Joseph-Edwards · Sep 11, 2026 · Sep 8, 2026 · Sep 9, 2026
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -4,19 +4,19 @@ Information for developers
 How to compile
 --------------
 
-To build ``libsemigroups_pybind11``, it is first required to have a system
-install of ``libsemigroups``. This is explained in full detail in the
-``libsemigroups``
+To build libsemigroups_pybind11_, it is first required to have a system
+install of libsemigroups_. This is explained in full detail in the
+libsemigroups_
 `documentation <https://libsemigroups.github.io/libsemigroups/md_install.html>`_.
 
-If you only intend to contribute to ``libsemigroups_pybind11``, and not 
-``libsemigroups``, it is sufficient to have the conda version of
-``libsemigroups``.
+If you only intend to contribute to libsemigroups_pybind11_, and not 
+libsemigroups_, it is sufficient to have the conda version of
+libsemigroups_.
 
-If you intend to develop both ``libsemigroups`` and ``libsemigroups_pybind11``,
-it is recommended to build ``libsemigroups`` from the sources. Furthermore, it is
-recommended to install ``libsemigroups`` without ``hpcombi``. Then, with
-``libsemigroups`` installed, the Python bindings can be ``pip`` installed. This
+If you intend to develop both libsemigroups_ and libsemigroups_pybind11_,
+it is recommended to build libsemigroups_ from the sources. Furthermore, it is
+recommended to install libsemigroups_ without ``hpcombi``. Then, with
+libsemigroups_ installed, the Python bindings can be ``pip`` installed. This
 may require the environment variable ``$PKG_CONFIG_PATH`` to be edited.
 
 To create an environment with, ``pip``, correct environment variables, and some
@@ -63,7 +63,7 @@ For a system-wide installation (requires sudo):
 In both cases, ``-j8`` instructs the compiler to use 8 threads (adjust based on your
 system).
 
-To build the Python bindings (with CCache) inside the ``libsemigroups_pybind11``
+To build the Python bindings (with CCache) inside the libsemigroups_pybind11_
 directory:
 
 .. code-block:: console
@@ -73,10 +73,10 @@ directory:
 Building the skeleton of a class
 --------------------------------
 
-If you are adding the bindings for a ``libsemigroups`` class that does not yet
-exist in ``libsemigroups_pybind11``, please consider running the script
+If you are adding the bindings for a libsemigroups_ class that does not yet
+exist in libsemigroups_pybind11_, please consider running the script
 ``generate_pybind11.py`` found in the ``etc/`` directory of
-``libsemigroups``.
+libsemigroups_.
 
 For example:
 
@@ -105,7 +105,7 @@ ________________________________
 A basic guide on how to create bindings for a simple function can be found
 `here <https://pybind11.readthedocs.io/en/stable/basics.html#creating-bindings-for-a-simple-function>`__.
 
-In the ``libsemigroups`` context, to bind the function ``bar`` from the class
+In the libsemigroups_ context, to bind the function ``bar`` from the class
 ``foo`` to the module ``m``:
 
 .. code-block:: cpp
@@ -235,13 +235,13 @@ the code for the bindings of the ``Runner`` class will start with:
   pybind11::class_<Runner, Reporter> runner(m, "Runner");
                            ^^^^^^^^
 
-Making your functions available in ``libsemigroups_pybind11``
+Making your functions available in libsemigroups_pybind11_
 -------------------------------------------------------------
 
 If you followed the instructions in the ``generate_pybind11.py`` script from the
-``libsemigroups`` project, the class you have added bindings for should now be
+libsemigroups_ project, the class you have added bindings for should now be
 available in ``_libsemigroups_pybind11`` (note the leading underscore). How to
-make this available in ``libsemigroups_pybind11`` depends on several factors.
+make this available in libsemigroups_pybind11_ depends on several factors.
 
 A class with no helpers or templates
 ____________________________________
@@ -366,7 +366,7 @@ A sample ``index.rst`` file may look like this:
   =====
 
     This page describes the functionality for the class in
-    ``libsemigroups_pybind11``.
+    libsemigroups_pybind11_.
 
 
   .. toctree::
@@ -413,7 +413,7 @@ _______________________________
 Inside `<docs/source/index.rst>`__, you will find the table of contents tree
 (toctree) for this project. Within that, you will find the names of files
 (without the ``.rst`` extension) of different classifications of structures that
-``libsemigroups_pybind11`` implements, such as congruences, digraphs, semigroups
+libsemigroups_pybind11_ implements, such as congruences, digraphs, semigroups
 and words. Within each of these files, there is another toctree containing
 the paths to the docs of various classes.
 
