Update sphinx requirement from >=3.2.1 to >=9.1.0

.coveragerc

@@ -1,8 +1,8 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = iranges
-# omit = bad_file.py
+source = src
+omit = tests/*
 
 [paths]
 source =

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "dependencies"

.github/workflows/build-docs.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v5

.github/workflows/publish-pypi.yml

@@ -1,65 +1,91 @@
-name: Publish to PyPI
+name: Publish to PyPI and GitHub Pages
 
 on:
   push:
-    tags:
-      - "*"
+    tags: "*"
 
 jobs:
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # macos-13 is an intel runner, higher macos's are apple silicon
-        # At some point, maybe get this to work on windows-latest
-        os: [ubuntu-latest, macos-latest]
-
+  build-and-test:
+    name: Build and Test
+    runs-on: ubuntu-latest
     steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v7
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
 
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v4.2.0
-        env:
-          CIBW_ARCHS_LINUX: x86_64
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.10"
-          CIBW_SKIP: pp*
+      - name: Install tox
+        run: python -m pip install tox
 
-      - uses: actions/upload-artifact@v4
+      - name: Test
+        run: tox -e default
+
+      - name: Build Project
+        run: tox -e build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl
+          name: python-package-distributions
+          path: dist/
 
-  build_sdist:
-    name: Build source distribution
+  build-docs:
+    name: Build Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          submodules: true
+          python-version: 3.12
+
+      - name: Install tox
+        run: python -m pip install tox
 
-      - name: Build sdist
-        run: pipx run build --sdist
+      - name: Build docs
+        run: tox -e docs
 
-      - uses: actions/upload-artifact@v4
+      - name: Add .nojekyll
+        run: touch ./docs/_build/html/.nojekyll
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v5
         with:
-          name: cibw-sdist
-          path: dist/*.tar.gz
+          path: ./docs/_build/html
 
-  upload_pypi:
-    needs: [build_wheels, build_sdist]
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build-and-test
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/IRanges
     permissions:
-      id-token: write
-
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
     steps:
-      - uses: actions/download-artifact@v4
+      - name: Download all the dists
+        uses: actions/download-artifact@v8
         with:
-          pattern: cibw-*
-          path: dist
-          merge-multiple: true
+          name: python-package-distributions
+          path: dist/
 
-      # This uses the trusted publisher workflow so no token is required.
-      - name: Publish to PyPI
+      - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
+
+  deploy-pages:
+    name: Deploy GitHub Pages
+    needs: build-docs
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

.github/workflows/run-tests.yml

@@ -31,29 +31,23 @@ jobs:
         python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         platform:
           - ubuntu-latest
-          # - macos-latest
-          # - windows-latest
+          - macos-latest
+          - windows-latest
     runs-on: ${{ matrix.platform }}
     name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
 
-      - uses: actions/setup-python@v5
-        id: setup-python
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox coverage
-
-      - name: Get latest CMake
-        uses: lukka/get-cmake@latest
+      - name: Install tox
+        run: python -m pip install tox coverage
 
       - name: Run tests
         run: >-
-          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
           tox
           -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
 
@@ -68,9 +62,9 @@ jobs:
           fi
 
       - name: Upload coverage reports to Codecov with GitHub Action
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v7
         if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           slug: ${{ github.repository }}
           flags: ${{ matrix.platform }} - py${{ matrix.python }}

.pre-commit-config.yaml

@@ -33,10 +33,12 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.2
   hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+    # Run the linter.
+    - id: ruff-check
+      args: [--fix, --exit-zero]
+    # Run the formatter.
     - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
@@ -51,3 +53,10 @@ repos:
 #   rev: v2.2.5
 #   hooks:
 #   - id: codespell
+
+- repo: https://github.com/PyCQA/bandit
+  rev: 1.7.9
+  hooks:
+    - id: bandit
+      args: ["-c", "pyproject.toml"]
+      additional_dependencies: ["bandit[toml]"]

docs/requirements.txt

@@ -5,5 +5,5 @@ myst-nb
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
-sphinx>=3.2.1
+sphinx>=9.1.0
 sphinx-autodoc-typehints

pyproject.toml

@@ -1,28 +1,63 @@
 [build-system]
-# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
-requires = ["setuptools>=46.1.0", "setuptools_scm[toml]>=5", "cmake", "pybind11", "numpy"]
+requires = [
+    "setuptools>=46.1.0",
+    "setuptools_scm[toml]>=5",
+    "cmake",
+    "pybind11",
+    "numpy",
+]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-# For smarter version schemes and other configuration options,
-# check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
 
 [tool.ruff]
 line-length = 120
-src = ["src"]
-# exclude = ["tests"]
-extend-ignore = ["F821"]
+src = [
+    "src",
+]
+exclude = [
+    "tests",
+    "docs",
+]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint]
+extend-ignore = [
+    "F821",
+]
+
+[tool.ruff.lint.pydocstyle]
 convention = "google"
 
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = [
+    "E402",
+    "F401",
+]
+
 [tool.ruff.format]
 docstring-code-format = true
 docstring-code-line-length = 20
 
-[tool.ruff.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
-
 [tool.black]
 force-exclude = "__init__.py"
+
+[tool.mypy]
+strict = true
+
+[tool.pytest.ini_options]
+addopts = "--cov --cov-report term-missing"
+testpaths = [
+    "tests",
+]
+
+[project.optional-dependencies]
+testing = [
+    "pytest>=9.1.1",
+    "pytest-cov>=7.1.0",
+]
+
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B110"]

setup.py

@@ -73,7 +73,7 @@ def build_cmake(self, ext):
             ext_modules=[CMakeExtension("iranges")],
             cmdclass={"build_ext": build_ext},
         )
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "