pyproject.toml

# The Selector library provides a set of tools for selecting a
# subset of the dataset and computing diversity.
#
# Copyright (C) 2023 The QC-Devs Community
#
# This file is part of Selector.
#
# Selector is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# Selector is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --


[project]
# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
name = "selector"
version = "0.0.1"
description = "Molecule selection with maximum diversity."
readme = "README.md"
#requires-python = ">=3.9,<4.0"
requires-python = ">=3.9"
# "LICENSE" is name of the license file, which must be in root of project folder
license = {file = "LICENSE"}
authors = [
    {name = "QC-Devs Community", email = "qcdevs@gmail.com"},
]
keywords = [
    "subset selection",
    "variable selection",
    "chemical diversity",
    "compound selection",
    "maximum diversity",
    "chemical library design",
    "compound acquisition",
]

# https://pypi.org/classifiers/
# Add PyPI classifiers here
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "License :: OSI Approved :: GNU (Version 3)",
    "Natural Language :: English",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]

# Required dependencies for install/usage of your package or application
# If you don't have any dependencies, leave this section empty
# Format for dependency strings: https://peps.python.org/pep-0508/
dependencies = [
    "bitarray~=2.5.1",
    "importlib-resources>=5.6.0",
    "numpy>=1.21.2",
    "pandas>=1.3.5",
    "pytest>=6.2.5",
    "scikit-learn>=1.0.1",
    "scipy==1.11.1",
    "setuptools>=58.0.4",
]

[project.scripts]
# Command line interface entrypoint scripts
# selector = "selector.__main__:main"

[project.urls]
# Use PyPI-standard names here
# Homepage
# Documentation
# Changelog
# Issue Tracker
# Source
# Discord server
homepage = "https://github.com/theochem/Selector"
documentation = "https://selector.qcdevs.org/"
repository = "https://github.com/theochem/Selector"

# Development dependencies
# pip install -e .[lint,test,exe]
# pip install -e .[dev]
[project.optional-dependencies]
lint = [
    # ruff linter checks for issues and potential bugs
    "ruff",
    # checks for unused code
    # "vulture",
    # # required for codespell to parse pyproject.toml
    # "tomli",
    # # validation of pyproject.toml
    # "validate-pyproject[all]",
    # automatic sorting of imports
    "isort",
    # # automatic code formatting to follow a consistent style
    # "black",
]

test = [
    # Handles most of the testing work, including execution
    # Docs: https://docs.pytest.org/en/stable/contents.html
    "pytest==7.4.0",
    # required by pytest
    "hypothesis",
    # "Coverage" is how much of the code is actually run (it's "coverage")
    # Generates coverage reports from test suite runs
    "pytest-cov>=3.0.0",

    "tomli",
    "scikit-learn>=1.0.1",
    # Better parsing of doctests
    "xdoctest",
    # Colors for doctest output
    "Pygments",
]

exe = [
    "setuptools",
    "wheel",
    "build",
    "tomli",
    "pyinstaller",
    "staticx;platform_system=='Linux'",
]

dev = [
    # https://hynek.me/articles/python-recursive-optional-dependencies/
    "selector[lint,test,exe]",

    # # Code quality tools
    # "mypy",

    # # Improved exception traceback output
    # # https://github.com/qix-/better-exceptions
    # "better_exceptions",

    # # Analyzing dependencies
    # # install graphviz to generate graphs
    # "graphviz",
    # "pipdeptree",
]


[tool.setuptools]
# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html
platforms = ["Linux", "Windows", "MacOS"]
include-package-data = true
# This just means it's safe to zip up the bdist
zip-safe = true

# Non-code data that should be included in the package source code
# https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[tool.setuptools.package-data]
selector = ["*.xml"]

# Python modules and packages that are included in the
# distribution package (and therefore become importable)
[tool.setuptools.packages.find]
exclude = ["tests", "tests_*", "examples"]


# PDM example
#[tool.pdm.scripts]
#isort = "isort selector"
#black = "black selector"
#format = {composite = ["isort", "black"]}
#check_isort = "isort --check selector tests"
#check_black = "black --check selector tests"
#vulture = "vulture --min-confidence 100 selector tests"
#ruff = "ruff check selector tests"
#fix = "ruff check --fix selector tests"
#codespell = "codespell --toml ./pyproject.toml"
#lint = {composite = ["vulture", "codespell", "ruff", "check_isort", "check_black"]}


#[tool.codespell]
## codespell supports pyproject.toml since version 2.2.2
## NOTE: the "tomli" package must be installed for this to work
## https://github.com/codespell-project/codespell#using-a-config-file
## NOTE: ignore words for codespell must be lowercase
#check-filenames = ""
#ignore-words-list = "word,another,something"
#skip = "htmlcov,.doctrees,*.pyc,*.class,*.ico,*.out,*.PNG,*.inv,*.png,*.jpg,*.dot"


[tool.black]
line-length = 100
# If you need to exclude directories from being reformatted by black
# force-exclude = '''
# (
#     somedirname
#     | dirname
#     | filename\.py
# )
# '''


[tool.isort]
profile = "black"
known_first_party = ["selector"]
# If you need to exclude files from having their imports sorted
#extend_skip_glob  = [
#    "selector/somefile.py",
#    "selector/somedir/*",
#]


