doc: link libsemigroups

Author: james-d-mitchell

docs/source/authors.rst

@@ -26,8 +26,9 @@ 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 some issues with the
   packaging.
 
 .. _nicolas thiery: http://nicolas.thiery.name/
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 

docs/source/data-structures/adapters/index.rst

@@ -11,10 +11,12 @@ Adapters
 ========
 
 This page describes some of the adapters used in ``libsemigroups_pybind11``.
-These are classes that permit the generic classes in ``libsemigroups`` to be
+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.
 
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 
+
 .. toctree::
     :maxdepth: 1
 

docs/source/data-structures/elements/index.rst

@@ -8,9 +8,11 @@
 Elements
 ========
 
-This page contains an overview summary of the functionality in ``libsemigroups``
+This page contains an overview summary of the functionality in libsemigroups_
 for defining elements of semigroups.
 
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 
+
 .. toctree::
     :maxdepth: 1
 

docs/source/data-structures/misc/libsemigroups-error.rst

@@ -25,7 +25,7 @@ Full API
 
     This is the main type of exception raised by the custom data-structures and
     algorithms of ``libsemigroups_pybind11``. It is raised when the underlying
-    C++ code from ``libsemigroups`` raises a ``LibsemigroupsException``.
+    C++ code from libsemigroups_ raises a ``LibsemigroupsException``.
 
     .. doctest:: python
 
@@ -48,4 +48,6 @@ Full API
         `issue tracker
         <https://github.com/libsemigroups/libsemigroups_pybind11/issues>`_.
 
-.. autofunction:: error_message_with_prefix
+.. autofunction:: error_message_with_prefix
+
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 

docs/source/data-structures/presentations/index.rst

@@ -8,7 +8,7 @@
 Presentations
 =============
 
-The ``libsemigroups`` C\ **++** library, and hence the
+The libsemigroups_ C\ **++** library, and hence the
 ``libsemigroups_pybind11`` Python package, implements several algorithms for
 computing with finitely presented semigroups and monoids. The implementation of
 the finite presentations on which these algorithms can be run is described
@@ -37,6 +37,8 @@ further details see, for example, :any:`Runner.run_for` and
 The classes and modules in ``libsemigroups_pybind11`` for finitely presented
 semigroups and monoids are:
 
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 
+
 .. toctree::
     :maxdepth: 1
 

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

@@ -10,9 +10,11 @@ Kambites
 
 On this page there are links to the documentation for the algorithms in
 ``libsemigroups_pybind11`` for small overlap monoids by Mark Kambites and the
-authors of ``libsemigroups``; see :cite:`Kambites2009aa`,
+authors of libsemigroups_; see :cite:`Kambites2009aa`,
 :cite:`Kambites2009ab`, and :cite:`Mitchell2021aa`.
 
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 
+
 .. toctree::
     :maxdepth: 1
 

docs/source/main-algorithms/todd-coxeter/index.rst

@@ -11,16 +11,18 @@ Todd-Coxeter
 ============
 
 This page contains documentation related to the implementation of the
-Todd-Coxeter algorithm :cite:`Coleman2022aa` in ``libsemigroups``.
+Todd-Coxeter algorithm :cite:`Coleman2022aa` in libsemigroups_.
 
 The purpose of this algorithm is to find the :any:`WordGraph` of the action of a
 semigroup or monoid on the classes of a 1-sided (right), or 2-sided congruence;
 see :cite:`Coleman2022aa` for more details.
 
-Similar to other places in ``libsemigroups`` it is possible to create a
+Similar to other places in libsemigroups_ it is possible to create a
 :any:`ToddCoxeter` object from a presentation consisting of strings or lists of
 integers.
 
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/ 
+
 .. toctree::
     :maxdepth: 1
 

src/cong.cpp

@@ -42,9 +42,9 @@ Class for running :any:`Kambites`,
 :any:`KnuthBendix`, and :any:`ToddCoxeter` in parallel.
 
 On this page we describe the functionality relating to the class
-:any:`Congruence` in ``libsemigroups``. This class can be used for computing a
+:any:`Congruence` in libsemigroups_. This class can be used for computing a
 congruence over a semigroup or monoid by running every applicable algorithm
-from ``libsemigroups`` (and some variants of the same algorithm) in parallel.
+from libsemigroups_ (and some variants of the same algorithm) in parallel.
 This class is provided for convenience, at present it is not very customisable,
 and lacks some of the fine grained control offered by the classes implementing
 individual algorithms, such as :any:`Kambites`,
@@ -248,7 +248,7 @@ obviously infinite; ``False`` is returned if it is not.
     congruence has infinitely many classes.
 )pbdoc");
     }  // bind_cong
-  }  // namespace
+  }    // namespace
 
   void init_cong(py::module& m) {
     bind_cong<word_type>(m, "CongruenceWord");

src/errors.cpp

@@ -80,14 +80,16 @@ namespace libsemigroups {
 Return whether :any:`LibsemigroupsError` messages have a C++ prefix.
 
 Since ``libsemigroups_pybind11`` is built on top of the C++ library
-``libsemigroups``, many of the errors thrown in ``libsemigroups_pybind11``
+libsemigroups_, many of the errors thrown in ``libsemigroups_pybind11``
 emanate from C++. This function returns whether :any:`LibsemigroupsError`
 messages contain a prefix that indicates which C++ function raised the
 exception.
 
 :return: Whether :any:`LibsemigroupsError` messages contain a prefix about the
   C++ function that raised the exception.
 :rtype: bool
+
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/
 )pbdoc");
     m.def("error_message_with_prefix",
           py::overload_cast<bool>(&error_message_with_prefix),
@@ -96,14 +98,16 @@ exception.
 Specify whether :any:`LibsemigroupsError` messages have a C++ prefix.
 
 Since ``libsemigroups_pybind11`` is built on top of the C++ library
-``libsemigroups``, many of the errors thrown in ``libsemigroups_pybind11``
+libsemigroups_, many of the errors thrown in ``libsemigroups_pybind11``
 emanate from C++. This function specifies whether :any:`LibsemigroupsError`
 messages should contain a prefix that indicates which C++ function raised the
 exception. By default, this information is not included.
 
 :param val: Whether :any:`LibsemigroupsError` messages should contain a prefix
   about the C++ function that raised the exception.
 :type val: bool
+
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/
 )pbdoc");
   }
 }  // namespace libsemigroups

src/word-graph.cpp

@@ -645,7 +645,7 @@ Adds a cycle consisting of *N* new nodes.
 Returns the adjacency matrix of a word graph.
 
 This function returns the adjacency matrix of the word graph *wg*. The
-type of the returned matrix depends on whether or not ``libsemigroups`` is
+type of the returned matrix depends on whether or not libsemigroups_ is
 compiled with `eigen <http://eigen.tuxfamily.org/>`_ enabled. The returned
 matrix has the number of edges with source ``s`` and target ``t`` in the
 ``(s, t)``-entry.
@@ -655,6 +655,8 @@ matrix has the number of edges with source ``s`` and target ``t`` in the
 
 :returns: The adjacency matrix.
 :rtype: numpy.ndarray | Matrix
+
+.. _libsemigroups: https://libsemigroups.github.io/libsemigroups/
 )pbdoc");
 
     m.def(