pyproject.toml

[build-system]
requires = ["setuptools>=77.0.3"]
build-backend = "setuptools.build_meta"

[project]
name = "coreax"
dynamic = ["version"]
description = "Jax coreset algorithms."
readme = "README.md"
requires-python = ">=3.10"
keywords = [
    "coreset",
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Typing :: Typed",
]
license = "Apache-2.0"
license-files = ["LICENSE"]
authors = [
    {name = "GCHQ", email = "oss@gchq.gov.uk"},
]
dependencies = [
    # NOTE: lower bounds are the lowest supported version when using the 'lowest'
    # resolution mode of uv on the latest supported version of Python - the bounds
    # are only sharp for the latest supported Python version.
    "equinox>=0.11.11",
    "flax>=0.10.0",
    "jax>=0.4.38",
    "jaxopt>=0.8.4",
    "jaxtyping>=0.2.31",
    "optax>=0.1.5",
    "scikit-learn>=1.5.0",
    "tqdm>=4.27",
    "typing-extensions>=4.12",
]

[dependency-groups]
# All tools for a developer including those for running pylint
dev = [
    # These dependencies are constrained more tightly as they're only used by package
    # developers, so compatibility is less of a concern
    {include-group = "doc"},
    {include-group = "test"},
    "pre-commit>=4.2.0",
    "pylint>=4.0.4",
    "pyright>=1.1.408",
]
# Compile documentation
doc = [
    "furo>=2024",
    "sphinx>=7",
    "sphinx-autodoc-typehints>=2",
    "sphinxcontrib-bibtex>=2",
    "sphobjinv>=2.1.0",
]
# Run unit tests with coverage assessment
test = [
    {include-group = "benchmark"},
    "beartype>=0.19",
    "pytest>=9",
    "pytest-cov>=6",
    "pytest-xdist>=3.2.0",
    "scipy>=1.14.1",
]
# Benchmarking - runs very similar code to examples with same dependencies plus more
benchmark = [
    {include-group = "example"},
    "torch>=2.5",
    "torchvision>=0.21",
    "umap-learn>=0.5.7",  # Earlier versions are incompatible.
    # Required for umap-learn - we constrain this so dependency solvers don't
    # erroneously backtrack.
    "llvmlite>=0.40.0",
]
# Example scripts
example = [
    "imageio>=2.19.4",
    "matplotlib>=3.9.0",
    "numpy>=2",
    "opencv-python-headless>=4.10.0.84",  # WARNING: Incompatible with other versions of opencv
]

[tool.uv]
# Exclude packages published less than 14 days ago from dependency resolution as a
# supply-chain security measure.
exclude-newer = "14 days"
# Provide lower bounds for transitive packages when using '--resolution lowest'. There
# are a lot of packages here as some of our dependencies don't provide lower bounds.
# These 'doc' dependency group is not constrained by this.
constraint-dependencies = [
    # Unconstrained (only specified to suppress uv warnings)
    "beautifulsoup4>0",
    "future>0",
    "msgpack>0",
    "orbax-checkpoint>=0,!=0.11.33; sys_platform == 'win32'",
    "orbax-checkpoint>=0; sys_platform != 'win32'",
    "sphinx-basic-ng>0",
    "sphinxcontrib-applehelp>0",
    "sphinxcontrib-devhelp>0",
    "sphinxcontrib-jsmath>0",
    "sphinxcontrib-qthelp>0",
    "tomli>0",
    "webencodings>0",
    # Constrained to the required lower-bounds on our highest supported Python version.
    "absl-py>=1.0.0",  # via optax
    "attrs>=18.1.0",  # via rich via flax
    "chex>=0.1.84",  # via optax
    "dm-tree>=0.1.8",  # via chex via optax
    "fsspec>=0.5.0",  # via torch
    "identify>=1.5.10",  # via pre-commit
    "isort>=5.1.0",  # via pylint
    "joblib>=1.4.0",  # via sklearn
    "ml-dtypes>=0.4.1",  # via jax
    "mpmath>=1.2.1",  # via torch
    "networkx>=1.3",  # via torch
    "numba>=0.61.0",  # via umap-learn
    "opt-einsum>=3.2.0",  # via jax
    "pillow>=11.0.0",  # via torchvision
    "pybtex>=0.22.0",  # via sphinxcontrib-bibtex
    "pynndescent>=0.5.13",  # via umap
    "pyparsing>=3.0.8",  # via matplotlib
    "python-dateutil>=2.9.0",  # via matplotlib
    "pyyaml>=6.0.1",  # via flax
    "setuptools>=5.0",  # via torch
    "six>=1.16.0",  # via absl-py via flax
    "tensorstore>=0.1.70",  # via flax
]
# Ensure we get the latest package versions available for each Python version
environments = [
    "python_version>='3.14'",
    "python_version=='3.13.*'",
    "python_version=='3.12.*'",
    "python_version=='3.11.*'",
    "python_version=='3.10.*'",
]

