libsemigroups · james-d-mitchell · Jun 11, 2025 · Jun 9, 2025 · Jun 10, 2025 · Jun 10, 2025
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -246,7 +246,7 @@ Each class that does not have a helper namespace should have a ``.rst`` file in
 
         The full license is in the file LICENSE, distributed with this software.
 
-    .. currentmodule:: _libsemigroups_pybind11
+    .. currentmodule:: libsemigroups_pybind11
 
     Class-Name
     ==========
@@ -311,7 +311,7 @@ A sample ``class-helpers.rst`` may look like this:
 
     The full license is in the file LICENSE, distributed with this software.
 
-  .. currentmodule:: _libsemigroups_pybind11
+  .. currentmodule:: libsemigroups_pybind11
 
   Class-name helpers
   ====================

diff --git a/docs/source/_ext/libsemigroups_pybind11_extensions.py b/docs/source/_ext/libsemigroups_pybind11_extensions.py
@@ -60,7 +60,9 @@ def doc_only_run(self):
         docstring = list(node.findall(condition=desc_content))
 
         if not docstring:
-            logger.warning(f"The docstring for {self.arguments[0]} cannot be found.")
+            logger.warning(
+                f"The docstring for {self.arguments[0]} cannot be found."
+            )
             return []
 
         return docstring
@@ -104,6 +106,7 @@ def no_doc_run(self):
     r"libsemigroups::Sims2": r"Sims2",
     r"libsemigroups::RepOrc": r"RepOrc",
     r"libsemigroups::MinimalRepOrc": r"MinimalRepOrc",
+    r"_?libsemigroups_pybind11\.": "",
 }
 
 # This dictionary should be of the form class_name -> (pattern, repl), where

diff --git a/docs/source/data-structures/elements/bipart.rst b/docs/source/data-structures/elements/bipart.rst
diff --git a/docs/source/data-structures/elements/bipart/class.rst b/docs/source/data-structures/elements/bipart/class.rst
@@ -0,0 +1,43 @@
+..
+    Copyright (c) 2021-2024 J. D. Mitchell
+
+    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
+
+The Bipartition class
+=====================
+
+.. autoclass:: Bipartition
+    :doc-only:
+    :class-doc-from: class
+
+Contents
+--------
+
+.. autosummary::
+    :signatures: short
+
+    ~Bipartition
+    Bipartition.copy
+    Bipartition.degree
+    Bipartition.is_transverse_block
+    Bipartition.iterator
+    Bipartition.left_blocks
+    Bipartition.lookup
+    Bipartition.number_of_blocks
+    Bipartition.number_of_left_blocks
+    Bipartition.number_of_right_blocks
+    Bipartition.one
+    Bipartition.rank
+    Bipartition.right_blocks
+
+Full API
+--------
+
+.. autoclass:: Bipartition
+    :members:
+    :class-doc-from: init
+    :inherited-members:
diff --git a/...ta-structures/elements/bipart-helpers.rst → ...ta-structures/elements/bipart/helpers.rst b/...ta-structures/elements/bipart-helpers.rst → ...ta-structures/elements/bipart/helpers.rst
diff --git a/docs/source/data-structures/elements/bipart/index.rst b/docs/source/data-structures/elements/bipart/index.rst
@@ -0,0 +1,18 @@
+..
+    Copyright (c) 2025 Joseph Edwards
+
+    Distributed under the terms of the GPL license version 3.
+
+    The full license is in the file LICENSE, distributed with this software.
+
+Bipartitions
+============
+
+This page describes the functionality for bipartitions in
+``libsemigroups_pybind11``.
+
+.. toctree::
+    :maxdepth: 1
+
+    class
+    helpers
diff --git a/...ource/data-structures/elements/blocks.rst → ...data-structures/elements/blocks/class.rst b/...ource/data-structures/elements/blocks.rst → ...data-structures/elements/blocks/class.rst
@@ -5,22 +5,14 @@
 
     The full license is in the file LICENSE, distributed with this software.
 
