Add option to suppress openmmtools and pymbar warnings

[cwalker7]

We get this warning numerous times throughout the replica exchange simulations and analysis:

Warning: The openmmtools.multistate API is experimental and may change in future releases

There are also these pymbar warnings totaling about ~3500 instances during test_native_contacts.py:

 cg_openmm/tests/test_native_contacts.py: 13 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/pymbar/mbar.py:725: RuntimeWarning: divide by zero encountered in log
    Log_W_nk[:, sa] = np.log(A_n[i, :]) + Log_W_nk[:, l]

cg_openmm/tests/test_native_contacts.py: 255 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/pymbar/mbar.py:1717: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    Ndiag = np.matrix(np.diag(N_k), dtype=np.float64)

cg_openmm/tests/test_native_contacts.py: 255 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/pymbar/mbar.py:1718: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    W = np.matrix(W, dtype=np.float64)

cg_openmm/tests/test_native_contacts.py: 2550 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/numpy/matrixlib/defmatrix.py:71: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    return matrix(data, dtype=dtype, copy=False)

cg_openmm/tests/test_native_contacts.py: 255 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/pymbar/mbar.py:1728: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    Sigma = np.matrix(np.diag(np.sqrt(S2)))

cg_openmm/tests/test_native_contacts.py: 255 tests with warnings
  /home/cwalker7/anaconda3/envs/cg_openmm_py37/lib/python3.7/site-packages/pymbar/mbar.py:1729: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
    V = np.matrix(V)