👁 TEMPLATE DEVIATIONS: synced file(s) with SciTools/.github

.github/dependabot.yml

@@ -9,6 +9,10 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every weekday
       interval: "daily"
+    groups:
+      dependencies:
+        patterns:
+          - "*"
     labels:
       - "new: pull request"
       - "bot"

.pre-commit-config.yaml

@@ -1,53 +1,105 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 # See https://pre-commit.ci/#configuration
+# See https://github.com/scientific-python/cookie#sp-repo-review
 
 ci:
   autofix_prs: false
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+
+
+# Alphabetised, for lack of a better order.
+files: |
+    (?x)(
+        benchmarks\/.+\.py|
+        docs\/.+\.py|
+        lib\/.+\.py|
+        noxfile\.py|
+        pyproject\.toml|
+        setup\.py|
+        src\/.+\.py
+    )
+minimum_pre_commit_version: 1.21.0
+
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.6.0"
-    hooks:
-      # Prevent giant files from being committed.
-    - id: check-added-large-files
-      # Check whether files parse as valid Python.
-    - id: check-ast
-      # Check for file name conflicts on case-insensitive file-systems.
-    - id: check-case-conflict
-      # Check for files that contain merge conflict strings.
-    - id: check-merge-conflict
-      # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
-    - id: debug-statements
-      # Check TOML file syntax.
-    - id: check-toml
-      # Check YAML file syntax.
-    - id: check-yaml
-      # Makes sure files end in a newline and only a newline
-    - id: end-of-file-fixer
-      exclude: nae.20100104-06_0001_0001.pp
-      # Replaces or checks mixed line ending
-    - id: mixed-line-ending
-      exclude: nae.20100104-06_0001_0001.pp
-      # Don't commit to main branch.
-      #- id: no-commit-to-branch
-      # Trims trailing whitespace
-    - id: trailing-whitespace
-      exclude: nae.20100104-06_0001_0001.pp
-
-  - repo: https://github.com/codespell-project/codespell
-    rev: "v2.3.0"
-    hooks:
-    - id: codespell
-      types_or: [python, markdown]
-      additional_dependencies: [tomli]
-
-  - repo: https://github.com/aio-libs/sort-all
-    rev: "v1.2.0"
-    hooks:
-      - id: sort-all
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+        # Prevent giant files from being committed.
+    -   id: check-added-large-files
+        # Check whether files parse as valid Python.
+    -   id: check-ast
+        # Check for file name conflicts on case-insensitive filesystems.
+    -   id: check-case-conflict
+        # Check for files that contain merge conflict strings.
+    -   id: check-merge-conflict
+        # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
+    -   id: debug-statements
+        # Check TOML file syntax.
+    -   id: check-toml
+        # Check YAML file syntax.
+    -   id: check-yaml
+        # Makes sure files end in a newline and only a newline.
+        # Duplicates Ruff W292 but also works on non-Python files.
+    -   id: end-of-file-fixer
+        # Replaces or checks mixed line ending.
+    -   id: mixed-line-ending
+        # Don't commit to main branch.
+    -   id: no-commit-to-branch
+        # Trims trailing whitespace.
+        # Duplicates Ruff W291 but also works on non-Python files.
+    -   id: trailing-whitespace
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.4.4"
+    hooks:
+    -   id: ruff
         types: [file, python]
+        args: [--fix, --show-fixes]
+    -   id: ruff-format
+        types: [file, python]
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+    -   id: codespell
+        types_or: [asciidoc, python, markdown, rst]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+    -   id: blacken-docs
+        types: [file, rst]
 
-  - repo: https://github.com/abravalheri/validate-pyproject
+-   repo: https://github.com/aio-libs/sort-all
+    rev: v1.2.0
+    hooks:
+    -   id: sort-all
+        types: [file, python]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.10.0'
+    hooks:
+    -   id: mypy
+        exclude: 'src\/mo_pack\/tests'
+
+-   repo: https://github.com/abravalheri/validate-pyproject
+    # More exhaustive than Ruff RUF200.
     rev: "v0.18"
     hooks:
-      - id: validate-pyproject
+    - id: validate-pyproject
+
+-   repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+    - id: sp-repo-review
+      additional_dependencies: ["repo-review[cli]"]
+      args: ["--show=errskip"]
+
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.7.0
+    hooks:
+      - id: numpydoc-validation
+        types: [file, python]
+        exclude: 'src\/mo_pack\/tests'

pyproject.toml

@@ -5,7 +5,6 @@ requires = [
     "oldest-supported-numpy",
     "setuptools>=64",
     "setuptools_scm[toml]>=8",
-    "wheel",
 ]
 # defined by PEP-517
 build-backend = "setuptools.build_meta"
@@ -52,9 +51,12 @@ ignore = [
 
 
 [tool.pytest.ini_options]
-addopts = ["-ra"]
+addopts = ["-ra", "--strict-config", "--strict-markers"]
+filterwarnings = ["error"]
+log_cli_level = "INFO"
 minversion = "6.0"
 testpaths = "src/mo_pack"
+xfail_strict = true
 
 
 [tool.setuptools]
@@ -79,3 +81,116 @@ mo_pack = ["tests/test_data/*.pp"]
 write_to = "src/mo_pack/_version.py"
 local_scheme = "dirty-tag"
 version_scheme = "release-branch-semver"
+
+
+[tool.numpydoc_validation]
+checks = [
+    "all",  # Enable all numpydoc validation rules, apart from the following:
+
+    # -> Docstring text (summary) should start in the line immediately
+    #    after the opening quotes (not in the same line, or leaving a
+    #    blank line in between)
+    "GL01",  # Permit summary line on same line as docstring opening quotes.
+
+    # -> Closing quotes should be placed in the line after the last text
+    #    in the docstring (do not close the quotes in the same line as
+    #    the text, or leave a blank line between the last text and the
+    #    quotes)
+    "GL02",  # Permit a blank line before docstring closing quotes.
+
+    # -> Double line break found; please use only one blank line to
+    #    separate sections or paragraphs, and do not leave blank lines
+    #    at the end of docstrings
+    "GL03",  # Ignoring.
+
+    # -> See Also section not found
+    "SA01",  # Not all docstrings require a "See Also" section.
+
+    # -> No extended summary found
+    "ES01",  # Not all docstrings require an "Extended Summary" section.
+
+    # -> No examples section found
+    "EX01",  # Not all docstrings require an "Examples" section.
+
+    # -> No Yields section found
+    "YD01",  # Not all docstrings require a "Yields" section.
+]
+exclude = [
+    '\.__eq__$',
+    '\.__ne__$',
+    '\.__repr__$',
+]
+
+[tool.repo-review]
+ignore = [
+    # https://learn.scientific-python.org/development/guides/style/#PC170
+    "PC170",  # Uses PyGrep hooks
+    # https://learn.scientific-python.org/development/guides/style/#PC180
+    "PC180",  # Uses prettier
+    # https://learn.scientific-python.org/development/guides/packaging-simple/#PY004
+    "PY004",  # Has docs folder
+    # https://learn.scientific-python.org/development/guides/docs/#readthedocsyaml
+    "RTD",    # ReadTheDocs
+
+    "PY007",  # TODO: Tox adoption blocked by SciTools/iris#5184.
+]
+
+[tool.mypy]
+# See https://mypy.readthedocs.io/en/stable/config_file.html
+ignore_missing_imports = true
+warn_unused_configs = true
+warn_unreachable = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+exclude = [
+    "src\\/mo_pack\\/tests$",
+]
+strict = true
+
+[tool.ruff]
+line-length = 88
+src = ["src"]
+
+[tool.ruff.format]
+preview = false
+
+[tool.ruff.lint]
+ignore = [
+    # NOTE: Non-permanent exclusions should be added to the ".ruff.toml" file.
+
+    # flake8-commas (COM)
+    # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+    "COM812",  # Trailing comma missing.
+    "COM819",  # Trailing comma prohibited.
+
+    # flake8-implicit-str-concat (ISC)
+    # https://docs.astral.sh/ruff/rules/single-line-implicit-string-concatenation/
+    # NOTE: This rule may cause conflicts when used with "ruff format".
+    "ISC001",  # Implicitly concatenate string literals on one line.
+    ]
+    preview = false
+    select = [
+        "ALL",
+        # list specific rules to include that is skipped using numpy convention.
+        "D212",  # Multi-line docstring summary should start at the first line
+    ]
+
+[tool.ruff.lint.isort]
+force-sort-within-sections = true
+
+[tool.ruff.lint.per-file-ignores]
+# All test scripts.
+
+"src/mo_pack/tests/*.py" = [
+    # https://docs.astral.sh/ruff/rules/undocumented-public-module/
+    "D100",  # Missing docstring in public module
+    "D101",  # Missing docstring in public class
+    "D102",  # Missing docstring in public method
+    "D205",  # 1 blank line required between summary line and description
+    "D401",  # 1 First line of docstring should be in imperative mood
+
+    "ANN",   # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "S101",  # Use of assert detected
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"

setup.py

@@ -1,31 +1,38 @@
-from setuptools import Command, Extension, setup
+"""Register the Cython extension."""
+
+from __future__ import annotations
 
 from pathlib import Path
+from typing import ClassVar
 
 from Cython.Build import cythonize
 import numpy as np
+from setuptools import Command, Extension, setup
 
 BASE_DIR = Path(__file__).resolve().parent
 PACKAGE_NAME = "mo_pack"
 SRC_DIR = BASE_DIR / "src"
 PACKAGE_DIR = SRC_DIR / PACKAGE_NAME
 
 
-class CleanCython(Command):
+class CleanCython(Command):  # type: ignore[misc]
+    """Command for purging artifacts built by Cython."""
+
     description = "Purge artifacts built by Cython"
-    user_options = []
+    user_options: ClassVar[list[tuple[str, str, str]]] = []
 
-    def initialize_options(self):
-        pass
+    def initialize_options(self: CleanCython) -> None:
+        """Set options/attributes/caches used by the command to default values."""
 
-    def finalize_options(self):
-        pass
+    def finalize_options(self: CleanCython) -> None:
+        """Set final values for all options/attributes used by the command."""
 
-    def run(self):
+    def run(self: CleanCython) -> None:
+        """Execute the actions intended by the command."""
         for path in PACKAGE_DIR.rglob("*"):
             if path.suffix in (".pyc", ".pyo", ".c", ".so"):
                 msg = f"clean: removing file {path}"
-                print(msg)
+                print(msg)  # noqa: T201
                 path.unlink()
 
 

src/mo_pack/__init__.py

@@ -2,10 +2,28 @@
 #
 # This file is part of mo_pack and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
-from ._packing import (compress_rle, compress_wgdos,
-                       decompress_rle, decompress_wgdos)
+"""Python bindings for the C library **libmo_unpack**.
+
+Provides Python bindings to the C library
+`libmo_unpack <https://github.com/SciTools/libmo_unpack>`_ , which contains
+packing methods used to encode and decode the data payloads of Met Office UM
+Post-Processing and Fields files.
+
+Supports both RLE and WGDOS encoding methods.
+
+"""
+
+from ._packing import compress_rle, compress_wgdos, decompress_rle, decompress_wgdos
 
 try:
     from ._version import version as __version__
 except ModuleNotFoundError:
     __version__ = "unknown"
+
+__all__ = [
+    "__version__",
+    "compress_rle",
+    "compress_wgdos",
+    "decompress_rle",
+    "decompress_wgdos",
+]