pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "versioningit~=2.0"]
build-backend = "setuptools.build_meta"

# Self-descriptive entries which should always be present
# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
[project]
name = "openfit"
description = "Molecular Density Fitting Using 3D Gaussian Functions"
dynamic = ["version"]
readme = "README.md"
authors = [
    { name = "Carlos Bueno", email = "carlos.bueno@rice.edu" }
]
license = "MIT"
license-files = ["LICENSE"]
# See https://pypi.org/classifiers/
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Physics",
]
requires-python = ">=3.10"
# Run-time dependencies. The core fitting code always imports these.
# Heavier, situational dependencies are kept lazy-imported and declared as
# optional extras below, so the core install stays lightweight.
dependencies = [
    "numpy",
    "scipy",
    "numba",
]

[project.urls]
"Source" = "https://github.com/cabb99/OpenFit"
"Documentation" = "https://openfit.readthedocs.io/"

[project.scripts]
openfit = "openfit.cli:main"

[project.optional-dependencies]
# OpenMM molecular dynamics integration (add_force / update_force).
openmm = [
  "openmm",
]
# Reading/writing density maps and trajectories.
io = [
  "mrcfile",
  "mdtraj",
]
# PDB/CIF/GRO parsing and the Scene-based workflow.
# MolScene is not on PyPI/conda yet, so install it from GitHub for now.
pdb = [
  "molscene @ git+https://github.com/cabb99/molscene",
]
# Plotting helpers
viz = [
  "matplotlib",
]
# YAML config support for `openfit run`.
cli = [
  "pyyaml",
]
# Structure-based-model integration (Fit.from_smog / from_smog_structure).
smog = [
  "OpenSMOG",
]
# OpenAWSEM coarse-grained force field (Fit.from_awsem).
awsem = [
  "openawsem @ git+https://github.com/cabb99/openawsem",
]
# Everything needed for the full feature set (awsem kept separate — heavy + git-only).
all = [
  "openmm",
  "mrcfile",
  "mdtraj",
  "molscene @ git+https://github.com/cabb99/molscene",
  "matplotlib",
  "pyyaml",
  "OpenSMOG",
]
test = [
  "pytest>=6.1.2",
  "pytest-cov",
]

[tool.setuptools]
# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
#
# As of version 0.971, mypy does not support type checking of installed zipped
# packages (because it does not actually import the Python packages).
# We declare the package not-zip-safe so that our type hints are also available
# when checking client code that uses our (installed) package.
# Ref:
# https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561
zip-safe = false
# Let setuptools discover the package in the current directory,
# but be explicit about non-Python files.
# See also:
#   https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration
# Note that behavior is currently evolving with respect to how to interpret the
# "data" and "tests" subdirectories. As of setuptools 63, both are automatically
# included if namespaces is true (default), even if the package is named explicitly
# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered
# recursively because of its __init__.py file, but the data subdirectory is excluded
# with include-package-data = false and namespaces = false.
include-package-data = false
[tool.setuptools.packages.find]
namespaces = false
where = ["."]

# Ref https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data
[tool.setuptools.package-data]
openfit = [
    "py.typed"
]

[tool.versioningit]
default-version = "1+unknown"

[tool.versioningit.format]
distance = "{base_version}+{distance}.{vcs}{rev}"
dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"

[tool.versioningit.vcs]
# The method key:
method = "git"  # <- The method name
# Parameters to pass to the method:
match = ["*"]
default-tag = "1.0.0"

[tool.versioningit.write]
file = "openfit/_version.py"

[tool.black]
line-length = 119
target-version = ["py310", "py311", "py312", "py313"]
# Generated by versioningit; never reformat it.
extend-exclude = "openfit/_version.py"