Add automerge bot for dependabot and pre-commit.ci PRs

.github/workflows/bot.yaml

@@ -0,0 +1,21 @@
+name: bot
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  auto-merge:
+    runs-on: ubuntu-latest
+    if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]') && github.repository == 'fcbg-platforms/nmod-wiki'
+    steps:
+      - name: Enable auto-merge for bot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pytest.yaml

@@ -17,29 +17,22 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.9, "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
       run:
         shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install package
-        run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools
-          python -m pip install --progress-bar off .[test]
-      - name: Display system information
-        run: nmod-wiki sys-info --developer
-      - name: Run pytest
-        run: pytest nmod_wiki --cov=nmod_wiki --cov-report=xml --cov-config=pyproject.toml
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v5
+      - uses: astral-sh/setup-uv@v4
+      - run: uv pip install --quiet --system .[test]
+      - run: nmod-wiki sys-info --developer
+      - run: pytest nmod_wiki --cov=nmod_wiki --cov-report=xml --cov-config=pyproject.toml
+      - uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml
           flags: unittests  # optional
@@ -55,27 +48,18 @@ jobs:
         python-version: ["3.11"]
     name: pip pre-release - py${{ matrix.python-version }}
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --progress-bar off --upgrade pip setuptools
-          python -m pip install --progress-bar off .[test]
-          python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy
-      - name: Display system information
-        run: nmod-wiki sys-info --developer
-      - name: Run pytest
-        run: pytest nmod_wiki --cov=nmod_wiki --cov-report=xml --cov-config=pyproject.toml
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v5
+      - uses: astral-sh/setup-uv@v4
+      - run: |
+          uv pip install --quiet --system .[test]
+          uv pip install --quiet --system --upgrade --prerelease allow --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
+      - run: nmod-wiki sys-info --developer
+      - run: pytest nmod_wiki --cov=nmod_wiki --cov-report=xml --cov-config=pyproject.toml
+      - uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml
           flags: unittests  # optional

doc/conf.py

@@ -18,7 +18,7 @@
 import nmod_wiki
 
 if TYPE_CHECKING:
-    from typing import Optional
+    pass
 
 # -- project information ---------------------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -187,7 +187,7 @@
 # https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
 
 
-def linkcode_resolve(domain: str, info: dict[str, str]) -> Optional[str]:
+def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     """Determine the URL corresponding to a Python object.
 
     Parameters

nmod_wiki/utils/_checks.py

@@ -13,10 +13,10 @@
 from ._docs import fill_doc
 
 if TYPE_CHECKING:
-    from typing import Any, Optional, Union
+    from typing import Any
 
 
-def ensure_int(item: Any, item_name: Optional[str] = None) -> int:
+def ensure_int(item: Any, item_name: str | None = None) -> int:
     """Ensure a variable is an integer.
 
     Parameters
@@ -72,7 +72,7 @@ def __instancecheck__(cls, other: Any) -> bool:
 }
 
 
-def check_type(item: Any, types: tuple, item_name: Optional[str] = None) -> None:
+def check_type(item: Any, types: tuple, item_name: str | None = None) -> None:
     """Check that item is an instance of types.
 
     Parameters
@@ -127,9 +127,9 @@ def check_type(item: Any, types: tuple, item_name: Optional[str] = None) -> None
 
 def check_value(
     item: Any,
-    allowed_values: Union[tuple, dict[Any, Any]],
-    item_name: Optional[str] = None,
-    extra: Optional[str] = None,
+    allowed_values: tuple | dict[Any, Any],
+    item_name: str | None = None,
+    extra: str | None = None,
 ) -> None:
     """Check the value of a parameter against a list of valid options.
 

nmod_wiki/utils/_docs.py

@@ -10,7 +10,8 @@
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
 # -- Documentation dictionary ----------------------------------------------------------
 docdict: dict[str, str] = dict()

nmod_wiki/utils/_docs.pyi

@@ -1,4 +1,5 @@
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
 
 docdict: dict[str, str]
 docdict_indented: dict[int, dict[str, str]]

nmod_wiki/utils/_imports.py

@@ -10,7 +10,6 @@
 
 if TYPE_CHECKING:
     from types import ModuleType
-    from typing import Optional
 
 # A mapping from import name to package name (on PyPI) when the package name
 # is different.
@@ -29,7 +28,7 @@ def import_optional_dependency(
     name: str,
     extra: str = "",
     raise_error: bool = True,
-) -> Optional[ModuleType]:
+) -> ModuleType | None:
     """Import an optional dependency.
 
     By default, if a dependency is missing an ImportError with a nice message will be

nmod_wiki/utils/config.py

@@ -12,10 +12,11 @@
 from ._checks import check_type
 
 if TYPE_CHECKING:
-    from typing import IO, Callable, Optional
+    from collections.abc import Callable
+    from typing import IO
 
 
-def sys_info(fid: Optional[IO] = None, developer: bool = False):
+def sys_info(fid: IO | None = None, developer: bool = False):
     """Print the system information for debugging.
 
