Add support for Sims for v1 release, please dont merge

docs/source/conf.py

@@ -161,7 +161,19 @@ def no_doc_run(self):
         r"libsemigroups::DynamicMatrix<libsemigroups::IntegerPlus<long long>, "
         r"libsemigroups::IntegerProd<long long>, libsemigroups::IntegerZero"
         r"<long long>, libsemigroups::IntegerOne<long long>, long long>"
-    ): "Matrix",
+    ): r"Matrix",
+    r"libsemigroups::SimsStats": r"SimsStats",
+    r"libsemigroups::Sims1": r"Sims1",
+    r"SimsSettingsSims1": r"Sims1",
+    r"libsemigroups::Sims2": r"Sims2",
+    r"SimsSettingsSims2": r"Sims2",
+    r"libsemigroups::RepOrc": r"RepOrc",
+    r"SimsSettingsRepOrc": r"RepOrc",
+    (
+        r"libsemigroups::DynamicMatrix<libsemigroups::BooleanPlus, "
+        r"libsemigroups::BooleanProd, libsemigroups::BooleanZero, "
+        r"libsemigroups::BooleanOne, int>"
+    ): r"Matrix",
 }
 
 # This dictionary should be of the form class_name -> (pattern, repl), where
@@ -216,6 +228,10 @@ def no_doc_run(self):
         ("PTransfBase16", "StaticPerm16"),
         ("Transf", "StaticPerm16"),
     ],
+    "Sims1": [("SubclassType", "Sims1")],
+    "Sims2": [("SubclassType", "Sims2")],
+    "RepOrc": [("SubclassType", "RepOrc")],
+    "MinimalRepOrc": [("SubclassType", "MinimalRepOrc")],
 }
 
 # This is what sphinx considers to be a signature

docs/source/index.rst

@@ -71,6 +71,7 @@ See the installation instructions:
    main-algorithms/knuth-bendix/index
    main-algorithms/konieczny/index
    main-algorithms/radoszewski-rytter/index
+   main-algorithms/sims/index
    main-algorithms/stephen/index
    main-algorithms/todd-coxeter/index
    main-algorithms/ukkonen/index

docs/source/main-algorithms/sims/index.rst

@@ -0,0 +1,20 @@
+.. Copyright (c) 2024 R. Cirpons
+
+   Distributed under the terms of the GPL license version 3.
+
+   The full license is in the file LICENSE, distributed with this software.
+
+Sims
+=======
+
+This page contains links to the functionality in ``libsemigroups_pybind11``
+related to Sims's low-index congruence algorithm
+:cite:`Anagnostopoulou-Merkouri2023aa` for finitely presented semigroups.
+
+.. toctree::
+   :maxdepth: 1
+
+   sims
+   sims-helpers
+
+

docs/source/main-algorithms/sims/sims-helpers.rst

@@ -0,0 +1,38 @@
+.. Copyright (c) 2024 R. Cirpons
+
+   Distributed under the terms of the GPL license version 3.
+
+   The full license is in the file LICENSE, distributed with this software.
+
+.. currentmodule:: _libsemigroups_pybind11
+
+Sims helpers
+============
+
+This page contains the documentation for various helper functions for
+manipulating ``Sims1``, ``Sims2``, ``RepOrc`` or ``MinimalRepOrc``  objects.
+All such functions are contained in the submodule
+``libsemigroups_pybind11.sims``.
+
+
+Contents
+--------
+
+.. currentmodule:: libsemigroups_pybind11.sims
+
+.. autosummary::
+   :nosignatures:
+
+   is_maximal_right_congruence
+   is_right_congruence
+   is_right_congruence_of_dual
+   is_two_sided_congruence
+   poset
+   right_generating_pairs
+   two_sided_generating_pairs
+
+Full API
+--------
+.. automodule:: libsemigroups_pybind11.sims
+   :members:
+   :imported-members:

