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

2014-03-31 Thread Tim Booth
Hi Andreas,

It works for me!  Could you share your failed build log, please?

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

Could it be due to my version of Python?  I'm on 2.7.3.  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.

Cheers,

TIM

On Sat, 2014-03-29 at 20:20 +, Andreas Tille wrote:
 Hi Tim,
 
 On Thu, Mar 27, 2014 at 03:46:01PM +0100, Andreas Tille wrote:
   My guess is that updating PyQi might help
   (https://pypi.python.org/pypi/pyqi/).  Did you already do that?
  
  No, I did not.  I just realised that this also has moved.  To bad if
  projects are moving and our watch files are pointing to the wrong
  location.  Since it might perfectly be the cause of the problem I could
  try to do this today evening / night if nobody will beat me.
 
 So pyqi is updated to the latest version in unstable and while biom
 was *running* with this latest version installed it does not *build*
 any more with this new version as (Build-)Depends.
 
 Any idea?
 
 Kind regards
 
Andreas. 
 

-- 
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


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

2014-03-31 Thread 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@l.d.o.

Kind regards

  Andreas.

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

2014-03-31 Thread Andreas Tille
Hi Tim,

On Mon, Mar 31, 2014 at 06:48:03PM +0100, Tim Booth wrote:
 ...
 Normally, 'export PYTHONPATH=.' is redundant but here it seems to be
 effective.

I can confirm this.  So I'll spend some cycles tomorrow to fix the
remaining lintian issues.  Thanks for your hint.

 No, just stick with what you have and use dh-linktree.  I'm so close to
 switching to the new 14.04 Ubuntu release that I might not even push
 this update for my 12.04 users unless someone specifically asks for it.
 I do appreciate the general importance of keeping our code in sync but
 in this case there's no point.

Many thanks for the clarification and thanks for checking the package

   Andreas. 

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

2014-03-29 Thread Andreas Tille
Hi Tim,

On Thu, Mar 27, 2014 at 03:46:01PM +0100, Andreas Tille wrote:
  My guess is that updating PyQi might help
  (https://pypi.python.org/pypi/pyqi/).  Did you already do that?
 
 No, I did not.  I just realised that this also has moved.  To bad if
 projects are moving and our watch files are pointing to the wrong
 location.  Since it might perfectly be the cause of the problem I could
 try to do this today evening / night if nobody will beat me.

So pyqi is updated to the latest version in unstable and while biom
was *running* with this latest version installed it does not *build*
any more with this new version as (Build-)Depends.

Any idea?

Kind regards

   Andreas. 

-- 
http://fam-tille.de


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

2014-03-27 Thread Andreas Tille
Hi,

On Wed, Mar 26, 2014 at 10:54:11AM -0400, Yaroslav Halchenko wrote:
 ok -- done -- see patch attached

I just realised that Biom-format has moved to a different location and
thus we missed the new version.  When inspecting this I realised that it
is not using Cython any more - so the problem will be fixed with the new
version automatically (Yaroslav, sorry for keeping you busy for no use
:-().

I have updated the packaging at

   svn://svn.debian.org/svn/debian-med/trunk/packages/python-biom-format/trunk/

and have the following questions (specifically also to Tim):

  1. Did you forwarded this patch to upstream?

 
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch?view=markup

 I think upstream would be interested in incorporating it.

  2. Tim, your latest changelog says: Rename add_metadata to something
 less generic.  It will die in the next release anyway.  Since the
 script did not died in 1.3.1 I wonder what next release you might
 mean.

  3. Will the packaging which I prepared in SVN work together with the
 latest qiime package?  This question is probably important before
 I'll upload it to unstable.

Kind regards

   Andreas.

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

2014-03-27 Thread Andreas Tille
Hi Tim,

On Thu, Mar 27, 2014 at 02:37:44PM +, Tim Booth wrote:
 Hi Andreas,
 
  I have updated the packaging at
  
 
  svn://svn.debian.org/svn/debian-med/trunk/packages/python-biom-format/trunk/
  
  and have the following questions (specifically also to Tim):
  
1. Did you forwarded this patch to upstream?
  
   
  http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch?view=markup
  
   I think upstream would be interested in incorporating it.
 
 No, I didn't send it.  Wasn't sure how they would take it.

Well, seems to be worth discussing.  I'll do since I also want to
approach them about unit tests (which vanished in the new version).

2. Tim, your latest changelog says: Rename add_metadata to something
   less generic.  It will die in the next release anyway.  Since the
   script did not died in 1.3.1 I wonder what next release you might
   mean.
 
 Don't take my word for it.  Run the script!
 
 ---
 $ add_biom_metadata
 
 This script no longer exists. ...
 ---
 
 If the script denies its own existence who are we to argue?

:-)
Seems we should not install this at all any more ...
 
3. Will the packaging which I prepared in SVN work together with the
   latest qiime package?  This question is probably important before
   I'll upload it to unstable.
 
 A quick build on my system failed.  Or rather it builds but when I run
 it:
 
 ---
 % biom   
 usage: biom command [args]
 
 The currently available commands are:
 
 The following commands could not be loaded:
add-metadataError: cannot import name
 make_command_in_collection_lookup_f
convert Error: cannot import name
 make_command_in_collection_lookup_f
show-install-info   Error: cannot import name
 make_command_out_collection_lookup_f
subset-tableError: cannot import name
 make_command_in_collection_lookup_f
summarize-table Error: cannot import name
 make_command_in_collection_lookup_f
validate-table  Error: cannot import name
 make_command_in_collection_lookup_f
 
 See 'biom help command' for more information on a specific command.
 ---
 
 My guess is that updating PyQi might help
 (https://pypi.python.org/pypi/pyqi/).  Did you already do that?

No, I did not.  I just realised that this also has moved.  To bad if
projects are moving and our watch files are pointing to the wrong
location.  Since it might perfectly be the cause of the problem I could
try to do this today evening / night if nobody will beat me.

This also scores one more point for the unit test which simply should
have made the build fail ...

 Also, can this now be arch=all or is there still something being
 compiled that I missed?

I think so.  I'm not done with the package anyway since it creates
a lintian error about google-spying in the docs.  Letting you have
a look in parallel has proven to be valuable. ;-)

Kind regards and thanks for testing

Andreas.

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

2014-03-27 Thread Tim Booth
Hi Andreas,

 I have updated the packaging at
 

 svn://svn.debian.org/svn/debian-med/trunk/packages/python-biom-format/trunk/
 
 and have the following questions (specifically also to Tim):
 
   1. Did you forwarded this patch to upstream?
 
  
 http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biom-format/trunk/debian/patches/smart_arse_fix.patch?view=markup
 
  I think upstream would be interested in incorporating it.

No, I didn't send it.  Wasn't sure how they would take it.

   2. Tim, your latest changelog says: Rename add_metadata to something
  less generic.  It will die in the next release anyway.  Since the
  script did not died in 1.3.1 I wonder what next release you might
  mean.

Don't take my word for it.  Run the script!

---
$ add_biom_metadata

This script no longer exists. ...
---

If the script denies its own existence who are we to argue?

   3. Will the packaging which I prepared in SVN work together with the
  latest qiime package?  This question is probably important before
  I'll upload it to unstable.

A quick build on my system failed.  Or rather it builds but when I run
it:

---
% biom   
usage: biom command [args]

The currently available commands are:

The following commands could not be loaded:
   add-metadataError: cannot import name
make_command_in_collection_lookup_f
   convert Error: cannot import name
make_command_in_collection_lookup_f
   show-install-info   Error: cannot import name
make_command_out_collection_lookup_f
   subset-tableError: cannot import name
make_command_in_collection_lookup_f
   summarize-table Error: cannot import name
make_command_in_collection_lookup_f
   validate-table  Error: cannot import name
make_command_in_collection_lookup_f

See 'biom help command' for more information on a specific command.
---

My guess is that updating PyQi might help
(https://pypi.python.org/pypi/pyqi/).  Did you already do that?

Also, can this now be arch=all or is there still something being
compiled that I missed?

Cheers,

TIM


-- 
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


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