Update doc and requirements.txt

docs/source/_ext/libsemigroups_pybind11_extensions.py

@@ -96,6 +96,9 @@ def no_doc_run(self):
 # replaced when the doc is built. It should be left empty.
 strings_replaced = set()
 
+# TODO(0): I think we ought to be able to get rid of almost all of the entries
+# in the filloeing two dictionaries
+
 # This dictionary should be of the form "bad type" -> "good type", and
 # replacements will be performed globally. Hyperlinks will be added in the
 # signature if "good type" is a valid (potentially user defined) python type
@@ -113,14 +116,12 @@ def no_doc_run(self):
 # "pattern" should be replaced by "repl" in the signature of all functions in
 # "class_name"
 class_specific_replacements = {
-    "Sims1": [("SubclassType", "Sims1"), ("SimsSettingsSims1", "Sims1")],
-    "Sims2": [("SubclassType", "Sims2"), ("SimsSettingsSims2", "Sims2")],
+    "Sims1": [("SimsSettingsSims1", "Sims1")],
+    "Sims2": [("SimsSettingsSims2", "Sims2")],
     "MinimalRepOrc": [
-        ("SubclassType", "MinimalRepOrc"),
         ("SimsSettingsMinimalRepOrc", "MinimalRepOrc"),
     ],
     "RepOrc": [
-        ("SubclassType", "RepOrc"),
         ("SimsSettingsRepOrc", "RepOrc"),
     ],
 }

docs/source/data-structures/words/to-string.rst

@@ -32,3 +32,4 @@ Full API
 .. autoclass:: ToString
     :class-doc-from: init
     :members:
+    :special-members: __call__

docs/source/data-structures/words/to-word.rst

@@ -32,3 +32,4 @@ Full API
 .. autoclass:: ToWord
     :class-doc-from: init
     :members:
+    :special-members: __call__

docs/source/main-algorithms/knuth-bendix/knuth-bendix.rst

@@ -54,7 +54,7 @@ Full API
     :members:
     :exclude-members: 
         options, run_for, run_until, run, finished, stopped, current_state, dead,
-        internal_generating_pairs, kill, last_report, report, report_every,
+        internal_generating_pairs, internal_presentation, kill, last_report, report, report_every,
         report_prefix, report_why_we_stopped, reset_last_report, reset_start_time,
         running, running_for, running_until, start_time, started, state,
         stopped_by_predicate, success, timed_out

etc/check-params.py

@@ -19,7 +19,7 @@ def warn(message):
     print(YELLOW + f"WARNING: {message}" + END_COLOUR)
 
 
-def extract_signature(func) -> tuple[dict[str, str], str]:
+def extract_signature(func, func_name) -> tuple[dict[str, str], str]:
     """Extract the parameters and typehints from the signature of a function
 
     This function interrogates the signature of a function and returns:
@@ -32,7 +32,7 @@ def extract_signature(func) -> tuple[dict[str, str], str]:
     for param in sig.find_all("em", class_="sig-param"):
         param_component = param.find_all("span", class_="n")
         if len(param_component) == 0 or len(param_component) > 2:
-            warn("unexpected element in doc. Skipping . . .")
+            warn(f"unexpected element in doc of {func_name}. Skipping . . .")
         elif len(param_component) == 1:
             param_to_typehint[param_component[0].get_text()] = ""
         else:
@@ -67,7 +67,6 @@ def extract_documented_signature(func, name) -> tuple[dict[str, str], str]:
     param_to_typehint = {}
     return_typehint = ""
     field_list = func.find("dl", class_="field-list simple")
-
     if not field_list:
         return param_to_typehint, return_typehint
 
@@ -157,7 +156,7 @@ def process_file(filename):
         content = f.read()
 
     soup = BeautifulSoup(content, "html.parser")
-    for func in soup.find_all("dl", class_="py function"):
+    for func in soup.find_all("dl", class_=lambda x: x in {"py function", "py method"}):
         first_segment = func.find("p")
         if first_segment and "Overloaded function" in first_segment.get_text():
             continue
@@ -167,7 +166,7 @@ def process_file(filename):
             sig_block = sig_block.parent.find_parent("dl").find("dt")
         func_name = sig_block["id"]
 
-        sig_params, sig_return_typehint = extract_signature(func)
+        sig_params, sig_return_typehint = extract_signature(func, func_name)
         doc_params, doc_return_typehint = extract_documented_signature(func, func_name)
 
         compare_parameters(sig_params, doc_params, func_name)

pyproject.toml

@@ -6,31 +6,23 @@
 #  * Use pre-commit
 #  * Use MyPy
 [build-system]
+build-backend = "setuptools.build_meta"
 requires = [
     "setuptools>=64",
     "setuptools-scm>=8",
     "pybind11",
     "pkgconfig",
     "packaging",
 ]
-build-backend = "setuptools.build_meta"
 
