Update linter and formatter config

.github/workflows/lint.yml

@@ -0,0 +1,75 @@
+name: Lint
+on: [pull_request, workflow_dispatch]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            compiler: g++
+          - os: macOS-latest
+            compiler: clang++
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      CXX: "ccache ${{ matrix.compiler }}"
+      CXXFLAGS: "-O2 -g"
+      UV_NO_SYNC: "1"
+      LD_LIBRARY_PATH: "/usr/local/lib"
+    steps:
+      # Setup environment
+      - uses: actions/checkout@v5
+      - name: Set up Python . . .
+        uses: actions/setup-python@v6
+        with:
+          python-version-file: "pyproject.toml"
+      - name: Install uv . . .
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+      - name: "Install libsemigroups_pybind11 dependencies . . ."
+        run: uv sync --locked --no-install-project --no-dev --group lint
+      - name: "Find the names of the Python files that will be linted"
+        run: echo "PYTHON_FILES=$(uv run ruff check --show-files | grep '\.py$' |  tr -s '\n' ' ')" >> $GITHUB_ENV
+
+      # Lint with ruff and cpplint
+      - name: "Lint with ruff . . ."
+        run: uv run ruff check
+      - name: "Check ruff formatting . . ."
+        run: uv run ruff format --diff
+      - name: "Lint with cpplint . . ."
+        run: uv run cpplint src/*.hpp src/*.cpp
+
+      # Build libsemigroups
+      - name: "macOS only: Install libsemigroups dependencies . . ."
+        if: ${{ matrix.os == 'macOS-latest' }}
+        run: brew install autoconf automake libtool
+      - name: "Setup ccache . . ."
+        uses: Chocobo1/setup-ccache-action@v1
+        with:
+          update_packager_index: false
+          install_ccache: true
+      - name: "Install libsemigroups . . ."
+        run: |
+          git clone --depth 1 --branch main https://github.com/libsemigroups/libsemigroups.git
+          cd libsemigroups
+          ./autogen.sh && ./configure CXX="$CXX" CXXFLAGS="$CXXFLAGS" --disable-hpcombi && sudo make install -j8
+          ccache -s
+
+      # Build libsemigroups_pybind11
+      - name: "Install libsemigroups_pybind11 . . ."
+        run: uv sync --locked --all-extras --no-dev --group lint
+
+      # Lint with ruff and cpplint
+      - name: "Lint with pylint . . ."
+        run: uv run pylint $PYTHON_FILES

.github/workflows/test-conda.yml

@@ -1,5 +1,10 @@
 name: Run tests (Conda libsemigroups)
-on: [pull_request, workflow_dispatch]
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - "stable-*"
+      - "rc-*"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Run tests and lint (GitHub libsemigroups)
+name: Run tests (GitHub libsemigroups)
 on: [pull_request, workflow_dispatch]
 
 concurrency:
@@ -62,5 +62,3 @@ jobs:
         run: uv run pytest
       - name: "Running doc tests . . ."
         run: uv run make doctest
-      - name: "Running ruff, pylint and cpplint . . ."
-        run: uv run make lint

Makefile

@@ -18,8 +18,11 @@ doctest:
 install:
 	pip3 install . --use-feature=in-tree-build
 
-black:
-	black setup.py tests/*.py src/libsemigroups_pybind11/*.py docs/source/conf.py
+format:
+# ruff format can't yet sort imports, so we require the ruff check line too
+# See https://github.com/astral-sh/ruff/issues/8232 for updates.
+	ruff check --select I --fix-only
+	ruff format
 
 check: doctest
 	pytest -vv tests/test_*.py

build_tools/__init__.py

@@ -1,19 +1,14 @@
-# -*- coding: utf-8 -*-
-
 # 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.
 
-"""
-This module provides some tools for building libsemigroups_pybind11.
-"""
+"""This module provides some tools for building libsemigroups_pybind11."""
 
 
 def minimum_libsemigroups_version():
-    """
-    Returns the minimum required version of libsemigroups required to build
+    """Returns the minimum required version of libsemigroups required to build
     libsemigroups_pybind11.
     """
     return "3.2.0"

build_tools/packaging_helpers.py

@@ -1,26 +1,25 @@
-# -*- coding: utf-8 -*-
-
 # 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.
 
-"""
-This submodule provides some more tools for building libsemigroups_pybind11.
-These tools rely on some non-built-in packages, so they have been placed in
-their own submodule to separate from the functions that need to be run in a bare
-Python environment.
+"""This submodule provides some more tools for building libsemigroups_pybind11.
+
+These tools rely on some non-built-in packages, so they have been placed in their own submodule to
+separate from the functions that need to be run in a bare Python environment.
 """
 
 import re
-from packaging import version
+
 import pkgconfig
+from packaging import version
+
 from . import minimum_libsemigroups_version
 
 
 def libsemigroups_version():
-    "Get the version of libsemigroups installed using pkg-config."
+    """Get the version of libsemigroups installed using pkg-config."""
 
     vers = pkgconfig.modversion("libsemigroups")
     if re.search(r"\d+\.\d+\.\d+-\d+-\w{7}", vers):
@@ -35,10 +34,8 @@ def compare_version_numbers(supplied, required):
     if isinstance(supplied, str) and isinstance(required, str):
         if "dev" in supplied:
             print(
-                (
-                    "\033[93mWarning: You are using a development version of libsemigroups. This "
-                    "may cause undocumented behaviour\033[0m"
-                )
+                "\033[93mWarning: You are using a development version of libsemigroups. This may "
+                "cause undocumented behaviour\033[0m"
             )
             return True
         return version.parse(supplied) >= version.parse(required)
@@ -73,15 +70,11 @@ def ld_library_path() -> str:
 
 
 def validate_libsemigroups():
-    DISCLAIMER = """
-    (You should not see this message unless you are installing
-    libsemigroups_pybind11 from its sources. If you are not installing from the
-    sources, please raise an issue at:
-    https://github.com/libsemigroups/libsemigroups_pybind11)"""
+    """Check if the installed version of libsemigroups is compatible with libsemigroups_pybind11"""
 
     if not pkgconfig.exists("libsemigroups"):
         raise ImportError(
-            f"""cannot locate the libsemigroups library.
+            """cannot locate the libsemigroups library.
     For more information about installing the libsemigroups library see
     https://libsemigroups.github.io/libsemigroups_pybind11/install.html.
 
@@ -93,7 +86,10 @@ def validate_libsemigroups():
     * $CONDA_PREFIX/lib/pkgconfig if your active conda environment has pkgconfig
     installed, and libsemigroups was installed with conda/mamba in this
     environment.
-    {DISCLAIMER}"""
+    (You should not see this message unless you are installing
+    libsemigroups_pybind11 from its sources. If you are not installing from the
+    sources, please raise an issue at:
+    https://github.com/libsemigroups/libsemigroups_pybind11)"""
         )
 
     if not compare_version_numbers(libsemigroups_version(), minimum_libsemigroups_version()):

docs/source/_ext/libsemigroups_pybind11_extensions.py

@@ -3,10 +3,9 @@
 """Custom functions and class for building the docs of libsemigroups_pybind11"""
 
 import re
-
 from inspect import getdoc
 
-from sphinx.addnodes import desc_content, desc, index
+from sphinx.addnodes import desc, desc_content, index
 from sphinx.ext.autodoc.directive import AutodocDirective
 from sphinx.util import logging
 from sphinx.util.display import progress_message
@@ -99,22 +98,16 @@ def no_doc_run(self):
 # 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
-type_replacements = {
-    r"_?libsemigroups_pybind11\.": "",
-}
+type_replacements = {r"_?libsemigroups_pybind11\.": ""}
 
 # This dictionary should be of the form class_name -> (pattern, repl), where
 # "pattern" should be replaced by "repl" in the signature of all functions in
 # "class_name"
 class_specific_replacements = {
     "Sims1": [("SimsSettingsSims1", "Sims1")],
     "Sims2": [("SimsSettingsSims2", "Sims2")],
-    "MinimalRepOrc": [
-        ("SimsSettingsMinimalRepOrc", "MinimalRepOrc"),
-    ],
-    "RepOrc": [
-        ("SimsSettingsRepOrc", "RepOrc"),
-    ],
+    "MinimalRepOrc": [("SimsSettingsMinimalRepOrc", "MinimalRepOrc")],
+    "RepOrc": [("SimsSettingsRepOrc", "RepOrc")],
     "PathsToRoots": [("forest_PathsFromToRootsCommon", "PathsToRoots")],
     "PathsFromRoots": [("forest_PathsFromToRootsCommon", "PathsFromRoots")],
 }
@@ -186,13 +179,7 @@ def sig_alternative(doc, signature, return_annotation):
 
 
 def change_sig(
-    app=None,
-    what=None,
-    name=None,
-    obj=None,
-    options=None,
-    signature=None,
-    return_annotation=None,
+    app=None, what=None, name=None, obj=None, options=None, signature=None, return_annotation=None
 ):
     """Make type replacement in function signatures"""
     if what == "class":
@@ -212,9 +199,7 @@ def change_sig(
 
 
 def make_only_doc(lines):
-    """
-    Extract the unique docstrings from a sequence of overloaded functions.
-    """
+    """Extract the unique docstrings from a sequence of overloaded functions."""
 
