pyproject.toml

[build-system]
# Lower bound: 1.27 is the first release with PEP 639 license metadata.
requires = ["hatchling>=1.27", "hatch-vcs"]
build-backend = "hatchling.build"


[project]
name = "pollux"
authors = [
  { name = "adrn", email = "adrian.prw@gmail.com" },
]
description = "A JAX framework for data-driven latent variable models, with models for stellar spectroscopy"
readme = "README.md"
license = "MIT"
license-files = ["LICENSE"]
requires-python = ">=3.12"
classifiers = [
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
  "Topic :: Scientific/Engineering",
  "Typing :: Typed",
]
dynamic = ["version"]
# Runtime dependencies only: everything imported by pollux itself. Development
# tooling lives in [dependency-groups] below.
dependencies = [
  "equinox>=0.11.12",
  "jax>=0.7.2",
  "jaxtyping>=0.3",           # the array-shape aliases in pollux.typing
  "numpyro>=0.19.0",
  "tqdm>=4.67.1",
  "typing-extensions>=4.15.0",  # TypeIs; only in typing from 3.13
  "xmmutablemap>=0.2.0",
]

# PEP 735 dependency groups. These are NOT published to PyPI: they are installed
# from a checkout, with `uv sync --only-group test` or, on pip >= 25.1,
# `pip install -e . --group test`.
[dependency-groups]
test = [
  "pytest>=8.3",
  "pytest-cov>=3",
]
docs = [
  "astropy>=7.2.0",
  "daft-pgm>=0.1.4",            # probabilistic graphical models, imported as `daft`
  "h5py>=3.16.0",
  "ipykernel>=6.30.1",
  "ipywidgets>=8.1.7",
  "matplotlib>=3.10.8",
  "myst-nb>=1.1.2",
  "nbconvert>=7.17.0",
  "rtds-action>=1.1.0",
  "sphinx-book-theme==1.1.3",
  "sphinx-prompt>=1.8.0",
  "sphinx>=7.0",
  "sphinx_autodoc_typehints>=3.0.0",
  "sphinx_copybutton>=0.5.2",
  "sphinx_design>=0.6.1",
  "sphinx_togglebutton>=0.3.2",
  "sphinxext-opengraph>=0.9.1",
]
dev = [
  {include-group = "test"},
  {include-group = "docs"},
  "hatch",
  "pre-commit",
  "twine",
  "ruff",
  # ty is pre-1.0 and its rules still move between releases; uv.lock pins the
  # exact version, so bump deliberately with `uv lock --upgrade-package ty`
  "ty>=0.0.70,<0.1",
]

[project.urls]
Homepage = "https://github.com/adrn/pollux"
"Bug Tracker" = "https://github.com/adrn/pollux/issues"
Discussions = "https://github.com/adrn/pollux/discussions"
Changelog = "https://github.com/adrn/pollux/releases"


[tool.hatch]
version.source = "vcs"
build.hooks.vcs.version-file = "src/pollux/_version.py"


[tool.pytest.ini_options]
minversion = "8.3"
addopts = [
    "-ra",
    "--showlocals",
    "--strict-markers",
    "--strict-config",
    "--doctest-modules",
  ]
xfail_strict = true
filterwarnings = [
  "error",
  "ignore:jax\\.core\\.call_p is deprecated:DeprecationWarning",
  "ignore:jax\\.core\\.closed_call_p is deprecated:DeprecationWarning",
]
log_cli_level = "INFO"
testpaths = ["src", "docs", "tests"]


[tool.coverage]
run.source = ["pollux"]
report.exclude_also = [
  '\.\.\.',
  'if typing.TYPE_CHECKING:',
]

[tool.ty.src]
include = ["src"]

# numpyro ships no py.typed marker, so ty reads its source directly. That is why
# it catches real API misuse there that mypy could not see at all -- but it also
# means numpyro's internal TypeVars (DistributionT, ConstraintT) and the loose
# return type of numpyro.sample surface as false positives in the module that
# does the sampling.
[[tool.ty.overrides]]
include = ["src/pollux/models/lvm.py"]
rules = { invalid-argument-type = "ignore", invalid-assignment = "ignore" }

# equinox's field() is a dataclass field factory; ty reads the descriptor type
# rather than the field's declared type.
[[tool.ty.overrides]]
include = ["src/pollux/data/data.py"]
rules = { invalid-assignment = "ignore" }


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

[tool.ruff.lint]
extend-select = [
  "B",        # flake8-bugbear
  "I",        # isort
  "ARG",      # flake8-unused-arguments
  "C4",       # flake8-comprehensions
  "EM",       # flake8-errmsg
  "ICN",      # flake8-import-conventions
  "G",        # flake8-logging-format
  "PGH",      # pygrep-hooks
  "PIE",      # flake8-pie
  "PL",       # pylint
  "PT",       # flake8-pytest-style
  "PTH",      # flake8-use-pathlib
  "RET",      # flake8-return
  "RUF",      # Ruff-specific
  "SIM",      # flake8-simplify
  "T20",      # flake8-print
  "UP",       # pyupgrade
  "YTT",      # flake8-2020
  "EXE",      # flake8-executable
  "NPY",      # NumPy specific rules
  "PD",       # pandas-vet
]
ignore = [
  "PLC0206",  # Extracting value from dictionary without calling `.items()`
  "PLR09",    # Too many <...>
  "PLR2004",  # Magic value used in comparison
  "ISC001",   # Conflicts with formatter
  "B905",      # zip() without explicit strict

]
# isort.required-imports = []
# Uncomment if using a _compat.typing backport
# typing-modules = ["pollux._compat.typing"]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20", "F841", "RUF059"]
"**/__init__.py" = ["F401", "F403"]
"docs/**" = ["T201"]