From 171356489c783b1322972fdddfba4702e496c3de Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:39:16 +0000
Subject: [PATCH 01/19] add timeout

---
 pytket/binders/passes.cpp                     |  4 ++-
 .../tket/Predicates/PassGenerators.hpp        |  3 ++-
 .../GreedyPauliOptimisation.hpp               |  2 +-
 tket/src/Predicates/PassGenerators.cpp        |  5 ++--
 .../GreedyPauliOptimisation.cpp               | 25 +++++++++++++------
 5 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/pytket/binders/passes.cpp b/pytket/binders/passes.cpp
index 6768b6d3a9..0edf619915 100644
--- a/pytket/binders/passes.cpp
+++ b/pytket/binders/passes.cpp
@@ -957,10 +957,12 @@ PYBIND11_MODULE(passes, m) {
       "\n:param allow_zzphase: If set to True, allows the algorithm to "
       "implement 2-qubit rotations using ZZPhase gates when deemed "
       "optimal. Defaults to False."
+      "\n:param timeout: Sets maximum out of time spent finding solution."
       "\n:return: a pass to perform the simplification",
       py::arg("discount_rate") = 0.7, py::arg("depth_weight") = 0.3,
       py::arg("max_lookahead") = 500, py::arg("max_tqe_candidates") = 500,
-      py::arg("seed") = 0, py::arg("allow_zzphase") = false);
+      py::arg("seed") = 0, py::arg("allow_zzphase") = false,
+      py::arg("timeout") = 100);
   m.def(
       "PauliSquash", &PauliSquash,
       "Applies :py:meth:`PauliSimp` followed by "
diff --git a/tket/include/tket/Predicates/PassGenerators.hpp b/tket/include/tket/Predicates/PassGenerators.hpp
index 9e7f87931c..59fe71bcfe 100644
--- a/tket/include/tket/Predicates/PassGenerators.hpp
+++ b/tket/include/tket/Predicates/PassGenerators.hpp
@@ -354,12 +354,13 @@ PassPtr gen_special_UCC_synthesis(
  * @param max_tqe_candidates
  * @param seed
  * @param allow_zzphase
+ * @param timeout
  * @return PassPtr
  */
 PassPtr gen_greedy_pauli_simp(
     double discount_rate = 0.7, double depth_weight = 0.3,
     unsigned max_lookahead = 500, unsigned max_tqe_candidates = 500,
-    unsigned seed = 0, bool allow_zzphase = false);
+    unsigned seed = 0, bool allow_zzphase = false, unsigned timeout = 100);
 
 /**
  * Generate a pass to simplify the circuit where it acts on known basis states.
diff --git a/tket/include/tket/Transformations/GreedyPauliOptimisation.hpp b/tket/include/tket/Transformations/GreedyPauliOptimisation.hpp
index de6bb19d5c..3cc6348582 100644
--- a/tket/include/tket/Transformations/GreedyPauliOptimisation.hpp
+++ b/tket/include/tket/Transformations/GreedyPauliOptimisation.hpp
@@ -643,7 +643,7 @@ Circuit greedy_pauli_set_synthesis(
 Transform greedy_pauli_optimisation(
     double discount_rate = 0.7, double depth_weight = 0.3,
     unsigned max_lookahead = 500, unsigned max_tqe_candidates = 500,
-    unsigned seed = 0, bool allow_zzphase = false);
+    unsigned seed = 0, bool allow_zzphase = false, unsigned timeout = 100);
 
 }  // namespace Transforms
 
diff --git a/tket/src/Predicates/PassGenerators.cpp b/tket/src/Predicates/PassGenerators.cpp
index 610caabd84..db8291daf5 100644
--- a/tket/src/Predicates/PassGenerators.cpp
+++ b/tket/src/Predicates/PassGenerators.cpp
@@ -1015,10 +1015,11 @@ PassPtr gen_synthesise_pauli_graph(
 
 PassPtr gen_greedy_pauli_simp(
     double discount_rate, double depth_weight, unsigned max_lookahead,
-    unsigned max_tqe_candidates, unsigned seed, bool allow_zzphase) {
+    unsigned max_tqe_candidates, unsigned seed, bool allow_zzphase,
+    unsigned timeout) {
   Transform t = Transforms::greedy_pauli_optimisation(
       discount_rate, depth_weight, max_lookahead, max_tqe_candidates, seed,
-      allow_zzphase);
+      allow_zzphase, timeout);
   OpTypeSet ins = {
       OpType::Z,
       OpType::X,
diff --git a/tket/src/Transformations/GreedyPauliOptimisation.cpp b/tket/src/Transformations/GreedyPauliOptimisation.cpp
index e052102656..0e59711f23 100644
--- a/tket/src/Transformations/GreedyPauliOptimisation.cpp
+++ b/tket/src/Transformations/GreedyPauliOptimisation.cpp
@@ -15,6 +15,8 @@
 #include "tket/Transformations/GreedyPauliOptimisation.hpp"
 
 #include <algorithm>
+#include <chrono>
+#include <future>
 #include <random>
 
 #include "tket/Circuit/PauliExpBoxes.hpp"
@@ -778,15 +780,22 @@ Circuit greedy_pauli_graph_synthesis(
 
 Transform greedy_pauli_optimisation(
     double discount_rate, double depth_weight, unsigned max_lookahead,
-    unsigned max_tqe_candidates, unsigned seed, bool allow_zzphase) {
+    unsigned max_tqe_candidates, unsigned seed, bool allow_zzphase,
+    unsigned timeout) {
   return Transform([discount_rate, depth_weight, max_lookahead,
-                    max_tqe_candidates, seed, allow_zzphase](Circuit& circ) {
-    circ = GreedyPauliSimp::greedy_pauli_graph_synthesis(
-        circ, discount_rate, depth_weight, max_lookahead, max_tqe_candidates,
-        seed, allow_zzphase);
-    // decompose the conditional CircBoxes
-    circ.decompose_boxes_recursively();
-    return true;
+                    max_tqe_candidates, seed, allow_zzphase,
+                    timeout](Circuit& circ) {
+    std::future<Circuit> future = std::async(
+        std::launch::async, GreedyPauliSimp::greedy_pauli_graph_synthesis, circ,
+        discount_rate, depth_weight, max_lookahead, max_tqe_candidates, seed,
+        allow_zzphase);
+    if (future.wait_for(std::chrono::seconds(timeout)) ==
+        std::future_status::ready) {
+      circ = future.get();
+      circ.decompose_boxes_recursively();
+      return true;
+    }
+    return false;
   });
 }
 

From e275cf81dc692d65aff399f79420778b74caa42c Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:47:50 +0000
Subject: [PATCH 02/19] add timeout to serialisation

