In [62]: c = np.ma.MaskedArray([3.4, 4.1, 6.3], mask=[False, True, False])

In [63]: np.testing.assert_array_almost_equal(c[:2], [3.4, np.nan])

In [64]: np.testing.assert_array_almost_equal(c, [3.4, np.nan, 6.3])
/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/core/arrayprint.py:686: UserWarning: Warning: converting a masked element to nan.
  s = self.format % x
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py in assert_array_compare(comparison, x, y, err_msg, verbose, header, precision, equal_nan, equal_inf)
    760 
--> 761         val = comparison(x, y)
    762 

/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py in compare(x, y)
    952         y = array(y, dtype=dtype, copy=False, subok=True)
--> 953         z = abs(x - y)
    954 

/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/ma/core.py in __sub__(self, other)
   4078             return NotImplemented
-> 4079         return subtract(self, other)
   4080 

/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/ma/core.py in __call__(self, a, b, *args, **kwargs)
   1045             np.seterr(divide='ignore', invalid='ignore')
-> 1046             result = self.f(da, db, *args, **kwargs)
   1047         # Get the mask for the result

ValueError: operands could not be broadcast together with shapes (3,) (2,) 

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-64-2c7b42e22a4d> in <module>()
----> 1 np.testing.assert_array_almost_equal(c, [3.4, np.nan, 6.3])

/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py in assert_array_almost_equal(x, y, decimal, err_msg, verbose)
    960     assert_array_compare(compare, x, y, err_msg=err_msg, verbose=verbose,
    961              header=('Arrays are not almost equal to %d decimals' % decimal),
--> 962              precision=decimal)
    963 
    964 

/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py in assert_array_compare(comparison, x, y, err_msg, verbose, header, precision, equal_nan, equal_inf)
    784         msg = build_err_msg([x, y], err_msg, verbose=verbose, header=header,
    785                             names=('x', 'y'), precision=precision)
--> 786         raise ValueError(msg)
    787 
    788 

ValueError: 
error during assertion:

Traceback (most recent call last):
  File "/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py", line 761, in assert_array_compare
    val = comparison(x, y)
  File "/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/testing/utils.py", line 953, in compare
    z = abs(x - y)
  File "/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/ma/core.py", line 4079, in __sub__
    return subtract(self, other)
  File "/export/tom/anaconda/envs/astropy/lib/python3.6/site-packages/numpy/ma/core.py", line 1046, in __call__
    result = self.f(da, db, *args, **kwargs)
ValueError: operands could not be broadcast together with shapes (3,) (2,) 


Arrays are not almost equal to 6 decimals
 x: MaskedArray([ 3.4,  nan,  6.3])
 y: array([ 3.4,  6.3])