Removed py3dmol as a dependency

pyproject.toml

@@ -23,7 +23,6 @@ ray = "2.10"
 sphinx-design = "^0.5.0"
 myst-nb = "^0.17.2"
 sphinx-copybutton = "^0.5.2"
-py3dmol = "^2.0.4"
 scipy = "1.9.3"
 urllib3 = "1.26.6"
 

symmer/utils.py

@@ -3,7 +3,6 @@
 import scipy as sp
 from typing import List, Tuple, Union
 from functools import reduce
-import py3Dmol
 from scipy.sparse import csr_matrix
 from scipy.sparse import kron as sparse_kron
 from symmer.operators.utils import _rref_binary
@@ -225,39 +224,6 @@ def gram_schmidt_from_quantum_state(state:Union[np.array, list, QuantumState]) -
 
     return M
 
-
-def Draw_molecule(
-        xyz_string: str, width: int = 400, height: int = 400, style: str = "sphere"
-    ) -> py3Dmol.view:
-    """Draw molecule from xyz string.
-
-    Note if molecule has unrealistic bonds, then style should be sphere. Otherwise stick style can be used
-    which shows bonds.
-
-    TODO: more styles at http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html
-
-    Args:
-        xyz_string (str): xyz string of molecule
-        width (int): width of image
-        height (int): Height of image
-        style (str): py3Dmol style ('sphere' or 'stick')
-
-    Returns:
-        view (py3dmol.view object). Run view.show() method to print molecule.
-    """
-    view = py3Dmol.view(width=width, height=height)
-    view.addModel(xyz_string, "xyz")
-    if style == "sphere":
-        view.setStyle({'sphere': {"radius": 0.2}})
-    elif style == "stick":
-        view.setStyle({'stick': {}})
-    else:
-        raise ValueError(f"unknown py3dmol style: {style}")
-
-    view.zoomTo()
-    return view
-
-
 def get_sparse_matrix_large_pauliwordop(P_op: PauliwordOp) -> csr_matrix:
     """
     In order to build the sparse matrix (e.g. above 18 qubits), this function goes through each pauli term

tests/test_symmer_utils.py

@@ -1,10 +1,9 @@
 from symmer.operators import PauliwordOp, QuantumState
-from symmer.utils import (exact_gs_energy, random_anitcomm_2n_1_PauliwordOp,Draw_molecule,
+from symmer.utils import (exact_gs_energy, random_anitcomm_2n_1_PauliwordOp,
                           tensor_list, gram_schmidt_from_quantum_state, product_list,
                           get_sparse_matrix_large_pauliwordop, matrix_allclose)
 import numpy as np
 from openfermion import QubitOperator
-import py3Dmol
 
 H2_sto3g = {'qubit_encoding': 'jordan_wigner',
  'unit': 'angstrom',
@@ -446,16 +445,6 @@ def test_gram_schmidt_from_quantum_state_numpy_array():
     assert np.allclose(U_gram[:, 0], psi_norm), 'first column of U_gram not correct'
     assert np.allclose(U_gram @ U_gram.conj().T, np.eye(2 ** nq)), 'U_gram not unitary'
 
-
-def test_Draw_molecule():
-
-    xyz = H2_sto3g['geometry']
-    viewer_sphere = Draw_molecule(xyz, width=400, height=400, style='sphere')
-    assert isinstance(viewer_sphere, py3Dmol.view)
-
-    viewer_stick = Draw_molecule(xyz, width=400, height=400, style='stick')
-    assert isinstance(viewer_stick, py3Dmol.view)
-
 def test_get_sparse_matrix_large_pauliwordop():
     for nq in range(2,6):
         n_terms = 10*nq