pyproject.toml

[project]
name = "bliss-toolkit"
version = "0.4.2"
description = "Bayesian Light Source Separator"
readme = "README.md"
requires-python = ">=3.12"
license = {text = "MIT"}
authors = [
    {name = "BLISS developers"}
]
keywords = ["cosmology", "blending", "weak lensing", "bayesian", "ml", "pytorch"]
dependencies = [
    "torch>=2.7.0",
    "torchvision>=0.22.0",
    "numpy>=1.18.5",
    "scipy>=1.4.1",
    "matplotlib>=3.3.3",
    "requests>=2.31.0",
    "torchmetrics>=1.4.0.post0",
    "lightning[extra]>=2.3.3",
    "einops>=0.8.0",
    "hydra-core>=1.0.4",
    "astropy>=6.1.1",
    "galsim>=2.4.10",
    "reproject>=0.11.0",
    "pyvo>=1.4.1",
    "colossus>=1.3.5",
    "lsstdesc-gcr-catalogs>=1.10.1",
    "anacal>=0.7.3",
    "pyccl>=3.2.1",
    "treecorr>=5.1.2",
    "camb>=1.6.5",
]

[[tool.uv.index]]
name = "pytorch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[tool.uv.sources]
torch = [{index = "pytorch-cu128"}]
torchvision = [{index = "pytorch-cu128"}]

[project.optional-dependencies]
dev = [
    "Sphinx>=4.0.2",
    "git-lfs>=1.6",
    "ipykernel>=6.29.5",
    "jupyter>=1.0.0",
    "nbstripout>=0.5.0",
    "plotly>=4.14.3",
    "pre-commit>=2.9.2",
    "pre-commit-hooks>=4.4.0",
    "pytest-cov>=2.10",
    "ruff>=0.8.0",
    "sphinx-rtd-theme>=0.5.2",
    "tqdm>=4.62.3",
    "nbsphinx>=0.9.2",
    "pypandoc>=1.11",
    "scikit-learn>=0.24.2",
    "seaborn>=0.13.0",
    "pyarrow>=15.0.0",
    "healpy>=1.16.6",
    "h5py>=3.11.0",
    "pytest>=8.2.2",
    "pytest-xdist>=3.5.0",
    "tensorboard>=2.20.0",
]

[project.scripts]
bliss = "bliss.main:main"

[project.urls]
Documentation = "https://prob-ml.github.io/bliss/"
Repository = "https://github.com/prob-ml/bliss"

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

[tool.hatch.build.targets.wheel]
packages = ["bliss"]

[tool.pytest.ini_options]
addopts = "-ra -v -n auto"
markers = [
  "run_first: mark test to run first for parallel test scheduling",
]
filterwarnings = [
  "ignore:numpy.core.* is deprecated:DeprecationWarning",
  "ignore:.*does not have many workers which may be a bottleneck.*:UserWarning",
  "ignore:GPU available but not used.*:UserWarning",
  "ignore:numpy.ndarray size changed:RuntimeWarning",
  "ignore:.*when logging on epoch level in distributed setting.*",
  "ignore:.*pkg_resources.declare_namespace.*:DeprecationWarning",
  "ignore:.*distutils Version classes are deprecated.*:DeprecationWarning",
  "ignore:.*Total length of `DataLoader` across ranks is zero.*:UserWarning",
  "ignore:.*Total length of `CombinedLoader` across ranks is zero.*:UserWarning",
  "ignore:.*Detected call of `lr_scheduler.step()` before `optimizer.step()`.*:UserWarning",
  "ignore:.*AMP with fp16 is not supported on CPU.*:UserWarning",
  "ignore:.*This process.*is multi-threaded, use of fork.*may lead to deadlocks.*:DeprecationWarning",
]
minversion = "6.0"
testpaths = [
  "tests",
]

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # Pyflakes
    "I",      # isort
    "N",      # pep8-naming
    "D",      # pydocstyle
    "S",      # flake8-bandit (security)
    "B",      # flake8-bugbear
    "A",      # flake8-builtins
    "C4",     # flake8-comprehensions
    "SIM",    # flake8-simplify
    "PL",     # Pylint
    "RUF",    # Ruff-specific rules
]

ignore = [
    # === Docstring Rules ===
    "D100", "D101", "D102", "D103", "D104", "D105", "D106", "D107",

    # === Security Rules ===
    "S101",   # Use of assert (useful for testing/development)
    "E731",   # Lambda assignment

    # === Naming Conventions ===
    "N812",   # Lowercase imported as non-lowercase (e.g., import F)
    "N817",   # CamelCase imported as acronym

    # === Pylint Rules ===
    "PLR0913",  # Too many arguments
    "PLR0914",  # Too many local variables
    "PLR0915",  # Too many statements
    "PLR0912",  # Too many branches
    "PLR0911",  # Too many return statements
    "PLR0917",  # Too many positional arguments
    "PLR2004",  # Magic value comparison
    "PLR0904",  # Too many public methods
    "PLW0603",  # Global statement
    "PLC0415",  # Import outside top-level

    # === Complexity ===
    "C901",   # Function too complex

    # === Ruff-specific ===
    "RUF012",  # Mutable class attributes (common in dataclass-like patterns)
    "RUF013",  # Implicit Optional (common pattern, not enforced before)
]

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

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["S101", "PLR2004", "D"]
"conftest.py" = ["D"]
"__init__.py" = ["D104"]
"case_studies/*" = ["D", "E501", "N803", "N806", "B006", "B007", "B028", "B905", "PLW2901", "RUF012", "RUF013", "S301", "S311"]
"*.ipynb" = ["E501", "N803", "N806", "B006", "B007", "B905", "E402", "F821", "RUF012", "RUF013"]