 [project]
-name = "libsemigroups_pybind11"
-dynamic = ["version"]
-description = "A python package for the libsemigroups C++ library."
-readme = "README.md"
 authors = [
     { name = "Reinis Cirpons", email = "rc234@st-andrews.ac.uk" },
     { name = "Joseph Edwards", email = "jde1@st-andrews.ac.uk" },
     { name = "James Mitchell", email = "jdm3@st-andrews.ac.uk" },
     { name = "Maria Tsalakou", email = "mt200@st-andrews.ac.uk" },
     { name = "Murray Whyte", email = "mw231@st-andrews.ac.uk" },
 ]
-# TODO: Uncomment and update
-# maintainers = [{ name = "My Organization", email = "myemail@email.com" }]
-requires-python = ">=3.9"
-dependencies = ["graphviz", "numpy", "typing_extensions"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Programming Language :: Python :: 3 :: Only",
@@ -43,67 +35,75 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Mathematics",
     "Natural Language :: English",
 ]
+dependencies = ["graphviz", "numpy", "typing_extensions"]
+description = "A python package for the libsemigroups C++ library."
+dynamic = ["version"]
 license = "GPL-3.0-or-later"
 license-files = ["LICENSE"]
+# TODO: Uncomment and update
+# maintainers = [{ name = "My Organization", email = "myemail@email.com" }]
+name            = "libsemigroups_pybind11"
+readme          = "README.md"
+requires-python = ">=3.9"
 
 [project.urls]
-Homepage = "https://github.com/libsemigroups/libsemigroups_pybind11"
+Changelog     = "https://libsemigroups.github.io/libsemigroups_pybind11/changelog.html"
 Documentation = "https://libsemigroups.github.io/libsemigroups_pybind11/"
-Issues = "https://github.com/libsemigroups/libsemigroups_pybind11/issues"
-Changelog = "https://libsemigroups.github.io/libsemigroups_pybind11/changelog.html"
+Homepage      = "https://github.com/libsemigroups/libsemigroups_pybind11"
+Issues        = "https://github.com/libsemigroups/libsemigroups_pybind11/issues"
 
 [project.optional-dependencies]
-test = ["pytest"]
 docs = [
     "sphinx_rtd_theme",
     "sphinx >=8.2",
     "sphinx-copybutton",
     "sphinxcontrib-bibtex",
 ]
+test = ["pytest"]
 
 [dependency-groups]
-test = ["pytest==8.3.3"]
-docs = [
-    "sphinx_rtd_theme==3.0.2",
-    "sphinx-copybutton==0.5.2",
-    "sphinx==8.2.3",
-    "sphinxcontrib-bibtex==2.6.3",
-]
 dev = [
     "accepts==2020.12.3",
     "argcomplete==3.6.2",
-    "beautifulsoup4==4.13.3",
+    "beautifulsoup4==4.13.4",
     "colorama==0.4.6",
-    "cpplint==2.0.0",
-    "eventlet==0.39.1",
-    "exceptiongroup==1.2.2",
-    "gevent==24.11.1",
+    "cpplint==2.0.2",
+    "eventlet==0.40.2",
+    "exceptiongroup==1.3.0",
+    "gevent==25.5.1",
     "graphviz==0.20.3",
-    "greenlet==3.1.1",
+    "greenlet==3.2.3",
     "numpy==2.0.2",
     "ox_profile==0.2.14",
     "packaging==24.2",
     "pexpect==4.9.0",
     "pkgconfig==1.5.5",
-    "pudb==2024.1.3",
-    "pybind11==2.13.6",
-    "pygments==2.19.1",
-    "pylint==3.3.5",
+    "pudb==2025.1",
+    "pybind11==3.0.0",
+    "pygments==2.19.2",
+    "pylint==3.3.7",
     "pyyaml==6.0.2",
-    "ruff==0.11.2",
+    "ruff==0.12.4",
     "setuptools==75.8.2",
     "tomli==2.2.1",
-    "twisted==24.11.0",
-    "typing_extensions==4.13.0",
+    "twisted==25.5.0",
+    "typing_extensions==4.14.1",
     "zope==5.13",
-    { include-group = "test" },
     { include-group = "docs" },
+    { include-group = "test" },
+]
+docs = [
+    "sphinx_rtd_theme==3.0.2",
+    "sphinx-copybutton==0.5.2",
+    "sphinx==8.2.3",
+    "sphinxcontrib-bibtex==2.6.5",
 ]
+test = ["pytest==8.4.1"]
 
