Fix a number of CodeQL code-scanning alerts

setup.py

@@ -11,26 +11,28 @@
 #   limitations under the License.
 
 import os
+import runpy
 
 from setuptools import find_packages, setup
 
 # This reads the __version__ variable from openfermion/_version.py
-__version__ = ''
-exec(open('src/openfermion/_version.py').read())
+__version__ = runpy.run_path('src/openfermion/_version.py')['__version__']
+assert __version__, 'Version string cannot be empty'
 
-# Readme file as long_description:
+# The readme file is used as the long_description:
 long_description = '===========\n' + 'OpenFermion\n' + '===========\n\n'
 with open('README.rst', 'r', encoding='utf-8') as readme:
     long_description += readme.read()
 
-# Read in package requirements.txt
-requirements = open('dev_tools/requirements/deps/runtime.txt').readlines()
+# Read in package requirements.txt.
+with open('dev_tools/requirements/deps/runtime.txt') as r:
+    requirements = r.readlines()
 requirements = [r.strip() for r in requirements]
 requirements = [r for r in requirements if not r.startswith('#')]
-# Resource estimates requirements.
-resource_requirements = open(
-    'dev_tools/requirements/deps/resource_estimates_runtime.txt'
-).readlines()
+
+# Read in resource estimates requirements.
+with open('dev_tools/requirements/deps/resource_estimates_runtime.txt') as r:
+    resource_requirements = r.readlines()
 resource_requirements = [r.strip() for r in resource_requirements]
 resource_requirements = [r for r in resource_requirements if not r.startswith('#')]
 

src/openfermion/chem/molecular_data.py

@@ -841,6 +841,7 @@ def save(self):
         try:
             os.remove("{}.hdf5".format(self.filename))
         except OSError:
+            # Nothing to do but carry on.
             pass
 
         shutil.move("{}.hdf5".format(tmp_name), "{}.hdf5".format(self.filename))

src/openfermion/chem/molecular_data_test.py

@@ -81,9 +81,7 @@ def test_name_molecule(self):
 
         # Check errors in naming
         with self.assertRaises(TypeError):
-            test_molecule = MolecularData(
-                self.geometry, self.basis, self.multiplicity, description=5
-            )
+            MolecularData(self.geometry, self.basis, self.multiplicity, description=5)
         correct_name = str('H2_sto-3g_singlet')
         test_molecule = self.molecule = MolecularData(
             self.geometry, self.basis, self.multiplicity, data_directory=DATA_DIRECTORY
@@ -222,11 +220,9 @@ def test_active_space(self):
         """Test simple active space truncation features"""
 
         # Start w/ no truncation
-        (
-            core_const,
-            one_body_integrals,
-            two_body_integrals,
-        ) = self.molecule.get_active_space_integrals(active_indices=[0, 1])
+        (core_const, one_body_integrals, two_body_integrals) = (
+            self.molecule.get_active_space_integrals(active_indices=[0, 1])
+        )
 
         self.assertAlmostEqual(core_const, 0.0)
         self.assertAlmostEqual(

src/openfermion/circuits/gates/four_qubit_gates.py

@@ -13,6 +13,7 @@
 
 from typing import Optional, Union
 
+import warnings
 import numpy as np
 import sympy
 
@@ -120,8 +121,10 @@ def _circuit_diagram_info_(self, args: cirq.CircuitDiagramInfoArgs) -> cirq.Circ
         if args.use_unicode_characters:
             wire_symbols = ('⇅', '⇅', '⇵', '⇵')
         else:
-            # pylint: disable=anomalous-backslash-in-string
-            wire_symbols = (r'/\ \/', r'/\ \/', '\/ /\\', '\/ /\\')
+            up_down = r'/\ \/'
+            # Split up this string to avoid SyntaxError in Python 3.12.
+            down_up = r'\/ /' + '\\'
+            wire_symbols = (up_down, up_down, down_up, down_up)
         return cirq.CircuitDiagramInfo(
             wire_symbols=wire_symbols, exponent=self._diagram_exponent(args)
         )

