generate_preset_pass_manager should take initial_layout as a list

[ajavadia]

What should we add?

Now that #10344 is merged, we should make the generate_preset_pass_manager function take an integer list for layout. This is a user entry point and should be easy to use. The Layout object is a pain to use all around (I would love to completely eliminate it, since it doesn't contain any more information than a list of int. The circuit qubits have an order).

[sbrandhsn]

We have a discussion about refactoring the Layout class in #11604 , @ajavadia could you give your opinion there? :-)

[ajavadia]

I think there are some other issues with the generate_preset_pass_manager. Even when an actual Layout object is supplied, it fails with TranspilerError: 'Sabre swap runs on physical circuits only.'. Needs more exploration.

[mtreinish]

@ajavadia do you have a re-create. I wrote a quick test to check this and it seems to at least work for my test:

        coupling_map_list = [[0, 1]]
            
        # Circuit that doesn't fit in the coupling map
        qc = QuantumCircuit(2)
        qc.h(0)
        qc.cx(0, 1)
        qc.cx(1, 0)
        qc.measure_all()
                        
        pm_list = generate_preset_pass_manager(
            optimization_level=optimization_level,
            coupling_map=coupling_map_list,
            basis_gates=["u", "cx"],
            seed_transpiler=42,
            initial_layout=[1, 0],
        )   
        pm_object = generate_preset_pass_manager(
            optimization_level=optimization_level,
            coupling_map=coupling_map_list,
            basis_gates=["u", "cx"],
            seed_transpiler=42,
            initial_layout=Layout.from_intlist([1, 0], *qc.qregs),
        )
        tqc_list = pm_list.run(qc)
        tqc_obj = pm_list.run(qc)
        self.assertIsInstance(pm_list, PassManager)
        self.assertIsInstance(pm_object, PassManager)
        
        self.assertEqual(tqc_list, tqc_obj)

(I checked the output circuits and they worked fine). Is the issue just the type hint for the argument?