-.. currentmodule:: _libsemigroups_pybind11
+.. currentmodule:: libsemigroups_pybind11
 
-Blocks
-======
+The Blocks class
+================
 
-This page contains an overview of the functionality in
-``libsemigroups_pybind11`` for blocks. See also :any:`Bipartition` for more
-details and context.
-
-There are a number of functions for computing things about :py:class:`Blocks`
-objects detailed below.
-
-.. toctree::
-    :maxdepth: 1
-
-    blocks-helpers
+.. autoclass:: Blocks
+    :doc-only:
+    :class-doc-from: class
 
 Contents
 --------
@@ -41,7 +33,6 @@ Full API
 --------
 
 .. autoclass:: Blocks
-    :class-doc-from: class
     :members:
+    :class-doc-from: init
     :inherited-members:
-    :special-members: __init__
diff --git a/...ta-structures/elements/blocks-helpers.rst → ...ta-structures/elements/blocks/helpers.rst b/...ta-structures/elements/blocks-helpers.rst → ...ta-structures/elements/blocks/helpers.rst
diff --git a/docs/source/data-structures/elements/blocks/index.rst b/docs/source/data-structures/elements/blocks/index.rst
@@ -0,0 +1,17 @@
+..
+    Copyright (c) 2025 Joseph Edwards
+
+    Distributed under the terms of the GPL license version 3.
+
+    The full license is in the file LICENSE, distributed with this software.
+
+Blocks
+======
+
+This page describes the functionality for blocks in ``libsemigroups_pybind11``.
+
+.. toctree::
+    :maxdepth: 1
+
+    class
+    helpers
diff --git a/docs/source/data-structures/elements/index.rst b/docs/source/data-structures/elements/index.rst
@@ -14,10 +14,8 @@ for defining elements of semigroups.
 .. toctree::
     :maxdepth: 1
 
-    bipart
-    blocks
+    bipart/index
+    blocks/index
     matrix/index
-    pperm
-    perm
-    pbr
-    transf
+    pbr/index
+    transformations/index
diff --git a/docs/source/data-structures/elements/matrix/bmat8-helpers.rst b/docs/source/data-structures/elements/matrix/bmat8-helpers.rst
@@ -5,10 +5,10 @@
 
     The full license is in the file LICENSE, distributed with this software.
 
-.. currentmodule:: _libsemigroups_pybind11
+.. currentmodule:: libsemigroups_pybind11
 
-The bmat8 submodule
-===================
+BMat8 helpers
+=============
 
 This page contains the documentation for various helper functions for
 manipulating :any:`BMat8` objects. All these functions are contained in the

diff --git a/docs/source/data-structures/elements/matrix/bmat8.rst b/docs/source/data-structures/elements/matrix/bmat8.rst
@@ -5,10 +5,10 @@
 
     The full license is in the file LICENSE, distributed with this software.
 
-.. currentmodule:: _libsemigroups_pybind11
+.. currentmodule:: libsemigroups_pybind11
 
-BMat8
-=====
+The BMat8 class
+===============
 
 .. autoclass:: BMat8
     :doc-only:
@@ -21,6 +21,8 @@ Contents
     :signatures: short
 
     ~BMat8
+    BMat8.copy
+    BMat8.degree
     BMat8.swap
     BMat8.to_int
 

diff --git a/docs/source/data-structures/elements/matrix/index.rst b/docs/source/data-structures/elements/matrix/index.rst
@@ -10,12 +10,13 @@
 Matrix
 ======
 
-It is possible to represent matrices over various semirings in
-``libsemigroups_pybind11``. The classes for matrices in
-``libsemigroups_pybind11`` are:
+This page describes the functionality for matrices over various semirings in
+``libsemigroups_pybind11``.
 
