ovo/pyproject.toml at develop · MSDLLCpapers/ovo · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "ovo"
version = "1.0.3"
description = "OVO: an open-source ecosystem for de novo protein design"
readme = "README.md"
requires-python = ">=3.10"
authors = [
    {name = "David Prihoda", email = "david.prihoda@msd.com"},
    {name = "Marco Ancona", email = "marco.ancona@msd.com"},
    {name = "Tereza Calounova", email = "tereza.calounova@msd.com"},
]

dependencies = [
    "numpy",
    "pandas>=2.2.3",
    "jinja2>=3.1.5",
    "streamlit>=1.55",
    "authlib",
    "boto3",
    "mypy-boto3",
    "mypy_boto3_s3",
    "mypy-boto3-omics",
    "mypy-boto3-logs",
    "biopython",
    "plotly",
    "streamlit-timeago>=0.1.3",
    "timeago",
    "sqlalchemy",
    "appdirs",
    "streamlit_js_eval",
    "humanize",
    "cmap",
    "biopandas",
    "nextflow < 26", # to avoid enabling strict parser by default
    "psutil",
    "typer",
    "rich",
    "pydantic",
    "pydantic-settings",
    "pyyaml",
    "scipy",
    "xlsxwriter>=3.2.5",
    "matplotlib>=3.9.4",
    "jsonschema",
    "openpyxl",
]

[dependency-groups]
dev = [
    # testing
    "pytest",
    "pytest-mock",
    # utilities
    "ruff",
    "python-dotenv",
    # live reloading for streamlit
    "watchdog",
    # building docs
    "sphinx",
    "myst-parser",
    "furo",
    "sphinx-autodoc2"
]

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

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
include = ["ovo*"]

[tool.setuptools.package-data]
"*" = ["*"]

[tool.pytest.ini_options]
pythonpath = ["."]
testpaths = ["tests", "ovo/pipelines"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = "-v --tb=short"

[tool.ruff]
line-length = 120
indent-width = 4
target-version = "py311" # target python version for linting
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]

[tool.ruff.lint]
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.
select = ["E4", "E7", "E9", "F"]
ignore = []

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"