---
 tket/src/Predicates/CompilerPass.cpp   | 3 ++-
 tket/src/Predicates/PassGenerators.cpp | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/tket/src/Predicates/CompilerPass.cpp b/tket/src/Predicates/CompilerPass.cpp
index f0a5461e4b..580aa29098 100644
--- a/tket/src/Predicates/CompilerPass.cpp
+++ b/tket/src/Predicates/CompilerPass.cpp
@@ -521,9 +521,10 @@ PassPtr deserialise(
       unsigned max_lookahead = content.at("max_lookahead").get<unsigned>();
       unsigned seed = content.at("seed").get<unsigned>();
       bool allow_zzphase = content.at("allow_zzphase").get<bool>();
+      unsigned timeout = content.at("timeout").get<unsigned>();
       pp = gen_greedy_pauli_simp(
           discount_rate, depth_weight, max_lookahead, max_tqe_candidates, seed,
-          allow_zzphase);
+          allow_zzphase, timeout);
 
     } else if (passname == "PauliSimp") {
       // SEQUENCE PASS - DESERIALIZABLE ONLY
diff --git a/tket/src/Predicates/PassGenerators.cpp b/tket/src/Predicates/PassGenerators.cpp
index db8291daf5..d33b83edff 100644
--- a/tket/src/Predicates/PassGenerators.cpp
+++ b/tket/src/Predicates/PassGenerators.cpp
@@ -1068,6 +1068,7 @@ PassPtr gen_greedy_pauli_simp(
   j["max_tqe_candidates"] = max_tqe_candidates;
   j["seed"] = seed;
   j["allow_zzphase"] = allow_zzphase;
+  j["timeout"] = timeout;
 
   return std::make_shared<StandardPass>(precons, t, postcon, j);
 }

From 4fea92626da91d86d146d5223c164c716c2bb004 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:48:09 +0000
Subject: [PATCH 03/19] Update changelog.rst

---
 pytket/docs/changelog.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pytket/docs/changelog.rst b/pytket/docs/changelog.rst
index df54b92f4e..dab6e73aa0 100644
--- a/pytket/docs/changelog.rst
+++ b/pytket/docs/changelog.rst
@@ -12,6 +12,7 @@ Features:
   conditions.
 * Add `custom_deserialisation` argument to `BasePass` and `SequencePass` 
   `from_dict` method to support construction of `CustomPass` from json.
+* Add `timeout` argument to `GreedyPauliSimp`.
 
 Fixes:
 

From 87aec9eb27c4c2bf01c21dee7db1adb0aeef8ad0 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:49:04 +0000
Subject: [PATCH 04/19] bump library

---
 pytket/conanfile.py | 2 +-
 tket/conanfile.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pytket/conanfile.py b/pytket/conanfile.py
index 094c0e3d89..e23892a53b 100644
--- a/pytket/conanfile.py
+++ b/pytket/conanfile.py
@@ -38,7 +38,7 @@ def requirements(self):
         self.requires("pybind11_json/0.2.14")
         self.requires("symengine/0.12.0")
         self.requires("tkassert/0.3.4@tket/stable")
-        self.requires("tket/1.3.39@tket/stable")
+        self.requires("tket/1.3.40@tket/stable")
         self.requires("tklog/0.3.3@tket/stable")
         self.requires("tkrng/0.3.3@tket/stable")
         self.requires("tktokenswap/0.3.9@tket/stable")
diff --git a/tket/conanfile.py b/tket/conanfile.py
index 147e674cb2..31633eef95 100644
--- a/tket/conanfile.py
+++ b/tket/conanfile.py
@@ -23,7 +23,7 @@
 
 class TketConan(ConanFile):
     name = "tket"
-    version = "1.3.39"
+    version = "1.3.40"
     package_type = "library"
     license = "Apache 2"
     homepage = "https://github.com/CQCL/tket"

From be649449917403214325f05d9046495630359262 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 10:57:16 +0000
Subject: [PATCH 05/19] Update transform.cpp

---
 pytket/binders/transform.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pytket/binders/transform.cpp b/pytket/binders/transform.cpp
index 21724759c3..cfd70bcec3 100644
--- a/pytket/binders/transform.cpp
+++ b/pytket/binders/transform.cpp
@@ -440,10 +440,12 @@ PYBIND11_MODULE(transform, m) {
           "\n:param allow_zzphase: If set to True, allows the algorithm to "
           "implement 2-qubit rotations using ZZPhase gates when deemed "
           "optimal. Defaults to False."
+          "\n:param timeout: Sets maximum out of time spent finding solution."
           "\n:return: a pass to perform the simplification",
           py::arg("discount_rate") = 0.7, py::arg("depth_weight") = 0.3,
           py::arg("max_tqe_candidates") = 500, py::arg("max_lookahead") = 500,
-          py::arg("seed") = 0, py::arg("allow_zzphase") = false)
+          py::arg("seed") = 0, py::arg("allow_zzphase") = false,
+          py::arg("timeout") = 100)
       .def_static(
           "ZZPhaseToRz", &Transforms::ZZPhase_to_Rz,
           "Fixes all ZZPhase gate angles to [-1, 1) half turns.")

From 02bb1d045e0dff129845b78ccc2ea2e9990f8407 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 11:03:18 +0000
Subject: [PATCH 06/19] Update test_GreedyPauli.cpp

---
 tket/test/src/test_GreedyPauli.cpp | 40 ++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/tket/test/src/test_GreedyPauli.cpp b/tket/test/src/test_GreedyPauli.cpp
index 366143ece4..dd855ea1b0 100644
--- a/tket/test/src/test_GreedyPauli.cpp
+++ b/tket/test/src/test_GreedyPauli.cpp
@@ -709,6 +709,46 @@ SCENARIO("Test GreedyPauliSimp for individual gates") {
     REQUIRE(test_unitary_comparison(circ, d, true));
   }
 }
+
+SCENARIO("Test greedy_pauli_optimisation timeout") {
+  GIVEN("Large circuit with ZZPhase, 0 second timeout.") {
+    Circuit circ(6);
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::X, Pauli::X}, 0.3)), {0, 1});
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Y, Pauli::X}, 0.2)),
+        {0, 1, 2});
+    circ.add_box(
+        PauliExpCommutingSetBox({
+            {{Pauli::I, Pauli::Y, Pauli::I, Pauli::Z}, 1.2},
+            {{Pauli::X, Pauli::Y, Pauli::Z, Pauli::I}, 0.8},
+            {{Pauli::I, Pauli::I, Pauli::I, Pauli::Z}, 1.25},
+        }),
+        {1, 2, 3, 4});
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::Y, Pauli::X}, 0.1)), {2, 3});
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Y, Pauli::X}, 0.11)),
+        {1, 3, 4});
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::Y, Pauli::Y}, 0.2)), {4, 5});
+    circ.add_box(
+        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Z, Pauli::X}, 0.15)),
+        {2, 4, 5});
+    circ.add_box(
+        PauliExpBox(
+            SymPauliTensor({Pauli::X, Pauli::X, Pauli::X, Pauli::X}, 0.25)),
+        {2, 4, 5, 0});
+    circ.add_box(
+        PauliExpBox(
+            SymPauliTensor({Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X}, 0.125)),
+        {1, 3, 5, 0});
+    Circuit d(circ);
+    REQUIRE(
+        !Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 0)
+             .apply(d));
+  }
+}
 SCENARIO("Test GreedyPauliSimp pass construction") {
   // test pass construction
   GIVEN("A circuit") {

