Re: Any volunteer to check two (hdf5 relatet?) issues with python-biom-format
Hi,
Am Tue, Oct 19, 2021 at 08:24:59PM +0530 schrieb Nilesh Patra:
> > 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.
Thanks to you both.
> > ...
> > > 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?
Its worth trying IMHO. Would you volunteer to do so?
Kind regards
Andreas.
--
http://fam-tille.de
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