[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)

[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-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?

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

Cheers,

TIM


-- 
Tim Booth <tbooth at 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