Format the doc

Author: james-d-mitchell

docs/source/authors.rst

@@ -1,10 +1,11 @@
-.. Copyright (c) 2021-2024 J. D. Mitchell
+..
+    Copyright (c) 2021-2024 J. D. Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
-.. _Authors:
+.. _authors:
 
 Authors
 =======
@@ -14,16 +15,19 @@ Authors
 - `Maria Tsalakou`_ (mt200@st-andrews.ac.uk)
 - Murray Whyte (mw231@st-andrews.ac.uk)
 
-.. _Joseph Edwards: https://github.com/Joseph-Edwards
-.. _James Mitchell: https://jdbm.me
-.. _Maria Tsalakou: https://mariatsalakou.github.io/
+.. _james mitchell: https://jdbm.me
+
+.. _joseph edwards: https://github.com/Joseph-Edwards
+
+.. _maria tsalakou: https://mariatsalakou.github.io/
 
 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.
-- Chinmaya Nagpal (chinmaya1011@gmail.com) resolved some issues with the packaging.
+- `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.
+- Chinmaya Nagpal (chinmaya1011@gmail.com) resolved some issues with the
+  packaging.
 
-.. _Nicolas Thiery: http://nicolas.thiery.name/
+.. _nicolas thiery: http://nicolas.thiery.name/

docs/source/biblio.rst

@@ -1,11 +1,12 @@
-.. Copyright (c) 2021-2024 J. D. Mitchell
+..
+    Copyright (c) 2021-2024 J. D. Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 Bibliography
 ============
 
 .. bibliography:: libsemigroups.bib
-   :all:
+    :all:

docs/source/changelog.rst

@@ -1,8 +1,9 @@
-.. Copyright (c) 2021-2024, J. D. Mitchell
+..
+    Copyright (c) 2021-2024, J. D. Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 Changelog
 =========
@@ -18,9 +19,9 @@ v0.10.0 (released 23/03/2023)
 
 This is a minor release adding some new functionality from ``libsemigroups``:
 
-* ukkonen: add support for ``Ukkonen`` + helpers by @james-d-mitchell in
+- ukkonen: add support for ``Ukkonen`` + helpers by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/132
-* present: add further manip. funcs by @james-d-mitchell in
+- present: add further manip. funcs by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/136
 
 v0.9.2 (released 22/03/2023)
@@ -33,20 +34,20 @@ v0.9.1 (released 21/03/2023)
 
 This is a minor release with some minor improvements:
 
-* stephen: make ``accepts/is_left_factor`` call more robust by @james-d-mitchell
+- stephen: make ``accepts/is_left_factor`` call more robust by @james-d-mitchell
   in https://github.com/libsemigroups/libsemigroups_pybind11/pull/129
-* tests: add libsemigroups v2.7.0 special case by @james-d-mitchell in
+- tests: add libsemigroups v2.7.0 special case by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/130
 
 v0.9.0 (released 06/03/2023)
 ----------------------------
 
-This is a minor release including two changes and some minor improvements to
-the doc:
+This is a minor release including two changes and some minor improvements to the
+doc:
 
-* Improve ``ActionDigraph`` colours by @MTWhyte in
+- Improve ``ActionDigraph`` colours by @MTWhyte in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/125
-* Add support for ``ActionDigraph::cbegin/cend_pstilo`` by @james-d-mitchell in
+- Add support for ``ActionDigraph::cbegin/cend_pstilo`` by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/127
 
 v0.8.0 (released 28/02/2023)
@@ -55,15 +56,15 @@ v0.8.0 (released 28/02/2023)
 This is a minor version that adds all the features from the namespace
 ``libsemigroups::presentation`` to the package, these are:
 
-* ``add_zero_rules``
-* ``are_rules_sorted``
-* ``change_alphabet``
-* ``letter`` and ``character``
-* ``first_unused_letter``
-* ``greedy_reduce_length``
-* ``longest_rule``, ``shortest_rule``, ``longest_rule_length``, and
+- ``add_zero_rules``
+- ``are_rules_sorted``
+- ``change_alphabet``
+- ``letter`` and ``character``
+- ``first_unused_letter``
+- ``greedy_reduce_length``
+- ``longest_rule``, ``shortest_rule``, ``longest_rule_length``, and
   ``shortest_rule_length``
-* ``make_semigroup``
+- ``make_semigroup``
 
 v0.7.3 (released 07/02/2023)
 ----------------------------
@@ -74,15 +75,14 @@ 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``.
+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``.
 
 v0.7.0 (released 15/12/2022)
 ----------------------------
@@ -91,13 +91,13 @@ 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``.
 
