Re: lintian

2002-11-08 Thread Andreas Tille
On Fri, 8 Nov 2002, Peter Hawkins wrote: Are lintian's current python dependency checks on crack or something? Just for the record: Same for me. Kind regards Andreas.

Re: [zope] New features of the zope package 2.5.1-2.5

2002-11-28 Thread Andreas Tille
On Wed, 27 Nov 2002, Luca - De Whiskey's - De Vitis wrote: Zope products will neither need to have any config, nor any templates file. They will simply get the answer to share/zope/restart question in their postinist (question to which the user have already answered) and configure acordingly.

Re: Need Help with Efforts to Package PreScript 2.2

2003-01-20 Thread Andreas Tille
On Mon, 20 Jan 2003, Federico Sevilla III wrote: To help Andreas Tille with getting all the prerequisites for work being done on packaging the Zope DocumentLibrary product I attempted to package PreScript. Thanks Federico for your efforts. By the way I regard PreScript as an interesting piece

Splitting ZODB from Zope package

2003-04-06 Thread Andreas Tille
Hello, ZODB has its own source tree http://www.zope.org/Wikis/ZODB/FrontPage and even sourceforge project http://sourceforge.net/projects/zodb/ It also has its usage without Zope http://www.zope.org/Documentation/Articles/ZODB1 I tried these examples but had some trouble get

Re: Splitting ZODB from Zope package

2003-04-07 Thread Andreas Tille
On Mon, 7 Apr 2003, Luca - De Whiskey's - De Vitis wrote: This is a good idea to me, and it's worth of trying: there are olso other packages which are included in Zope source for convenience (like ZPT, or ZEO) for which we can try as well. In fact your plan to package ZEO separately was one

Woody backports of Python2.[23]

2003-08-20 Thread Andreas Tille
Hi, are there any apt-get sources for Python2.[23] for Woody? Kind regards Andreas.

Re: gnue-* package should be updated, maybe NMUed

2003-09-12 Thread Andreas Tille
On Fri, 12 Sep 2003, Matthias Klose wrote: PS: I'm away until Sep. 21. Then you should fix your vacation message which was saying October ... Kind regards Andreas.

Re: RFS: I search sponsor for Zope/Debian Packages

2003-10-06 Thread Andreas Tille
On Fri, 3 Oct 2003, Nicolas Ledez wrote: Hello, I'm french and I would like to be a Debian Developper, a search a sponsor. Sorry for mass-maling but nobody anser me to debian-mentors. I foreward this mail to debian-python list which might be more apropriate or even the zope packaging list on

Enough time for curator?

2003-10-20 Thread Andreas Tille
Hi, your package curator is one of the package which depends from Python 2.1. Recently there was a move to Python 2.3 as default Python version. The bug against curator to update to a recent Python version is 64 days old. MOreover the curator version in Debian is about one and a half year old

Re: [Pkg-zope-developers] Re: Duplicate debconf templates in zope-* packages

2003-11-14 Thread Andreas Tille
On Thu, 13 Nov 2003, Denis Barbier wrote: This was your original point, then Andreas Tille and Federico Di Gregorio replied that this explanation does not apply here because all packages depend on Zope, you agreed and proposed to drop templates, and everyone was happy... but this never

Re: Duplicate debconf templates in zope-* packages

2003-11-14 Thread Andreas Tille
On Fri, 14 Nov 2003, Luca - De Whiskey's - De Vitis wrote: Actually my proposed sentence is not accurate, but something more might be added to that paragraph. zope-* .postinst and only those files expect a shared question to be available at configuration time. zope package is the only one

Bug#226315: ITP: zope-testcase -- unit testing framework and TestCase for Zope (fwd)

2004-01-06 Thread Andreas Tille
a mistake in my mail forwarding regime mails to [EMAIL PROTECTED] where not delivered to me since 29.10.2003 I'm sorry for the delay. -- Forwarded message -- Date: Mon, 05 Jan 2004 21:45:35 +0100 From: Andreas Tille [EMAIL PROTECTED] To: Debian Bug Tracking System [EMAIL PROTECTED

Re: Bug#226315: ITP: zope-testcase -- unit testing framework and TestCase for Zope (fwd)

2004-01-09 Thread Andreas Tille
On Fri, 9 Jan 2004, Donovan Baarda wrote: We've been using ZopeTestCase for unit tests on our zope products. I recommend it to anyone doing zope product development. Great. The package is in incomming new and will need about 5 to 10 days normally to enter the archive. I'd like it very much

Re: [Zope] A few questions...

2005-01-26 Thread Andreas Tille
On Wed, 26 Jan 2005, Fabio Tranchitella wrote: reason I'd like to see a dh_zope debhelper script, so the packages This would be really great. (at least the easy ones) could get rid of their templates and their maintainer scripts. I know that Luca De Vitis started working on it, and I tried to mail

Re: Problems using python-support

2006-08-09 Thread Andreas Tille
On Wed, 9 Aug 2006, Josselin Mouette wrote: As Gnumed doesn't ship a .pth file, the .path doesn't need to be updated. Well, I did so in 0.1 packages but was unsure whether this might be useful with new Python policy. Would you advise me to continue using Gnumed.pth that contained Gnumed

Re: RFS: pondus

2008-02-05 Thread Andreas Tille
On Tue, 5 Feb 2008, Piotr O?arowski wrote: no need to upload it anywhere anymore, just inject it into the repo (please remember about svn-inject's -o option [1]) and ping me. Well, there are two options for using a SVN reporitory: debian-python and debian-med. As you can read in the thread

Re: python-openopt

2008-05-29 Thread Andreas Tille
On Thu, 28 May 2008, Yaroslav Halchenko wrote: Within your project we are going to make use of OpenOpt project http://scipy.org/scipy/scikits/wiki/OpenOpt which as you see is a part of scikits. Just added the project to Debian Science tasks files and rerendered the web sentinel page

Re: Packaging question on private extension modules

2008-06-01 Thread Andreas Tille
On Sat, 31 May 2008, Manuel Prinz wrote: I have a Python application with private extension modules, so the package is Arch: any. Because there is no way (at least I'm not aware of that) to split the package because the modules are private, I can't seperate the large part of the app out to

Re: Packaging question on private extension modules

2008-06-01 Thread Andreas Tille
On Sun, 1 Jun 2008, Manuel Prinz wrote: The package is pdb2pqr, you can find it here: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/ Without having a look into this ... The current version puts everything to /usr/lib/pdb2pqr as that seems to please lintian. I tried to

Yet another list statistics for debian-python

2009-01-17 Thread Andreas Tille
Hi, as you can read in my lightning talk at DebConf http://people.debian.org/~tille/talks/200808_lightning/ I did some investigation on who is frequently posting on our mailing lists. I now created graphs until end of last year and write a short summary for those lists I regard worth a

[Help] Failed to apply new Python policy to GNUmed packages

2009-03-26 Thread Andreas Tille
Hi, I tried to implement the Python policy [1] using python-support to the new GNUmed packages but failed. If I try the basic essence of the /usr/bin/gnumed script I get: $ python -m Gnumed.wxpython.gnumed Traceback (most recent call last): File /usr/lib/python2.5/runpy.py, line 85, in

Re: [Help] Failed to apply new Python policy to GNUmed packages

2009-03-29 Thread Andreas Tille
On Sat, 28 Mar 2009, Emilio Pozuelo Monfort wrote: That is, you're now shipping some modules in a private location This is what I understood as recommendation in #516037. (usr/share is not in PYTHONPATH), so they are not found when you try to import them. You could ship Gnumed in

Re: [Help] Failed to apply new Python policy to GNUmed packages

2009-03-29 Thread Andreas Tille
On Sun, 29 Mar 2009, Karsten Hilbert wrote: Well, you are trying to solve two things at once: 1) make the python -m calling convention work 2) move GNUmed modules to a private location While, yes, this WAS recommended in that report I tried furiously to argue against doing both at once

Re: [Help] Failed to apply new Python policy to GNUmed packages

2009-03-29 Thread Andreas Tille
On Sun, 29 Mar 2009, Karsten Hilbert wrote: - My suggestion would be: - call gnumed.py with the python -m ... option if that works - this would rid us of that hardcoded path - a great thing - leave modules where they are and GNUmed finds them by default - if the Debian package

Re: [Help] Failed to apply new Python policy to GNUmed packages

2009-03-29 Thread Andreas Tille
On Sun, 29 Mar 2009, Emilio Pozuelo Monfort wrote: You're missing a 'export' before setting the variable (or call python in the same line you set it). Uhm - stupid me. That's a beginners fault ... :-( In the first releases of gnumed-client package I used Gnumed.pth but dropped this since I

Verifying module dependencies (Was: [Help] Failed to apply new Python policy to GNUmed packages)

2009-03-30 Thread Andreas Tille
On Sat, 28 Mar 2009, Emilio Pozuelo Monfort wrote: I got an error that mx.DateTime can't be imported, so you probably need to depend on python-egenix-mxdatetime). Thanks to Emilio I was able to fix the gnumed-client package which was in fact lacking the python-egenix-mxdatetime build

Re: [Help] Failed to apply new Python policy to GNUmed packages

2009-03-30 Thread Andreas Tille
On Mon, 30 Mar 2009, Emilio Pozuelo Monfort wrote: I think pysupport does this for you. When the default interpreter changes, it will regenerate all the .pyc files for the new one. This lets me relax a bit more, but hmmm, I'm not fully convinced ... And FWIW I've just noticed that your