@@ -497,3 +497,5 @@ whilst contributing are::
   ├── tests/
   │   └── test_class_name.py
   └── CONTRIBUTING.rst (this file!)
+
+.. _libsemigroups_pybind11: https://libsemigroups.github.io/libsemigroups_pybind11/
diff --git a/docs/source/_static/links.rst b/docs/source/_static/links.rst
@@ -4,3 +4,14 @@
 .. _Graphviz: https://www.graphviz.org
 .. _pybind11: https://pybind11.readthedocs.io/en/stable/#
 .. _HPCombi: https://libsemigroups.github.io/HPCombi/
+.. _GAP: https://www.gap-system.org/
+.. _ACE: https://gap-packages.github.io/ace/
+.. _Cython: https://cython.org/
+.. _cppyy: https://cppyy.readthedocs.io/en/latest/
+.. _Eigen: https://libeigen.gitlab.io/
+.. _pip: https://pip.pypa.io/en/stable/
+.. _mamba: https://mamba.readthedocs.io/en/latest/
+.. _Anaconda: https://www.anaconda.com/docs/main
+.. _Miniconda: https://continuumio-docs.readthedocs-hosted.com/miniconda/
+
+.. |libsemigroups_pybind11| replace:: :doc:`libsemigroups_pybind11 </index>`
diff --git a/docs/source/authors.rst b/docs/source/authors.rst
@@ -29,7 +29,7 @@ Contributors
 
 - `Nicolas Thiery`_ helped the authors understand the ecosystem for integrating
   C++ code into python, and to some preliminary versions of the python bindings
-  for libsemigroups_ using cython, and cppyy.
+  for libsemigroups_ using Cython_, and cppyy_.
 - Chinmaya Nagpal (chinmaya1011@gmail.com) resolved a great many issues with the
   packaging.
 - James Swent (jws20@st-andrews.ac.uk) contributed several implementations for

diff --git a/docs/source/changelog-v0.rst b/docs/source/changelog-v0.rst
@@ -11,13 +11,13 @@ Changelog - version 0
 v0.10.1 (released 29/03/2023)
 -----------------------------
 
-This release increases the required version of ``libsemigroups`` to v2.7.1,
+This release increases the required version of libsemigroups_ to v2.7.1,
 which contains some bug fixes.
 
 v0.10.0 (released 23/03/2023)
 -----------------------------
 
-This is a minor release adding some new functionality from ``libsemigroups``:
+This is a minor release adding some new functionality from libsemigroups_:
 
 - ukkonen: add support for ``Ukkonen`` + helpers by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/132
@@ -70,26 +70,26 @@ v0.7.3 (released 07/02/2023)
 ----------------------------
 
 This is a minor version with some improvements and adjustments for forthcoming
-changes in ``libsemigroups``.
+changes in libsemigroups_.
 
 v0.7.2 (released 12/01/2023)
 ----------------------------
 
-This is a minor change related to some forthcoming changes in ``libsemigroups``.
+This is a minor change related to some forthcoming changes in libsemigroups_.
 
 v0.7.1 (released 11/01/2023)
 ----------------------------
 
 This is a very minor release updating the required versions of some dependencies
-to permit the ``libsemigroups_pybind11`` wheel to be built with python 3.11, and
-to adapt for some recent changes in ``libsemigroups``.
+to permit the |libsemigroups_pybind11| wheel to be built with python 3.11, and
+to adapt for some recent changes in libsemigroups_.
 
 v0.7.0 (released 15/12/2022)
 ----------------------------
 
 This release contains a number of improvements and fixes, and adds support for
-the library of finite semigroup and monoid presentations in ``libsemigroups``
-and the ``Stephen`` class from ``libsemigroups``.
+the library of finite semigroup and monoid presentations in libsemigroups_
+and the ``Stephen`` class from libsemigroups_.
 
 - Add functionality for the presentation helper ``replace_word`` by @MTWhyte in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/84
@@ -104,23 +104,23 @@ v0.6.0 (released 02/12/2022)
 ----------------------------
 
 This release contains a number of improvements and fixes, and adds support for
-the ``Konieczny`` class from ``libsemigroups``.
+the ``Konieczny`` class from libsemigroups_.
 