 .. toctree::
     :maxdepth: 1
 
     bmat8
+    bmat8-helpers
     matrix
+    matrix-helpers
diff --git a/docs/source/data-structures/elements/matrix/matrix-helpers.rst b/docs/source/data-structures/elements/matrix/matrix-helpers.rst
@@ -7,8 +7,8 @@
 
 .. currentmodule:: libsemigroups_pybind11
 
-The matrix submodule
-====================
+Matrix helpers
+==============
 
 This page contains the documentation for various helper functions for
 manipulating :any:`Matrix` objects. All these functions are contained in the

diff --git a/docs/source/data-structures/elements/matrix/matrix.rst b/docs/source/data-structures/elements/matrix/matrix.rst
@@ -26,12 +26,7 @@ While :py:class:`Matrix` is not a class the objects returned by
 as if it was a class.
 
 Some helper functions for :py:class:`Matrix` objects are documented in the
-submodule ``matrix``.
-
-.. toctree::
-    :maxdepth: 1
-
-    matrix-helpers
+submodule :any:`libsemigroups_pybind11.matrix`.
 
 .. doctest::
 
@@ -155,40 +150,6 @@ MatrixKind
 ----------
 
 .. autoclass:: MatrixKind
-    :show-inheritance:
-
-    .. autoattribute:: Boolean
-
-        For matrices over the Boolean semiring.
-
-    .. autoattribute:: Integer
-
-        For matrices over the usual ring of integers.
-
-    .. autoattribute:: MaxPlus
-
-        For matrices over the max-plus semiring.
-
-    .. autoattribute:: MinPlus
-
-        For matrices over the min-plus semiring.
-
-    .. autoattribute:: ProjMaxPlus
-
-        For projective matrices over the max-plus semiring.
-
-    .. autoattribute:: MaxPlusTrunc
-
-        For matrices over the truncated max-plus semiring.
-
-    .. autoattribute:: MinPlusTrunc
-
-        For matrices over the truncated min-plus semiring.
-
-    .. autoattribute:: NTP
-
-        For matrices over the semiring of natural numbers quotiented by `t = t +
-        p`.
 
 ..
     TODO later summary

diff --git a/docs/source/data-structures/elements/pbr.rst → ...ce/data-structures/elements/pbr/class.rst b/docs/source/data-structures/elements/pbr.rst → ...ce/data-structures/elements/pbr/class.rst
@@ -7,35 +7,29 @@
 
 .. currentmodule:: libsemigroups_pybind11
 
-PBR
-===
+The PBR class
+=============
 
-This page contains an overview of the functionality in
-``libsemigroups_pybind11`` for partitioned binary relations (PBRs).
-
-There are a number of functions for computing things about :py:class:`PBR`
-objects detailed below.
-
-.. toctree::
-    :maxdepth: 1
-
-    pbr-helpers
+.. autoclass:: PBR
+    :doc-only:
+    :class-doc-from: class
 
 Contents
 --------
 
 .. autosummary::
     :signatures: short
 
+    ~PBR
     PBR.copy
     PBR.degree
     PBR.number_of_points
+    PBR.product_inplace
 
 Full API
 --------
 
 .. autoclass:: PBR
-    :class-doc-from: class
     :members:
+    :class-doc-from: init
     :inherited-members:
-    :special-members: __init__
diff --git a/.../data-structures/elements/pbr-helpers.rst → .../data-structures/elements/pbr/helpers.rst b/.../data-structures/elements/pbr-helpers.rst → .../data-structures/elements/pbr/helpers.rst
diff --git a/docs/source/data-structures/elements/pbr/index.rst b/docs/source/data-structures/elements/pbr/index.rst
@@ -0,0 +1,18 @@
+..
+    Copyright (c) 2025 Joseph Edwards
+
+    Distributed under the terms of the GPL license version 3.
+
+    The full license is in the file LICENSE, distributed with this software.
+
+Partitioned binary relations (PBRs)
+===================================
+
+This page describes the functionality for partitioned binary relations (PBRs) in
+``libsemigroups_pybind11``.
+
+.. toctree::
+    :maxdepth: 1
+
+    class
+    helpers