First pass formatting changes to docs

docs/source/conf.py

@@ -55,7 +55,9 @@ 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
@@ -101,7 +103,9 @@ 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"
@@ -158,6 +162,8 @@ def no_doc_run(self):
         r"libsemigroups::IntegerProd<long long>, libsemigroups::IntegerZero"
         r"<long long>, libsemigroups::IntegerOne<long long>, long long>"
     ): r"Matrix",
+    r"libsemigroups::Sims1": r"Sims1",
+    r"SimsSettingsSims1": r"Sims1",
 }
 
 # This dictionary should be of the form class_name -> (pattern, repl), where
@@ -181,6 +187,10 @@ def no_doc_run(self):
     "FroidurePinPBR": [(r"\bPBR\b", "Element")],
     "SchreierSimsPerm1": [(r"\bPerm1\b", "Element")],
     "ReversiblePaths": [(r"\bPaths\b", "ReversiblePaths")],
+    "Sims1": [("SubclassType", "Sims1")],
+    "Sims2": [("SubclassType", "Sims2")],
+    "RepOrc": [("SubclassType", "RepOrc")],
+    "MinimalRepOrc": [("SubclassType", "MinimalRepOrc")],
 }
 
 # This is what sphinx considers to be a signature
@@ -302,7 +312,8 @@ def make_only_doc(lines):
     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)
+            "documentation has not been repeated. Invoked in:\n"
+            + "\n".join(lines)
         )
 
     # If the new doc shouldn't be overloaded, remove the "Overloaded
@@ -312,7 +323,9 @@ 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
+):  # pylint:disable=too-many-arguments,too-many-positional-arguments
     """
     Edit docstring to only include one version of the doc for an overloaded
     function if necessary
@@ -322,7 +335,9 @@ 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
+):  # pylint:disable=too-many-arguments,too-many-positional-arguments
     """Indent overloaded function documentation and format signatures"""
     overloading = False
     overloaded_function = ""
@@ -395,7 +410,9 @@ def fix_overloads(app, what, name, obj, options, lines):  # pylint:disable=too-m
 }
 
 
-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
+):  # pylint:disable=too-many-arguments,too-many-positional-arguments
     """Remove any special decorations from the documentation"""
     for i in range(len(lines) - 1, -1, -1):
         for bad, good in docstring_replacements.items():