[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 Thu, Mar 27, 2014 at 02:37:44PM +0000, 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-metadata        Error: 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-table        Error: 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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