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Replace no-longer-available SciPy constructs (#935)
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In SciPy 1.14, they removed the `.A` sparse matrix attribute; users
are now supposed to call `.toarray()` instead.
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@mhucka
mhucka authored Feb 4, 2025
1 parent 52278cf commit 6066fee
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Showing 2 changed files with 37 additions and 41 deletions.
2 changes: 1 addition & 1 deletion src/openfermion/linalg/linear_qubit_operator_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,7 @@ def test_matvec_compare(self):
[LinearQubitOperator(qubit_operator) * v for v in numpy.identity(16)]
)
),
mat_expected.A,
mat_expected.toarray(),
)
)

Expand Down
76 changes: 36 additions & 40 deletions src/openfermion/linalg/sparse_tools_test.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -140,16 +140,24 @@ def test_qubit_jw_fermion_integration(self):
class JordanWignerSparseTest(unittest.TestCase):
def test_jw_sparse_0create(self):
expected = csc_matrix(([1], ([1], [0])), shape=(2, 2))
self.assertTrue(numpy.allclose(jordan_wigner_sparse(FermionOperator('0^')).A, expected.A))
self.assertTrue(
numpy.allclose(
jordan_wigner_sparse(FermionOperator('0^')).toarray(), expected.toarray()
)
)

def test_jw_sparse_1annihilate(self):
expected = csc_matrix(([1, -1], ([0, 2], [1, 3])), shape=(4, 4))
self.assertTrue(numpy.allclose(jordan_wigner_sparse(FermionOperator('1')).A, expected.A))
self.assertTrue(
numpy.allclose(jordan_wigner_sparse(FermionOperator('1')).toarray(), expected.toarray())
)

def test_jw_sparse_0create_2annihilate(self):
expected = csc_matrix(([-1j, 1j], ([4, 6], [1, 3])), shape=(8, 8), dtype=numpy.complex128)
self.assertTrue(
numpy.allclose(jordan_wigner_sparse(FermionOperator('0^ 2', -1j)).A, expected.A)
numpy.allclose(
jordan_wigner_sparse(FermionOperator('0^ 2', -1j)).toarray(), expected.toarray()
)
)

def test_jw_sparse_0create_3annihilate(self):
Expand All @@ -159,13 +167,17 @@ def test_jw_sparse_0create_3annihilate(self):
dtype=numpy.complex128,
)
self.assertTrue(
numpy.allclose(jordan_wigner_sparse(FermionOperator('0^ 3', -1j)).A, expected.A)
numpy.allclose(
jordan_wigner_sparse(FermionOperator('0^ 3', -1j)).toarray(), expected.toarray()
)
)

def test_jw_sparse_twobody(self):
expected = csc_matrix(([1, 1], ([6, 14], [5, 13])), shape=(16, 16))
self.assertTrue(
numpy.allclose(jordan_wigner_sparse(FermionOperator('2^ 1^ 1 3')).A, expected.A)
numpy.allclose(
jordan_wigner_sparse(FermionOperator('2^ 1^ 1 3')).toarray(), expected.toarray()
)
)

def test_qubit_operator_sparse_n_qubits_too_small(self):
Expand All @@ -174,7 +186,9 @@ def test_qubit_operator_sparse_n_qubits_too_small(self):

def test_qubit_operator_sparse_n_qubits_not_specified(self):
expected = csc_matrix(([1, 1, 1, 1], ([1, 0, 3, 2], [0, 1, 2, 3])), shape=(4, 4))
self.assertTrue(numpy.allclose(qubit_operator_sparse(QubitOperator('X1')).A, expected.A))
self.assertTrue(
numpy.allclose(qubit_operator_sparse(QubitOperator('X1')).toarray(), expected.toarray())
)

def test_get_linear_qubit_operator_diagonal_wrong_n(self):
"""Testing with wrong n_qubits."""
Expand Down Expand Up @@ -364,8 +378,8 @@ def test_jw_restrict_operator(self):
restricted_hamiltonian = jw_number_restrict_operator(
hamiltonian_sparse, target_electrons, n_qubits
)
true_eigvals, _ = eigh(hamiltonian_sparse.A)
test_eigvals, _ = eigh(restricted_hamiltonian.A)
true_eigvals, _ = eigh(hamiltonian_sparse.toarray())
test_eigvals, _ = eigh(restricted_hamiltonian.toarray())

self.assertAlmostEqual(norm(true_eigvals[:6] - test_eigvals[:6]), 0.0)