     Parameters
@@ -134,7 +135,7 @@ def _list_dependencies_info(
 
 
 @lru_cache(maxsize=1)
-def _get_gpu_info() -> tuple[Optional[str], Optional[str]]:
+def _get_gpu_info() -> tuple[str | None, str | None]:
     """Get the GPU information."""
     try:
         from pyvista import GPUInfo

nmod_wiki/utils/config.pyi

@@ -1,4 +1,5 @@
-from typing import IO, Callable
+from collections.abc import Callable
+from typing import IO
 
 from packaging.requirements import Requirement
 

nmod_wiki/utils/logs.py

@@ -13,14 +13,14 @@
 from ._fixes import WrapStdOut
 
 if TYPE_CHECKING:
-    from typing import Callable, Optional, Union
+    from collections.abc import Callable
 
 
 _PACKAGE: str = __package__.split(".")[0]
 
 
 @fill_doc
-def _init_logger(*, verbose: Optional[Union[bool, str, int]] = None) -> logging.Logger:
+def _init_logger(*, verbose: bool | str | int | None = None) -> logging.Logger:
     """Initialize a logger.
 
     Assigns sys.stdout as the first handler of the logger.
@@ -47,11 +47,11 @@ def _init_logger(*, verbose: Optional[Union[bool, str, int]] = None) -> logging.
 
 
 def add_file_handler(
-    fname: Union[str, Path],
+    fname: str | Path,
     mode: str = "a",
-    encoding: Optional[str] = None,
+    encoding: str | None = None,
     *,
-    verbose: Optional[Union[bool, str, int]] = None,
+    verbose: bool | str | int | None = None,
 ) -> None:
     """Add a file handler to the logger.
 
@@ -83,7 +83,7 @@ def add_file_handler(
 
 
 @fill_doc
-def set_log_level(verbose: Optional[Union[bool, str, int]]) -> None:
+def set_log_level(verbose: bool | str | int | None) -> None:
     """Set the log level for the logger.
 
     Parameters
@@ -167,7 +167,7 @@ class _use_log_level:  # noqa: N801
     %(verbose)s
     """
 
-    def __init__(self, verbose: Optional[Union[bool, str, int]] = None):
+    def __init__(self, verbose: bool | str | int | None = None):
         self._old_level = logger.level
         self._level = verbose
 
@@ -182,7 +182,7 @@ def warn(
     message: str,
     category: Warning = RuntimeWarning,
     module: str = _PACKAGE,
-    ignore_namespaces: Union[tuple[str, ...] | list[str]] = (_PACKAGE,),
+    ignore_namespaces: tuple[str, ...] | list[str] = (_PACKAGE,),
 ) -> None:
     """Emit a warning with trace outside the requested namespace.
 

nmod_wiki/utils/logs.pyi

@@ -1,6 +1,6 @@
 import logging
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable
 
 from _typeshed import Incomplete
 

nmod_wiki/utils/tests/test_logs.py

@@ -9,7 +9,6 @@
 
 if TYPE_CHECKING:
     from pathlib import Path
-    from typing import Optional, Union
 
 
 def test_default_log_level(caplog: pytest.LogCaptureFixture):
@@ -68,7 +67,7 @@ def test_verbose(caplog: pytest.LogCaptureFixture):
 
     # function
     @verbose
-    def foo(verbose: Optional[Union[bool, str, int]] = None):
+    def foo(verbose: bool | str | int | None = None):
         """Foo function."""
         logger.debug("101")
 
@@ -94,12 +93,12 @@ def __init__(self):
             pass
 
         @verbose
-        def foo(self, verbose: Optional[Union[bool, str, int]] = None):
+        def foo(self, verbose: bool | str | int | None = None):
             logger.debug("101")
 
         @staticmethod
         @verbose
-        def foo2(verbose: Optional[Union[bool, str, int]] = None):
+        def foo2(verbose: bool | str | int | None = None):
             logger.debug("101")
 
     foo = Foo()

pyproject.toml

@@ -16,7 +16,7 @@ classifiers = [
   'Programming Language :: Python :: 3.10',
   'Programming Language :: Python :: 3.11',
   'Programming Language :: Python :: 3.12',
-  'Programming Language :: Python :: 3.9',
+  'Programming Language :: Python :: 3.13',
 ]
 dependencies = [
   'click',
@@ -38,7 +38,7 @@ maintainers = [
 ]
 name = 'nmod_wiki'
 readme = 'README.md'
-requires-python = '>=3.9'
+requires-python = '>=3.10'
 version = '0.1.0'
 
 [project.optional-dependencies]
@@ -128,7 +128,7 @@ minversion = '8.0'
 [tool.ruff]
 extend-exclude = []
 line-length = 88
-target-version = 'py39'
+target-version = 'py310'
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -138,15 +138,12 @@ line-ending = "lf"
 ignore = []
 select = ['A', 'B', 'D', 'E', 'F', 'G', 'I', 'LOG', 'NPY', 'PIE', 'PT', 'T20', 'UP', 'W']
 
-
 [tool.ruff.lint.per-file-ignores]
 '*' = [
   'B904', # 'Within an except clause, raise exceptions with raise ... from ...'
   'D100', # 'Missing docstring in public module'
   'D104', # 'Missing docstring in public package'
   'D107', # 'Missing docstring in __init__'
-  'UP007', # 'Use `X | Y` for type annotations', requires python 3.10
-  'UP038', # 'Use X | Y in {} call instead of (X, Y)', requires python 3.10
 ]
 '*.pyi' = ['E501']
 '__init__.py' = ['F401']

tools/stubgen.py

@@ -41,7 +41,7 @@
     objects = [
         node
         for node in module_ast.body
-        if isinstance(node, (ast.ClassDef, ast.FunctionDef))
+        if isinstance(node, (ast.ClassDef | ast.FunctionDef))
     ]
     for node in objects:
         docstring = getattr(module, node.name).__doc__