[project]
name = "pymol-mcp"
version = "0.1.0"
description = "A headless PyMOL MCP server for molecular visualization, GROMACS/LAMMPS MD workflows, and clathrate-hydrate cage analysis."
readme = "README.md"
requires-python = ">=3.11"
license = { text = "MIT" }
authors = [{ name = "wjgoarxiv" }]
keywords = ["mcp", "pymol", "molecular-visualization", "gromacs", "lammps", "clathrate-hydrate", "md-analysis"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Chemistry",
]

# NOTE: `pymol` (pymol-open-source) is provided by the conda environment, NOT pip.
# The server MUST run in an interpreter that can `import pymol2` (e.g. conda env `viz`).
dependencies = [
    "fastmcp>=3.4.0",
    "numpy>=1.24",
    "scipy>=1.11",
]

[project.optional-dependencies]
# Universal trajectory/format bridge (GROMACS xtc/trr, LAMMPS dump, AMBER NetCDF, ...).
# GPL-2.0-or-later — kept OUT of the hard dependency set and lazily imported.
md = ["MDAnalysis>=2.7"]
dev = ["pytest>=8", "pytest-timeout>=2"]

[project.scripts]
pymol-mcp = "pymol_mcp.__main__:main"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/pymol_mcp"]

[tool.hatch.build.targets.sdist]
exclude = [
    "/.litcodex",
    "/.litopencode",
    "/.pr-checkouts",
    "/video/node_modules",
    "/video/out",
    "/video/.remotion",
    "/video/public/frames",
]

[tool.pytest.ini_options]
addopts = "-q"
testpaths = ["tests"]