Expand All @@ -375,15 +389,15 @@ def test_jw_restrict_operator_hopping_to_1_particle(self):
hop_restrict = jw_number_restrict_operator(hop_sparse, 1, n_qubits=4)
expected = csc_matrix(([1, 1], ([0, 2], [2, 0])), shape=(4, 4))

self.assertTrue(numpy.allclose(hop_restrict.A, expected.A))
self.assertTrue(numpy.allclose(hop_restrict.toarray(), expected.toarray()))

def test_jw_restrict_operator_interaction_to_1_particle(self):
interaction = FermionOperator('3^ 2^ 4 1')
interaction_sparse = jordan_wigner_sparse(interaction, n_qubits=6)
interaction_restrict = jw_number_restrict_operator(interaction_sparse, 1, n_qubits=6)
expected = csc_matrix(([], ([], [])), shape=(6, 6))

self.assertTrue(numpy.allclose(interaction_restrict.A, expected.A))
self.assertTrue(numpy.allclose(interaction_restrict.toarray(), expected.toarray()))

def test_jw_restrict_operator_interaction_to_2_particles(self):
interaction = FermionOperator('3^ 2^ 4 1') + FermionOperator('4^ 1^ 3 2')
Expand All @@ -396,7 +410,7 @@ def test_jw_restrict_operator_interaction_to_2_particles(self):
# in the 2-particle subspace (1, 4) and (2, 3) are 7th and 9th.
expected = csc_matrix(([-1, -1], ([7, 9], [9, 7])), shape=(dim, dim))

self.assertTrue(numpy.allclose(interaction_restrict.A, expected.A))
self.assertTrue(numpy.allclose(interaction_restrict.toarray(), expected.toarray()))

def test_jw_restrict_operator_hopping_to_1_particle_default_nqubits(self):
interaction = FermionOperator('3^ 2^ 4 1') + FermionOperator('4^ 1^ 3 2')
Expand All @@ -410,7 +424,7 @@ def test_jw_restrict_operator_hopping_to_1_particle_default_nqubits(self):
# in the 2-particle subspace (1, 4) and (2, 3) are 7th and 9th.
expected = csc_matrix(([-1, -1], ([7, 9], [9, 7])), shape=(dim, dim))

self.assertTrue(numpy.allclose(interaction_restrict.A, expected.A))
self.assertTrue(numpy.allclose(interaction_restrict.toarray(), expected.toarray()))

def test_jw_restrict_jellium_ground_state_integration(self):
n_qubits = 4
Expand Down Expand Up @@ -582,7 +596,7 @@ def test_get_ground_state_hermitian(self):
)
expected_state = csc_matrix(
([1j, 1], ([1, 2], [0, 0])), shape=(4, 1), dtype=numpy.complex128
).A
).toarray()
expected_state /= numpy.sqrt(2.0)

self.assertAlmostEqual(ground[0], -2)
Expand Down Expand Up @@ -753,9 +767,7 @@ def setUp(self):
-1 + int(numpy.log2(self.hf_state1.shape[0])) - self.reversed_occupied_orbitals1[i]
)

self.reversed_hf_state_index1 = sum(
2**index for index in self.reversed_occupied_orbitals1
)
self.reversed_hf_state_index1 = sum(2**index for index in self.reversed_occupied_orbitals1)

