pyproject.toml

# https://peps.python.org/pep-0517/
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# https://peps.python.org/pep-0621/
[project]
name = "dacapo-ml"
description = "Framework for deployment of volumetric machine learning models, and easy composition of training jobs."
readme = "README.md"
requires-python = ">=3.10"
# license = { text = "BSD 3-Clause License" }
authors = [
    { email = "pattonw@janelia.hhmi.org", name = "Will Patton" },
    { email = "rhoadesj@hhmi.org", name = "Jeff Rhoades" },
    { email = "zouinkhim@hhmi.org", name = "Marwan Zouinkhi" },
    { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Typing :: Typed",
]
dynamic = ["version"]
dependencies = [
        "numpy>=1.22.4",
        "pyyaml",
        "zarr",
        "cattrs",
        "pymongo",
        "tqdm",
        "simpleitk",
        "lazy-property",
        "neuroglancer",
        "torch",
        "fibsem_tools",
        "attrs",
        "bokeh",
        "numpy-indexed>=0.3.7",
        "daisy",
        "funlib.math>=0.1",
        "funlib.geometry>=0.2",
        "mwatershed>=0.1",
        "cellmap-models",
        "funlib.persistence>=0.3.0",
        "gunpowder>=1.3",
        # "lsds>=0.1.3",
        # "lsds @ git+https://github.com/funkelab/lsd",
        "lsds",
        "xarray",
        "cattrs",
        "numpy-indexed",
        "click",
        "pyyaml",
        "scipy",
        ]

# extras
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
[project.optional-dependencies]
test = ["pytest==7.4.4", "pytest-cov", "pytest-lazy-fixture"]
dev = [
    "black",
    "mypy",
    "pdbpp",
    "rich",
    "ruff",
    "pre-commit",
]
docs = [
    "sphinx-autodoc-typehints",
    "sphinx-autoapi",
    "sphinx-click",
    "sphinx-rtd-theme",
    "myst-parser",
]
examples = [
    "ipython",
    "ipykernel",
    "jupyter",
]
pretrained = [
    "pyqt5",
    "empanada-napari",
    "cellmap-models",
    ]
all = ["dacapo-ml[test,dev,docs,examples,pretrained]"]

[project.urls]
homepage = "https://github.io/janelia-cellmap/dacapo"
repository = "https://github.com/janelia-cellmap/dacapo"

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

# https://hatch.pypa.io/latest/config/build/#file-selection
# [tool.hatch.build.targets.sdist]
# include = ["/src", "/tests"]
[tool.hatch.metadata]
allow-direct-references = true

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

[project.scripts]
dacapo = "dacapo.cli:cli"

# https://github.com/charliermarsh/ruff
[tool.ruff]
line-length = 88
target-version = "py310"
src = ["dacapo"]

[tool.ruff.lint]
# https://beta.ruff.rs/docs/rules/
# We may want to enable some of these options later
select = [
    "E",    # style errors
#    "W",    # style warnings
    "F",    # flakes
#    "D",    # pydocstyle
#    "I",    # isort
#    "UP",   # pyupgrade
#    "C4",   # flake8-comprehensions
#    "B",    # flake8-bugbear
#    "A001", # flake8-builtins
#    "RUF",  # ruff-specific rules
]
extend-ignore = ["E501"]

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]
"__init__.py" = ["F401"]

# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["tests"]
filterwarnings = [
    "error",
    "ignore::DeprecationWarning",
    ]
    
# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "dacapo/**/"
strict = false
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true
exclude = [
    "scratch/*",
    "examples/*",
]


# # module specific overrides
[[tool.mypy.overrides]]
module = [
    "cellmap_models.*",
    "funlib.*",
    "toml.*", 
    "gunpowder.*",
    "scipy.*",
    "augment.*",
    "tifffile.*",
    "daisy.*",
    "lazy_property.*",
    "skimage.*",
    "fibsem_tools.*",
    "neuroglancer.*",
    "tqdm.*",
    "zarr.*",
    "pymongo.*",
    "bson.*",
    "affogato.*",
    "SimpleITK.*",
    "bokeh.*",
    "lsd.*",
    "yaml.*",
    "pytest_lazyfixture.*",
    "neuclease.dvid.*",
    "mwatershed.*",
    "numpy_indexed.*",
    "empanada_napari.*",
    "napari.*",
    "empanada.*",
    "IPython.*",
]
ignore_missing_imports = true

# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "\\.\\.\\.",
    "raise NotImplementedError()",
]
[tool.coverage.run]
source = ["dacapo"]

# https://github.com/mgedmin/check-manifest#configuration
[tool.check-manifest]
ignore = [
    ".github_changelog_generator",
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "tests/**/*",
]