From 9862430bab6b4ba23440ab6ab016f3ad8468a84e Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 11:10:05 +0000
Subject: [PATCH 07/19] update stubs

---
 pytket/pytket/_tket/passes.pyi    | 3 ++-
 pytket/pytket/_tket/transform.pyi | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/pytket/pytket/_tket/passes.pyi b/pytket/pytket/_tket/passes.pyi
index 650273f020..f2efed5973 100644
--- a/pytket/pytket/_tket/passes.pyi
+++ b/pytket/pytket/_tket/passes.pyi
@@ -444,7 +444,7 @@ def GlobalisePhasedX(squash: bool = True) -> BasePass:
     
     It is not recommended to use this pass with symbolic expressions, as in certain cases a blow-up in symbolic expression sizes may occur.
     """
-def GreedyPauliSimp(discount_rate: float = 0.7, depth_weight: float = 0.3, max_lookahead: int = 500, max_tqe_candidates: int = 500, seed: int = 0, allow_zzphase: bool = False) -> BasePass:
+def GreedyPauliSimp(discount_rate: float = 0.7, depth_weight: float = 0.3, max_lookahead: int = 500, max_tqe_candidates: int = 500, seed: int = 0, allow_zzphase: bool = False, timeout: int = 100) -> BasePass:
     """
     Construct a pass that converts a circuit into a graph of Pauli gadgets to account for commutation and phase folding, and resynthesises them using a greedy algorithm adapted from arxiv.org/abs/2103.08602. The method for synthesising the final Clifford operator is adapted from arxiv.org/abs/2305.10966.
     
@@ -454,6 +454,7 @@ def GreedyPauliSimp(discount_rate: float = 0.7, depth_weight: float = 0.3, max_l
     :param max_lookahead:  Maximum lookahead when evaluating each Clifford gate candidate. Default to 500.
     :param seed:  Unsigned integer seed used for sampling candidates and tie breaking. Default to 0.
     :param allow_zzphase: If set to True, allows the algorithm to implement 2-qubit rotations using ZZPhase gates when deemed optimal. Defaults to False.
+    :param timeout: Sets maximum out of time spent finding solution.
     :return: a pass to perform the simplification
     """
 def GuidedPauliSimp(strat: pytket._tket.transform.PauliSynthStrat = pytket._tket.transform.PauliSynthStrat.Sets, cx_config: pytket._tket.circuit.CXConfigType = pytket._tket.circuit.CXConfigType.Snake) -> BasePass:
diff --git a/pytket/pytket/_tket/transform.pyi b/pytket/pytket/_tket/transform.pyi
index 4801b4238c..ce620128b2 100644
--- a/pytket/pytket/_tket/transform.pyi
+++ b/pytket/pytket/_tket/transform.pyi
@@ -165,7 +165,7 @@ class Transform:
         It is not recommended to use this transformation with symbolic expressions, as in certain cases a blow-up in symbolic expression sizes may occur.
         """
     @staticmethod
-    def GreedyPauliSimp(discount_rate: float = 0.7, depth_weight: float = 0.3, max_tqe_candidates: int = 500, max_lookahead: int = 500, seed: int = 0, allow_zzphase: bool = False) -> Transform:
+    def GreedyPauliSimp(discount_rate: float = 0.7, depth_weight: float = 0.3, max_tqe_candidates: int = 500, max_lookahead: int = 500, seed: int = 0, allow_zzphase: bool = False, timeout: int = 100) -> Transform:
         """
         Convert a circuit into a graph of Pauli gadgets to account for commutation and phase folding, and resynthesises them using a greedy algorithm adapted from arxiv.org/abs/2103.08602. The method for synthesising the final Clifford operator is adapted from arxiv.org/abs/2305.10966.
         
@@ -175,6 +175,7 @@ class Transform:
         :param max_lookahead:  Maximum lookahead when evaluating each Clifford gate candidate. Default to 500.
         :param seed:  Unsigned integer seed used for sampling candidates and tie breaking. Default to 0.
         :param allow_zzphase: If set to True, allows the algorithm to implement 2-qubit rotations using ZZPhase gates when deemed optimal. Defaults to False.
+        :param timeout: Sets maximum out of time spent finding solution.
         :return: a pass to perform the simplification
         """
     @staticmethod

From a147bb4d1deba3f5acd4fb52a536a2032037ff65 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 11:29:17 +0000
Subject: [PATCH 08/19] fix serialisation

---
 pytket/tests/passes_serialisation_test.py | 6 ++----
 schemas/compiler_pass_v1.json             | 9 +++++++--
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/pytket/tests/passes_serialisation_test.py b/pytket/tests/passes_serialisation_test.py
index 3c76194963..dbfcf168a2 100644
--- a/pytket/tests/passes_serialisation_test.py
+++ b/pytket/tests/passes_serialisation_test.py
@@ -20,8 +20,6 @@
 from pathlib import Path
 from typing import Any, Dict, List
 
-from sympy import Expr
-
 from pytket.circuit import Node, Circuit, Qubit, OpType
 from pytket.predicates import Predicate
 from pytket.architecture import Architecture
@@ -36,7 +34,6 @@
     CommuteThroughMultis,
     RepeatWithMetricPass,
     RebaseCustom,
-    CXMappingPass,
     FullMappingPass,
     DefaultMappingPass,
     AASRouting,
@@ -299,6 +296,7 @@ def nonparam_predicate_dict(name: str) -> Dict[str, Any]:
             "max_tqe_candidates": 100,
             "seed": 2,
             "allow_zzphase": True,
+            "timeout": 5000,
         }
     ),
     # lists must be sorted by OpType value
@@ -699,7 +697,7 @@ def tk1_rep(a: ParamType, b: ParamType, c: ParamType) -> Circuit:
     np_pass = dm_pass_0.get_sequence()[2]
     d_pass = dm_pass.get_sequence()[1]
     assert d_pass.to_dict()["StandardPass"]["name"] == "DelayMeasures"
-    assert d_pass.to_dict()["StandardPass"]["allow_partial"] == False
+    assert not d_pass.to_dict()["StandardPass"]["allow_partial"]
     assert p_pass.to_dict()["StandardPass"]["name"] == "PlacementPass"
     assert np_pass.to_dict()["StandardPass"]["name"] == "NaivePlacementPass"
     assert r_pass.to_dict()["StandardPass"]["name"] == "RoutingPass"
diff --git a/schemas/compiler_pass_v1.json b/schemas/compiler_pass_v1.json
index b8175c8b92..d36580d3d8 100644
--- a/schemas/compiler_pass_v1.json
+++ b/schemas/compiler_pass_v1.json
@@ -373,6 +373,10 @@
         "allow_zzphase": {
           "type": "boolean",
           "definition": "parameter controlling the use of ZZPhase gates in \"GreedyPauliSimp\""
+        },
+        "timeout": {
+          "type": "number",
+          "definition": "parameter controlling the maximum runtime of \"GreedyPauliSimp\""
         }
       },
       "required": [
@@ -903,9 +907,10 @@
               "max_lookahead",
               "max_tqe_candidates",
               "seed",
-              "allow_zzphase"
+              "allow_zzphase",
+              "timeout"
             ],
-            "maxProperties": 7
+            "maxProperties": 8
           }
         },
         {

