pyproject.toml

[project]
name = "biotite"
requires-python = ">=3.11"
description = "A comprehensive library for computational molecular biology"
readme = "README.rst"
authors = [{name = "The Biotite contributors"}]
license = "BSD-3-Clause"
license-files = ["LICENSE.rst"]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
  # Wheels compiled with NumPy 2.0 are backward compatible with NumPy 1.x
  # https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice
  "numpy >= 1.25",
  "biotraj >= 1.0, < 2.0",
  "requests >= 2.12",
  "msgpack >= 0.5.6",
  "networkx >= 2.0",
  "packaging >= 24.0",
]
dynamic = ["version"]

[project.optional-dependencies]
test = [
  "pytest",
  "pytest-codspeed",
]
lint = [
  "ruff == 0.9.7",
  "numpydoc == 1.8.0",
]

[project.urls]
homepage = "https://www.biotite-python.org"
repository = "https://github.com/biotite-dev/biotite"
documentation = "https://www.biotite-python.org"

[tool.ruff.lint]
# pyflakes, pycodestyle isort and varibale naming
select = ["F", "E", "W", "I", "TID", "N"]
ignore = [
    # In docstrings long lines are often intentional
    # Most other ocassions are caught by the ruff formatter
    "E501",
    # Due to constants and class placeholders defined in functions
    "N806",
]

[tool.ruff.lint.per-file-ignores]
# Due to `* import` of BCIF encoding
"src/biotite/setup_ccd.py" = ["F405", "F403"]
# Due to imports after the PATH has been adjusted
"doc/conf.py" = ["E402"]
# Due to `from .module import *` imports in `__init__.py` modules
"__init__.py" = ["F403", "TID252"]
# Due to package existence check before other modules are imported
"src/biotite/interface/**/__init__.py" = ["E402"]
# Due to pymol scripts that are evaluated in other example scripts
"doc/examples/**/*_pymol.py" = ["F821"]
# Due to 'Table' class used as parametrized argument in test functions
"benchmarks/sequence/align/benchmark_kmers.py" = ["N803"]

[tool.ruff.lint.flake8-tidy-imports]
ban-relative-imports = "all"

[tool.ruff.lint.isort]
# No separator lines between import sections
no-lines-before = [
    "future",
    "standard-library",
    "third-party",
    "first-party",
    "local-folder",
]
order-by-type = true
known-first-party = ["biotite"]

[tool.numpydoc_validation]
# The description of each rule is documented at
# https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks
checks = [
  "all",
  # ... except:
  "GL08",  # Properties do not have a docstring
  "SS03",  # Sometimes the citation comes after the period
  "SS05",  # Too error-prone; classes do not use infinite verbs
  "SS06",  # Sometimes summaries are a bit longer
  "ES01",  # Some functions are simple enough to not need an extended summary
  "PR06",  # The types are quite descriptive (include shape, dtype, etc.)
  "RT02",  # In Biotite all return values have names
  # Intentionally not all docstrings contain these sections
  "YD01",
  "SA01",
  "EX01",
]
exclude = [
  '__init__$', # Subpackage descriptions are not Numpydoc formatted
  '\._[_a-z0-9]+$',  # Do not validate private or special methods
  # Dataclasses: Numpydoc complains about additional constructor parameters,
  # but the constructor is absent
  'sdf.Metadata\.Key',
  'header.Header',
  'throttle.ThrottleStatus',
  # Numpydoc does not accept the parameters of inherited constructors
  "query.DepositGrouping",
  "query.UniprotGrouping",
  # Function uses args/kwargs, but docstring describes parameter
  'geometry.index_',
  'query.FieldQuery',
  'query.SimilarityQuery',
  'query.IdentityQuery',
  'query.StructureQuery',
  'query.SuperOrSubstructureQuery',
  'query.SuperstructureQuery',
  'query.SubstructureQuery',
  # Numpydoc expects a return value for decorators
  'application.requires_state',
  'version.requires_version',
  'object.validate',
  # Usage of the return value is not intended
  'display.show',
  'display.play',
]

[tool.pytest.ini_options]
testpaths = [
  "tests",
  "benchmarks"
]
python_files = [
  "test_*.py",
  "benchmark_*.py",
]
python_functions = [
  "test_*",
  "benchmark_*",
]
filterwarnings = [
  # Appears in loading NetCDF trajectory files
  "ignore:The 'netCDF4' Python package is not installed.",
  "ignore:Input structure has no associated 'BondList'",
]

[tool.hatch.build.targets.sdist]
exclude = [
  "tests",
  "benchmarks",
  "doc",
  "environment.yml",
  # .github, .gitignore, .gitattributes
  ".git*",
]
artifacts = [
  "src/biotite/structure/info/components.bcif"
]

[tool.hatch.build.targets.wheel]
artifacts = [
  "src/biotite/structure/info/components.bcif"
]

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.hooks.vcs]
version-file = "src/biotite/version.py"

[tool.hatch.build.targets.wheel.hooks.cython]
dependencies = ["hatch-cython"]

[tool.hatch.build.targets.wheel.hooks.cython.options]
include_numpy = true
compile_py = false
define_macros = [
    ["NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION"],
]

[build-system]
requires = [
    "hatchling",
    "hatch-vcs == 0.4",
    "hatch-cython == 0.5",
    "numpy >= 2.0",
    "cython >= 3.0",
]
build-backend = "hatchling.build"