Cleanups + add Congruence

.gitignore

@@ -19,3 +19,4 @@ docs/source/api/Perm.rst
 docs/source/api/Transf.rst
 gh-pages/
 htmlcov
+.cache

Makefile

@@ -22,6 +22,7 @@ check: doctest
 	pytest -vv tests/test_*.py
 
 lint:
+	ruff check --exit-zero setup.py tests/*.py libsemigroups_pybind11/*.py docs/source/conf.py
 	pylint --exit-zero setup.py tests/*.py libsemigroups_pybind11/*.py docs/source/conf.py
 	cpplint src/*.hpp src/*.cpp
 

docs/source/conf.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 # pylint:disable=redefined-builtin, invalid-name, too-many-arguments,
 # pylint:disable=unbalanced-tuple-unpacking, unused-argument, too-many-locals
-# pylint:disable=unused-import
+# pylint:disable=unused-import, too-many-positional-arguments
 """
 This provides configuration for the generation of the docs
 """
@@ -56,7 +56,9 @@ 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
@@ -102,7 +104,9 @@ def no_doc_run(self):
 source_suffix = ".rst"
 master_doc = "index"
 project = "libsemigroups_pybind11"
-copyright = "2021-2024, Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
+copyright = (
+    "2021-2024, Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
+)
 author = "Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte"
 version = "1.0.0"
 release = "1.0.0"
@@ -225,7 +229,7 @@ def sig_alternative(doc, signature, return_annotation):
     return new_sig, return_annotation
 
 
-def change_sig(  # pylint: disable=too-many-arguments,too-many-positional-arguments
+def change_sig(
     app=None,
     what=None,
     name=None,
@@ -300,10 +304,12 @@ def make_only_doc(lines):
         del lines[-3:]
 
     if not called_correctly:
-        raise RuntimeError(
-            ":only-document-once: has been invoked in a function where "
-            "documentation has not been repeated. Invoked in:\n" + "\n".join(lines)
+        print(
+            "\033[93m:only-document-once: has been invoked in a function where "
+            "documentation has not been repeated. Invoked in:\n"
+            + "\n\033[0m".join(lines)
         )
+        return
 
     # If the new doc shouldn't be overloaded, remove the "Overloaded
     # function" part
@@ -312,7 +318,7 @@ def make_only_doc(lines):
             del lines[0]
 
 
-def only_doc_once(app, what, name, obj, options, lines):  # pylint:disable=too-many-arguments,too-many-positional-arguments
+def only_doc_once(app, what, name, obj, options, lines):
     """
     Edit docstring to only include one version of the doc for an overloaded
     function if necessary
@@ -322,7 +328,7 @@ def only_doc_once(app, what, name, obj, options, lines):  # pylint:disable=too-m
         make_only_doc(lines)
 
 
-def fix_overloads(app, what, name, obj, options, lines):  # pylint:disable=too-many-arguments,too-many-positional-arguments
+def fix_overloads(app, what, name, obj, options, lines):
     """Indent overloaded function documentation and format signatures"""
     overloading = False
     overloaded_function = ""
@@ -339,8 +345,11 @@ def fix_overloads(app, what, name, obj, options, lines):  # pylint:disable=too-m
         # Start overloading and capture the name of the overloaded function
         if "Overloaded function." in line:
             overloading = True
-            m = re.search(r"\s*?\d+\. (.*?)\(", input[i + 2])
-            if not m:
+            try:
+                m = re.search(r"\s*?\d+\. (.*?)\(", input[i + 2])
+                if not m:
+                    return
+            except IndexError:
                 return
             overloaded_function = m.group(1)
             new_name = re.sub(r"^.*\.", "", name)
@@ -389,20 +398,24 @@ def fix_overloads(app, what, name, obj, options, lines):  # pylint:disable=too-m
 # replacements will be made in each docstring, and will be useful for removing
 # things like the signatures that sphinx inserts into every docstring
 docstring_replacements = {
+    r"_current_index_of.*$": "",
+    r"_number_of_classes.*$": "",
     r"aho_corasick_dot\(.*\)(\s*->\s*(\w+::)*\w*)?": "",
+    r"congruence_non_trivial_classes.*$": "",
+    r"congruence_partition.*$": "",
+    r"kambites_normal_forms.*$": "",
+    r"knuth_bendix_non_trivial_classes.*$": "",
     r"pbr_one\(\*args, \*\*kwargs\)": "",
-    r"word_graph_dot\(.*\)(\s*->\s*(\w+::)*\w*)?": "",
     r"todd_coxeter_is_non_trivial.*$": "",
     r"todd_coxeter_non_trivial_class.*$": "",
+    r"todd_coxeter_normal_forms.*$": "",
     r"todd_coxeter_partition.*$": "",
     r"todd_coxeter_redundant_rule.*$": "",
-    r"todd_coxeter_str_normal_forms.*$": "",
-    r"todd_coxeter_word_normal_forms.*$": "",
-    r"kambites_normal_forms.*$": "",
+    r"word_graph_dot\(.*\)(\s*->\s*(\w+::)*\w*)?": "",
 }
 
 
-def remove_doc_annotations(app, what, name, obj, options, lines):  # pylint:disable=too-many-arguments,too-many-positional-arguments
+def remove_doc_annotations(app, what, name, obj, options, lines):
     """Remove any special decorations from the documentation"""
     for i in range(len(lines) - 1, -1, -1):
         for bad, good in docstring_replacements.items():

docs/source/index.rst

@@ -65,15 +65,15 @@ See the installation instructions:
    :caption: Main Algorithms
    :hidden:
 
-   main-algorithms/action/index.rst
-   main-algorithms/cong-intf/index.rst
+   main-algorithms/action/index
    main-algorithms/congruences/index
    main-algorithms/froidure-pin/index
    main-algorithms/kambites/index
    main-algorithms/knuth-bendix/index
    main-algorithms/konieczny/index
    main-algorithms/radoszewski-rytter/index
    main-algorithms/schreier-sims/index
+   main-algorithms/sims/index
    main-algorithms/stephen/index
    main-algorithms/todd-coxeter/index
 

docs/source/main-algorithms/congruences/cong.rst

@@ -1,12 +1,39 @@
-.. Copyright (c) 2021-2024 J. D. Mitchell
+.. Copyright (c) 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
 
-Congruence
-==========
+The CongruenceWord class
+========================
 
-TODO
+.. autoclass:: CongruenceWord
+   :doc-only:
+   :class-doc-from: class
+
+Contents
+--------
+
+.. autosummary::
+   :nosignatures:
+
+   ~CongruenceWord
+   CongruenceWord.add_generating_pair
+   CongruenceWord.contains
+   CongruenceWord.copy
+   CongruenceWord.currently_contains
+   CongruenceWord.generating_pairs
+   CongruenceWord.init
+   CongruenceWord.max_threads
+   CongruenceWord.number_of_classes
+   CongruenceWord.number_of_runners
+   CongruenceWord.presentation
+
+Full API
+--------
+
+.. autoclass:: CongruenceWord
+   :class-doc-from: init
+   :members: