Fixing typing issues associated with openfermion v1.6.1

src/benchq/problem_embeddings/block_encodings/double_factorized_hamiltonian.py

@@ -57,11 +57,7 @@ def get_double_factorized_hamiltonian_block_encoding(
     lam = compute_lambda_df(h1, eri_rr, LR)
 
     allowable_phase_estimation_error = 1
-    (
-        step_cost,
-        total_cost,
-        num_qubits,
-    ) = _get_double_factorized_qpe_info(
+    (step_cost, total_cost, num_qubits,) = _get_double_factorized_qpe_info(
         h1,
         eri,
         threshold,

src/benchq/problem_ingestion/hamiltonian_from_file.py

@@ -9,7 +9,7 @@
 import h5py
 import numpy as np
 import openfermion as of
-from openfermion import InteractionOperator, jordan_wigner
+from openfermion import InteractionOperator, QubitOperator, jordan_wigner
 from orquestra.integrations.cirq.conversions import from_openfermion
 from orquestra.quantum.operators import PauliSum, PauliTerm
 from orquestra.quantum.utils import ensure_open
@@ -115,7 +115,7 @@ def _get_hamiltonian_from_hdf5(file_name: str) -> PauliSum:
     if "q_matrix" in data.keys():
         return _qaoa_hamiltonian_from_hdf5(data)
     elif "basis" in data.attrs:
-        return _molecule_hamiltonian_from_hdf5(data)
+        return from_openfermion(_molecule_hamiltonian_from_hdf5(data))
     else:
         raise ValueError(
             f"Hamiltonian extraction failed for {file_name}. "
@@ -165,16 +165,16 @@ def _qaoa_hamiltonian_from_hdf5(data: h5py.File) -> PauliSum:
     return hamiltonian
 
 
-def _molecule_hamiltonian_from_hdf5(data: h5py.File) -> PauliSum:
+def _molecule_hamiltonian_from_hdf5(data: h5py.File) -> QubitOperator:
     """Given a file with a hamiltonian, generate hamiltonian terms corresponding to it.
     This function only accepts hamiltonians in the format with one and two body terms as
     attributes of the hdf5 file.
 
     Args:
-        data (h5py.File): a file with a hamiltonian described by one and two body terms
+        data: A file with a hamiltonian described by one and two body terms.
 
     Returns:
-        PauliSum: the terms of the haimltonian
+        The Jordan-Wigner transformed Hamiltonian.
     """
     one_body_term = data["one_body_tensor"]
     two_body_term = data["two_body_tensor"]
@@ -184,5 +184,4 @@ def _molecule_hamiltonian_from_hdf5(data: h5py.File) -> PauliSum:
         one_body_tensor=one_body_term,
         two_body_tensor=two_body_term,
     )
-    hamiltonian = jordan_wigner(hamiltonian)
-    return hamiltonian
+    return jordan_wigner(hamiltonian)

src/benchq/problem_ingestion/molecular_hamiltonians/_hamiltonian_generation.py

@@ -415,9 +415,10 @@ def _get_molecular_data(
 
     molecular_data.hf_energy = float(mean_field_object.e_tot)
 
-    molecular_data._pyscf_data = pyscf_data = {}
-    pyscf_data["mol"] = molecule
-    pyscf_data["scf"] = mean_field_object
+    molecular_data._pyscf_data = {  # type: ignore
+        "mol": molecule,
+        "scf": mean_field_object,
+    }
 
     molecular_data.canonical_orbitals = mean_field_object.mo_coeff.astype(float)
     molecular_data.orbital_energies = mean_field_object.mo_energy.astype(float)