On Tue, 19 Oct, 2021, 8:15 pm olivier sallou, <[email protected]>
wrote:
> 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'))
>
or..... a ".decode()" with m['BODY_SITE']
:)
I had made this change locally a few hours ago.
> ...
> > 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 wonder if it's a problem with the the version of h5py in the archive?
Because these seem to run fine upstream.
Might be worth raising this problem upstream?
Nilesh
>
