genSurvPy/pyproject.toml at develop · DiogoRibeiro7/genSurvPy · GitHub

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[project]
name = "gen_surv"
version = "3.1.2"
description = "Simulate survival data with a known truth: twelve models spanning proportional hazards, accelerated failure time, competing risks, cure fractions, recurrent events and multi-state processes"
readme = "README.md"
requires-python = ">=3.11,<3.14"
license = "MIT"
license-files = ["LICENSE"]
authors = [
    { name = "Diogo Ribeiro", email = "diogo.debastos.ribeiro@gmail.com" },
]
keywords = [
    "survival-analysis",
    "simulation",
    "synthetic-data",
    "cox-model",
    "accelerated-failure-time",
    "competing-risks",
    "recurrent-events",
    "multi-state-models",
    "cure-models",
    "markov-model",
    "time-dependent",
    "statistics",
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
dependencies = [
    "numpy (>=2.3.3,<3.0.0)",
    "pandas (>=2.3.3,<3.0.0)",
    "scipy (>=1.17.1,<2.0.0)",
    "typer (>=0.19.2,<0.20.0)",
    "click (>=8.3.0,<9.0.0)",
    "matplotlib (>=3.10.7,<4.0.0)",
    "lifelines (>=0.30.3,<0.31.0)",
    "pyarrow (>=25.0.1,<26)",
    "pyreadr (>=0.5.3,<0.6.0)",
]

[project.urls]
Homepage = "https://diogoribeiro7.github.io/genSurvPy/"
Documentation = "https://diogoribeiro7.github.io/genSurvPy/"
Repository = "https://github.com/DiogoRibeiro7/genSurvPy"
Issues = "https://github.com/DiogoRibeiro7/genSurvPy/issues"
Changelog = "https://github.com/DiogoRibeiro7/genSurvPy/blob/main/CHANGELOG.md"

[project.scripts]
gen_surv = "gen_surv.cli:app"

[tool.poetry]
packages = [{ include = "gen_surv" }]

[tool.poetry.group.dev.dependencies]
pytest = ">=9.1.1,<10.0.0"
pytest-cov = "^7.0.0"
pytest-benchmark = "^5.3.0"
mypy = "^1.18.2"
invoke = ">=3.0.3,<4.0.0"
hypothesis = "^6.142.1"
tomli = "^2.3.0"
black = ">=26.5.1,<27.0"
isort = ">=8.0.1,<9"
flake8 = ">=6.1,<8.0"
scikit-survival = ">=0.28.0,<0.29"
pre-commit = "^4.6.2"

# Dependencies of the research studies under research/, not of the package.
# The published gen-surv wheel must not acquire these merely because a paper
# uses them, so they live in their own group rather than in the runtime list.
#
# PyYAML was previously undeclared: the research configuration loader imports
# it, but it was only present transitively through mkdocs and pre-commit, so a
# clean install without the docs group would have failed at load_study.
#
# scikit-survival is also in the dev group, where the package's own sksurv
# adapter tests need it. It is repeated here so a research-only install works
# without pulling the whole development toolchain.
[tool.poetry.group.research.dependencies]
pyyaml = "^6.0"
scikit-survival = ">=0.25,<0.29"

[tool.poetry.group.docs.dependencies]
mkdocs = ">=1.6,<2.0"
mkdocs-material = ">=9.5,<10.0"
mkdocstrings = { extras = ["python"], version = ">=1.0.6,<2.0" }

[tool.pytest.ini_options]
markers = [
    "slow: slow performance tests",
]

[tool.black]
line-length = 88
target-version = ['py311']
include = '\.pyi?$'

[tool.isort]
profile = "black"
line_length = 88

[tool.flake8]
max-line-length = 88
extend-ignore = ["E203", "W503", "E501", "W291", "W293", "W391", "E402", "E302", "E305"]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true

[[tool.mypy.overrides]]
module = [
    "typer",
    "typer.models",
    "matplotlib",
    "matplotlib.*",
    "lifelines",
    "lifelines.*",
    "sklearn",
    "sklearn.*",
    "numpy",
    "numpy.*",
    "pandas",
    "pandas.*",
    "scipy",
    "scipy.*",
    "pyreadr",
    "sksurv",
    "sksurv.*",
]
ignore_missing_imports = true

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"