Re: [Zope-dev] The future of Zope{2, 3} and Plone in Debian and Ubuntu

2009-06-24 Thread Andreas Tille
On Wed, Jun 24, 2009 at 11:21:45AM +0200, Fabio Tranchitella wrote: * 2009-06-24 11:20, Sebastien Douche wrote: Is it possible to keep Python 2.4 with a warning like we don't provide support on this version ? No, it is not possible. ... in Debian stable. What about experimental? Also

Re: please upload python2.6 to unstable

2010-01-11 Thread Andreas Tille
On Tue, Jan 12, 2010 at 07:18:03AM +0100, Sandro Tosi wrote: 1) Upload python2.6 to unstable within the next 7 days, or 2) RFA python2.6 and all relevant python packages within the next 7 days. ... Easy as it can be, just leave Python to Debian, and step over. I have no doubt there will

Re: please upload python2.6 to unstable

2010-01-12 Thread Andreas Tille
On Tue, Jan 12, 2010 at 12:06:09AM -0800, Steve Langasek wrote: A group hijack is still a hijack. I don't know why you try to make this sound like some sort of noble enterprise for the good of Debian. I never said it is a noble enterprise. I would simply call it common sense that a group

Re: please upload python2.6 to unstable

2010-01-12 Thread Andreas Tille
On Tue, Jan 12, 2010 at 02:37:49AM -0800, Steve Langasek wrote: Really? Here are some other words that go hand-in-hand with 'package hijack': - vigilante - antisocial - arrogant - acrimonious - disrespectful - demotivating Are you really sure that these attributes will not fit

Re: please upload python2.6 to unstable

2010-01-12 Thread Andreas Tille
On Tue, Jan 12, 2010 at 02:59:35AM -0800, Steve Langasek wrote: As log as you leave it as the maintainer's prerogative to nack the takeover, then that's fine. Sure. That's what I intended to say when I said: ... if I do not hear from you until 7 days I assume you agree. The alternative

Help with Python 2.6 migration

2010-07-10 Thread Andreas Tille
Hi, I wanted to upgrade the package epigrass to recent upstream version and to build against Python 2.6. Unfortunately I was running into a problem and I'm wondering what might be the reason. $ epigrass Traceback (most recent call last): File /usr/bin/epigrass, line 5, in module from

Help with conversion to dh_python2 needed

2011-04-07 Thread Andreas Tille
Hi, I tried to fix #616887 and commited some intermediate packaging stuff to Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mgltools/bhtree/trunk/ When trying to build the package I get: dh_python2 Traceback (most recent call last): File

Re: Help with conversion to dh_python2 needed

2011-04-07 Thread Andreas Tille
Hi, On Thu, Apr 07, 2011 at 12:53:51PM +0200, Piotr Ożarowski wrote: you're not building extensions for all supported Python versions (see previous thread on this mailing list). I will finish namespace feature this weekend and ask python-defaults maintainers to upload new version to unstable

Re: Help with conversion to dh_python2 needed

2011-04-07 Thread Andreas Tille
On Thu, Apr 07, 2011 at 02:07:59PM +0200, Sandro Tosi wrote: (as it can be seen in SVN).  However this does not seem to be the correct solution to avoid this problem.  Perhaps I missed the point in this advise so what exactly do I have to do to build extensions for all supported Python

Re: Help with my Debian package for Orange

2011-06-30 Thread Andreas Tille
On Thu, Jun 30, 2011 at 10:08:57AM +0200, Mitar wrote: btw -- we should list it among http://blends.alioth.debian.org/science/tasks/machine-learning Sure. ;-) care to join the project or commit the entry for the tasks page? I can join the project and commit the entry. Just tell me

Re: Help with my Debian package for Orange

2011-06-30 Thread Andreas Tille
On Thu, Jun 30, 2011 at 10:12:50AM +0200, Mitar wrote: On Thu, Jun 30, 2011 at 10:08 AM, Mitar mmi...@gmail.com wrote: No, but this is also something I will need help with. ;-) And mostly I think that I have over-complicated rules file. ;-) Yes. :-) Have a look into rules files that are

Re: Help with my Debian package for Orange

2011-06-30 Thread Andreas Tille
On Thu, Jun 30, 2011 at 12:28:21PM +0200, Mitar wrote: I have been reading all this but I must say it does not help a beginner in any way. Ahh, sorry. I think some best-practices examples would be most useful. To just copy/paste and adapt. Saying look into rules files also does not help