[project.urls]
Documentation = "https://coreax.readthedocs.io/en/latest/"
Repository = "https://github.com/gchq/coreax"
Issues = "https://github.com/gchq/coreax/issues"
Changelog = "https://github.com/gchq/coreax/blob/main/CHANGELOG.md"

[tool.setuptools]
packages = [
    "coreax",
    "coreax.kernels",
    "coreax.solvers",
]

[tool.setuptools.dynamic]
version = {attr = "coreax.__version__"}

[tool.pyright]
exclude = [
    # Exclude snippets for documentation as most variables not properly defined
    "documentation/source/snippets",
    # Exclusions that would have been generated automatically if this section weren't
    # specified
    "**/node_modules",
    "**/__pycache__",
    "**/.*",
]
venvPath = "."
venv = ".venv"

[tool.pytest.ini_options]
minversion = "9.0"
filterwarnings = [
    "error",
    "ignore::ImportWarning:umap",
    "ignore::DeprecationWarning:jaxopt",
]

[tool.ruff]
src = [".", "examples"]

[tool.ruff.lint]
preview = true
select = [
    "B",      # flake8-bugbear
    "C90",    # McCabe
    "D",      # pydocstyle
    "E",      # pycodestyle [error]
    "F",      # pyflakes
    "G010",   # logging-warn
    "I",      # isort
    "N",      # pep8-naming
    "PGH005", # invalid-mock-access
    "PL",     # pylint
    "S102",   # exec-builtin
    "S307",   # suspicious-eval-usage
    "TD",     # flake8-todo
    "UP",     # pyupgrade
    "W",      # pycodestyle [warning]
]

ignore = [
    # Incompatible with ruff format
    "D206",    # indent-with-spaces
    "E111",    # indentation-with-invalid-multiple
    "E114",    # indentation-with-invalid-multiple-comment
    "E117",    # over-indented
    "W191",    # tab-indentation
    # Incompatible with other pydocstyle rules
    "D203",    # one-blank-line-before-class
    "D212",    # multi-line-summary-first-line
    # Incompatible with jaxtyping
    "F722",    # forward-annotation-syntax-error
    # Opinionated ignores
    "PLR6301", # no-self-use (opinionated)
    "TD002",   # missing-todo-author (opinionated)
]

[tool.ruff.lint.per-file-ignores]
"documentation/source/conf.py" = [
    "E402",  # Allow module imports not at the top of the file - conf.py does weird
             # things with imports that necessitate this
]
"documentation/source/snippets/*" = [
    "D100",  # Allow missing module docstring - these are snippets, not full modules
    "F821",  # Allow undefined names - the snippets are *snippets*, not complete code
]
"examples/*" = [
    "PLR0914",  # Ignore "too many locals"
    "PLR0915",  # Ignore "too many statements"
    # In both cases, the example code is meant to be more verbose so it's easier to
    # understand and can serve as its own documentation.
]
"tests/*" = [
    "D200",  # Allow "one-line docstring not on one line" - test docstrings can be
             # quite long, so sometimes the extra six characters are really needed
    "PLR0904",  # Ignore "too many public methods" - test classes are really just
                # namespaces, so the usual concerns here don't apply
]

[tool.ruff.lint.pylint]
max-args = 10
max-locals = 20
allow-dunder-method-names = ["__check_init__", "__jax_array__"]

[tool.ruff.lint.isort]
combine-as-imports = true
force-wrap-aliases = true

[tool.coverage.run]
command_line = "-m pytest tests/unit --cov"
branch = true
relative_files = true
source = ["coreax"]

[tool.coverage.report]
show_missing = true
sort = "Cover"
exclude_also = [
    "pass",
    "raise RuntimeError",
    "if TYPE_CHECKING:",
    "raise$",
    "\\.\\.\\.",
]