     # To keep track of unique strings
     sigs = set()
@@ -240,9 +225,7 @@ def make_only_doc(lines):
                 deleting = False
                 sigs.add(sig)
                 lines[i - 3] = re.sub(
-                    r"\d+(\. .*)\(.*$",
-                    str(overload_counter) + r"\1" + sig,
-                    lines[i - 3],
+                    r"\d+(\. .*)\(.*$", str(overload_counter) + r"\1" + sig, lines[i - 3]
                 )
                 overload_counter += 1
 
@@ -273,8 +256,7 @@ def make_only_doc(lines):
 
 
 def only_doc_once(app, what, name, obj, options, lines):
-    """
-    Edit docstring to only include one version of the doc for an overloaded
+    """Edit docstring to only include one version of the doc for an overloaded
     function if necessary
     """
 
@@ -327,9 +309,7 @@ def fix_overloads(app, what, name, obj, options, lines):
                     return_annotation = m.group(3)
                 # Make replacements in signature
                 signature, return_annotation = change_sig(
-                    name=name,
-                    signature=signature,
-                    return_annotation=return_annotation,
+                    name=name, signature=signature, return_annotation=return_annotation
                 )
 
                 # Add adjusted content to the output
@@ -338,10 +318,7 @@ def fix_overloads(app, what, name, obj, options, lines):
                     f"{new_name}{signature} -> {return_annotation}"
                 )
                 lines[i + offset] = new_line
-                lines.insert(
-                    i + offset + 1,
-                    f"{parent_indent}{indent}:noindex:",
-                )
+                lines.insert(i + offset + 1, f"{parent_indent}{indent}:noindex:")
                 overload_counter += 1
                 offset += 1
             else:
@@ -397,26 +374,19 @@ def check_string_replacements(app, env):
     for bad_type, good_type in type_replacements.items():
         if bad_type not in strings_replaced:
             any_warnings = True
-            logger.warning(
-                f'"{bad_type}" -> "{good_type}"',
-                type="unused-replacement",
-            )
+            logger.warning(f'"{bad_type}" -> "{good_type}"', type="unused-replacement")
 
     for class_name, repls in class_specific_replacements.items():
         for pattern, repl in repls:
             if pattern not in strings_replaced:
                 any_warnings = True
                 logger.warning(
-                    f'"{pattern}" -> "{repl}" in {class_name}',
-                    type="unused-replacement",
+                    f'"{pattern}" -> "{repl}" in {class_name}', type="unused-replacement"
                 )
     for bad_string, good_string in docstring_replacements.items():
         if bad_string not in strings_replaced:
             any_warnings = True
-            logger.warning(
-                f'"{bad_string}" -> "{good_string}"',
-                type="unused-replacement",
-            )
+            logger.warning(f'"{bad_string}" -> "{good_string}"', type="unused-replacement")
     if any_warnings:
         logger.info(f"Please correct this in {__file__}")
 

docs/source/conf.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 # pylint: disable=invalid-name, line-too-long
-"""
-This provides configuration for the generation of the docs
+"""This provides configuration for the generation of the docs.
 
 More detail of the available configuration options can be found in the
 following places:
@@ -110,10 +108,7 @@
 # The titles_only option stops the page sections and toc (which have the
 # same names) from being duplicated in the sidebar on the Konieczny and
 # FroidurePin pages.
-html_theme_options = {
-    "titles_only": True,
-    "style_nav_header_background": "#2980B9",
-}
+html_theme_options = {"titles_only": True, "style_nav_header_background": "#2980B9"}
 
 # The project logo
 html_logo = "../pictures/libsemigroups_pybind11_logo.svg"
@@ -137,13 +132,7 @@
 
 # How to group the document tree into manual pages.
 man_pages = [
-    (
-        master_doc,
-        "libsemigroups_pybind11",
-        "libsemigroups_pybind11 Documentation",
-        author,
-        1,
-    )
+    (master_doc, "libsemigroups_pybind11", "libsemigroups_pybind11 Documentation", author, 1)
 ]
 
 ############ Options for the Python domain ############