Re: RFS: DPMT: python-hl7 0.2.0

2011-07-13 Thread Andreas Tille
Hi John, On Wed, Jul 13, 2011 at 09:12:46AM -0500, John Paulett wrote: I am the upstream maintainer of python-hl7 [1] and have packaged it for Debian. I was hoping that a DD may be able to review the package with me and potentially sponsor the package [2]. I have worked with the DPMT before

Re: RFS: DPMT: python-hl7 0.2.0

2011-07-13 Thread Andreas Tille
On Wed, Jul 13, 2011 at 09:43:39AM -0500, John Paulett wrote: In regards to the XML file licensing--it is currently a non-issue in this release, since that code as not been fully merged upstream. We will address any issues upstream before releasing a new version of python-hl7. OK, so the

Re: RFS: DPMT: python-hl7 0.2.0

2011-07-14 Thread Andreas Tille
On Wed, Jul 13, 2011 at 05:02:33PM -0500, John Paulett wrote: I corrected debian/copyright in subversion (the parsing error on was caused by empty lines inside the license). I also corrected the License short name. Thanks for fixing this. As I am packaging novice, please advise if this

Re: Please add me to the team

2012-08-10 Thread Andreas Tille
Hi Laszlo, On Fri, Aug 10, 2012 at 12:43:51PM +0200, Laszlo Kajan wrote: But sometimes the Debian Med group decides that packs are better off in their specialized teams. That's probably a bit missleading wording. There is no such decision making process in the Debian Med team - we adopted

Re: Advise on packaging a new Python module

2012-11-08 Thread Andreas Tille
Hi, On Wed, Nov 07, 2012 at 12:30:41PM +0100, Tomás Di Domenico wrote: Thank you very much for your input, Jakub and Dmitry. I'll start working on those changes right away. And yes, it would be very nice to try and get a Python3 version up. In fact, I'm quite interested in learning how to

Re: Second round of advise on packaging python-csb

2012-11-15 Thread Andreas Tille
Hi Tomás, On Wed, Nov 14, 2012 at 04:42:19PM +0100, Tomás Di Domenico wrote: Ideally, the documentation should be rebuilt from source. Right, things get a bit blurry for me here. When upstream releases a new version, they take a snapshot from their repository and build the release

Re: Revisiting team joining procedures

2012-11-15 Thread Andreas Tille
On Wed, Nov 14, 2012 at 08:04:11PM +0100, Jakub Wilk wrote: I'm afraid that this creates false impression that we'd accept anyone, without any questions asked. This is not the case. As a DPMT admin I required that the applicant: 1) either had existing Python-related packages in the archive;

Re: Recommending get-orig-source for packages ?

2013-12-03 Thread Andreas Tille
On Wed, Dec 04, 2013 at 11:59:33AM +0800, Paul Wise wrote: uscan to grow features for removing files from upstream tarballs, in a declarative way preferably. That's in devscripts git and will be included in the next devscripts version. (see [1]) The default dh get-orig-source to invoke

Re: Recommending get-orig-source for packages ?

2013-12-04 Thread Andreas Tille
Hi, On Wed, Dec 04, 2013 at 09:12:49AM +0100, Jakub Wilk wrote: * Andreas Tille andr...@an3as.eu, 2013-12-04, 08:43: uscan to grow features for removing files from upstream tarballs, in a declarative way preferably. That's in devscripts git and will be included in the next devscripts version

Re: Recommending get-orig-source for packages ?

2013-12-04 Thread Andreas Tille
On Wed, Dec 04, 2013 at 08:49:02PM +0900, Charles Plessy wrote: better solution and migrating the existing information, Andreas will complain. s/complain/comply/ perhaps? D'oh as well. Indeed, I meant will not complain, sorry for the noise... I think all readers had the proper mind

Re: Recommending get-orig-source for packages ?

2013-12-04 Thread Andreas Tille
On Wed, Dec 04, 2013 at 11:30:01AM +0100, Jakub Wilk wrote: AFAICS they way get_main_source_dir() is currently implemented lets malicious upstream to plant files in their tarball that would cause arbitrary code execution... Would you mind proposing a proper fix and forward it to the

Re: Recommending get-orig-source for packages ?

2013-12-09 Thread Andreas Tille
Hi Ben, On Fri, Dec 06, 2013 at 09:07:01PM +1100, Ben Finney wrote: I was just thinking a link might be useful for folks landing on the LibraryStyleGuide page, but I don't feel strongly about it. I have written URL:https://wiki.debian.org/BenFinney/software/repack, do you think that is

Re: Review and sponsoring request: pymia (Python module)

2013-12-10 Thread Andreas Tille
Hi Gert, On Tue, Dec 10, 2013 at 12:41:38PM +0100, Gert Wollny wrote: I've prepared the new package 'pymia' to close the ITP #694439. I've seen that the package python-mia has already been added to the debian-med:imaging-development task :). There is also the python 3 version python3-mia,

