pyproject.toml

[project]
name = "odyssey"
version = "0.1.0"
description = "A toolkit to develop clinical foundation models using electronic health records"
readme = "README.md"
authors = [{name = "Vector AI Engineering", email = "odyssey@vectorinstitute.ai"}]
license = "Apache-2.0"
repository = "https://github.com/VectorInstitute/odyssey"
documentation = "https://vectorinstitute.github.io/odyssey/"
requires-python = ">=3.12"
dependencies = [
    "lightning>=2.0.0",
    "scikit-learn>=1.2.2",
    # torch is not pinned here — install the wheel matching your CUDA version:
    #   CPU:       uv pip install torch
    #   CUDA 12.8: uv pip install torch --index-url https://download.pytorch.org/whl/cu128
    #   CUDA 12.4: uv pip install torch --index-url https://download.pytorch.org/whl/cu124
    "torch>=2.0.0",
    "tqdm>=4.60.0",
    "wandb>=0.15.0",
    "pandas>=2.2.1",
    "sqlalchemy>=2.0.28",
    "psycopg2-binary>=2.9.9",
    "fhir-resources>=5.1.1",
    "pyarrow>=15.0.1",
    "plotly>=5.7.0",
    "tokenizers>=0.15.2",
    "transformers>=5.0.0",
    "captum>=0.7.0",
    "scikit-multilearn>=0.2.0",
    "numpy>=1.26.4",
    # polars is pinned by meds-transforms 0.6.1 (~=1.30.0); will lift when that updates
    "polars>=1.30.0",
    "meds>=0.4.0",
    "meds-transforms>=0.6.1",
]

[project.optional-dependencies]
# mamba-ssm requires CUDA/nvcc; install on GPU hosts with --no-build-isolation:
#   uv sync --extra cuda --no-build-isolation
#   or: pip install mamba-ssm>=2.3.0 --no-build-isolation
cuda = [
    "mamba-ssm>=2.3.0",
]

[dependency-groups]
dev = [
    "pytest>=9.0.3",
    "pre-commit>=4.0.0",
    "pytest-cov>=3.0.0",
    "codecov>=2.1.13",
    "nbstripout>=0.6.1",
    "mypy>=1.7.0",
    "ruff>=0.3.0",
    "nbqa[toolchain]>=1.7.0",
]
docs = [
    "mkdocs>=1.5.0",
    "mkdocs-material>=9.0.0",
    "mkdocstrings[python]>=0.24.0",
]

# Default dependency groups to be installed
[tool.uv]
default-groups = ["dev"]

[tool.mypy]
plugins = ["numpy.typing.mypy_plugin"]
ignore_missing_imports = true
install_types = true
pretty = true
namespace_packages = true
explicit_package_bases = true
non_interactive = true
warn_unused_configs = true
allow_any_generics = false
allow_subclassing_any = false
allow_untyped_calls = false
allow_untyped_defs = false
allow_incomplete_defs = false
check_untyped_defs = true
allow_untyped_decorators = false
warn_redundant_casts = true
warn_unused_ignores = true
warn_return_any = true
implicit_reexport = false
strict_equality = true
extra_checks = true

[tool.ruff]
include = ["*.py", "pyproject.toml", "*.ipynb"]
exclude = []
line-length = 88

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
docstring-code-format = true

[tool.ruff.lint]
select = [
    "A", # flake8-builtins
    "B", # flake8-bugbear
    "COM", # flake8-commas
    "C4", # flake8-comprehensions
    "RET", # flake8-return
    "SIM", # flake8-simplify
    "ICN", # flake8-import-conventions
    "Q", # flake8-quotes
    "RSE", # flake8-raise
    "D", # pydocstyle
    "E", # pycodestyle
    "F", # pyflakes
    "I", # isort
    "W", # pycodestyle
    "N", # pep8-naming
    "ERA", # eradicate
    "PL", # pylint
]
fixable = ["A", "B", "COM", "C4", "RET", "SIM", "ICN", "Q", "RSE", "D", "E", "F", "I", "W", "N", "ERA", "PL"]
ignore = [
    "B905", # `zip()` without an explicit `strict=` parameter
    "E501", # line too long
    "D203", # 1 blank line required before class docstring
    "D213", # Multi-line docstring summary should start at the second line
    "PLR2004", # Replace magic number with named constant
    "PLR0913", # Too many arguments
    "COM812", # Missing trailing comma
    "ERA001", # Found commented-out code (too many false positives with math comments)
    "A001", # Ignore variable `input` is shadowing a Python builtin (common for torch)
    "A002", # Ignore variable `input` is shadowing a Python builtin in function (common for torch)
    "D301", # r-strings for docstrings with backslashes
]

# Ignore import violations in all `__init__.py` files.
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402", "F401", "F403", "F811"]
# Ignoring undocumented public functions, public init, magic method in tests folder
"tests/*" = ["D103", "D105", "D107"]

[tool.ruff.lint.pep8-naming]
ignore-names = ["X*", "setUp"]

[tool.ruff.lint.isort]
lines-after-imports = 2

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

[tool.ruff.lint.pycodestyle]
max-doc-length = 88

[tool.pytest.ini_options]
markers = [
    "integration_test: marks tests as integration tests",
]

[tool.coverage]
    [tool.coverage.run]
    source=["odyssey"]
    omit=["tests/*", "*__init__.py"]

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