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