From e3716f1ea6aa6212900727a2b8a9581113757bdc Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 11:30:44 +0000
Subject: [PATCH 09/19] Update test_GreedyPauli.cpp

---
 tket/test/src/test_GreedyPauli.cpp | 47 ++++--------------------------
 1 file changed, 6 insertions(+), 41 deletions(-)

diff --git a/tket/test/src/test_GreedyPauli.cpp b/tket/test/src/test_GreedyPauli.cpp
index dd855ea1b0..73675929d8 100644
--- a/tket/test/src/test_GreedyPauli.cpp
+++ b/tket/test/src/test_GreedyPauli.cpp
@@ -620,8 +620,12 @@ SCENARIO("Complete synthesis") {
             SymPauliTensor({Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X}, 0.125)),
         {1, 3, 5, 0});
     Circuit d(circ);
-    REQUIRE(Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true)
-                .apply(d));
+    REQUIRE(
+        !Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 0)
+             .apply(d));
+    REQUIRE(
+        Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 10)
+            .apply(d));
     REQUIRE(test_unitary_comparison(circ, d, true));
   }
   GIVEN("Select TQE over ZZPhase") {
@@ -710,45 +714,6 @@ SCENARIO("Test GreedyPauliSimp for individual gates") {
   }
 }
 
-SCENARIO("Test greedy_pauli_optimisation timeout") {
-  GIVEN("Large circuit with ZZPhase, 0 second timeout.") {
-    Circuit circ(6);
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::X, Pauli::X}, 0.3)), {0, 1});
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Y, Pauli::X}, 0.2)),
-        {0, 1, 2});
-    circ.add_box(
-        PauliExpCommutingSetBox({
-            {{Pauli::I, Pauli::Y, Pauli::I, Pauli::Z}, 1.2},
-            {{Pauli::X, Pauli::Y, Pauli::Z, Pauli::I}, 0.8},
-            {{Pauli::I, Pauli::I, Pauli::I, Pauli::Z}, 1.25},
-        }),
-        {1, 2, 3, 4});
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::Y, Pauli::X}, 0.1)), {2, 3});
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Y, Pauli::X}, 0.11)),
-        {1, 3, 4});
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::Y, Pauli::Y}, 0.2)), {4, 5});
-    circ.add_box(
-        PauliExpBox(SymPauliTensor({Pauli::Z, Pauli::Z, Pauli::X}, 0.15)),
-        {2, 4, 5});
-    circ.add_box(
-        PauliExpBox(
-            SymPauliTensor({Pauli::X, Pauli::X, Pauli::X, Pauli::X}, 0.25)),
-        {2, 4, 5, 0});
-    circ.add_box(
-        PauliExpBox(
-            SymPauliTensor({Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X}, 0.125)),
-        {1, 3, 5, 0});
-    Circuit d(circ);
-    REQUIRE(
-        !Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 0)
-             .apply(d));
-  }
-}
 SCENARIO("Test GreedyPauliSimp pass construction") {
   // test pass construction
   GIVEN("A circuit") {

From 278474796618314937930a3f08bd3e233df777eb Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 13:41:05 +0000
Subject: [PATCH 10/19] optionally relabel classical expressions when renaming
 units

---
 pytket/binders/circuit/Circuit/main.cpp          |  7 ++++++-
 pytket/tests/predicates_test.py                  |  4 +++-
 tket/include/tket/Circuit/Circuit.hpp            | 16 +++++++++-------
 tket/src/Circuit/basic_circ_manip.cpp            |  4 ++--
 .../Transformations/GreedyPauliOptimisation.cpp  |  3 +--
 5 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/pytket/binders/circuit/Circuit/main.cpp b/pytket/binders/circuit/Circuit/main.cpp
index 867996beb1..ce999432c5 100644
--- a/pytket/binders/circuit/Circuit/main.cpp
+++ b/pytket/binders/circuit/Circuit/main.cpp
@@ -322,7 +322,12 @@ void def_circuit(py::class_<Circuit, std::shared_ptr<Circuit>> &pyCircuit) {
       .def(
           "flatten_registers", &Circuit::flatten_registers,
           "Combines all qubits into a single register namespace with "
-          "the default name, and likewise for bits")
+          "the default name, and likewise for bits"
+          "\n\n:param relabel_classical_expression: Determines whether python "
+          "classical expressions held in `ClassicalExpBox` have their "
+          "expression "
+          "relabelled to match relabelled Bit.",
+          py::arg("relabel_classical_expression") = true)
 
       // Circuit composition:
       .def(
diff --git a/pytket/tests/predicates_test.py b/pytket/tests/predicates_test.py
index ffc0f26064..b18180c48c 100644
--- a/pytket/tests/predicates_test.py
+++ b/pytket/tests/predicates_test.py
@@ -1040,6 +1040,7 @@ def test_greedy_pauli_synth() -> None:
     ).SWAP(regb[1], rega[0])
     d = circ.copy()
     pss = GreedyPauliSimp(0.5, 0.5)
+    assert not GreedyPauliSimp(0.5, 0.5, timeout = 0).apply(d)
     assert pss.apply(d)
     assert np.allclose(circ.get_unitary(), d.get_unitary())
     assert d.name == "test"
@@ -1062,7 +1063,8 @@ def test_greedy_pauli_synth() -> None:
     circ.measure_all()
     circ.Reset(0)
     circ.add_pauliexpbox(pg1, [2, 3])
-    assert GreedyPauliSimp(0.5, 0.5, 100, 100, 0, True).apply(circ)
+    assert not GreedyPauliSimp(0.5, 0.5, 100, 100, 0, True, 0).apply(circ)
+    assert GreedyPauliSimp(0.5, 0.5, 100, 100, 0, True, 100).apply(circ)
     # PauliExpBoxes implemented using ZZPhase
     d = Circuit(4, 4, name="test")
     d.H(0)
diff --git a/tket/include/tket/Circuit/Circuit.hpp b/tket/include/tket/Circuit/Circuit.hpp
index 64a4f338c9..73777c89c7 100644
--- a/tket/include/tket/Circuit/Circuit.hpp
+++ b/tket/include/tket/Circuit/Circuit.hpp
@@ -749,9 +749,12 @@ class Circuit {
   /**
    * Convert all quantum and classical bits to use default registers.
    *
+   * @param relabel_classical_expression Whether expressions in ClassicalExpBox
+   *  have their expr updated to match the input wires
+   *
    * @return mapping from old to new unit IDs
    */
-  unit_map_t flatten_registers();
+  unit_map_t flatten_registers(bool relabel_classical_expression = true);
 
