Fix a number of CodeQL code-scanning alerts (#1074)

This addresses a number of alerts by CodeQL. Many more remain, but at
least it's a start.

Author: mhucka

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

@@ -120,8 +120,10 @@ 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/sparse_tools_test.py

@@ -1192,6 +1192,11 @@ def test_single_quad_two_mode(self):
         expected = numpy.kron(self.Id, self.p)
         self.assertTrue(numpy.allclose(res, expected))
 
+    def test_single_quad_op_sparse_invalid_quadrature(self):
+        """Test ValueError for invalid quadrature in single_quad_op_sparse."""
+        with self.assertRaisesRegex(ValueError, "Invalid value x for quadrature parameter."):
+            single_quad_op_sparse(n_modes=1, mode=0, quadrature='x', hbar=1.0, trunc=2)
+
     def test_boson_operator_sparse_trunc(self):
         op = BosonOperator('0')
         with self.assertRaises(ValueError):

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