The error is reproducible if the array is of dtype=object:

import numpy  as np

label0 = np.random.random((50, 3)).astype(object)
np.cov(label0, rowvar=False)

AttributeError: 'float' object has no attribute 'shape'

If possible you should convert it to a numeric type. For example:

np.cov(label0.astype(float), rowvar=False)  # works

Note: object arrays are rarely useful (they are slow and not all NumPy functions deal gracefully with these - like in this case), so it could make sense to check where it came from and also fix that.

np.cov with 2 1d arrays works:

In [202]: np.cov(np.arange(10),np.arange(10))
Out[202]: 
array([[9.16666667, 9.16666667],
       [9.16666667, 9.16666667]])

But if one of the arrays is object dtype, I get your error:

In [203]: np.cov(np.arange(10),np.arange(10).astype(object))
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-203-db3c70a7640d> in <module>()
----> 1 np.cov(np.arange(10),np.arange(10).astype(object))

/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py in cov(m, y, rowvar, bias, ddof, fweights, aweights)
   2300             w *= aweights
   2301 
-> 2302     avg, w_sum = average(X, axis=1, weights=w, returned=True)
   2303     w_sum = w_sum[0]
   2304 

/usr/local/lib/python3.6/dist-packages/numpy/lib/function_base.py in average(a, axis, weights, returned)
    389 
    390     if returned:
--> 391         if scl.shape != avg.shape:
    392             scl = np.broadcast_to(scl, avg.shape).copy()
    393         return avg, scl

AttributeError: 'float' object has no attribute 'shape'

Solution was linked on reshaped method on documentation page.

Insted of Y.reshape(-1,1) you need to use:

Y.values.reshape(-1,1)