CodeEntropy/pyproject.toml at main · CCPBioSim/CodeEntropy · GitHub

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[build-system]
# Build the package with [flit](https://flit.readthedocs.io)
requires = ["flit_core >=3.4,<4"]
build-backend = "flit_core.buildapi"

[project]
# See https://www.python.org/dev/peps/pep-0621/
name = "CodeEntropy"
dynamic = ["version"]
description = "CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics."
authors = [
    {name = "Arghya 'Argo' Chakravorty", email = "arghyac@umich.edu"},
    {name = "Donald Chung-HK", email = "donald.chung@stfc.ac.uk"},
    {name = "Sarah Fegan", email = "sarah.fegan@stfc.ac.uk"},
    {name = "James Gebbie-Rayet", email = "james.gebbie@stfc.ac.uk"},
    {name = "Sarah Harris", email="sarah.harris@sheffield.ac.uk"},
    {name = "Richard Henchman", email="rhen7213@uni.sydney.edu.au"},
    {name = "Jonathan Higham", email="j.higham4@lancaster.ac.uk"},
    {name = "Jas Kalayan", email = "jas.kalayan@stfc.ac.uk"},
    {name = "Ioana Papa", email = "iapapa1@sheffield.ac.uk"},
]
maintainers = [
    {name = "Harry Swift", email = "harry.swift@stfc.ac.uk"}
]
readme = "README.md"
license = { file = "LICENSE" }
classifiers = [
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Development Status :: 5 - Production/Stable"
]
keywords = ["entropy", "macromolecular systems", "MD simulation"]
requires-python = ">=3.12"
dependencies = [
    "numpy>=2.3,<3.0",
    "mdanalysis>=2.10,<3.0",
    "pandas>=3,<3.1",
    "psutil>=7.1,<8.0",
    "PyYAML>=6.0,<7.0",
    "python-json-logger>=4.0,<5.0",
    "rich>=14.2,<15.0",
    "art>=6.5,<7.0",
    "networkx>=3.6,<3.7",
    "matplotlib>=3.10,<3.11",
    "waterEntropy>=2,<2.3",
    "requests>=2.32,<3.0",
    "rdkit>=2025.9.5",
]

[project.urls]
Homepage = "https://ccpbiosim.github.io/CodeEntropy/"
Repository = "https://github.com/CCPBioSim/CodeEntropy"
Documentation = "https://codeentropy.readthedocs.io"

[project.optional-dependencies]
testing = [
    "pytest>=9.0,<10.0",
    "pytest-cov>=7.0,<8.0",
    "pytest-sugar>=1.1,<2.0",
    "pytest-xdist"
]
pre-commit = [
    "pre-commit>=4.5,<5.0",
    "ruff>=0.15,<0.16",
    "pylint>=4.0,<5.0",
    "rstcheck>=6.2,<7.0"
]
docs = [
    "sphinx>=9.1,<9.2",
    "nbsphinx>=0.9,<1.0",
    "sphinx_rtd_theme>=3,<3.2",
    "sphinxcontrib-contentui>=0.2,<1.0",
    "sphinxcontrib-details-directive>=0.1,<1.0",
    "sphinx_copybutton>=0.5,<1.0",
    "furo>=2025.0,<2026.0",
    "markupsafe>=3.0,<4.0"
]

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

[tool.pytest.ini_options]
testpaths = ["tests"]

addopts = "-n auto -vv -ra"

markers = [
  "regression: end-to-end regression tests against baselines",
  "slow: long-running regression tests (20-30+ minutes)",
]

[tool.ruff]
line-length = 88
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "I", "B", "UP"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"