Help with packaging of python executable and its modules

2014-02-07 Thread Andreas Tille
Hi folks, I have commited some packaging for a bioinformatics package arden to git://anonscm.debian.org/debian-med/arden.git Since it expects to find its modules under the pretty generic name core I decided to move the modules under /usr/share/pyshared/arden/core and tried to patch the

Re: Help with packaging of python executable and its modules

2014-02-07 Thread Andreas Tille
Hi Julian, On Fri, Feb 07, 2014 at 02:41:10PM +0100, Julian Taylor wrote: I assume this is a python application and not a library? It is an application including some private modules which I like to be compiled into *.pyc. don't install into pyshared, its an implementational detail that

Next time help needed, now with a real Python library (pysam)

2014-02-07 Thread Andreas Tille
Hi folks, since it worked out pretty well with my more simple question I'm impudent enough to come up with a more tricky question: I need to tackle git://anonscm.debian.org/debian-med/pysam.git as a predependency of another package but it seems I need to tweek the build process initially

Re: Next time help needed, now with a real Python library (pysam)

2014-02-07 Thread Andreas Tille
Hi Olivier, On Fri, Feb 07, 2014 at 06:08:20PM +0100, Olivier Sallou wrote: You could first try deleting: 130 from distribute_setup import use_setuptools 131 use_setuptools() if setuptools is already installed. Patch commited - thanks for the hint. How can I prevent the build

Re: Help with packaging of python executable and its modules

2014-02-10 Thread Andreas Tille
Hi Piotr, On Mon, Feb 10, 2014 at 12:53:50PM +0100, Piotr Ożarowski wrote: good that you ask, I will use this opportunity to dispel a myth: dh_python* tools (or any other dh_* tool which doesn't have install in its name AFAIK) do not install files. dh_python* is not supposed to install

HELP: dh_python2 fails to install files if an additional binary package is added

2014-02-11 Thread Andreas Tille
Hi, I'm working on python-pysam in the Debian Med team at git://anonscm.debian.org/debian-med/pysam.git The package was created nicely until I added an additional binary package python-pysam-tests covering the test data in a separate file (since it us usually not needed but might be helpful

Re: HELP: something other than dh_python2 fails to install files if an additional binary package is added

2014-02-11 Thread Andreas Tille
On Tue, Feb 11, 2014 at 09:48:43AM +0100, Piotr Ożarowski wrote: [Andreas Tille, 2014-02-11] directory. I can reproduce this behavious by simply deleting the python-pysam-tests paragraph in debian/control. this part is very important Obviously. It seems that there is some problem

Re: HELP: something other than dh_python2 fails to install files if an additional binary package is added

2014-02-11 Thread Andreas Tille
Hi Piotr, On Tue, Feb 11, 2014 at 10:21:43AM +0100, Piotr Ożarowski wrote: this part is very important It seems that there is some problem in dh_python (or a related tool argh! dh_python2 doesn't install files :-P `echo '/usr/lib/python2.*/*' debian/python-pysam.install` fixes

Python coding help: Has anybody seen this syntax

2014-02-13 Thread Andreas Tille
Hi, I'm trying to package spades[1] and found the following code inside an __init__.py file: ... class YAMLObjectMetaclass(type): The metaclass for YAMLObject. def __init__(cls, name, bases, kwds): super(YAMLObjectMetaclass, cls).__init__(name, bases, kwds) if

[Help] Bug#739631: python-pysam: FTBFS: ImportError: No module named pysam

2014-02-20 Thread Andreas Tille
Hi, I have built the package in pbuilder and wonder why it does not build in autobuilders. Any clue? The package is maintained at git://anonscm.debian.org/debian-med/python-pysam.git Any hint is welcome Andreas. - Forwarded message from Aaron M. Ucko u...@debian.org - Date:

Re: [Help] Bug#739631: python-pysam: FTBFS: ImportError: No module named pysam

2014-02-24 Thread Andreas Tille
Hi Piotr, On Fri, Feb 21, 2014 at 02:42:37PM +0100, Piotr Ożarowski wrote: /me continues promoting pybuild: Thanks for this nice promotion demo - it worked nicely. Thanks for the patch Andreas. PS: What is the best place to read about this in the first place. -- http://fam-tille.de

Help needed for python-biopython which splits up modules into two packages per Python version

2014-03-04 Thread Andreas Tille
Hi, I tried to work on python-biopython which according to authors request supports also Python3 and so I tried to put this into the packaging at svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/ The problem is that I seem to have messed up the debian/*.install files

Re: Help needed for python-biopython which splits up modules into two packages per Python version