docs/source/main-algorithms/sims/sims.rst

@@ -0,0 +1,76 @@
+.. Copyright (c) 2024 R. Cirpons
+
+   Distributed under the terms of the GPL license version 3.
+
+   The full license is in the file LICENSE, distributed with this software.
+
+.. currentmodule:: _libsemigroups_pybind11
+
+Sims
+====
+
+On this page we describe the functionality relating to the Sims's
+low-index congruence algorithm for semigroups and monoids that is available in
+``libsemigroups_pybind11``. This page contains a details of the methods
+of the classes:
+
+* :py:class:`Sims1` for computing finite index right congruences,
+* :py:class:`Sims2` for computing finite index two-sided congruences,
+* :py:class:`RepOrc` for computing small degree transformation representations of a finite semigroup or monoid,
+* :py:class:`MinimalRepOrc` for computing minimal degree transformation representations of a finite semigroup or monoid.
+
+.. doctest::
+
+   >>> from libsemigroups_pybind11 import Sims1, Presentation, presentation
+   >>> p = Presentation([0, 1])
+   >>> presentation.add_rule(p, [0, 1], [1, 0])
+   >>> sims = Sims1(p)
+   >>> sims.number_of_congruences(4)
+   117
+
+Contents
+--------
+
+.. autosummary::
+   :nosignatures:
+
+   ~Sims1
+   ~Sims2
+   ~RepOrc
+   ~MinimalRepOrc
+   ~SimsStats
+   ~SimsRefinerFaithful
+   ~SimsRefinerIdeals
+
+Full API
+--------
+
+.. autoclass:: Sims1
+   :members:
+   :inherited-members:
+
+.. autoclass:: Sims2
+   :members:
+   :inherited-members:
+
+.. autoclass:: RepOrc
+   :members:
+   :inherited-members:
+
+.. autoclass:: MinimalRepOrc
+   :members:
+   :inherited-members:
+
+.. autoclass:: SimsStats
+   :members:
+   :inherited-members:
+
+.. autoclass:: SimsRefinerFaithful
+   :members:
+   :inherited-members:
+   :special-members: __call__
+
+.. autoclass:: SimsRefinerIdeals
+   :members:
+   :inherited-members:
+   :special-members: __call__

libsemigroups_pybind11/__init__.py

@@ -64,6 +64,12 @@
         Dot,
         PBR,
         Ukkonen,
+        Sims1,
+        Sims2,
+        RepOrc,
+        MinimalRepOrc,
+        SimsRefinerFaithful,
+        SimsRefinerIdeals,
     )
 except ModuleNotFoundError as e:
     raise ModuleNotFoundError(

libsemigroups_pybind11/sims.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2024 R. Cirpons
+#
+# Distributed under the terms of the GPL license version 3.
+#
+# The full license is in the file LICENSE, distributed with this software.
+
+# pylint: disable=no-name-in-module, invalid-name, unused-import, fixme,
+# pylint: disable=unidiomatic-typecheck
+
+"""
+This package provides the user-facing python part of libsemigroups_pybind11 for
+the Sims class from libsemigroups.
+"""
+
+from _libsemigroups_pybind11 import (
+    right_generating_pairs,
+    two_sided_generating_pairs,
+    is_right_congruence,
+    is_right_congruence_of_dual,
+    is_two_sided_congruence,
+    is_maximal_right_congruence,
+    poset,
+)

pyproject.toml

@@ -10,3 +10,11 @@ requires = [
 ]
 
 build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+markers = [
+    "quick",
+    "standard",
+    "extreme",
+    "fail",
+]

src/main.cpp

@@ -154,6 +154,7 @@ namespace libsemigroups {
     init_present(m);
     init_inverse_present(m);
     init_to_present(m);
+    init_sims(m);
     init_transf(m);
     init_ranges(m);
     init_words(m);

src/main.hpp

@@ -42,6 +42,7 @@ namespace libsemigroups {
   void init_present(py::module&);
   void init_inverse_present(py::module&);
   void init_to_present(py::module&);
+  void init_sims(py::module&);
   void init_transf(py::module&);
   void init_ranges(py::module&);
   void init_words(py::module&);