Bugfix/greedy pauli simp ignores the qubit permutation of the original circuit (#2072)

* Fix GreedyPauliSimp ignoring implicit qubit permutation

* Update changelog

* Bump tket version

---------

Co-authored-by: yao-cqc <yao.tang@quantinuum.com>

Author: yao-cqc

TKET_VERSION

@@ -1 +1 @@
-2.1.63
+2.1.64

pytket/docs/changelog.md

@@ -3,6 +3,7 @@
 ## Unreleased
 
 - Fix segfault from `Circuit::get_resources()` with 0-qubit gates.
+- Fix `GreedyPauliSimp` ignoring implicit qubit permutation.
 
 ## 2.10.3 (October 2025)
 

tket/src/Transformations/GreedyPauliOptimisation.cpp

@@ -751,6 +751,7 @@ Circuit greedy_pauli_graph_synthesis_flag(
     throw GreedyPauliSimpError("max_tqe_candidates must be greater than 0.");
   }
   Circuit circ_flat(circ);
+  circ_flat.replace_all_implicit_wire_swaps();
   unsigned n_qubits = circ_flat.n_qubits();
   unsigned n_bits = circ_flat.n_bits();
   // empty circuit

tket/test/src/test_GreedyPauli.cpp

@@ -142,6 +142,15 @@ SCENARIO("Clifford synthesis") {
   }
 }
 SCENARIO("Complete synthesis") {
+  GIVEN("Qubit permutation circuit") {
+    Circuit circ(3);
+    circ.add_op<unsigned>(OpType::SWAP, {0, 1});
+    circ.add_op<unsigned>(OpType::SWAP, {1, 2});
+    circ.replace_SWAPs();
+    Circuit d(circ);
+    REQUIRE(Transforms::greedy_pauli_optimisation().apply(d));
+    REQUIRE(test_unitary_comparison(circ, d, true));
+  }
   GIVEN("1Q Simple Circuit") {
     Circuit circ(1);
     circ.add_op<unsigned>(OpType::Sdg, {0});