2014-03-04 Thread Andreas Tille
Hi, On Tue, Mar 04, 2014 at 05:26:51PM +0100, Piotr Ożarowski wrote: [Andreas Tille, 2014-03-04] I tried to work on python-biopython which according to authors request supports also Python3 and so I tried to put this into the packaging at svn://anonscm.debian.org/debian-med/trunk

Compiled C modules are not found by test suite (Was: Help needed for python-biopython which splits up modules into two packages per Python version)

2014-03-05 Thread Andreas Tille
Hi again On Tue, Mar 04, 2014 at 07:18:08PM +0100, Andreas Tille wrote: you can force pybuild to move BioSQL files to a different location (hint: --ext-dest-dir --ext-pattern or equivalent PYBUILD_* vars) but IMO it's cleaner to use *.install files for that Hmmm, you say *.install files

Re: Compiled C modules are not found by test suite (Was: Help needed for python-biopython which splits up modules into two packages per Python version)

2014-03-14 Thread Andreas Tille
On Wed, Mar 12, 2014 at 01:20:38AM -0400, Éric Araujo wrote: Le 05/03/2014 10:31, Andreas Tille a écrit : I have noted another problem: I worked a bit on the tests and noticed that those tests that are including compiled C code are failing. Is there anything in addition I need to do to make

Re: Compiled C modules are not found by test suite (Was: Help needed for python-biopython which splits up modules into two packages per Python version)

2014-03-15 Thread Andreas Tille
Hi Éric, On Fri, Mar 14, 2014 at 07:15:26PM -0400, Éric Araujo wrote: There are two ways to fix that: either make distutils build the extensions alongside the Python modules, or make the test import all code from the build directory. I’m surprised that this isn’t a common issue for PMPT.

Re: Compiled C modules are not found by test suite (Was: Help needed for python-biopython which splits up modules into two packages per Python version)

2014-03-17 Thread Andreas Tille
Hi Piotr, On Sat, Mar 15, 2014 at 12:52:41PM +0100, Piotr Ożarowski wrote: pybuild takes care of distutils cannot find files it build in previous step and has to build them again problem. I just checked python-biopython and all .so files are in the right location (yey pybuild! :). The

BioPython: Different test suite results when debuild and pdebuild

2014-04-25 Thread Andreas Tille
Hi, I have started anyother try to finalise BioPython which is prepared at Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/ I try to run as much tests of the test suite as possible in the build process and I also added autopkgtest based on upstream's unit

Re: BioPython: Different test suite results when debuild and pdebuild

2014-04-25 Thread Andreas Tille
On Fri, Apr 25, 2014 at 10:57:33AM +0200, Etienne Millon wrote: LC_ALL=C.UTF-8 dh_auto_tests -- ... Works! Thanks a lot for this really helpful hint Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of unsubscribe.

BioPython: Some Python modules not found in tests at package build time

2014-04-25 Thread Andreas Tille
Hi, as I wrote in my last mail I have started anyother try to finalise BioPython which is prepared at Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/ I hope the final problem with the tests is that I get output like test_GraphicsBitmaps ... skipping.

Re: BioPython: Some Python modules not found in tests at package build time

2014-04-25 Thread Andreas Tille
Hi, On Fri, Apr 25, 2014 at 03:05:42PM +0200, Andreas Tille wrote: Hi, as I wrote in my last mail I have started anyother try to finalise BioPython which is prepared at Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/ I hope the final problem

Re: BioPython: Some Python modules not found in tests at package build time

2014-04-25 Thread Andreas Tille
[Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] Hi again, On Fri, Apr 25, 2014 at 03:32:21PM +0200, Andreas Tille wrote: test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman' skipping. Check the fonts

Re: BioPython: Some Python modules not found in tests at package build time

2014-04-28 Thread Andreas Tille
Hi, On Sat, Apr 26, 2014 at 09:12:45PM +0200, Jakub Wilk wrote: * Andreas Tille andr...@an3as.eu, 2014-04-25, 16:08: [Debian Python Modules Team python-modules-t...@lists.alioth.debian.org in CC since it maintains python-reportlab] ITYM s/maintains/is in Uploaders of/. It makes a big

Re: BioPython: Some Python modules not found in tests at package build time

2014-04-29 Thread Andreas Tille
Hi, On Mon, Apr 28, 2014 at 03:39:59PM +0200, Jakub Wilk wrote: ITYM s/maintains/is in Uploaders of/. It makes a big difference here... Does this mean that not any member of the team could upload a fixed package? I don't know that. What I know is that there were no commits to the

Re: Bug#747494: python3-biopython: Does not use C implementations of cpairwise2 functions

2014-05-09 Thread Andreas Tille
Hi Jamie, thanks for your bug report. I think this should work out of the box but I personally not comfortable with cpython to know how this could be fixed. I keep the Debian Python list in CC - perhaps they might have some helpful advise. It seems this module is not affected by the test suite