   //_________________________________________________
 
@@ -1044,7 +1047,8 @@ class Circuit {
    * @return true iff circuit was modified
    */
   template <typename UnitA, typename UnitB>
-  bool rename_units(const std::map<UnitA, UnitB> &qm);
+  bool rename_units(
+      const std::map<UnitA, UnitB> &qm, bool relabel_classicalexpbox = true);
 
   /** Automatically rewire holes when removing vertices from the circuit? */
   enum class GraphRewiring { Yes, No };
@@ -1718,7 +1722,8 @@ JSON_DECL(Circuit)
 /** Templated method definitions */
 
 template <typename UnitA, typename UnitB>
-bool Circuit::rename_units(const std::map<UnitA, UnitB> &qm) {
+bool Circuit::rename_units(
+    const std::map<UnitA, UnitB> &qm, bool relabel_classicalexpbox) {
   // Can only work for Unit classes
   static_assert(std::is_base_of<UnitID, UnitA>::value);
   static_assert(std::is_base_of<UnitID, UnitB>::value);
@@ -1767,21 +1772,18 @@ bool Circuit::rename_units(const std::map<UnitA, UnitB> &qm) {
           "Unit already exists in circuit: " + pair.first.repr());
     TKET_ASSERT(modified);
   }
-
   // For every ClassicalExpBox, update its logic expressions
-  if (!bm.empty()) {
+  if (!bm.empty() && relabel_classicalexpbox) {
     BGL_FORALL_VERTICES(v, dag, DAG) {
       Op_ptr op = get_Op_ptr_from_Vertex(v);
       if (op->get_type() == OpType::ClassicalExpBox) {
         const ClassicalExpBoxBase &cbox =
             static_cast<const ClassicalExpBoxBase &>(*op);
         // rename_units is marked as const to get around the Op_ptr
-        // cast, but it can still mutate a python object
         modified |= cbox.rename_units(bm);
       }
     }
   }
-
   return modified;
 }
 
diff --git a/tket/src/Circuit/basic_circ_manip.cpp b/tket/src/Circuit/basic_circ_manip.cpp
index ca3d27faa3..9bb8b11902 100644
--- a/tket/src/Circuit/basic_circ_manip.cpp
+++ b/tket/src/Circuit/basic_circ_manip.cpp
@@ -422,7 +422,7 @@ void Circuit::remove_edge(const Edge& edge) {
   boost::remove_edge(edge, this->dag);
 }
 
-unit_map_t Circuit::flatten_registers() {
+unit_map_t Circuit::flatten_registers(bool relabel_classical_expression) {
   unit_map_t rename_map;
   unsigned q_index = 0;
   unsigned c_index = 0;
@@ -434,7 +434,7 @@ unit_map_t Circuit::flatten_registers() {
     }
   }
   try {
-    rename_units(rename_map);
+    rename_units(rename_map, relabel_classical_expression);
   } catch (const std::exception& e) {
     std::stringstream ss;
     ss << "Unable to flatten registers: " << e.what();
diff --git a/tket/src/Transformations/GreedyPauliOptimisation.cpp b/tket/src/Transformations/GreedyPauliOptimisation.cpp
index 0e59711f23..e0c1890a7a 100644
--- a/tket/src/Transformations/GreedyPauliOptimisation.cpp
+++ b/tket/src/Transformations/GreedyPauliOptimisation.cpp
@@ -742,7 +742,6 @@ Circuit greedy_pauli_graph_synthesis(
   if (max_tqe_candidates == 0) {
     throw GreedyPauliSimpError("max_tqe_candidates must be greater than 0.");
   }
-
   Circuit circ_flat(circ);
   unsigned n_qubits = circ_flat.n_qubits();
   unsigned n_bits = circ_flat.n_bits();
@@ -752,7 +751,7 @@ Circuit greedy_pauli_graph_synthesis(
   if (name != std::nullopt) {
     new_circ.set_name(name.value());
   }
-  unit_map_t unit_map = circ_flat.flatten_registers();
+  unit_map_t unit_map = circ_flat.flatten_registers(false);
   unit_map_t rev_unit_map;
   for (const auto& pair : unit_map) {
     rev_unit_map.insert({pair.second, pair.first});

From 8cda1151a8ee89a0053f11bb50ecd8a570be487f Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 13:43:00 +0000
Subject: [PATCH 11/19] Update predicates_test.py

---
 pytket/tests/predicates_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pytket/tests/predicates_test.py b/pytket/tests/predicates_test.py
index b18180c48c..167420afdf 100644
--- a/pytket/tests/predicates_test.py
+++ b/pytket/tests/predicates_test.py
@@ -1040,7 +1040,7 @@ def test_greedy_pauli_synth() -> None:
     ).SWAP(regb[1], rega[0])
     d = circ.copy()
     pss = GreedyPauliSimp(0.5, 0.5)
-    assert not GreedyPauliSimp(0.5, 0.5, timeout = 0).apply(d)
+    assert not GreedyPauliSimp(0.5, 0.5, timeout=0).apply(d)
     assert pss.apply(d)
     assert np.allclose(circ.get_unitary(), d.get_unitary())
     assert d.name == "test"

From 809d385bcc7862939e9f765df164e0cd3114c18d Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:52:17 +0000
Subject: [PATCH 12/19] update flattenrelabelregisters