 - Add missing header include in cong.cpp by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/77
 - Remove trivial rules by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/79
 - Fix string encoding in ``KnuthBendix`` by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/82
-- Add support for ``Konieczny`` from ``libsemigroups`` by @james-d-mitchell in
+- Add support for ``Konieczny`` from libsemigroups_ by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/80
 - Better ``__repr__`` for ``KnuthBendix`` by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/86
 
 v0.5.0 (released 16/11/2022)
 ----------------------------
 
-This is a minor release adding support for the ``libsemigroups`` class
+This is a minor release adding support for the libsemigroups_ class
 ``Kambites`` for computing small overlap monoids.
 
 v0.4.3 (released 09/11/2022)
@@ -133,20 +133,20 @@ package.
 v0.4.2 (released 28/10/2022)
 ----------------------------
 
-Update for version 2.3.2 of ``libsemigroups`` which contains some bugfixes.
+Update for version 2.3.2 of libsemigroups_ which contains some bugfixes.
 
 v0.4.1 (released 11/10/2022)
 ----------------------------
 
-Update for version 2.3.1 of ``libsemigroups`` which contains some bugfixes in
+Update for version 2.3.1 of libsemigroups_ which contains some bugfixes in
 the ``Sims1`` class, the ``Presentation`` class and its helper functions.
 
 v0.4.0 (released 04/10/2022)
 ----------------------------
 
 This is a minor release with a couple of new features added:
 
-- ``libsemigroups`` constants ``POSITIVE_INFINITY``, ``NEGATIVE_INFINITY``, and
+- libsemigroups_ constants ``POSITIVE_INFINITY``, ``NEGATIVE_INFINITY``, and
   ``UNDEFINED`` are properly supported;
 - ``libsemigroups::matrix_helper::pow`` is added as a method for ``__pow__`` for
   some types of matrices (those not defined over a runtime semiring);
@@ -156,15 +156,15 @@ and some minor improvements (the tests now use ``pytest`` exclusively).
 v0.3.0 (released 29/09/2022)
 ----------------------------
 
-This is a minor release adding support for the ``libsemigroups`` class ``Sims1``
+This is a minor release adding support for the libsemigroups_ class ``Sims1``
 for computing low index congruences, and some further minor changes to the
 ``Presentation`` class.
 
 v0.2.2 (released 16/09/2022)
 ----------------------------
 
 A very minor release to futureproof some tests against new versions of
-``libsemigroups``.
+libsemigroups_.
 
 v0.2.1 (released 12/09/2022)
 ----------------------------
@@ -174,7 +174,7 @@ A very minor release trying to fix an issue in the release process.
 v0.2.0 (released 10/09/2022)
 ----------------------------
 
-This is a minor release adding support for the ``libsemigroups`` class template
+This is a minor release adding support for the libsemigroups_ class template
 ``Presentation`` by @MTWhyte and @james-d-mitchell in:
 
 https://github.com/libsemigroups/libsemigroups_pybind11/pull/49
@@ -211,13 +211,13 @@ v0.1.4 (released 12/11/2021)
 ----------------------------
 
 Yet another minor release updating the C++ code for some forthcoming changes in
-``libsemigroups``.
+libsemigroups_.
 
 v0.1.3 (released 11/11/2021)
 ----------------------------
 
 A minor release updating the C++ code for some forthcoming changes in
-``libsemigroups``.
+libsemigroups_.
 
 v0.1.2 (released 11/11/2021)
 ----------------------------
@@ -238,5 +238,5 @@ Some minor issues were resolved and the function ``follow_path`` was added for
 v0.0.0 (released 24/09/2021)
 ----------------------------
 
-First release of the package, some functionality of ``libsemigroups`` is not yet
+First release of the package, some functionality of libsemigroups_ is not yet
 available.
diff --git a/docs/source/changelog-v1.rst b/docs/source/changelog-v1.rst
@@ -102,14 +102,14 @@ v1.0.0 (released 12/08/2025)
 ----------------------------
 
 This is a major release that significantly expands the API of
-``libsemigroups_pybind11`` to expose much of the functionality implemented in
+|libsemigroups_pybind11| to expose much of the functionality implemented in
 version 3 of libsemigroups_. The extent of the changes made in this release
 means that it is likely that any code written with earlier versions of
-``libsemigroups_pybind11`` will no longer work.
+|libsemigroups_pybind11| will no longer work.
 