Re: Bug#747494: python3-biopython: Does not use C implementations of cpairwise2 functions

2014-05-10 Thread Andreas Tille
Hi Jamie, On Sat, May 10, 2014 at 09:22:29AM +1200, Jamie Norrish wrote: from .cpairwise2 import rint, _make_score_matrix_fast should do the trick. Indeed. This was actually reported and fixed a couple of months ago upstream[1]; I foolishly didn't check the closed bugs there

Re: Help with python-biom-format needed

2014-05-21 Thread Andreas Tille
On Wed, May 21, 2014 at 12:12:37PM +0200, Jakub Wilk wrote: * Andreas Tille andr...@an3as.eu, 2014-05-21, 09:52: svn://anonscm.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ (Unrelated to your question:) Since you are already repacking .orig.tar, please get rid

Re: Help with python-biom-format needed

2014-05-21 Thread Andreas Tille
Hi, sorry for the confusion. On Wed, May 21, 2014 at 01:02:23PM +0200, Jakub Wilk wrote: * Piotr Ożarowski pi...@debian.org, 2014-05-21, 11:14: svn://anonscm.debian.org/debian-med/trunk/packages/python-biom-format/trunk/ Unfortunately the new version has a problem when it comes to

Re: Help with python-biom-format needed

2014-05-21 Thread Andreas Tille
Hi Jakub, On Wed, May 21, 2014 at 03:38:36PM +0200, Jakub Wilk wrote: I strongly recommend rebuilding everything from source. With my latest commit I'm recreating the *.c files using cython. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to

Re: Help with python-biom-format needed

2014-05-21 Thread Andreas Tille
Hi, On Wed, May 21, 2014 at 03:33:22PM +0200, Jakub Wilk wrote: With the attached patch I got the package almost building. Almost, becasue the tests fail: Just to let you know: The package requires a new versioned Build-Depends pyqi (= 0.3.2) which I just uploaded. Thanks for your help

Re: Bug#753590: ITP: python-pyqtgraph -- Scientific Graphics and GUI Library for Python

2014-07-05 Thread Andreas Tille
Hi Gianfranco, On Sat, Jul 05, 2014 at 10:41:09AM +0100, Gianfranco Costamagna wrote: Hi Andreas, thanks for doing this! I propose also to change the maintainer if you think is better, don't know ;) IMHO the maintainer should be a team (either Debian Science or Debian Python) and it seems

Failed to switch to pybuild for dicompyler

2014-08-25 Thread Andreas Tille
Hi, I tried to use dicompyler and followed the hint I had received in a similar case[1] and used: DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') export PYBUILD_INSTALL_ARGS=--install-lib=/usr/share/$(DEBPKGNAME) --install-scripts=/usr/share/$(DEBPKGNAME)

Help with old mathplotlib API (nxutils) needed

2014-09-10 Thread Andreas Tille
Hi, I'm trying to upgrade dicompyler[1] but I seem to have some final problem: $ dicompyler Traceback (most recent call last): File /usr/share/dicompyler/dicompyler_app.py, line 10, in module import dicompyler.main File /usr/share/dicompyler/__init__.py, line 10, in module from main

Re: Python applications: private dirs and PYTHONPATH issue

2014-09-10 Thread Andreas Tille
Hi Piotr, On Wed, Sep 10, 2014 at 04:03:40PM +0200, Piotr Ożarowski wrote: if you install your script to the same directory as the application¹ then all you need is `dh_link /usr/bin/foo /usr/share/pkgname/foo` in debian/rules or adequate line in debian/pkgname.links file. No need to write

Re: Python applications: private dirs and PYTHONPATH issue

2014-09-11 Thread Andreas Tille
Hi Piotr, On Wed, Sep 10, 2014 at 07:09:37PM +0200, Piotr Ożarowski wrote: [Andreas Tille, 2014-09-10] Copying dicompyler.egg-info to /tmp/buildd/dicompyler-0.4.2/debian/dicompyler/usr/share/dicompyler/dicompyler-0.4.2.egg-info running install_scripts Installing dicompyler script

Re: Python applications: private dirs and PYTHONPATH issue

2014-09-11 Thread Andreas Tille
Hi, On Thu, Sep 11, 2014 at 10:30:42AM +0200, Piotr Ożarowski wrote: [Andreas Tille, 2014-09-11] pkg_resources.DistributionNotFound: pil=1.1.7 python{,3}-pil provides Pillow egg-info Matthias: should python-imaging provide pil.egg.info file (for older libraries/applications like

Re: Help to run test suite for python-pysam needed (does not find libhts)

