Removed unnecessary qiskit transpilation pass that was failing

[pediejo]

Reviving skipped tests

Context: In the previous PR, some tests were skipped to enable all tests to pass. The purpose of this PR is to revive these skipped tests.
Solution: @max-radin discovered that the errors were occurring during a qiskit transpilation pass. We determined that this transpilation likely only served to slightly speed up the simulation of the circuits and hence didn't impact the correctness of the test. This transpilation pass was simply removed, which enabled the previously failing tests to pass.

Please verify that you have completed the following steps

• I have self-reviewed my code.
• I have included test cases validating introduced feature/fix.
• I have updated documentation.

[github-actions]

🚀 Code Coverage

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You are using PYTHON: my_little_venv/bin/python3
Python Version: Python 3.11.9
Repository: https://github.com/zapatacomputing/benchq
Python Modules Covered: src.benchq/problem_embeddings/block_encodings src.benchq/problem_embeddings/qaoa src.benchq/problem_embeddings/time_marching src.benchq/problem_embeddings/qsp src.benchq/problem_embeddings/trotter src.benchq/algorithms/data_structures src.benchq/algorithms/gsee src.benchq/problem_ingestion/solid_state_hamiltonians src.benchq/problem_ingestion/plasma_hamiltonians src.benchq/problem_ingestion/molecular_hamiltonians src.benchq/compilation/graph_states src.benchq/compilation/circuits
-------------------------------------------------------------------------------
my_little_venv/bin/python3 -m coverage report --show-missing
Name                                                                                    Stmts   Miss  Cover   Missing
---------------------------------------------------------------------------------------------------------------------
src/benchq/algorithms/data_structures/algorithm_implementation.py                          20      1    95%   37
src/benchq/algorithms/data_structures/error_budget.py                                      19      0   100%
src/benchq/algorithms/gsee/ld_gsee.py                                                      15      0   100%
src/benchq/algorithms/gsee/qpe_gsee.py                                                     16     16     0%   1-24
src/benchq/algorithms/profolio_optimization.py                                              6      6     0%   4-27
src/benchq/algorithms/time_evolution.py                                                    30      0   100%
src/benchq/compilation/circuits/compile_to_native_gates.py                                121      1    99%   149
src/benchq/compilation/circuits/pyliqtr_transpilation.py                                   32      0   100%
src/benchq/compilation/graph_states/circuit_compilers.py                                   36     15    58%   14-19, 92-93, 97-104
src/benchq/compilation/graph_states/compiled_data_structures.py                            54      1    98%   102
src/benchq/compilation/graph_states/implementation_compiler.py                             42      4    90%   86-89
src/benchq/compilation/graph_states/initialize_julia.py                                    14      0   100%
src/benchq/compilation/graph_states/substrate_scheduler/python_substrate_scheduler.py      30      6    80%   36, 44, 52, 57-59
src/benchq/conversions/_circuit_translations.py                                            28      1    96%   53
src/benchq/conversions/_openfermion_pyliqtr.py                                             18      0   100%
src/benchq/conversions/_operator_translations.py                                           30      4    87%   35, 40, 45, 58
src/benchq/decoder_modeling/decoder.py                                                     48      1    98%   116
src/benchq/decoder_modeling/decoder_resource_estimator.py                                  30      0   100%
src/benchq/magic_state_distillation/autoccz_factories.py                                   45      0   100%
src/benchq/magic_state_distillation/litinski_factories.py                                   9      0   100%
src/benchq/magic_state_distillation/small_footprint_factories.py                            8      8     0%   1-81
src/benchq/mlflow/data_logging.py                                                          44      1    98%   43
src/benchq/problem_embeddings/block_encodings/double_factorized_hamiltonian.py             14      0   100%
src/benchq/problem_embeddings/block_encodings/offset_tridiagonal.py                        27      0   100%
src/benchq/problem_embeddings/block_encodings/offset_tridiagonal_utils.py                  40      0   100%
src/benchq/problem_embeddings/qaoa/_qaoa.py                                                14      4    71%   47-50
src/benchq/problem_embeddings/qpe.py                                                       29      0   100%
src/benchq/problem_embeddings/qsp/_lin_and_dong_qsp.py                                     34      0   100%
src/benchq/problem_embeddings/qsp/_qsp.py                                                 114      2    98%   313, 315
src/benchq/problem_embeddings/qsp/get_qsp_phases.py                                       193    184     5%   79-182, 203-225, 239-261, 277-284, 304-371, 397-428
src/benchq/problem_embeddings/qsp/get_qsp_polynomial.py                                    42      3    93%   112-115
src/benchq/problem_embeddings/quantum_program.py                                          106     28    74%   42, 56-59, 78, 86, 96, 143-149, 152-155, 169-176, 184-188
src/benchq/problem_embeddings/time_marching/_time_marching.py                             107     14    87%   75, 287-314
src/benchq/problem_embeddings/time_marching/compression_gadget.py                          13      0   100%
src/benchq/problem_embeddings/time_marching/matrix_properties.py                           13      0   100%
src/benchq/problem_embeddings/trotter/_trotter.py                                          12      2    83%   13, 26
src/benchq/problem_ingestion/hamiltonian_from_file.py                                      74      2    97%   94, 120
src/benchq/problem_ingestion/molecular_hamiltonians/_common_molecules.py                   13      0   100%
src/benchq/problem_ingestion/molecular_hamiltonians/_compute_lambda.py                     18      0   100%
src/benchq/problem_ingestion/molecular_hamiltonians/_hamiltonian_generation.py            161     11    93%   136, 139, 145, 148, 167, 230, 240, 322-324, 539
src/benchq/problem_ingestion/plasma_hamiltonians/vlasov.py                                 12      0   100%
src/benchq/problem_ingestion/solid_state_hamiltonians/fermi_hubbard.py                      7      3    57%   17-29
src/benchq/problem_ingestion/solid_state_hamiltonians/heisenberg.py                        20     14    30%   19-44
src/benchq/problem_ingestion/solid_state_hamiltonians/ising.py                             90     43    52%   17-24, 42-49, 53-75, 79-91
src/benchq/quantum_hardware_modeling/devitt_surface_code.py                                14      0   100%
src/benchq/quantum_hardware_modeling/fowler_surface_code.py                                 6      0   100%
src/benchq/quantum_hardware_modeling/hardware_architecture_models.py                      117      6    95%   50, 93, 207-211, 264, 270
src/benchq/resource_estimators/azure_estimator.py                                          42     29    31%   19, 58-73, 86-119
src/benchq/resource_estimators/default_estimators.py                                       69     43    38%   129-131, 164, 178-192, 234-281, 292-309
src/benchq/resource_estimators/graph_estimator.py                                         129      9    93%   131, 312, 385-389, 405-417
src/benchq/resource_estimators/openfermion_estimator.py                                    61      2    97%   68, 172
src/benchq/resource_estimators/resource_info.py                                            75      0   100%
src/benchq/timing.py                                                                       17      0   100%
src/benchq/visualization_tools/plot_graph_state.py                                         76     69     9%   19-230
src/benchq/visualization_tools/plot_substrate_scheduling.py                                28     15    46%   26-47
src/benchq/visualization_tools/resource_allocation.py                                     119     53    55%   112-115, 119-143, 146-220
---------------------------------------------------------------------------------------------------------------------
TOTAL                                                                                    2601    601    77%