-* Add functionality for the presentation helper ``replace_word`` by @MTWhyte in
+- Add functionality for the presentation helper ``replace_word`` by @MTWhyte in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/84
-* Out neighbours for action digraphs by @james-d-mitchell in
+- Out neighbours for action digraphs by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/91
-* Add functionality for the ``fpsemi-examples`` presentations by @MTWhyte in
+- Add functionality for the ``fpsemi-examples`` presentations by @MTWhyte in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/85
-* Stephen by @james-d-mitchell in
+- Stephen by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/93
 
 v0.6.0 (released 02/12/2022)
@@ -106,15 +106,15 @@ 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``.
 
-* Add missing header include in cong.cpp by @james-d-mitchell in
+- 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
+- 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
+- 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
+- Better ``__repr__`` for ``KnuthBendix`` by @james-d-mitchell in
   https://github.com/libsemigroups/libsemigroups_pybind11/pull/86
 
 v0.5.0 (released 16/11/2022)
@@ -127,8 +127,8 @@ v0.4.3 (released 09/11/2022)
 ----------------------------
 
 This is a very minor release which contains no functional changes, or bugfixes,
-but exists to allow zenodo.org to pick up the release and generate a doi for
-the package.
+but exists to allow zenodo.org to pick up the release and generate a doi for the
+package.
 
 v0.4.2 (released 28/10/2022)
 ----------------------------
@@ -141,25 +141,24 @@ v0.4.1 (released 11/10/2022)
 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);
+- ``libsemigroups::matrix_helper::pow`` is added as a method for ``__pow__`` for
+  some types of matrices (those not defined over a runtime semiring);
 
 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`` for computing low index congruences, and some further minor changes
-to the ``Presentation`` class.
+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)
 ----------------------------
@@ -184,15 +183,15 @@ v0.1.8 (released 27/01/2022)
 ----------------------------
 
 This is a very minor release which contains no functional changes, or bugfixes,
-but exists to fix an issue related to the wheel created for pypi on mac os x
-arm machines.
+but exists to fix an issue related to the wheel created for pypi on mac os x arm
+machines.
 
 v0.1.7 (released 27/01/2022)
 ----------------------------
 
 This is a very minor release which contains no functional changes, or bugfixes,
-but exists to fix an issue related to the wheel created for pypi on mac os x
-arm machines.
+but exists to fix an issue related to the wheel created for pypi on mac os x arm
+machines.
 
 v0.1.6 (released 02/12/2021)
 ----------------------------
@@ -239,5 +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 available.
+First release of the package, some functionality of ``libsemigroups`` is not yet
+available.

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

@@ -1,8 +1,9 @@
-.. Copyright (c) 2024 James Mitchell
+..
+    Copyright (c) 2024 James Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 .. currentmodule:: libsemigroups_pybind11
 
@@ -11,14 +12,14 @@ The ImageLeftAction class
 
 .. autoclass:: ImageLeftAction
     :doc-only:
-    :class-doc-from: class 
+    :class-doc-from: class
 
 Contents
 --------
 
 .. autosummary::
     :signatures: short
-    
+
     ~ImageLeftAction
     ImageLeftAction.__call__
 

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

@@ -1,8 +1,9 @@
-.. Copyright (c) 2024 James Mitchell
+..
+    Copyright (c) 2024 James Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 .. currentmodule:: libsemigroups_pybind11
 
@@ -11,14 +12,14 @@ The ImageRightAction class
 
 .. autoclass:: ImageRightAction
     :doc-only:
-    :class-doc-from: class 
+    :class-doc-from: class
 
 Contents
 --------
 
 .. autosummary::
     :signatures: short
-    
+
     ~ImageRightAction
     ImageRightAction.__call__
 

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

@@ -1,8 +1,9 @@
-.. Copyright (c) 2024 James Mitchell
+..
+    Copyright (c) 2024 James Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 .. currentmodule:: libsemigroups_pybind11
 
@@ -12,11 +13,10 @@ Adapters
 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. 
+types.
 
 .. toctree::
-   :maxdepth: 1
+    :maxdepth: 1
 
-   imagerightaction
-   imageleftaction
-  
+    imagerightaction
+    imageleftaction

docs/source/data-structures/elements/bipart-helpers.rst

@@ -1,8 +1,9 @@
-.. Copyright (c) 2024 J. D. Mitchell
+..
+    Copyright (c) 2024 J. D. Mitchell
 
-   Distributed under the terms of the GPL license version 3.
+    Distributed under the terms of the GPL license version 3.
 
-   The full license is in the file LICENSE, distributed with this software.
+    The full license is in the file LICENSE, distributed with this software.
 
 Bipartition helpers
 ===================
@@ -11,6 +12,6 @@ This page contains the documentation for various helper functions for
 manipulating bipartitions.
 
 .. automodule:: libsemigroups_pybind11.bipartition
-   :members:
-   :imported-members:
-   :exclude-members: Bipartition
+    :members:
+    :imported-members:
+    :exclude-members: Bipartition