---
 pytket/binders/passes.cpp                       | 7 +++++--
 pytket/docs/changelog.rst                       | 2 ++
 pytket/pytket/_tket/circuit.pyi                 | 4 +++-
 pytket/pytket/_tket/passes.pyi                  | 3 ++-
 schemas/compiler_pass_v1.json                   | 5 +++--
 tket/include/tket/Predicates/PassGenerators.hpp | 2 +-
 tket/src/Predicates/CompilerPass.cpp            | 2 +-
 tket/src/Predicates/PassGenerators.cpp          | 5 +++--
 8 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/pytket/binders/passes.cpp b/pytket/binders/passes.cpp
index 0edf619915..3d96b982a9 100644
--- a/pytket/binders/passes.cpp
+++ b/pytket/binders/passes.cpp
@@ -752,9 +752,12 @@ PYBIND11_MODULE(passes, m) {
       "FlattenRelabelRegistersPass", &gen_flatten_relabel_registers_pass,
       "Removes empty Quantum wires from the Circuit and relabels all Qubit to "
       "a register from passed name. \n\n:param label: Name to relabel "
-      "remaining Qubit to, default 'q'.\n:return: A pass that removes empty "
+      "remaining Qubit to, default 'q'.\n:param relabel_classical_expressions: "
+      "Whether to relabel arguments of expressions held in `ClassicalExpBox`. "
+      "\n:return: A pass that removes empty "
       "wires and relabels.",
-      py::arg("label") = q_default_reg());
+      py::arg("label") = q_default_reg(),
+      py::arg("relabel_classical_expressions") = true);
 
   m.def(
       "RenameQubitsPass", &gen_rename_qubits_pass,
diff --git a/pytket/docs/changelog.rst b/pytket/docs/changelog.rst
index dab6e73aa0..5e2b38e137 100644
--- a/pytket/docs/changelog.rst
+++ b/pytket/docs/changelog.rst
@@ -13,6 +13,8 @@ Features:
 * Add `custom_deserialisation` argument to `BasePass` and `SequencePass` 
   `from_dict` method to support construction of `CustomPass` from json.
 * Add `timeout` argument to `GreedyPauliSimp`.
+* Add option to not relabel `ClassicalExpBox` when calling `rename_units`
+  and `flatten_registers`
 
 Fixes:
 
diff --git a/pytket/pytket/_tket/circuit.pyi b/pytket/pytket/_tket/circuit.pyi
index 4cbc158def..f153fd5fd0 100644
--- a/pytket/pytket/_tket/circuit.pyi
+++ b/pytket/pytket/_tket/circuit.pyi
@@ -2104,9 +2104,11 @@ class Circuit:
         :param types: the set of operation types of interest
         :return: the circuit depth with respect to operations matching an element of `types`
         """
-    def flatten_registers(self) -> dict[pytket._tket.unit_id.UnitID, pytket._tket.unit_id.UnitID]:
+    def flatten_registers(self, relabel_classical_expression: bool = True) -> dict[pytket._tket.unit_id.UnitID, pytket._tket.unit_id.UnitID]:
         """
         Combines all qubits into a single register namespace with the default name, and likewise for bits
+        
+        :param relabel_classical_expression: Determines whether python classical expressions held in `ClassicalExpBox` have their expression relabelled to match relabelled Bit.
         """
     def free_symbols(self) -> set[sympy.Symbol]:
         """
diff --git a/pytket/pytket/_tket/passes.pyi b/pytket/pytket/_tket/passes.pyi
index f2efed5973..b928a2e970 100644
--- a/pytket/pytket/_tket/passes.pyi
+++ b/pytket/pytket/_tket/passes.pyi
@@ -410,11 +410,12 @@ def FlattenRegisters() -> BasePass:
     """
     Merges all quantum and classical registers into their respective default registers with contiguous indexing.
     """
-def FlattenRelabelRegistersPass(label: str = 'q') -> BasePass:
+def FlattenRelabelRegistersPass(label: str = 'q', relabel_classical_expressions: bool = True) -> BasePass:
     """
     Removes empty Quantum wires from the Circuit and relabels all Qubit to a register from passed name. 
     
     :param label: Name to relabel remaining Qubit to, default 'q'.
+    :param relabel_classical_expressions: Whether to relabel arguments of expressions held in `ClassicalExpBox`. 
     :return: A pass that removes empty wires and relabels.
     """
 def FullMappingPass(arc: pytket._tket.architecture.Architecture, placer: pytket._tket.placement.Placement, config: typing.Sequence[pytket._tket.mapping.RoutingMethod]) -> BasePass:
diff --git a/schemas/compiler_pass_v1.json b/schemas/compiler_pass_v1.json
index d36580d3d8..dbd68c9e18 100644
--- a/schemas/compiler_pass_v1.json
+++ b/schemas/compiler_pass_v1.json
@@ -648,9 +648,10 @@
           },
           "then": {
             "required": [
-              "label"
+              "label",
+              "relabel_classical_registers"
             ],
-            "maxProperties": 2
+            "maxProperties": 3
           }
         },
         {
diff --git a/tket/include/tket/Predicates/PassGenerators.hpp b/tket/include/tket/Predicates/PassGenerators.hpp
index 59fe71bcfe..f4bcb4a8d4 100644
--- a/tket/include/tket/Predicates/PassGenerators.hpp
+++ b/tket/include/tket/Predicates/PassGenerators.hpp
@@ -110,7 +110,7 @@ PassPtr gen_clifford_push_through_pass();
  * Qubits removed from the Circuit are preserved in the bimap, but not updated
  * to a new labelling.
  */
-PassPtr gen_flatten_relabel_registers_pass(const std::string& label);
+PassPtr gen_flatten_relabel_registers_pass(const std::string& label, bool relabel_classical_expressions = true);
 /**
  * Pass to rename some or all qubits according to the given map.
  *
diff --git a/tket/src/Predicates/CompilerPass.cpp b/tket/src/Predicates/CompilerPass.cpp
index 580aa29098..5176f207a6 100644
--- a/tket/src/Predicates/CompilerPass.cpp
+++ b/tket/src/Predicates/CompilerPass.cpp
@@ -469,7 +469,7 @@ PassPtr deserialise(
       pp = gen_euler_pass(q, p, s);
     } else if (passname == "FlattenRelabelRegistersPass") {
       pp = gen_flatten_relabel_registers_pass(
-          content.at("label").get<std::string>());
+          content.at("label").get<std::string>(), content.at("relabel_classical_expressions").get<bool>());
     } else if (passname == "RoutingPass") {
       Architecture arc = content.at("architecture").get<Architecture>();
       std::vector<RoutingMethodPtr> con = content.at("routing_config");
diff --git a/tket/src/Predicates/PassGenerators.cpp b/tket/src/Predicates/PassGenerators.cpp
index d33b83edff..bbf14ab895 100644
--- a/tket/src/Predicates/PassGenerators.cpp
+++ b/tket/src/Predicates/PassGenerators.cpp
@@ -354,7 +354,7 @@ PassPtr gen_clifford_push_through_pass() {
   return std::make_shared<StandardPass>(precons, t, pc, j);
 }
 
-PassPtr gen_flatten_relabel_registers_pass(const std::string& label) {
+PassPtr gen_flatten_relabel_registers_pass(const std::string& label, bool relabel_classical_expressions) {
   Transform t =
       Transform([=](Circuit& circuit, std::shared_ptr<unit_bimaps_t> maps) {
         unsigned n_qubits = circuit.n_qubits();
@@ -366,7 +366,7 @@ PassPtr gen_flatten_relabel_registers_pass(const std::string& label) {
           relabelling_map.insert({all_qubits[i], Qubit(label, i)});
         }
 
