Re: Any volunteer to check two (hdf5 relatet?) issues with python-biom-format

[olivier sallou <olivier.sallou@irisa.fr>]

On Mon, 2021-10-18 at 12:30 +0200, Andreas Tille wrote:
> Hi,
> 
> I wanted to update python-biom-format, but the build time test ends
> up in
> 
> 
> FAILED
> biom/tests/test_table.py::TableTests::test_from_hdf5_custom_parsers -

can be fixed with:

            self.assertIn(m['BODY_SITE'], ('GUT', 'SKIN'))
=>
            self.assertIn(m['BODY_SITE'], (b'GUT', b'SKIN'))

> ...
> FAILED
> biom/tests/test_table.py::TableTests::test_to_hdf5_missing_metadata_s
> ample
this second test issue seems to be linked with hdf5 library.
Seems it does not accept NULL values:

	"E   ValueError: VLEN strings do not support embedded NULLs"

while test tries to set some null values and see if converted to empty
strings.

I am not hdf5 user so cannot really test,  but if h5py dep does not
accept null.... maybe we should just skip the test.

Olivier
> 
> 
> Any help would be welcome
> 
>        Andreas.
> 
> 

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438