new: Update setup files and requirements.

.gitignore

@@ -59,4 +59,3 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
-

MANIFEST.in

@@ -0,0 +1,3 @@
+include README.md
+include LICENSE
+include requirements*.txt

requirements-dev.txt

@@ -0,0 +1,10 @@
+bandit>=1.7.5
+black>=23.3.0
+isort>=5.12.0
+mypy>=1.4.1
+pycodestyle>=2.10.0
+pydocstyle>=6.3.0
+pylint>=2.17.4
+pytest>=7.3.2
+pytest-cov>=4.1.0
+pytest-xdist>=3.3.1

setup.cfg

@@ -0,0 +1,107 @@
+[pycodestyle]
+exclude=.*,__pycache__,test,*venv,*virtualenv*
+# Ignore E402 import not at top of file, pylint will catch and we do not want double ignore lines in the code.
+# Ignore E501 line too long, up to maintainers/contributors to use best judgement.
+# Ignore E722 bare except, pylint will catch and we do not want double ignore lines in the code.
+# Ignore W503 break before binary operator, both W503 and W504 are enabled by default meaning no breaks could be made.
+ignore=E402,E501,E722,W503
+
+[pydocstyle]
+convention=google
+match-dir=^(?!\.|__pycache__|test|venv|virtualenv).*
+# PEP257 "D204 1 blank line after class docstring" is inconsistent depending on pydocstyle version. Add for consistency.
+add-select=D204
+
+[pylint]
+# Pylint requires a full list of disables, or a full list of includes, and cannot be partially overridden.
+# The following list starts with the pylint defaults, followed by project specifics.
+# Do not modify the pylint defaults without adding a comment as to why, and only comment out instead of remove.
+disable=raw-checker-failed,
+        bad-inline-option,
+        locally-disabled,
+        file-ignored,
+        suppressed-message,
+        useless-suppression,
+        deprecated-pragma,
+        use-symbolic-message-instead,
+        # PyAtop specific modifications.
+        # W1203, allow f-strings to be used in logging messages.
+        logging-fstring-interpolation,
+        # C0301 line too long, up to maintainers/contributors to use best judgement.
+        line-too-long,
+        # R0801 duplicate code, up to maintainers/contributors to use best judgement.
+        duplicate-code,
+        # W0221 arguments-differ, disabled until pylint known is resolved to prevent flagging variadics such as kwargs.
+        arguments-differ,
+        # R0903 too-few-public-methods, custom classes are allowed to have low amount of public functions.
+        too-few-public-methods,
+
+[pylint.MASTER]
+ignore=__pycache__,build,test
+# Use jobs 0 to autodetect CPUs on system for parallel performance.
+jobs=0
+
+[pylint.DESIGN]
+max-args=6
+max-attributes=10
+
+[pylint.TYPECHECK]
+# Property setters and getters are dynamic attributes, allow these to be overridden in subclasses.
+generated-members=fset,fget
+
+[isort]
+profile=black
+force_single_line=True
+
+[tool:pytest]
+norecursedirs=.* __pycache__ site-packages venv virtualenv virtualenvs
+filterwarnings =
+    # Promote all warnings to errors to ensure performance, forwards compatibility, and code quality.
+    error
+
+[mypy]
+exclude=(__pycache__)/
+ignore_missing_imports=True
+warn_unused_configs=True
+show_error_codes=True
+incremental=False
+follow_imports=skip
+# There is no option for an enable list, so a full disable list must be provided instead.
+disable_error_code=attr-defined,
+        name-defined,
+        call-arg,
+        arg-type,
+        call-overload,
+        valid-type,
+        var-annotated,
+        override,
+        return,
+        return-value,
+        assignment,
+        type-arg,
+        type-var,
+        union-attr,
+        index,
+        operator,
+        list-item,
+        dict-item,
+        typeddict-item,
+        has-type,
+        import,
+        no-redef,
+        func-returns-value,
+        abstract,
+        valid-newtype,
+        str-format,
+        str-bytes-safe,
+        exit-return,
+        no-untyped-call,
+        redundant-cast,
+        comparison-overlap,
+        no-any-unimported,
+        no-any-return,
+        unreachable,
+        name-match,
+        syntax,
+        misc
+disallow_untyped_defs=True

setup.py

@@ -1,36 +1,78 @@
-"""Setup configuration and dependencies for the pyatop library."""
+"""Set up configuration and dependencies for the pyatop library."""
 
 import os
-import setuptools
+from pathlib import Path
+
+from setuptools import find_packages
+from setuptools import setup
 
 ROOT_DIR = os.path.dirname(os.path.realpath(__file__))
 
 
-def _find_version() -> str:
+def _find_version(module_path: str, file: str = "__init__.py") -> str:
     """Locate semantic version from a text file in a compatible format with setuptools."""
     # Do not import the module within the library, as this can cause an infinite import. Read manually.
-    init_file = os.path.join(ROOT_DIR, 'pyatop', '__init__.py')
-    with open(init_file, 'rt') as file_in:
+    init_file = os.path.join(ROOT_DIR, module_path, file)
+    with open(init_file, "rt", encoding="utf-8") as file_in:
         for line in file_in.readlines():
-            if '__version__' in line:
+            if "__version__" in line:
                 # Example:
-                # __version__ = '1.5.0' -> 1.5.0
-                version = line.split()[2].replace("'", '')
+                # __version__ = "1.2.3" -> 1.2.3
+                version = line.split()[2].replace('"', "")
     return version
 
 
-setuptools.setup(
-    name='pyatop',
-    version=_find_version(),
-    description='Utilities for reading ATOP files natively in Python.',
-    maintainer='David Fritz',
-    maintainer_email='[email protected]',
-    url='https://github.com/dfrtz/pyatop',
-    packages=setuptools.find_packages(ROOT_DIR, include=['pyatop*'], exclude=['*test']),
-    python_requires='>=3.6',
+def read_requirements_file(extra_type: str | None) -> list[str]:
+    """Read local requirement file basic on the type."""
+    extra_type = f"-{extra_type}" if extra_type else ""
+    with open(f"requirements{extra_type}.txt", encoding="utf-8") as input_file:
+        lines = (line.strip() for line in input_file)
+        return [req for req in lines if req and not req.startswith("#")]
+
+
+setup(
+    name="pyatop",
+    description="Utilities for reading ATOP files natively in Python",
+    long_description=Path("README.md").read_text(encoding="utf-8"),
+    long_description_content_type="text/markdown",
+    version=_find_version("pyatop"),
+    author="David Fritz",
+    url="https://github.com/dfrtz/pyatop",
+    project_urls={
+        "Issue Tracker": "https://github.com/dfrtz/pyatop/issues",
+        "Source Code": "https://github.com/dfrtz/pyatop",
+    },
+    license="MIT",
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Topic :: Software Development",
+        "Topic :: Scientific/Engineering",
+        "Typing :: Typed",
+        "Operating System :: POSIX :: Linux",
+    ],
+    platforms=[
+        "Linux",
+    ],
+    test_suite="pytest",
+    packages=find_packages(ROOT_DIR, include=["pyatop*"], exclude=["*test", "tests*"]),
+    include_package_data=True,
+    python_requires=">=3.10",
+    extras_require={
+        "dev": [
+            *read_requirements_file("dev"),
+        ],
+    },
     entry_points={
-        'console_scripts': [
-            'pyatop = pyatop.atop_reader:main',
+        "console_scripts": [
+            "pyatop = pyatop.atop_reader:main",
         ]
     },
 )

utils/pydocstyle_patched.py

@@ -0,0 +1,20 @@
+#! /usr/bin/env python
+
+"""Static analysis tool for checking docstring conventions and style.
+
+Patched to account for google convention not working properly due to numpy checks:
+https://github.com/PyCQA/pydocstyle/issues/514
+"""
+
+from pydocstyle import cli
+from pydocstyle.checker import ConventionChecker
+
+
+def main() -> None:
+    """Run pydocstyle after disabling numpy convention checking."""
+    ConventionChecker.NUMPY_SECTION_NAMES = ()
+    cli.main()
+
+
+if __name__ == "__main__":
+    main()