pyproject.toml

# https://peps.python.org/pep-0517/

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
# read more about configuring hatch at:
# https://hatch.pypa.io/latest/config/build/

# https://hatch.pypa.io/latest/config/metadata/
[tool.hatch.version]
source = "vcs"

[tool.hatch.build.targets.wheel]
only-include = ["src"]
sources = ["src"]

# https://peps.python.org/pep-0621/
[project]
name = "careamics"
dynamic = ["version"]
description = "Toolbox for running N2V and friends."
readme = "README.md"
requires-python = ">=3.9"
license = { text = "BSD-3-Clause" }
authors = [
    { name = 'CAREamics team', email = 'rse@fht.org' },
    { name = 'Ashesh', email = 'ashesh.ashesh@fht.org' },
    { name = 'Federico Carrara', email = 'federico.carrara@fht.org' },
    { name = 'Melisande Croft', email = 'melisande.croft@fht.org' },
    { name = 'Joran Deschamps', email = 'joran.deschamps@fht.org' },
    { name = 'Vera Galinova', email = 'vera.galinova@fht.org' },
    { name = 'Igor Zubarev', email = 'igor.zubarev@fht.org' },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "License :: OSI Approved :: BSD License",
    "Typing :: Typed",
]
dependencies = [
    'numpy<2.0.0',
    'torch>=2.0.0',
    'torchvision',
    'bioimageio.core>=0.7.0',
    'tifffile',
    'psutil',
    'pydantic>=2.5,<2.9',
    'pytorch_lightning>=2.2.0',
    'pyyaml',
    'typer==0.12.3',
    'scikit-image<=0.23.2',
    'zarr<3.0.0',
]

[project.optional-dependencies]
# development dependencies and tooling
dev = [
    "pre-commit",
    "pytest",
    "pytest-cov",
    "onnx",
    "sybil",      # doctesting
]

# notebooks
examples = ["jupyter", "careamics-portfolio", "matplotlib"]

# loggers
wandb = ["wandb"]
tensorboard = ["tensorboard", "protobuf==3.20.3"]

[project.urls]
homepage = "https://careamics.github.io/"
repository = "https://github.com/CAREamics/careamics"

# cli
[project.scripts]
careamics = "careamics.cli.main:run"

# https://beta.ruff.rs/docs
[tool.ruff]
line-length = 88
target-version = "py39"
src = ["src"]
lint.select = [
    "E",  # style errors
    "W",  # style warnings
    "F",  # flakes
    "D",  # pydocstyle
    "I",  # isort
    "UP", # pyupgrade
    # "S",    # bandit
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
]
lint.ignore = [
    "D100", # Missing docstring in public module
    "D107", # Missing docstring in __init__
    "D203", # 1 blank line required before class docstring
    "D212", # Multi-line docstring summary should start at the first line
    "D213", # Multi-line docstring summary should start at the second line
    "D401", # First line should be in imperative mood
    "D413", # Missing blank line after last section
    "D416", # Section name should end with a colon

    # incompatibility with mypy
    "RUF005", # collection-literal-concatenation, in prediction_utils.py:30

    # version specific
    "UP007", # Replace Union by |, mandatory for py3.9
]
show-fixes = true

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

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]
"setup.py" = ["D"]

[tool.black]
line-length = 88

# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src/**/"
strict = false
# allow_untyped_defs = false
# allow_untyped_calls = false
# disallow_any_generics = false
# ignore_missing_imports = false


# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["src/careamics", "tests"] # add src/careamics for doctest discovery
filterwarnings = [
    # "error",
    # "ignore::UserWarning",
]
addopts = "-p no:doctest"

markers = [
    # "gpu: marks tests as requiring gpu",
    "lvae: marks tests as testing lvae",
]

# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
exclude_lines = [
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "raise NotImplementedError()",
    "except PackageNotFoundError:",
]

[tool.coverage.run]
source = ["src/careamics"]
omit = ["src/careamics/lvae_training/*"]

# https://github.com/mgedmin/check-manifest#configuration
# add files that you want check-manifest to explicitly ignore here
# (files that are in the repo but shouldn't go in the package)
[tool.check-manifest]
ignore = [
    ".github_changelog_generator",
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "setup.py",
    "tests/**/*",
]

[tool.numpydoc_validation]
checks = [
    "all",  # report on all checks, except the below
    "EX01", # Example section not found
    "SA01", # See Also section not found
    "ES01", # Extended Summar not found
    "GL01", # Docstring text (summary) should start in the line immediately
    # after the opening quotes
    "GL02", # Closing quotes should be placed in the line after the last text 
    # in the docstring
    "GL03", # Double line break found
]
exclude = [ # don't report on objects that match any of these regex
    "test_*",
    "src/careamics/lvae_training/*",
]