From 53bcc24bf4c91c477e67e08cb898ac21b094c728 Mon Sep 17 00:00:00 2001
From: reiniscirpons <rc234@st-andrews.ac.uk>
Date: Wed, 4 Dec 2024 09:23:31 +0000
Subject: [PATCH] Fix some issues from rebase

---
 include/libsemigroups/sims.hpp | 30 +++++++++++++++++++++---------
 include/libsemigroups/sims.tpp | 13 ++++++-------
 src/sims.cpp                   |  2 +-
 tests/test-sims.cpp            |  4 ++--
 4 files changed, 30 insertions(+), 19 deletions(-)

diff --git a/include/libsemigroups/sims.hpp b/include/libsemigroups/sims.hpp
index 53874c634..291a690d6 100644
--- a/include/libsemigroups/sims.hpp
+++ b/include/libsemigroups/sims.hpp
@@ -2946,12 +2946,14 @@ namespace libsemigroups {
     using node_type    = uint32_t;
     using KnuthBendix_ = KnuthBendix<>;
     std::vector<KnuthBendix_> _knuth_bendices;
+    Presentation<word_type>   _presentation;
 
    public:
     //! Default constructor.
     explicit SimsRefinerIdeals()
         : _knuth_bendices(std::thread::hardware_concurrency() + 1,
-                          KnuthBendix_()) {
+                          KnuthBendix_()),
+          _presentation() {
       init();
     }
 
@@ -2962,6 +2964,7 @@ namespace libsemigroups {
     //!
     //! \returns A reference to \c *this.
     SimsRefinerIdeals& init() {
+      _presentation.init();
       _knuth_bendices[0].init();
       std::fill(_knuth_bendices.begin() + 1,
                 _knuth_bendices.end(),
@@ -2981,7 +2984,8 @@ namespace libsemigroups {
     template <typename Word>
     explicit SimsRefinerIdeals(Presentation<Word> const& p)
         : _knuth_bendices(std::thread::hardware_concurrency() + 1,
-                          KnuthBendix_(congruence_kind::twosided, p)) {
+                          KnuthBendix_()),
+          _presentation() {
       init(p);
     }
 
@@ -3006,9 +3010,18 @@ namespace libsemigroups {
     //! terminate on certain inputs.
     //!
     //! \sa presentation(Presentation<std::string> const&)
-    template <typename Word>
-    SimsRefinerIdeals& init(Presentation<Word> const& p) {
-      _knuth_bendices[0].init(congruence_kind::twosided, p).run();
+    SimsRefinerIdeals& init(Presentation<word_type> const& p) {
+      _presentation = p;
+      _knuth_bendices[0].init(congruence_kind::twosided, _presentation).run();
+      std::fill(_knuth_bendices.begin() + 1,
+                _knuth_bendices.end(),
+                _knuth_bendices[0]);
+      return *this;
+    }
+
+    SimsRefinerIdeals& init(Presentation<std::string> const& p) {
+      _presentation = to_presentation<word_type>(p);
+      _knuth_bendices[0].init(congruence_kind::twosided, _presentation).run();
       std::fill(_knuth_bendices.begin() + 1,
                 _knuth_bendices.end(),
                 _knuth_bendices[0]);
@@ -3024,13 +3037,12 @@ namespace libsemigroups {
     //! This function returns the defining presentation of a SimsRefinerIdeals
     //! instance.
     //!
-    //! \returns A const reference to `Presentation<std::string>`.
+    //! \returns A const reference to `Presentation<word_type>`.
     //!
     //! \exceptions
     //! \noexcept
-    [[nodiscard]] Presentation<std::string> const&
-    presentation() const noexcept {
-      return _knuth_bendices[0].presentation();
+    [[nodiscard]] Presentation<word_type> const& presentation() const noexcept {
+      return _presentation;
     }
 
     //! \brief Check if a word graph can be extended to one defining a Rees
diff --git a/include/libsemigroups/sims.tpp b/include/libsemigroups/sims.tpp
index b15407c1f..8a7fd5aa3 100644
--- a/include/libsemigroups/sims.tpp
+++ b/include/libsemigroups/sims.tpp
@@ -171,19 +171,18 @@ namespace libsemigroups {
           // TODO(2) avoid the copy here
           copy.induced_subgraph_no_checks(static_cast<Node>(0),
                                           wg.number_of_active_nodes());
-          tc.init(congruence_kind::onesided, copy)
-              .add_generating_pair_no_checks(
-                  wx.cbegin(), wx.cend(), wy.cbegin(), wy.cend());
-          LIBSEMIGROUPS_ASSERT(tc.word_graph().number_of_nodes()
-                               == wg.number_of_active_nodes());
+          tc.init(congruence_kind::onesided, copy);
+          todd_coxeter::add_generating_pair(tc, wx, wy);
+          // LIBSEMIGROUPS_ASSERT(tc.word_graph().number_of_nodes()
+          //                      == wg.number_of_active_nodes());
           // fmt::print("x = {}, y = {}\n", x, y);
           // fmt::print("wx = {}, wy = {}\n", wx, wy);
           // std::cout << copy << std::endl;
           // fmt::print("tc.number_of_classes() == {}\n",
           // tc.number_of_classes()); fmt::print("copy.number_of_nodes() ==
           // {}\n", copy.number_of_nodes());
-          LIBSEMIGROUPS_ASSERT(tc.number_of_classes()
-                               < wg.number_of_active_nodes());
+          // LIBSEMIGROUPS_ASSERT(tc.number_of_classes()
+          //                      < wg.number_of_active_nodes());
           if (tc.number_of_classes() > 1) {
             return false;
           }
diff --git a/src/sims.cpp b/src/sims.cpp
index 86bff3dd9..d5470c081 100644
--- a/src/sims.cpp
+++ b/src/sims.cpp
@@ -1525,7 +1525,7 @@ namespace libsemigroups {
       auto const& v = p.second;
       // TODO(1) change this to be const_contains for knuth
       // bendix when we have it
-      if (!kb.contains(u.cbegin(), u.cend(), v.cbegin(), v.cend())) {
+      if (!knuth_bendix::contains(kb, u, v)) {
         auto beta
             = word_graph::follow_path_no_checks(wg, 0, u.cbegin(), u.cend());
         if (sink == UNDEFINED) {
diff --git a/tests/test-sims.cpp b/tests/test-sims.cpp
index 996c5d76c..0ecc4c874 100644
--- a/tests/test-sims.cpp
+++ b/tests/test-sims.cpp
@@ -4242,7 +4242,7 @@ namespace libsemigroups {
   LIBSEMIGROUPS_TEST_CASE("Sims2",
                           "119",
                           "2-sided ideals Jura's example",
-                          "[fail][sims1][no-valgrind]") {
+                          "[quick][sims1][no-valgrind]") {
     // TODO(0) change category back to quick, these fail
     // currently because of changes to the api in
     // ToddCoxeter
@@ -4404,7 +4404,7 @@ namespace libsemigroups {
   LIBSEMIGROUPS_TEST_CASE("Sims2",
                           "123",
                           "Adding and removing pruners",
-                          "[fail][low-index]") {
+                          "[quick][low-index]") {
     // TODO(0) change category back to quick, these fail
     // currently because of changes to the api in
     // ToddCoxeter