Repository: Qiskit/qiskit
Issue category: Feature Request

Issue:
generate_preset_pass_manager should take initial_layout as a list
### What should we add?

Now that https://github.com/Qiskit/qiskit/pull/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).


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

Patch:
diff --git a/qiskit/transpiler/preset_passmanagers/__init__.py b/qiskit/transpiler/preset_passmanagers/__init__.py
index d8a7fc9b5158..8d653ed3a1a9 100644
--- a/qiskit/transpiler/preset_passmanagers/__init__.py
+++ b/qiskit/transpiler/preset_passmanagers/__init__.py
@@ -136,7 +136,7 @@ def generate_preset_pass_manager(
         instruction_durations (InstructionDurations): Dictionary of duration
             (in dt) for each instruction.
         timing_constraints (TimingConstraints): Hardware time alignment restrictions.
-        initial_layout (Layout): Initial position of virtual qubits on
+        initial_layout (Layout | List[int]): Initial position of virtual qubits on
             physical qubits.
         layout_method (str): The :class:`~.Pass` to use for choosing initial qubit
             placement. Valid choices are ``'trivial'``, ``'dense'``,


Test patch:
diff --git a/test/python/transpiler/test_preset_passmanagers.py b/test/python/transpiler/test_preset_passmanagers.py
index 0382c83ab754..ae1837bf111b 100644
--- a/test/python/transpiler/test_preset_passmanagers.py
+++ b/test/python/transpiler/test_preset_passmanagers.py
@@ -1436,6 +1436,38 @@ def test_generate_preset_pass_manager_with_list_coupling_map(self):
         # Ensure the DAGs from both methods are identical
         self.assertEqual(transpiled_circuit_list, transpiled_circuit_object)
 
+    @data(0, 1, 2, 3)
+    def test_generate_preset_pass_manager_with_list_initial_layout(self, optimization_level):
+        """Test that generate_preset_pass_manager can handle list based initial layouts."""
+        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)
+
 
 @ddt
 class TestIntegrationControlFlow(QiskitTestCase):