vEcolisRNA/pyproject.toml at sRNA-regulation · vivarium-collective/vEcolisRNA · GitHub

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[build-system]
requires = [
    "setuptools",
    "wheel",
    "Cython",
    "numpy"
]
build-backend = "setuptools.build_meta"

[project]
name = "vEcoli"
version = "1.1.0"
description = "Whole Cell E. coli Model"
requires-python = "==3.12.9"
dependencies = [
    "numpy",
    "scipy",
    "biopython",
    "cvxpy",
    "cython",
    "dill",
    "duckdb",
    "gcsfs",
    "pyarrow",
    "ipdb",
    "ipython",
    "line-profiler",
    "altair",
    "numba",
    "orjson",
    # Constraint can be removed once cvxpy supports newer ortools
    # than 9.12, need 9.11 to support newer protobuf (see gh-326)
    "ortools<9.11",
    "pandas",
    "polars",
    "pymunk",
    "scikit-image",
    "scikit-learn",
    "seaborn",
    "swiglpk",
    "sympy",
    "tqdm",
    "unum",
    "vivarium-core",
    "imageio[ffmpeg]",
    "statsmodels",
    "ecos",
    "matplotlib",
    "iteround",
    "stochastic-arrow",
    "autograd",
    "xmltodict",
    # Required to save Altair charts as PNG
    "vl-convert-python",
    "plotly>=6.2.0",
    "kaleido>=1.0.0",
    "pandas-stubs==2.3.0.250703",
    "scipy-stubs==1.16.1.0",
]

[project.optional-dependencies]
dev = [
    "pytest",
    "pytest-cov",
    "mypy",
    "ruff",
    "pre-commit",
    "jupyter",
    "marimo[sql,lsp]"
]
docs = [
    "Sphinx",
    "sphinx-rtd-theme",
    "nbsphinx"
]

[tool.setuptools]
packages = [
    "configs",
    "ecoli",
    "reconstruction",
    "runscripts",
    "validation",
    "wholecell"
]