pyproject.toml

# -*- coding: utf-8 -*-
# The Procrustes library provides a set of functions for transforming
# a matrix to make it as similar as possible to a target matrix.
#
# Copyright (C) 2017-2022 The QC-Devs Community
#
# This file is part of Procrustes.
#
# Procrustes 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.
#
# Procrustes 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]
name = "qc-procrustes"
description = "Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other."
readme = {file = 'README.md', content-type='text/markdown'}
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
    {name = "QC-Devs Community", email = "qcdevs@gmail.com"},
]
keywords = [
    "procrustes analysis",
    "statistical shape analysis",
    "qudratic assignment problem",
    "matrix transformation",
    "generalized procrustes analysis",
    "orthogonal procrustes problem",
    "symmetric procrustes problem",
    "rotational procrustes problem",
    "permutation procrustes problem",
    "softassign method",
    "molecule alignment",
    "chemical structure similarity",

]

classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "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",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Mathematics",
    'Topic :: Scientific/Engineering :: Physics',
    'Topic :: Scientific/Engineering :: Chemistry',
    'Intended Audience :: Science/Research',
]

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

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

[project.urls]
homepage = "https://github.com/theochem/procrustes"
documentation = "https://procrustes.qcdevs.org/"
repository = "https://github.com/theochem/procrustes/"

[build-system]
requires = ["setuptools>=64", "setuptools-scm>=8", "wheel", "build"]
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]
platforms = ["Linux", "Windows", "MacOS"]
include-package-data = true
zip-safe = true

[tool.setuptools.package-data]
procrustes = ["*.xml"]

[tool.setuptools.packages.find]
exclude = ["*/*/tests", "tests_*", "doc", "tools/conda.recipe", "tools/conda.recipe/*"]

[tool.black]
line-length = 100

[tool.isort]
# https://github.com/PyCQA/isort/blob/main/pyproject.toml
line_length = 100
profile = "black"
known_first_party = ["procrustes"]
skip = [
    "procrustes/__init__.py"
]

[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
]

[tool.ruff.per-file-ignores]
"__init__.py" = ["F401", "E501"]
"procrustes/somefile.py" = ["E402", "E501"]
"procrustes/somedir/*" = ["E501"]

[tool.mypy]
python_version = "3.11"
follow_imports = "skip"
ignore_missing_imports = true
files = "procrustes"
exclude = [
    "doc",
    "docs",
    "tools/conda.recipe",
    "tools/conda.recipe/*",
]

# Configuration for pytest
# https://docs.pytest.org/en/latest/reference/customize.html#pyproject-toml
[tool.pytest.ini_options]
addopts = [
    "--import-mode=importlib",
    "--cache-clear",
    "--showlocals",
    "-v",
    "-r a",
    "--cov-report=term-missing",
    "--cov=procrustes",
]
# directory containing the tests
testpaths = [
    "procrustes/tests",
    "procrustes/test",
]
norecursedirs = [
    ".vscode",
    "__pycache__",
    "build",
]
filterwarnings = [
    "ignore::DeprecationWarning"
]
markers = [
    "slow: lower-importance tests that take an excessive amount of time",
]

[tool.coverage.run]
omit = [
    'procrustes/test/*',
]

[tool.vulture]
exclude = [
    "somedir",
    "*somefile.py",
]

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

[tool.pylint."MESSAGES CONTROL"]
max-line-length = 100
disable = [
    "too-many-arguments",
    "too-many-locals",
    # "wrong-import-order",
    "fixme",
    "too-many-branches",
    "too-many-statements",
    "too-many-lines",
    "unnecessary-lambda-assignment",
    "no-else-return",
    "no-member",
    "too-many-branches",
    "too-many-positional-arguments",
]

[tool.pylint."MASTER"]
# ingore the __init__.py files
# ignore-patterns = "__init__.py"
# https://pylint.readthedocs.io/en/stable/user_guide/configuration/all-options.html#ignore
ignore = [
    "procrustes/test/__init__.py",
    "procrustes/__init__.py",
    ]