def test_1body_hopping_operator_1D(self):
operator = FermionOperator('2^ 0')
Expand Down Expand Up @@ -884,9 +896,7 @@ def test_1d5_with_spin_10particles(self):
)
self.hf_state_index3 = numpy.sum(2**occupied_states)

self.hf_state3 = csc_matrix(
([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1)
)
self.hf_state3 = csc_matrix(([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1))

self.orbital_occupations3 = [digit == '1' for digit in bin(self.hf_state_index3)[2:]][::-1]
self.occupied_orbitals3 = [
Expand All @@ -899,9 +909,7 @@ def test_1d5_with_spin_10particles(self):
-1 + int(numpy.log2(self.hf_state3.shape[0])) - self.reversed_occupied_orbitals3[i]
)

self.reversed_hf_state_index3 = sum(
2**index for index in self.reversed_occupied_orbitals3
)
self.reversed_hf_state_index3 = sum(2**index for index in self.reversed_occupied_orbitals3)

operator = (
FermionOperator('6^ 0^ 1^ 3 5 4', 2)
Expand Down Expand Up @@ -946,9 +954,7 @@ def test_1d5_with_spin_7particles(self):
)
self.hf_state_index3 = numpy.sum(2**occupied_states)

self.hf_state3 = csc_matrix(
([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1)
)
self.hf_state3 = csc_matrix(([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1))

self.orbital_occupations3 = [digit == '1' for digit in bin(self.hf_state_index3)[2:]][::-1]
self.occupied_orbitals3 = [
Expand All @@ -961,9 +967,7 @@ def test_1d5_with_spin_7particles(self):
-1 + int(numpy.log2(self.hf_state3.shape[0])) - self.reversed_occupied_orbitals3[i]
)

self.reversed_hf_state_index3 = sum(
2**index for index in self.reversed_occupied_orbitals3
)
self.reversed_hf_state_index3 = sum(2**index for index in self.reversed_occupied_orbitals3)

operator = (
FermionOperator('6^ 0^ 1^ 3 5 4', 2)
Expand Down Expand Up @@ -1006,9 +1010,7 @@ def test_3d2_spinless(self):
)
self.hf_state_index3 = numpy.sum(2**occupied_states)

self.hf_state3 = csc_matrix(
([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1)
)
self.hf_state3 = csc_matrix(([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1))

self.orbital_occupations3 = [digit == '1' for digit in bin(self.hf_state_index3)[2:]][::-1]
self.occupied_orbitals3 = [
Expand All @@ -1021,9 +1023,7 @@ def test_3d2_spinless(self):
-1 + int(numpy.log2(self.hf_state3.shape[0])) - self.reversed_occupied_orbitals3[i]
)

self.reversed_hf_state_index3 = sum(
2**index for index in self.reversed_occupied_orbitals3
)
self.reversed_hf_state_index3 = sum(2**index for index in self.reversed_occupied_orbitals3)

operator = (
FermionOperator('4^ 2^ 3^ 5 5 4', 2)
Expand Down Expand Up @@ -1066,9 +1066,7 @@ def test_3d2_with_spin(self):
)
self.hf_state_index3 = numpy.sum(2**occupied_states)

self.hf_state3 = csc_matrix(
([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1)
)
self.hf_state3 = csc_matrix(([1.0], ([self.hf_state_index3], [0])), shape=(2**n_qubits, 1))

self.orbital_occupations3 = [digit == '1' for digit in bin(self.hf_state_index3)[2:]][::-1]
self.occupied_orbitals3 = [
Expand All @@ -1081,9 +1079,7 @@ def test_3d2_with_spin(self):
-1 + int(numpy.log2(self.hf_state3.shape[0])) - self.reversed_occupied_orbitals3[i]
)

self.reversed_hf_state_index3 = sum(
2**index for index in self.reversed_occupied_orbitals3
)
self.reversed_hf_state_index3 = sum(2**index for index in self.reversed_occupied_orbitals3)

operator = (
FermionOperator('4^ 2^ 3^ 5 5 4', 2)
Expand Down

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