR: tasks/gbrv.py (ScriptTestCase)
--
Traceback (most recent call last):
File /tmp/buildd/python-ase-3.9.1.4567/ase/test/__init__.py, line 50, in
testfile
exec(compile(fd.read(), self.filename, 'exec'),
File /usr/lib/python3.4/encodings/ascii.py, line 26, in decode
return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 488:
ordinal not in range(128)
--
Ran 142 tests in 46.282s
FAILED (errors=1)
E: pybuild pybuild:256: test: plugin custom failed with: exit code=1: python3.4
/tmp/buildd/python-ase-3.9.1.4567/setup.py test
dh_auto_test: pybuild --test -i python{version} -p 3.4 --dir . returned exit
code 13
...
So if you build in an unstable chroot you do not get this error?
I did get hundreds of Lintian warnings though, e.g.
W: python-ase source: binaries-have-file-conflict python-ase python3-ase
usr/bin/ase-build
Well, the build at my side did not finalise so I can not look into the
binary but it seems that the package does install not only binaries but
also has some executables in /usr/bin. Setup.py simply installs these
for each run and so you get the files in /usr/bin in both packages which
will lead to a conflict between both packages.
I had a similar situation in DendroPy
git://anonscm.debian.org/debian-med/python-dendropy.git
and solved this by a separate package delivering the tools in /usr/bin.
I decided for the Python 3 version of the tool.
Is this normal for packages that produce Python2 and Python3 binaries?
This is normal for all packages installing the same file name.
What about the recommended packages; python-gtk2, python-matplotlib and
python-scipy?
Should those become python3-matplotlib and python3-scipy?
Sure. I missed this piece.
It seems that
there is no python3-gtk2.
I'm not sure. May be you clarify this with
debian-pyt...@lists.debian.org.
I must admit I am not comfortable with this change you have made.
If you want to push on a quick update I'm fine with reverting this
change. However, at some point in time you will need to do it anyway.
Its youe choice when you want to do this.
Kind regards
Andreas.
--
http://fam-tille.de
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Re: updated python-ase / gpaw
Hi Graham, On Fri, Jul 24, 2015 at 04:09:22PM +0200, Graham Inggs wrote: Update: new upstream version 3.9.1.4567 was released. I have updated my packaging and I would like someone to review and hopefully sponsor the upload. Thanks for your work on this. Andreas did already offer [2]. I noticed that ase also should work with Python 3 and thus added a Python 3 package. Unfortunately 1 of 142 fails. Would you mind having a look into this? I also used cme fix dpkg-control to solve some minor issues in d/control. Feel free to ping me if you either have a solution for the Python 3 issue or if you have problems solving it. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150724145350.gf26...@an3as.eu
Re: [Debichem-devel] updated python-ase / gpaw
Hi Andreas On 24 July 2015 at 18:14, Andreas Tille andr...@an3as.eu wrote: I was building in an unstable chroot which obviously used Python 3.4 (not 3.5). The log said: Sorry, I was confused. I think I saw that Ubuntu have already switched to 3.5. So if you build in an unstable chroot you do not get this error? I have limited connectivity until next week. I tried building with your changes on the first machine available which happened to be running Ubuntu 14.04. (What I pushed to git was tested against unstable using sbuild though) If you want to push on a quick update I'm fine with reverting this change. However, at some point in time you will need to do it anyway. Its youe choice when you want to do this. At this stage, I'd prefer if we uploaded a Python2-only version. I can then look at the test case failure you saw, and Python3 in more detail, over the coming weeks. Regards Graham -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/CAM8zJQufD_3nCY0owRu+6ir-3XJY7Kf=gw0=3f4o5shbepz...@mail.gmail.com
Re: updated python-ase / gpaw
On 15/07/2015 20:09, Graham Inggs wrote: I've been working on the python-ase packaging in git [1]. ... [1] http://anonscm.debian.org/cgit/debichem/packages/python-ase.git Update: new upstream version 3.9.1.4567 was released. I have updated my packaging and I would like someone to review and hopefully sponsor the upload. Andreas did already offer [2]. [2] https://lists.debian.org/debian-science/2015/07/msg00098.html -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55b24712.6090...@nerve.org.za
Re: [Debichem-devel] updated python-ase / gpaw
Hi Graham. On Fri, Jul 24, 2015 at 07:04:08PM +0200, Graham Inggs wrote: If you want to push on a quick update I'm fine with reverting this change. However, at some point in time you will need to do it anyway. Its youe choice when you want to do this. At this stage, I'd prefer if we uploaded a Python2-only version. OK, I commented out the Python 3 changes and uploaded. Regarding the /usr/bin issue: Alternatively to a separate tools package there is the option to use the alternatives system. I can then look at the test case failure you saw, and Python3 in more detail, over the coming weeks. OK. Thanks for your work on this Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150725052620.gu26...@an3as.eu