src/openfermion/circuits/primitives/optimal_givens_decomposition_test.py

@@ -106,7 +106,6 @@ def test_col_eliminate():
     # mixing U[1, 0] and U[0, 0]
     unitary_original = unitary.copy()
     gmat = givens_matrix_elements(unitary[0, 0], unitary[1, 0], which='right')
-    vec = numpy.array([[unitary[0, 0]], [unitary[1, 0]]])
     fullgmat = create_givens(gmat, 0, 1, 3)
     zeroed_unitary = fullgmat.dot(unitary)
 

src/openfermion/linalg/erpa.py

@@ -1,4 +1,5 @@
 """Code to generate the eigenvalue problem for the ERPA equations"""
+
 from typing import Dict, Tuple, Union
 from itertools import product
 import numpy
@@ -11,7 +12,7 @@
 def erpa_eom_hamiltonian(
     h_ijkl: numpy.ndarray, tpdm: numpy.ndarray, p: int, q: int, r: int, s: int
 ) -> Union[float, complex]:
-    """
+    r"""
     Evaluate $\sum_{a,b,c,d}h_{a, b, d, c}<\psi[p^ q, [a^ b^ c d, r^ s]]\psi>$
 
     Args:

src/openfermion/linalg/sparse_tools.py

@@ -1162,6 +1162,8 @@ def single_quad_op_sparse(n_modes, mode, quadrature, hbar, trunc):
         op = numpy.sqrt(hbar / 2) * (b + b.conj().T)
     elif quadrature == 'p':
         op = -1j * numpy.sqrt(hbar / 2) * (b - b.conj().T)
+    else:
+        raise ValueError(f'Invalid value {quadrature} for quadrature parameter.')
 
     Id = [scipy.sparse.identity(trunc, dtype=complex, format='csc')]
     operator_list = Id * mode + [op] + Id * (n_modes - mode - 1)

src/openfermion/linalg/wave_fitting.py

@@ -40,7 +40,7 @@ def fit_known_frequencies(
 
 
 def prony(signal: numpy.ndarray) -> Tuple[numpy.ndarray, numpy.ndarray]:
-    """Estimates amplitudes and phases of a sparse signal using Prony's method.
+    r"""Estimates amplitudes and phases of a sparse signal using Prony's method.
 
     Single-ancilla quantum phase estimation returns a signal
     $g(k)=\sum (aj*exp(i*k*phij))$, where aj and phij are the amplitudes

src/openfermion/linalg/wedge_product.py

@@ -67,7 +67,7 @@ def generate_parity_permutations(seq):
 
 
 def wedge(left_tensor, right_tensor, left_index_ranks, right_index_ranks):
-    """
+    r"""
     Implement the wedge product between left_tensor and right_tensor
 
     The wedge product is defined as

src/openfermion/resource_estimates/molecule/pyscf_utils.py

@@ -1,5 +1,5 @@
 # coverage:ignore
-""" Drivers for various PySCF electronic structure routines """
+"""Drivers for various PySCF electronic structure routines"""
 from typing import Tuple, Optional
 import sys
 import h5py
@@ -82,6 +82,9 @@ def localize(pyscf_mf, loc_type='pm', verbose=0):
         loc_virt_mo = lo.ER(pyscf_mf.mol, pyscf_mf.mo_coeff[:, virt_idx]).kernel(verbose=verbose)
         print("DONE")
 
+    else:
+        raise ValueError(f'Invalid value {loc_type} for localization type parameter.')
+
     # overwrite orbitals with localized orbitals
     pyscf_mf.mo_coeff[:, docc_idx] = loc_docc_mo.copy()
     pyscf_mf.mo_coeff[:, socc_idx] = loc_socc_mo.copy()

src/openfermion/resource_estimates/pbc/thc/factorizations/thc_jax.py

@@ -943,6 +943,7 @@ def kpoint_thc_via_isdf(
     if verbose:
         print("Time for BFGS {:.4f}".format(time.time() - start))
     start = time.time()
+    opt_params = ()
     if perform_adagrad_opt:
         if save_checkpoints:
             chkfile_name = f"{checkpoint_basename}_adagrad.h5"

src/openfermion/resource_estimates/thc/spacetime.py

@@ -28,9 +28,6 @@ def qubit_vs_toffoli(lam, dE, eps, n, chi, beta, M, algorithm='half', verbose=Fa
         verbose (bool) - do additional printing of intermediates?
 
