[Debian-med-packaging] Bug#742691: New version of python-biom-format (Was: Bug#742691: please make robust against ad-hoc (pre/post released) versions of cython)

[Andreas Tille]

Hi Tim,

On Mon, Mar 31, 2014 at 03:14:58PM +0100, Tim Booth wrote:
> It works for me!  Could you share your failed build log, please?

The cruxial part is

$ pyqi make-bash-completion --command-config-module biom.interfaces.optparse.config --driver-name biom -o debian/bash-completion
Traceback (most recent call last):
  File "/usr/bin/pyqi", line 177, in <module>
    optparse_main(cmd_obj, argv[1:])
  File "/usr/lib/python2.7/dist-packages/pyqi/core/interfaces/optparse/__init__.py", line 276, in optparse_main
    result = optparse_cmd(local_argv[1:])
  File "/usr/lib/python2.7/dist-packages/pyqi/core/interface.py", line 40, in __call__
    cmd_result = self.CmdInstance(**cmd_input)
  File "/usr/lib/python2.7/dist-packages/pyqi/core/command.py", line 137, in __call__
    result = self.run(**kwargs)
  File "/usr/lib/python2.7/dist-packages/pyqi/commands/make_bash_completion.py", line 79, in run
    cfg_mod = _get_cfg_module(cfg_mod_path)
  File "/usr/lib/python2.7/dist-packages/pyqi/commands/make_bash_completion.py", line 23, in _get_cfg_module
    mod = importlib.import_module(desc)
  File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named biom.interfaces.optparse.config


which works with pyqi 0.2.0 but not with pyqi 0.3.1.

I have

$ python --version
Python 2.7.6


> I built PyQi from your latest SVN and then built the latest biom-format
> against it.  What's more, I had the build log from building against PyQi
> 0.2.0 and I diffed it with the new build log.  They were essentially
> identical.
> 
> The only things I changed in the PyQi build -
> 1) I used the pristine tarball rather that repacking it to a -dfsg.

This should not be the problem - I just excluded binary chunks from
sphinx doc builds.

> 2) I disabled dh-linktree as I don't have it on Ubuntu 12.04.

If this might be a problem for your purpose I'm fine with a patch which
does not rely in dh-linktree.  I think you have worked around the JS links
issue in dh_installdocs of python-biom-format.  I think the most elegant
way to cope with this for the moment would be to comment "--with linktree"
in d/rules and use the d/linktrees as "data" to set the links manually
in override_dh_installdocs (similarly as you did in python-biom-format).
If this plan might sound to vague I'm fine with implementing this to
make sure we are working on the same code in Debian and BioLinux and can
easily switch to the more elegant linktrees later.
 
> Could it be due to my version of Python?  I'm on 2.7.3.

This might be possible (see above).

> I'm due to
> start building stuff for Ubuntu 14.04 this week, so at that point I'll
> be on a system much closer to what you have with Debian Unstable.  Right
> now I'm at the point of maximum divergence.

Can you perhaps test the pyqi call to create a bash-completion file on
14.04.  Than we can be quite sure that the Python version has probably
some influence.  Otherwise I'd go on asking on debian-python at l.d.o.

Kind regards

          Andreas.

-- 
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