pyproject.toml

[project]
name = "HSSM"
version = "0.3.0"
description = "Bayesian inference for hierarchical sequential sampling models."
authors = [
    { name = "Alexander Fengler", email = "alexander_fengler@brown.edu" },
    { name = "Paul Xu", email = "yang_xu@brown.edu" },
    { name = "Carlos Paniagua", email = "carlos_paniagua@brown.edu" },
    { name = "Krishn Bera", email = "krishn_bera@brown.edu" },
    { name = "Aisulu Omar", email = "aisulu_omar@brown.edu" },
    { name = "Michael Frank", email = "michael_frank@brown.edu" },
]
readme = "README.md"
license = { file = "LICENSE" }
keywords = ["HSSM", "sequential sampling models", "bayesian", "bayes", "mcmc"]

requires-python = ">=3.11,<3.14"
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]

dependencies = [
    "absl-py>=2.3.1",
    "arviz>=0.22.0",
    "bambi>=0.17.2",
    "cloudpickle>=3.0.0",
    "hddm-wfpt>=0.1.6",
    "huggingface-hub>=0.34.0",
    "jaxonnxruntime>=0.3.0",
    "numpyro>=0.19",
    "onnx>=1.16.0",
    "pandas>=2.2,<3",
    "pymc>=5.26.0",
    "seaborn>=0.13.2",
    "ssm-simulators>=0.12.2",
    "tqdm>=4.66.0",
]

[project.urls]
homepage = "https://lnccbrown.github.io/HSSM/"
documentation = "https://lnccbrown.github.io/HSSM/"
repository = "https://github.com/lnccbrown/HSSM"

[project.optional-dependencies]
cuda12 = ["jax[cuda12]>=0.5.2"]

[dependency-groups]
dev = [
    "coverage>=7.6.4",
    "mypy>=1.11.1",
    "pytest-cov>=6.0.0",
    "pytest-xdist>=3.6.1",
    "pytest>=8.3.1",
    "pytest-random-order>=1.1.1",
    "pytest-rerunfailures>=15.0",
    "pytest-timeout>=2.3.1",
    "ruff>=0.15.0",
    "types-PyYAML",
    "pre-commit>=4.1.0",
    "onnxruntime>=1.17.1",
]

notebook = [
    "graphviz>=0.20.3",
    "ipykernel>=6.29.5",
    "ipython>=8.31.0",
    "ipywidgets>=8.1.2",
    "jupyterlab>=4.2.4",
    "mistune>=3.0.2",
    "nbconvert>=7.16.5",
    "nb-clean>=4.0.1",
    "nbval>=0.11.0",
    "ptpython>=3.0.29",
    "pyarrow>=20.0.0",
    "lanfactory>=0.6.1",
    "zeus-mcmc>=2.5.4",
    "bayesflow>=2.0.10",
    "keras>=3",
]

docs = [
    "mkdocs-material>=9.5.21",
    "mkdocs>=1.6.0",
    "mkdocs-jupyter>=0.25.1",
    "mkdocstrings-python>=1.10.0",
]

[tool.ruff]
line-length = 88
target-version = "py310"
exclude = ["*.ipynb"]

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
unfixable = ["E711"]

select = [
    # pydocstyle
    "D",
    # pyflakes
    "F",
    # pycodestyle
    "E",
    "I",
    "W",
    # flake8-2020
    "YTT",
    # flake8-bugbear
    "B",
    # flake8-quotes
    "Q",
    # pylint
    "PLE",
    "PLR",
    "PLW",
    # misc lints
    "PIE",
    # flake8-pyi
    "PYI",
    # tidy imports
    "TID",
    # type-checking imports
    "TCH",
]

ignore = [
    # space before : (needed for how black formats slicing)
    # "E203",  # not yet implemented
    # module level import not at top of file
    "E402",
    # do not assign a lambda expression, use a def
    "E731",
    # line break before binary operator
    # "W503",  # not yet implemented
    # line break after binary operator
    # "W504",  # not yet implemented
    # controversial
    "B006",
    # controversial
    "B007",
    # controversial
    "B008",
    # setattr is used to side-step mypy
    "B009",
    # getattr is used to side-step mypy
    "B010",
    # tests use assert False
    "B011",
    # tests use comparisons but not their returned value
    "B015",
    # false positives
    "B019",
    # Loop control variable overrides iterable it iterates
    "B020",
    # Function definition does not bind loop variable
    "B023",
    # zip()` without an explicit `strict=
    "B905",
    # Functions defined inside a loop must not use variables redefined in the loop
    # "B301",  # not yet implemented
    # Too many arguments to function call
    "PLR0913",
    # Too many returns
    "PLR0911",
    # Too many branches
    "PLR0912",
    # Too many statements
    "PLR0915",
    # Global statements are discouraged
    "PLW0603",
    # Implement of __eq__ without __hash__ function
    "PLW1641",
    # Docstrings should not be included in stubs
    "PYI021",
    # Use typing_extensions.TypeAlias for type aliases
    # "PYI026",  # not yet implemented
    # Use "collections.abc.*" instead of "typing.*" (PEP 585 syntax)
    # "PYI027",  # not yet implemented
    # while int | float can be shortened to float, the former is more explicit
    # "PYI041",  # not yet implemented

    # Additional checks that don't pass yet
    # Within an except clause, raise exceptions with ...
    "B904",
    # Magic number
    "PLR2004",
    # Consider `elif` instead of `else` then `if` to remove indentation level
    "PLR5501",
    # Ignore "Use `float` instead of `int | float`."
    "PYI041",
    # Allow importing from parent modules
    "TID252",
]

exclude = [".github", "docs", "notebook", "tests/*"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.mypy]
ignore_missing_imports = true

[tool.pytest]

[tool.pytest.ini_options]
testpaths = ["tests"]
log_cli = true
log_cli_level = "INFO" # set minimum log level for console output
addopts = [
    "--cov=.",
    "--cov-report=term-missing",
    "--cov-report=xml",
    "--exitfirst",
    "--capture=no",
    "--timeout=360",
    "--reruns=2",
    "--reruns-delay=5",
]
markers = [
    "slow: marks tests as slow (add --runslow option to run these tests)",
]

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

[tool.hatch.build.targets.sdist]
exclude = [
    "docs/**", # remove all docs content from the source tarball
]

[tool.hatch.build.targets.wheel]
packages = ["src/hssm"] # keep as-is so only package code goes into the wheel

[[tool.uv.index]]
name = "pypi"
url = "https://pypi.org/simple/"

[[tool.uv.index]]
name = "testpypi"
url = "https://test.pypi.org/simple/"
publish-url = "https://test.pypi.org/legacy/"