# https://beta.ruff.rs/docs
[tool.ruff]
line-length = 100
show-source = true

# Rules: https://beta.ruff.rs/docs/rules
# If you violate a rule, lookup the rule on the Rules page in ruff docs.
# Many rules have links you can click with a explanation of the rule and how to fix it.
# If there isn't a link, go to the project the rule was source from (e.g. flake8-bugbear)
# and review it's docs for the corresponding rule.
# If you're still confused, ask a fellow developer for assistance.
# You can also run "ruff rule <rule>" to explain a rule on the command line, without a browser or internet access.
select = [
    "E",    # pycodestyle
    "F",    # Pyflakes
    "W",    # Warning
    "B",    # flake8-bugbear
    "A",    # flake8-builtins
    "C4",   # flake8-comprehensions
    "T10",  # flake8-debugger
    "EXE",  # flake8-executable,
    "ISC",  # flake8-implicit-str-concat
    "G",    # flake8-logging-format
    "PIE",  # flake8-pie
    "T20",  # flake8-print
    "PT",   # flake8-pytest-style
    "RSE",  # flake8-raise
    "RET",  # flake8-return
    "TID",  # flake8-tidy-imports
    "ARG",  # flake8-unused-arguments
    "PGH",  # pygrep-hooks
    "PLC",  # Pylint Convention
    "PLE",  # Pylint Errors
    "PLW",  # Pylint Warnings
    "RUF",  # Ruff-specific rules

    # ** Things to potentially enable in the future **
    # DTZ requires all usage of datetime module to have timezone-aware
    # objects (so have a tz argument or be explicitly UTC).
    # "DTZ",  # flake8-datetimez
    # "PTH",  # flake8-use-pathlib
    # "SIM",  # flake8-simplify
]

# Files to exclude from linting
extend-exclude = [
    "*.pyc",
    "__pycache__",
    "*.egg-info",
    ".eggs",
    # check point files of jupyter notebooks
    "*.ipynb_checkpoints",
    ".tox",
    ".git",
    "build",
    "dist",
    "docs",
    "examples",
    "htmlcov",
    "notebooks",
    ".cache",
    "_version.py",
]

# Linting error codes to ignore
ignore = [
    "F403",    # unable to detect undefined names from star imports
    "F405",    # undefined locals from star imports
    "W605",    # invalid escape sequence
    "A003",    # shadowing python builtins
    "RET505",  # unnecessary 'else' after 'return' statement
    "RET504",  # Unnecessary variable assignment before return statement
    "RET507",  # Unnecessary {branch} after continue statement
    "PT011",   # pytest-raises-too-broad
    "PT012",   # pytest.raises() block should contain a single simple statement
    "PLW0603", # Using the global statement to update is discouraged
    "PLW2901", # for loop variable overwritten by assignment target
    "G004",    # Logging statement uses f-string
    "PIE790",  # no-unnecessary-pass
    "PIE810",  # multiple-starts-ends-with
    "PGH003",  # Use specific rule codes when ignoring type issues
    "PLC1901", # compare-to-empty-string
]

# Linting error codes to ignore on a per-file basis
[tool.ruff.per-file-ignores]
"__init__.py" = ["F401", "E501"]
"selector/somefile.py" = ["E402", "E501"]
"selector/somedir/*" = ["E501"]


# Configuration for mypy
# https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file
[tool.mypy]
python_version = "3.9"
follow_imports = "skip"
ignore_missing_imports = true
files = "selector"  # directory mypy should analyze
# Directories to exclude from mypy's analysis
exclude = [
    "selector/somedir",
    "selector/somefile\\.py",
    "dirname",
]


# Configuration for pytest
# https://docs.pytest.org/en/latest/reference/customize.html#pyproject-toml
[tool.pytest.ini_options]
addopts = [
    # Allow test files to have the same name in different directories.
    "--import-mode=importlib",
    "--cache-clear",
    "--showlocals",
    "-v",
    "-r a",
    "--cov-report=term-missing",
    "--cov=selector",
]
# directory containing the tests
testpaths = [
    "selector/tests",
    "selector/methods/tests",
]
norecursedirs = [
    ".vscode",
    "__pycache__",
    "build",
]
# Warnings that should be ignored
filterwarnings = [
    "ignore::DeprecationWarning"
]
# custom markers that can be used using pytest.mark
markers = [
    "slow: lower-importance tests that take an excessive amount of time",
]


# Configuration for coverage.py
[tool.coverage.run]
# files or directories to exclude from coverage calculations
omit = [
    'selector/somedir/*',
    'selector/somefile.py',
]


# Configuration for vulture
[tool.vulture]
# Files or directories to exclude from vulture
# The syntax is a little funky
exclude = [
    "somedir",
    "*somefile.py",
]

# configuration for bandit
[tool.bandit]
exclude_dirs = [
    "selector/tests",
    "selector/methods",
]
skips = [
    "B101", # Ignore assert statements
    "B311", # Ignore pseudo-random generators
    "B404", # Ignore subprocess import
    "B603", # Ignore subprocess call
    "B607", # Ignore subprocess call
]