-        circuit.rename_units(relabelling_map);
+        circuit.rename_units(relabelling_map, relabel_classical_expressions);
         changed |= update_maps(maps, relabelling_map, relabelling_map);
         return changed;
       });
@@ -376,6 +376,7 @@ PassPtr gen_flatten_relabel_registers_pass(const std::string& label) {
   nlohmann::json j;
   j["name"] = "FlattenRelabelRegistersPass";
   j["label"] = label;
+  j["relabel_classical_expressions"] = relabel_classical_expressions;
   return std::make_shared<StandardPass>(precons, t, postcons, j);
 }
 

From 533c90742ee8e430edffdbe5c7734f6a07146006 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 15:58:11 +0000
Subject: [PATCH 13/19] reformat, add false to rename_units again

---
 tket/include/tket/Predicates/PassGenerators.hpp      | 3 ++-
 tket/src/Predicates/CompilerPass.cpp                 | 3 ++-
 tket/src/Predicates/PassGenerators.cpp               | 3 ++-
 tket/src/Transformations/GreedyPauliOptimisation.cpp | 2 +-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/tket/include/tket/Predicates/PassGenerators.hpp b/tket/include/tket/Predicates/PassGenerators.hpp
index f4bcb4a8d4..699f9b9edc 100644
--- a/tket/include/tket/Predicates/PassGenerators.hpp
+++ b/tket/include/tket/Predicates/PassGenerators.hpp
@@ -110,7 +110,8 @@ PassPtr gen_clifford_push_through_pass();
  * Qubits removed from the Circuit are preserved in the bimap, but not updated
  * to a new labelling.
  */
-PassPtr gen_flatten_relabel_registers_pass(const std::string& label, bool relabel_classical_expressions = true);
+PassPtr gen_flatten_relabel_registers_pass(
+    const std::string& label, bool relabel_classical_expressions = true);
 /**
  * Pass to rename some or all qubits according to the given map.
  *
diff --git a/tket/src/Predicates/CompilerPass.cpp b/tket/src/Predicates/CompilerPass.cpp
index 5176f207a6..2caeafe08f 100644
--- a/tket/src/Predicates/CompilerPass.cpp
+++ b/tket/src/Predicates/CompilerPass.cpp
@@ -469,7 +469,8 @@ PassPtr deserialise(
       pp = gen_euler_pass(q, p, s);
     } else if (passname == "FlattenRelabelRegistersPass") {
       pp = gen_flatten_relabel_registers_pass(
-          content.at("label").get<std::string>(), content.at("relabel_classical_expressions").get<bool>());
+          content.at("label").get<std::string>(),
+          content.at("relabel_classical_expressions").get<bool>());
     } else if (passname == "RoutingPass") {
       Architecture arc = content.at("architecture").get<Architecture>();
       std::vector<RoutingMethodPtr> con = content.at("routing_config");
diff --git a/tket/src/Predicates/PassGenerators.cpp b/tket/src/Predicates/PassGenerators.cpp
index bbf14ab895..eb5f50317b 100644
--- a/tket/src/Predicates/PassGenerators.cpp
+++ b/tket/src/Predicates/PassGenerators.cpp
@@ -354,7 +354,8 @@ PassPtr gen_clifford_push_through_pass() {
   return std::make_shared<StandardPass>(precons, t, pc, j);
 }
 
-PassPtr gen_flatten_relabel_registers_pass(const std::string& label, bool relabel_classical_expressions) {
+PassPtr gen_flatten_relabel_registers_pass(
+    const std::string& label, bool relabel_classical_expressions) {
   Transform t =
       Transform([=](Circuit& circuit, std::shared_ptr<unit_bimaps_t> maps) {
         unsigned n_qubits = circuit.n_qubits();
diff --git a/tket/src/Transformations/GreedyPauliOptimisation.cpp b/tket/src/Transformations/GreedyPauliOptimisation.cpp
index e0c1890a7a..bf88e4a265 100644
--- a/tket/src/Transformations/GreedyPauliOptimisation.cpp
+++ b/tket/src/Transformations/GreedyPauliOptimisation.cpp
@@ -770,7 +770,7 @@ Circuit greedy_pauli_graph_synthesis(
   for (auto it = measures.begin(); it != measures.end(); ++it) {
     new_circ.add_measure(it->left, it->right);
   }
-  new_circ.rename_units(rev_unit_map);
+  new_circ.rename_units(rev_unit_map, false);
   new_circ.replace_SWAPs();
   return new_circ;
 }

From 747d44b93e91a664e3398d96a47d6fe6b1478963 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 16:04:23 +0000
Subject: [PATCH 14/19] bump library

---
 pytket/conanfile.py | 2 +-
 tket/conanfile.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pytket/conanfile.py b/pytket/conanfile.py
index e23892a53b..b42d4657d3 100644
--- a/pytket/conanfile.py
+++ b/pytket/conanfile.py
@@ -38,7 +38,7 @@ def requirements(self):
         self.requires("pybind11_json/0.2.14")
         self.requires("symengine/0.12.0")
         self.requires("tkassert/0.3.4@tket/stable")
-        self.requires("tket/1.3.40@tket/stable")
+        self.requires("tket/1.3.41@tket/stable")
         self.requires("tklog/0.3.3@tket/stable")
         self.requires("tkrng/0.3.3@tket/stable")
         self.requires("tktokenswap/0.3.9@tket/stable")
diff --git a/tket/conanfile.py b/tket/conanfile.py
index 31633eef95..872160e0a2 100644
--- a/tket/conanfile.py
+++ b/tket/conanfile.py
@@ -23,7 +23,7 @@
 
 class TketConan(ConanFile):
     name = "tket"
-    version = "1.3.40"
+    version = "1.3.41"
     package_type = "library"
     license = "Apache 2"
     homepage = "https://github.com/CQCL/tket"

From 8ad64e8e3445ba1db3c8548d302ffa38bc838e0e Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 17:15:59 +0000
Subject: [PATCH 15/19] Update passes_serialisation_test.py

---
 pytket/tests/passes_serialisation_test.py | 30 ++---------------------
 1 file changed, 2 insertions(+), 28 deletions(-)

diff --git a/pytket/tests/passes_serialisation_test.py b/pytket/tests/passes_serialisation_test.py
index a1edefa9d7..14e2f42193 100644
--- a/pytket/tests/passes_serialisation_test.py
+++ b/pytket/tests/passes_serialisation_test.py
@@ -16,41 +16,15 @@
 from pathlib import Path
 from typing import Any, Dict, List
 
