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test_serialize_hdf5_masked failed for 3.1rc1 · Issue #8134 · astropy/astropy · GitHub

test_serialize_hdf5_masked failed for 3.1rc1 #8134

Description

I just tested astropy 3.1rc1 into a python 3.7.1 environment with numpy=1.15.4 and h5py=2.8.0.

1 failed, 11370 passed, 264 skipped, 67 xfailed, 3106 warnings, 2 error in 245.20 seconds

I show the output from the one failure below, but I posted the full testing log at this gist.

========================================================== FAILURES ==========================================================
_________________________________________________ test_serialize_hdf5_masked _________________________________________________

tbl = <Table length=3>
       col0
      object
------------------
0.9999999999969589
                --
 3.000000000000469

    def _encode_mixins(tbl):
        """Encode a Table ``tbl`` that may have mixin columns to a Table with only
        astropy Columns + appropriate meta-data to allow subsequent decoding.
        """
        from ...table import serialize
        from ...table.table import has_info_class
        from ... import units as u
        from ...utils.data_info import MixinInfo, serialize_context_as

        # If PyYAML is not available then check to see if there are any mixin cols
        # that *require* YAML serialization.  HDF5 already has support for
        # Quantity, so if those are the only mixins the proceed without doing the
        # YAML bit, for backward compatibility (i.e. not requiring YAML to write
        # Quantity).
        try:
>           import yaml
E           ModuleNotFoundError: No module named 'yaml'

/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/io/misc/hdf5.py:206: ModuleNotFoundError

During handling of the above exception, another exception occurred:

tmpdir = local('/private/var/folders/xj/6rkkv6w11vxg2ryy8whq850c0000gn/T/pytest-of-aphearin/pytest-0/test_serialize_hdf5_masked0')

    @pytest.mark.skipif('not HAS_H5PY')
    def test_serialize_hdf5_masked(tmpdir):
        tm = Time([1, 2, 3], format='cxcsec')
        tm[1] = np.ma.masked

        fn = str(tmpdir.join('tempfile.hdf5'))
        t = Table([tm])
>       t.write(fn, path='root', serialize_meta=True)

/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/time/tests/test_mask.py:178:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/table/table.py:2592: in write
    io_registry.write(self, *args, **kwargs)
/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/io/registry.py:560: in write
    writer(data, *args, **kwargs)
/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/io/misc/hdf5.py:298: in write_table_hdf5
    compatibility_mode=compatibility_mode)
/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/io/misc/hdf5.py:316: in write_table_hdf5
    table = _encode_mixins(table)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

tbl = <Table length=3>
       col0
      object
------------------
0.9999999999969589
                --
 3.000000000000469

    def _encode_mixins(tbl):
        """Encode a Table ``tbl`` that may have mixin columns to a Table with only
        astropy Columns + appropriate meta-data to allow subsequent decoding.
        """
        from ...table import serialize
        from ...table.table import has_info_class
        from ... import units as u
        from ...utils.data_info import MixinInfo, serialize_context_as

        # If PyYAML is not available then check to see if there are any mixin cols
        # that *require* YAML serialization.  HDF5 already has support for
        # Quantity, so if those are the only mixins the proceed without doing the
        # YAML bit, for backward compatibility (i.e. not requiring YAML to write
        # Quantity).
        try:
            import yaml
        except ImportError:
            for col in tbl.itercols():
                if (has_info_class(col, MixinInfo) and
                        col.__class__ is not u.Quantity):
                    raise TypeError("cannot write type {} column '{}' "
                                    "to HDF5 without PyYAML installed."
>                                   .format(col.__class__.__name__, col.info.name))
E                   TypeError: cannot write type Time column 'col0' to HDF5 without PyYAML installed.

/anaconda3/envs/astropy_testing/lib/python3.7/site-packages/astropy/io/misc/hdf5.py:213: TypeError

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