From d33d50e1a43c883e7b39a062290a715d02b50612 Mon Sep 17 00:00:00 2001
From: TimWeaving <weaving.timothy@gmail.com>
Date: Tue, 8 Oct 2024 17:36:09 +0100
Subject: [PATCH] Removed py3dmol as a dependency

---
 poetry.lock                | 16 +---------------
 pyproject.toml             |  1 -
 symmer/utils.py            | 34 ----------------------------------
 tests/test_symmer_utils.py | 13 +------------
 4 files changed, 2 insertions(+), 62 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 74091227..bf3ad990 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2558,20 +2558,6 @@ files = [
 [package.extras]
 tests = ["pytest"]
 
-[[package]]
-name = "py3dmol"
-version = "2.4.0"
-description = "An IPython interface for embedding 3Dmol.js views in Jupyter notebooks"
-optional = false
-python-versions = "*"
-files = [
-    {file = "py3Dmol-2.4.0-py2.py3-none-any.whl", hash = "sha256:e7d27ffdf9326850e4c6dac55ec047ce023ffaf87d8032278982a4d3d78d3973"},
-    {file = "py3Dmol-2.4.0.tar.gz", hash = "sha256:5cbeb125771abdedf051845bbb8df30306338a92a1852c9934c3ec85ba482a78"},
-]
-
-[package.extras]
-ipython = ["IPython"]
-
 [[package]]
 name = "pycodestyle"
 version = "2.8.0"
@@ -3790,4 +3776,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.8"
-content-hash = "17a853a1287459499c42a8559227f2b5d1ef4ddedd10f531f02ffce9baa9ebb5"
+content-hash = "0ebae7433e51c9b3d5a63553a4d6ab65144b44e911cd041d345d4b49e563cdc3"
diff --git a/pyproject.toml b/pyproject.toml
index 3a246ffb..87b55f8d 100644
--- a/pyproject.toml
+++ b/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"
 
diff --git a/symmer/utils.py b/symmer/utils.py
index a961f971..c61c2b49 100644
--- a/symmer/utils.py
+++ b/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
diff --git a/tests/test_symmer_utils.py b/tests/test_symmer_utils.py
index 52601126..e714dc45 100644
--- a/tests/test_symmer_utils.py
+++ b/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