-from pytket.circuit import Node, Circuit, Qubit, OpType
-from pytket.predicates import Predicate
-from pytket.architecture import Architecture
-from pytket.placement import Placement, GraphPlacement
-import pytket.circuit_library as _library
-
-from pytket.passes import (
-    BasePass,
-    SequencePass,
-    RemoveRedundancies,
-    RepeatUntilSatisfiedPass,
-    CommuteThroughMultis,
-    RepeatWithMetricPass,
-    RebaseCustom,
-    FullMappingPass,
-    DefaultMappingPass,
-    AASRouting,
-    SquashCustom,
-    CustomPass,
-)
 import pytest
 from jsonschema import Draft7Validator, ValidationError  # type: ignore
 from referencing import Registry
 from referencing.jsonschema import DRAFT7
 
 import pytket.circuit_library as _library
+from pytket.architecture import Architecture
+from pytket.circuit import Circuit, Node, OpType, Qubit
 from pytket.circuit.named_types import ParamType
-
-
-
-
-
-
-
-
 from pytket.mapping import (
     BoxDecompositionRoutingMethod,
     LexiLabellingMethod,

From 2f3446b7a1f633281151ec3cb18256ce6833ab4d Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Fri, 8 Nov 2024 17:16:16 +0000
Subject: [PATCH 16/19] bump library version

---
 pytket/conanfile.py | 2 +-
 tket/conanfile.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pytket/conanfile.py b/pytket/conanfile.py
index 0b13ea52cf..b12e296e0b 100644
--- a/pytket/conanfile.py
+++ b/pytket/conanfile.py
@@ -38,7 +38,7 @@ def requirements(self):
         self.requires("pybind11_json/0.2.14")
         self.requires("symengine/0.12.0")
         self.requires("tkassert/0.3.4@tket/stable")
-        self.requires("tket/1.3.41@tket/stable")
+        self.requires("tket/1.3.42@tket/stable")
         self.requires("tklog/0.3.3@tket/stable")
         self.requires("tkrng/0.3.3@tket/stable")
         self.requires("tktokenswap/0.3.9@tket/stable")
diff --git a/tket/conanfile.py b/tket/conanfile.py
index 872160e0a2..a30f2f1de8 100644
--- a/tket/conanfile.py
+++ b/tket/conanfile.py
@@ -23,7 +23,7 @@
 
 class TketConan(ConanFile):
     name = "tket"
-    version = "1.3.41"
+    version = "1.3.42"
     package_type = "library"
     license = "Apache 2"
     homepage = "https://github.com/CQCL/tket"

From 6a288a891629bd5362339f68288e076439f56868 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Mon, 11 Nov 2024 08:05:32 +0000
Subject: [PATCH 17/19] Update test_GreedyPauli.cpp

---
 tket/test/src/test_GreedyPauli.cpp | 35 +++++++++++++++++++++++++++---
 1 file changed, 32 insertions(+), 3 deletions(-)

diff --git a/tket/test/src/test_GreedyPauli.cpp b/tket/test/src/test_GreedyPauli.cpp
index 73675929d8..629b8d21e3 100644
--- a/tket/test/src/test_GreedyPauli.cpp
+++ b/tket/test/src/test_GreedyPauli.cpp
@@ -619,10 +619,39 @@ SCENARIO("Complete synthesis") {
         PauliExpBox(
             SymPauliTensor({Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X}, 0.125)),
         {1, 3, 5, 0});
+
+    circ.add_box(
+        PauliExpBox(SymPauliTensor(
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
+             Pauli::X},
+            0.125)),
+        {1, 3, 5, 0, 2, 4});
+
+    circ.add_box(
+        PauliExpBox(SymPauliTensor(
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
+             Pauli::X},
+            0.125)),
+        {0, 1, 2, 3, 4, 5});
+
+    circ.add_box(
+        PauliExpBox(SymPauliTensor(
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
+             Pauli::X},
+            0.125)),
+        {5, 2, 4, 1, 3, 0});
+
+    circ.add_box(
+        PauliExpBox(SymPauliTensor(
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
+             Pauli::X},
+            0.125)),
+        {0, 5, 1, 4, 3, 2});
+
     Circuit d(circ);
-    REQUIRE(
-        !Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 0)
-             .apply(d));
+    REQUIRE(!Transforms::greedy_pauli_optimisation(
+                 0.7, 0.3, 500, 500, 0, true, timeout = 0)
+                 .apply(d));
     REQUIRE(
         Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 10)
             .apply(d));

From 5071d1ee4cafd78de7d66c1f86b8ee4adc7667b2 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Mon, 11 Nov 2024 08:24:05 +0000
Subject: [PATCH 18/19] Update test_GreedyPauli.cpp

---
 tket/test/src/test_GreedyPauli.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tket/test/src/test_GreedyPauli.cpp b/tket/test/src/test_GreedyPauli.cpp
index 629b8d21e3..ec436dc50e 100644
--- a/tket/test/src/test_GreedyPauli.cpp
+++ b/tket/test/src/test_GreedyPauli.cpp
@@ -649,9 +649,9 @@ SCENARIO("Complete synthesis") {
         {0, 5, 1, 4, 3, 2});
 
     Circuit d(circ);
-    REQUIRE(!Transforms::greedy_pauli_optimisation(
-                 0.7, 0.3, 500, 500, 0, true, timeout = 0)
-                 .apply(d));
+    REQUIRE(
+        !Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 0)
+             .apply(d));
     REQUIRE(
         Transforms::greedy_pauli_optimisation(0.7, 0.3, 500, 500, 0, true, 10)
             .apply(d));

From 6596f5d984a8999d8985e2904e289667e2e390c6 Mon Sep 17 00:00:00 2001
From: Silas Dilkes <36165522+sjdilkes@users.noreply.github.com>
Date: Mon, 11 Nov 2024 08:33:08 +0000
Subject: [PATCH 19/19] Update test_GreedyPauli.cpp

---
 tket/test/src/test_GreedyPauli.cpp | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/tket/test/src/test_GreedyPauli.cpp b/tket/test/src/test_GreedyPauli.cpp
index ec436dc50e..6d62f74bd5 100644
--- a/tket/test/src/test_GreedyPauli.cpp
+++ b/tket/test/src/test_GreedyPauli.cpp
@@ -622,29 +622,25 @@ SCENARIO("Complete synthesis") {
 
     circ.add_box(
         PauliExpBox(SymPauliTensor(
-            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
-             Pauli::X},
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::X},
             0.125)),
         {1, 3, 5, 0, 2, 4});
 
     circ.add_box(
         PauliExpBox(SymPauliTensor(
-            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
-             Pauli::X},
+            {Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X},
             0.125)),
         {0, 1, 2, 3, 4, 5});
 
     circ.add_box(
         PauliExpBox(SymPauliTensor(
-            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
-             Pauli::X},
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Z, Pauli::Z, Pauli::X},
             0.125)),
         {5, 2, 4, 1, 3, 0});
 
     circ.add_box(
         PauliExpBox(SymPauliTensor(
-            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::Z,
-             Pauli::X},
+            {Pauli::X, Pauli::Z, Pauli::Y, Pauli::Y, Pauli::Z, Pauli::X},
             0.125)),
         {0, 5, 1, 4, 3, 2});