 [tool.codespell]
-skip = "./.git,./docs/_build/*,./gh-pages"
-ignore-words-list = "nd,toword,groupe,theses"
 ignore-multiline-regex = "codespell:begin-ignore.*codespell:end-ignore"
+ignore-words-list      = "nd,toword,groupe,theses"
+skip                   = "./.git,./docs/_build/*,./gh-pages"
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -129,25 +129,25 @@ lint.select = ["E", "F", "B"]
 # docstring-code-format = true
 
 [tool.pytest.ini_options]
-minversion = "6.0"
-testpaths = ["tests"]
-addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+addopts              = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
 console_output_style = "progress"
-filterwarnings = ["error"]
-markers = ["quick", "standard", "extreme", "fail"]
+filterwarnings       = ["error"]
+log_cli_level        = "INFO"
+markers              = ["quick", "standard", "extreme", "fail"]
+minversion           = "6.0"
+testpaths            = ["tests"]
 verbosity_test_cases = 1
-xfail_strict = true
-log_cli_level = "INFO"
+xfail_strict         = true
 
 [tool.pylint.main]
 ignore-paths = "src/libsemigroups_pybind11/_version.py"
-jobs = 0
+jobs         = 0
 
 [tool.pylint.miscellaneous]
 # List of note tags to take in consideration, separated by a comma.
 # notes = ["TODO", "FIXME", "REVIEW"]
 disable = ["R0801", "fixme"]
-notes = []
+notes   = []
 
 [tool.pylint.similarities]
 ignore-imports = "yes"

requirements.txt

@@ -1,34 +1,34 @@
 accepts==2020.12.3
 argcomplete==3.6.2
-beautifulsoup4==4.13.3
+beautifulsoup4==4.13.4
 colorama==0.4.6
-cpplint==2.0.0
-eventlet==0.39.1
-exceptiongroup==1.2.2
-gevent==24.11.1
+cpplint==2.0.2
+eventlet==0.40.2
+exceptiongroup==1.3.0
+gevent==25.5.1
 graphviz==0.20.3
-greenlet==3.1.1
-numpy==2.0.2;
+greenlet==3.2.3
+numpy==2.0.2
 ox_profile==0.2.14
 packaging==24.2
 pexpect==4.9.0
 pkgconfig==1.5.5
-pudb==2024.1.3
-pybind11==2.13.6
-pygments==2.19.1
-pylint==3.3.5
-pytest==8.3.3
+pudb==2025.1
+pybind11==3.0.0
+pygments==2.19.2
+pylint==3.3.7
+pytest==8.4.1
 pyyaml==6.0.2
-ruff==0.11.2
+ruff==0.12.4
 setuptools==75.8.2
 sphinx_rtd_theme==3.0.2
 sphinx-copybutton==0.5.2
 # We are being slightly deceptive here. Compiling with sphinx==7.4.7 will work,
 # but will cause warnings
 sphinx==8.2.3;python_version>="3.11"
 sphinx==7.4.7;python_version<="3.10"
-sphinxcontrib-bibtex==2.6.3
+sphinxcontrib-bibtex==2.6.5
 tomli==2.2.1
-twisted==24.11.0
-typing_extensions==4.13.0
+twisted==25.5.0
+typing_extensions==4.14.1
 zope==5.13

src/action.cpp

@@ -221,14 +221,14 @@ Returns the number of generators.
                                      self.generators().cend());
           },
           R"pbdoc(
-:sig=(self: Action) -> Iterator[Element]:
+:sig=(self: Action) -> collections.abc.Iterator[Element]:
 
 Returns an iterator yielding the generators.
 
 :returns:
    An iterator yielding the generators.
 :rtype:
-   Iterator[Element]
+   collections.abc.Iterator[Element]
 
 :complexity:
    Constant.
@@ -405,7 +405,7 @@ of the strongly connected component containing ``self[pos]``.
           },
           py::arg("x"),
           R"pbdoc(
-:sig=(self: Action, x: Element) -> Point:
+:sig=(self: Action, x: Point) -> Point:
 
 Returns the root point of a strongly connected component containing an
 ``Point``.
@@ -428,7 +428,7 @@ Returns the root point of a strongly connected component containing an
           [](Action_& self, index_type pos) { return self.root_of_scc(pos); },
           py::arg("pos"),
           R"pbdoc(
-:sig=(self: Action, pos: Point) -> Point:
+:sig=(self: Action, pos: int) -> Point:
 
 Returns the root point of a strongly connected component.