pyproject.toml

# The B3DB provides a rich molecule database for
# Blood-Brain Barrier (BBB) permeability.
#
# Copyright (C) 2021-2025 The QC-Devs Community
# This file is part of B3DB.
#
# B3DB is dedicated to the public domain under the terms of CC0 1.0 Universal.
#
# A full copy of the CC0 1.0 Universal license can be found at:
# https://creativecommons.org/publicdomain/zero/1.0/legalcode
#
# --


[project]
# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
name = "qc-B3DB"
description = "A rich molecule dataset for Blood-Brain Barrier (BBB) permeability."
readme = {file = 'README.md', content-type='text/markdown'}
requires-python = ">=3.9"
# "LICENSE" is name of the license file, which must be in root of project folder
license = "CC0-1.0"
authors = [
    {name = "QC-Devs Community", email = "qcdevs@gmail.com"},
]
keywords = [
    "Blood-Brain Barrier",
    "BBB",
    "drug discovery",
    "BBB permeability",
    "CNS drug delivery",
    "molecule database",
]

# https://pypi.org/classifiers/
# Add PyPI classifiers here
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Natural Language :: English",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: Unix",
    "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",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Chemistry",
]

dynamic = [
    "dependencies",
    "optional-dependencies",
    "version",
    ]

[project.scripts]
# Command line interface entrypoint scripts

[project.urls]
# Use PyPI-standard names here
# Homepage
# Documentation
# Changelog
# Issue Tracker
# Source
# Discord server
homepage = "https://github.com/theochem/B3DB"
documentation = "https://github.com/theochem/B3DB"
repository = "https://github.com/theochem/B3DB"

[build-system]
# Minimum requirements for the build system to execute.
requires = ["setuptools>=64", "setuptools-scm>=8", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.dynamic]
dependencies = {file = ["requirements.txt"]}
# optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}

[tool.setuptools_scm]
# can be empty if no extra settings are needed, presence enables setuptools-scm

[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

# Python modules and packages that are included in the
# distribution package (and therefore become importable)
[tool.setuptools.packages.find]
where = ["."]
include = ["B3DB"]
exclude = [
    "*/*/tests",
    "tests_*",
    "data_curation",
    "data_curation/*",
    "cleaning",
    "notebooks",
    "grouping",
    "preprocessing",
    "raw_data",
    "data_curation/**/*",
    "notebooks/**/*",
]

# 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]
B3DB = ["*.csv", "*.tsv", "*.tsv.gz"]

[tool.setuptools.exclude-package-data]
# exclude all files in data_curation folder from all packages
"*" = [
    "data_curation/*",
    "data_curation/**/*",
    "notebooks/*",
    "notebooks/**/*",
    "*.pyc",
    "__pycache__/*",
    "*.egg-info/*",
    ".git*",
    ".github/*",
    "build/*",
    "dist/*",
    ".tox/*",
    ".pytest_cache/*",
    ".coverage",
    "htmlcov/*",
    ".mypy_cache/*",
    ".ruff_cache/*",
]




[tool.black]
line-length = 100

[tool.isort]
profile = "black"
known_first_party = ["B3DB"]
# If you need to exclude files from having their imports sorted
#extend_skip_glob  = [
#    "B3DB/somefile.py",
#    "B3DB/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"]
"B3DB/somefile.py" = ["E402", "E501"]
"B3DB/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 = "B3DB"  # directory mypy should analyze
# Directories to exclude from mypy's analysis
exclude = [
    "book",
]


# 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=B3DB",
]
# directory containing the tests
testpaths = [
    "B3DB/measures/tests",
    "B3DB/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 = [
#     'B3DB/measures/tests/*',
#     'B3DB/methods/tests/*',
# ]


# 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 = [
    "B3DB/measures/tests",
    "B3DB/methods/tests",
]
skips = [
    "B101", # Ignore assert statements
    "B311", # Ignore pseudo-random generators
    "B404", # Ignore subprocess import
    "B603", # Ignore subprocess call
    "B607", # Ignore subprocess call
]