-The structure of ``libsemigroups_pybind11`` is very tightly linked to the
+The structure of |libsemigroups_pybind11| is very tightly linked to the
 structure of libsemigroups_. Therefore, some of the differences between
-v0.10.1 and v1.0.0 of ``libsemigroups_pybind11`` will be related to the
+v0.10.1 and v1.0.0 of |libsemigroups_pybind11| will be related to the
 differences between v2 and v3 of libsemigroups_, such as changes to class names
 and interfaces. These changes can be found in the
 `libsemigroups changelog <https://libsemigroups.github.io/libsemigroups/md_changelog-v3.html>`_.
diff --git a/docs/source/data-structures/adapters/index.rst b/docs/source/data-structures/adapters/index.rst
@@ -10,7 +10,7 @@
 Adapters
 ========
 
-This page describes some of the adapters used in ``libsemigroups_pybind11``.
+This page describes some of the adapters used in |libsemigroups_pybind11|.
 These are classes that permit the generic classes in libsemigroups_ to be
 used with arbitrary types, provided that the adapters are implemented for these
 types.

diff --git a/docs/source/data-structures/constants/index.rst b/docs/source/data-structures/constants/index.rst
@@ -10,7 +10,7 @@
 Constants
 =========
 
-This page describes some of the constants used in ``libsemigroups_pybind11``.
+This page describes some of the constants used in |libsemigroups_pybind11|.
 
 Constant types
 --------------

diff --git a/docs/source/data-structures/elements/bipart/index.rst b/docs/source/data-structures/elements/bipart/index.rst
@@ -9,7 +9,7 @@ Bipartitions and blocks
 =======================
 
 This page describes the functionality for bipartitions and blocks in
-``libsemigroups_pybind11``.
+|libsemigroups_pybind11|.
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/source/data-structures/elements/matrix/index.rst b/docs/source/data-structures/elements/matrix/index.rst
@@ -11,7 +11,7 @@ Matrix
 ======
 
 This page describes the functionality for matrices over various semirings in
-``libsemigroups_pybind11``.
+|libsemigroups_pybind11|.
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/source/data-structures/elements/pbr/index.rst b/docs/source/data-structures/elements/pbr/index.rst
@@ -9,7 +9,7 @@ Partitioned binary relations (PBRs)
 ===================================
 
 This page describes the functionality for partitioned binary relations (PBRs) in
-``libsemigroups_pybind11``.
+|libsemigroups_pybind11|.
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/source/data-structures/elements/transformations/index.rst b/docs/source/data-structures/elements/transformations/index.rst
@@ -9,7 +9,7 @@ Transformations
 ===============
 
 This page describes the functionality for various partial transformations in
-``libsemigroups_pybind11``.
+|libsemigroups_pybind11|.
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/source/data-structures/enums/congruence-kind.rst b/docs/source/data-structures/enums/congruence-kind.rst
@@ -11,7 +11,7 @@ The congruence_kind enum
 ========================
 
 This page describes the enum class :any:`congruence_kind` in
-``libsemigroups_pybind11`` for representing the whether a congruence is one- or
+|libsemigroups_pybind11| for representing the whether a congruence is one- or
 two-sided.
 
 .. seealso:: 

diff --git a/docs/source/data-structures/enums/index.rst b/docs/source/data-structures/enums/index.rst
@@ -9,7 +9,7 @@ Enums
 =====
 
 In this section, we describe the :any:`Enum <enum.Enum>` classes available in
-``libsemigroups_pybind11``.
+|libsemigroups_pybind11|.
 
 .. toctree::
     :maxdepth: 1

diff --git a/docs/source/data-structures/enums/matrix-kind.rst b/docs/source/data-structures/enums/matrix-kind.rst
@@ -11,7 +11,7 @@ The MatrixKind enum
 ===================
 
 This page describes the enum class :any:`MatrixKind` in
-``libsemigroups_pybind11`` for representing the semiring of elements in a
+|libsemigroups_pybind11| for representing the semiring of elements in a
 matrix.
 
 .. seealso::

diff --git a/docs/source/data-structures/enums/order.rst b/docs/source/data-structures/enums/order.rst
@@ -10,7 +10,7 @@
 The Order enum
 ===============
 
-This page describes the enum class :any:`Order` in ``libsemigroups_pybind11``
+This page describes the enum class :any:`Order` in |libsemigroups_pybind11|
 for representing the order of words.
 
 Full API

diff --git a/docs/source/data-structures/enums/paths-algorithm.rst b/docs/source/data-structures/enums/paths-algorithm.rst
@@ -10,7 +10,7 @@
 The paths.algorithm enum
 ========================
 
-This page describes the enum class :any:`paths.algorithm` in ``libsemigroups_pybind11``.
+This page describes the enum class :any:`paths.algorithm` in |libsemigroups_pybind11|.
 
 Full API
 --------