[build-system]
build-backend = "setuptools.build_meta:__legacy__"
requires = [ "cython>=3", "numpy~=2.0,<2.5", "setuptools", "versioneer[toml]" ]

[project]
name = "mdtraj"
description = "MDTraj: A modern, open library for the analysis of molecular dynamics trajectories"
readme = { file = "README.md", content-type = "text/markdown" }
keywords = []
license = "LGPL-2.1-OR-later"
license-files = [ "LICEN[CS]E*" ]
authors = [
  { name = "Robert McGibbon", email = "rmcgibbo@gmail.com" },
]
requires-python = ">=3.12"
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Intended Audience :: Developers",
  "Intended Audience :: Science/Research",
  "Operating System :: MacOS",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: POSIX",
  "Operating System :: Unix",
  "Programming Language :: C",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Scientific/Engineering :: Chemistry",
]
dynamic = [ "version" ]
dependencies = [
  "numpy~=2.0,<2.5",
  "packaging",
  "pyparsing",
  "scipy",
]
optional-dependencies.all = [ "mdtraj[optional]", "mdtraj[tests]" ]
optional-dependencies.optional = [ "netcdf4", "networkx", "pandas", "pyarrow", "tables" ]
optional-dependencies.tests = [ "pytest", "pytest-recording", "pytest-rerunfailures", "pytest-xdist" ]
urls.download = "https://github.com/mdtraj/mdtraj/releases/latest"
urls.homepage = "https://mdtraj.org"
urls.issues = "https://githubcom/mdtraj/mdtraj/issues"
urls.source = "https://github.com/mdtraj/mdtraj"
scripts.mdconvert = "mdtraj.scripts.mdconvert:entry_point"
scripts.mdinspect = "mdtraj.scripts.mdinspect:entry_point"

[tool.setuptools]
packages.find.where = [ "." ]
package-data."mdtraj.formats.pdb" = [ "data/*" ]

[tool.ruff]
line-length = 119
extend-exclude = [ "mdtraj/_version.py" ]
lint.select = [
  "E",
  "F",
  "I",
  "NPY",
  "UP",
  "W",
]
lint.per-file-ignores."*" = [ "NPY002", "UP031" ]
# Would really, really like to get rid of F403, though F401 is okay
lint.per-file-ignores."__init__.py" = [ "F401", "F403" ]
lint.per-file-ignores."mdtraj/core/trajectory.py" = [ "F401" ]
lint.per-file-ignores."mdtraj/geometry/__init__.py" = [ "F403", "F405" ]
lint.per-file-ignores."mdtraj/utils/unit/**" = [ "F403", "F405" ]

[tool.pytest]
ini_options.testpaths = [
  "examples",
  "tests",
]
ini_options.addopts = "-v -ra"
ini_options.filterwarnings = [
  "ignore:.*Casting *:mdtraj.utils.validation.TypeCastPerformanceWarning",
  "ignore:.*Function restrict_atoms is deprecated;.*:DeprecationWarning",
  "ignore:.*object name is a Python keyword.*:tables.NaturalNameWarning",
  "ignore:.*The 'netCDF4' Python package.*:UserWarning",
  "ignore:.*top= kwargs ignored since this file parser does not support it.*:UserWarning",
  "ignore:.*Unlikely unit cell *:UserWarning",
  "ignore:.*Using or importing the ABCs from 'collections' instead of.*:DeprecationWarning",
]

[tool.coverage]
run.omit = [
  "*test_*.py",
  "*testing/*.py",
]
report.exclude_lines = [
  "@overload",
  "if TYPE_CHECKING:",
  "pragma: no cover",
  "raise NotImplementedError",
]

[tool.versioneer]
VCS = "git"
style = "pep440"
versionfile_source = "mdtraj/_version.py"
versionfile_build = "mdtraj/_version.py"
tag_prefix = ""
parentdir_prefix = "mdtraj-"