Fix tracking of routing permutation in Sabre with disjoint backends

qiskit/transpiler/passes/layout/sabre_layout.py

@@ -328,6 +328,19 @@ def run(self, dag):
                 for initial, final in enumerate(component.final_permutation)
             }
         )
+
+        # The coupling map may have been split into more components than the DAG.  In this case,
+        # there will be some physical qubits unaccounted for in our `final_layout`.  Strictly the
+        # `if` check is unnecessary, but we can avoid the loop for most circuits and backends.
+        if len(final_layout) != len(physical_qubits):
+            used_qubits = {
+                qubit for component in components for qubit in component.coupling_map.graph.nodes()
+            }
+            for index, qubit in enumerate(physical_qubits):
+                if index in used_qubits:
+                    continue
+                final_layout[qubit] = index
+
         if self.property_set["final_layout"] is None:
             self.property_set["final_layout"] = final_layout
         else:

releasenotes/notes/sabre-disjoint-routing-85c6f6481c9ffca4.yaml

@@ -0,0 +1,15 @@
+---
+fixes:
+  - |
+    When :class:`.SabreLayout` is used to do both layout and routing simultaneously (as is the case
+    for the default options to :func:`.transpile` and :func:`.generate_preset_pass_manager`) on a
+    :class:`.Target` or :class:`.CouplingMap` with disjoint connectivity, and the input circuit fits
+    into a single component of the coupling map, the routing permutation will now be tracked
+    correctly.
+
+    Previously, any qubits in the coupling map that were not connected, even indirectly, to a qubit
+    used by the routed circuit would not be included in the final routing permutation.  This could
+    cause surprising behaviour a long way from the point of failure, even if compilation appeared to
+    succeed, such as calls to :meth:`.TranspileLayout.final_index_layout` raising :exc:`KeyError`.
+
+    This bug did not affect backends that were fully connected, as most are.

test/python/transpiler/test_sabre_layout.py

@@ -470,6 +470,21 @@ def test_with_partial_layout(self):
         layout = pm.property_set["layout"]
         self.assertEqual([layout[q] for q in qc.qubits], [3, 1, 2, 5, 4, 6, 7, 8])
 
+    def test_dag_fits_in_one_component(self):
+        """Test that the output is valid if the DAG all fits in a single component of a disjoint
+        coupling map.."""
+        qc = QuantumCircuit(3)
+        qc.cx(0, 1)
+        qc.cx(1, 2)
+        qc.cx(2, 0)
+
+        disjoint = CouplingMap([(0, 1), (1, 2), (3, 4), (4, 5)])
+        layout_routing_pass = SabreLayout(disjoint, seed=2025_02_12, swap_trials=1, layout_trials=1)
+        out = layout_routing_pass(qc)
+        self.assertEqual(len(out.layout.initial_layout), len(out.layout.final_layout))
+        self.assertEqual(out.layout.initial_index_layout(filter_ancillas=False), [1, 0, 2, 3, 4, 5])
+        self.assertEqual(out.layout.final_index_layout(filter_ancillas=False), [2, 0, 1, 3, 4, 5])
+
 
 class TestSabrePreLayout(QiskitTestCase):
     """Tests the SabreLayout pass with starting layout created by SabrePreLayout."""