np.isclose(a, b, rtol=10**-5, atol=10**-8)
checks:
np.abs(a - b) <= (atol + rtol * np.abs(b))
This means that for your values ~1000 and the defaults it will return True
if the differences are
<= (10**-8 + 10**-5 * np.abs(1000))
<= 0.01000001
So your values are within that distance, thus it evaluates to True.
If your requirement is
I need to compare these values up to 3 decimal places only.
Then you don't want a relative tolerance, and instead you want only to specify an absolute tolerance.
np.isclose([1000.01, 1000.0013, 1000.0047, 1000.0041, 1000.0045],
[1000.02, 1000.0014, 1000.0052, 1000.0052, 1000.005500001],
rtol=0, atol=10**-3)
#array([False, True, True, False, False])