2014-09-25 Thread Andreas Tille
Hi, in Git[1] I tried to implement the additional hint from upstream https://github.com/pysam-developers/pysam/issues/34 but this does not change anything. :-( Any further help would be welcome Andreas. On Thu, Sep 25, 2014 at 02:48:25PM +0200, Andreas Tille wrote: Hi, I tried

Re: [Debian-med-packaging] Help to run test suite for python-pysam needed (does not find libhts)

2014-09-25 Thread Andreas Tille
Ups, sorry, done. Andreas. On Thu, Sep 25, 2014 at 03:32:49PM +0200, Gert Wollny wrote: Hi Andreas, I tried to have a look, but ... On Thu, 2014-09-25 at 14:48 +0200, Andreas Tille wrote: [1] git://git.debian.org/git/debian-med/python-pysam.git Could you git push --all --tags

Re: [Debian-med-packaging] Help to run test suite for python-pysam needed (does not find libhts)

2014-09-25 Thread Andreas Tille
]http://web.archiveorange.com/archive/v/WK9riEUrSSGTqb90VM4v On Thu, 2014-09-25 at 16:22 +0200, Andreas Tille wrote: Ups, sorry, done. Andreas. On Thu, Sep 25, 2014 at 03:32:49PM +0200, Gert Wollny wrote: Hi Andreas, I tried to have a look, but ... On Thu, 2014

How to use Debian packaged lapack in python-miso

2015-02-16 Thread Andreas Tille
Hi, I intent to package python MISO on behalf of the Debian Med team. The packaging code is in SVN at Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-miso/trunk/ It builds and runs the test suite but I'd like to drop the lapack code copy. I have not found any chance to

Re: How to use Debian packaged lapack in python-miso

2015-02-17 Thread Andreas Tille
investigations (svn up) to drop at least f2c and has added a remark about lapack in d/README.source. Some dynamic linking of f2c would help enhancing the package as well. Kind regards Andreas. 2015-02-16 13:59 GMT+00:00 Andreas Tille andr...@an3as.eu: Hi, I intent to package python MISO

Need help python module testing at package build time: python-matplotlib-venn

2015-05-05 Thread Andreas Tille
Hi, I'd like to package python-matplotlib-venn since a Debian Med package depends from this module. I injected the packaging to svn://anonscm.debian.org/debian-med/trunk/packages/python-mathplotlib-venn/trunk/ Unfortunately I'm running into:

Help needed for broken clean target of python module

2015-06-22 Thread Andreas Tille
Hi, I have commited some initial packaging attempt for python-dendropy Vcs-Git: git://anonscm.debian.org/debian-med/python-dendropy.git but the clean target fails and I have no idea why: ... dh_auto_clean -O--buildsystem=pybuild I: pybuild base:170: python2.7 setup.py clean Traceback

Help needed for python-skbio

2015-07-29 Thread Andreas Tille
Hi, I intend to package python-skbio as a predependency of a Debian Med package upgrade. I have prepared the packaging in SVN[1] but it does not build but fails with a strange error, that I have never seen in Python modules: ... Copying scikit_bio.egg-info to

Re: Some remaining test failures (Was: Please help clarifying licensed)

2015-07-29 Thread Andreas Tille
. In principle, I might be able forcibly ignore the error by opening the file stream with: stream = open(path, errors=ignore) but without being able to rproduce the problem on my end, cannot test the solution. -- jeet On 7/29/15 7:27 AM, Andreas Tille wrote: Hi Jeet, On Wed

Strange *.so names in pbuild do require tricks for test suite (Was: Trying to run build time tests using nosetest for python-pysam)

2015-07-21 Thread Andreas Tille
Hi Bas, On Mon, Jul 20, 2015 at 11:06:22AM +0200, sebastic wrote: On 2015-07-20 10:54, Andreas Tille wrote: unfortunately I did not got any response from Debian Python team and I'm simply lost how to run the tests. Maybe change the dh_auto_test override to something like

Re: Strange *.so names in pbuild do require tricks for test suite (Was: Trying to run build time tests using nosetest for python-pysam)

2015-07-21 Thread Andreas Tille
Hi Piotr, thanks for your quick help! On Tue, Jul 21, 2015 at 05:29:18PM +0200, Piotr Ożarowski wrote: [Piotr Ożarowski, 2015-07-21] export PYBUILD_TEST_NOSE=1 if tests are not installed, add also: export PYBUILD_TEST_ARGS={dir}/tests While it looks a lot more elegant if I do

Trying to run build time tests using nosetest for python-pysam

2015-07-15 Thread Andreas Tille
Hi, I tried to add build-time tests for python-pysam[1]. I admit I'm a bit confused about the fact that this involves compiler calls like: ... warning: no files found matching 'tests/tabix_data' writing manifest file 'pysam.egg-info/SOURCES.txt' skipping 'pysam/csamtools.c' Cython extension

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