     """
-    # only valid algorithms accepted
-    assert algorithm in ['half', 'full']
-
     # The number of iterations for the phase estimation.
     iters = np.ceil(pi * lam / (dE * 2))
     # The number of bits used for each register.
@@ -487,8 +484,12 @@ def qubit_vs_toffoli(lam, dE, eps, n, chi, beta, M, algorithm='half', verbose=Fa
 
         colors = [color_dict[i] for i in labels]
 
+    else:
+        raise ValueError(f'Invalid value {algorithm} for algorithm parameter.')
+
     # check lists are at least consistent
-    assert all(len(element) == len(tgates) for element in [qubits, labels, colors])
+    if not all(len(element) == len(tgates) for element in [qubits, labels, colors]):
+        raise RuntimeError('Failed to get a consistent result.')
 
     return tgates, qubits, labels, colors
 
@@ -579,10 +580,11 @@ def group_steps(labels, tgates, qubits):
         grouped_labels = ['R', 'QROM', 'I-QROM', 'QROM', 'R']
         grouped_tgates = [ 13,     30,       14,     40,  20]  (sum)
         grouped_qubits = [ 10,     30,        4,     70,  60]  (mean)
-
     """
-    assert len(labels) == len(tgates)
-    assert len(labels) == len(qubits)
+    if len(labels) != len(tgates):
+        raise ValueError('Number of labels must equal number of Toffoli gates.')
+    if len(labels) != len(qubits):
+        raise ValueError('Number of labels must equal number of qubits.')
 
     # Key function -- group identical nearest neighbors in labels (x[0])
     key_func = lambda x: x[0]
@@ -604,5 +606,6 @@ def group_steps(labels, tgates, qubits):
         grouped_qubits.append(np.mean([i[1] for i in group]))
 
     # sanity check -- shouldn't be losing total value in toffoli
-    assert np.sum(tgates) == np.sum(grouped_tgates)
+    if np.sum(tgates) != np.sum(grouped_tgates):
+        raise RuntimeError('Sum of Toffoli gates does not equal sum of grouped gates.')
     return grouped_labels, grouped_tgates, grouped_qubits

src/openfermion/transforms/opconversions/jordan_wigner.py

@@ -294,6 +294,8 @@ def jordan_wigner_two_body(p, q, r, s, coefficient=1.0):
                 a, b = p, r
                 coefficient = -coefficient
             c = q
+        else:
+            raise RuntimeError('Invalid parameter combination.')
 
         # Get operators.
         parity_string = tuple((z, 'Z') for z in range(a + 1, b))

src/openfermion/transforms/opconversions/term_reordering.py

@@ -189,6 +189,8 @@ def normal_ordered_ladder_term(term, coefficient, parity=-1):
         Op = FermionOperator
     elif parity == 1:
         Op = BosonOperator
+    else:
+        raise ValueError(f'Invalid value {parity} for parity parameter')
 
     ordered_term = Op()
 

src/openfermion/utils/bch_expansion.py

@@ -16,7 +16,7 @@
 
 
 def bch_expand(*ops, **kwargs):
-    """Compute $\log[e^{x_1} ... e^{x_N}]$ using the BCH formula.
+    r"""Compute $\log[e^{x_1} ... e^{x_N}]$ using the BCH formula.
 
     This implementation is explained in arXiv:1712.01348.
 
@@ -65,7 +65,7 @@ def _bch_expand_multiple_terms(*ops, **kwargs):
 
 
 def _bch_expand_two_terms(x, y, order=6):
-    """Compute $\log[e^x e^y]$ using the Baker-Campbell-Hausdorff formula.
+    r"""Compute $\log[e^x e^y]$ using the Baker-Campbell-Hausdorff formula.
 
     Args:
         x: An operator for which multiplication and addition are supported.