shell/pyproject.toml at main · laviolette-lab/shell · GitHub

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

[project]
name = "lavlab-shell"
dynamic = ["version"]
description = "SHELL Highlights Epithelium and Lumen Locations — whole-slide H&E segmentation"
readme = "README.md"
requires-python = ">=3.10,<3.13"
license = "MIT"
keywords = [
    "histopathology",
    "segmentation",
    "whole-slide-image",
    "H&E",
    "deep-learning",
]
authors = [{ name = "barrettMCW", email = "mjbarrett@mcw.edu" }]
classifiers = [
    "Development Status :: 4 - Beta",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: Implementation :: CPython",
]
dependencies = [
    "numpy",
    "scipy",
    "torch",
    "monai",
    "pyvips",
    "openslide-python",
    "macenko-pca",
    "scikit-image",
]

[project.optional-dependencies]
omero = ["omero-py", "zeroc-ice"]

[project.scripts]
shell = "shell.cli:main"
lavlab-shell = "shell.cli:main"

[project.urls]
Documentation = "https://github.com/laviolette-lab/shell#readme"
Issues = "https://github.com/laviolette-lab/shell/issues"
Source = "https://github.com/laviolette-lab/shell"

[tool.hatch.version]
path = "src/shell/__about__.py"

[tool.hatch.build.targets.wheel]
packages = ["src/shell"]

[tool.hatch.envs.default]
dependencies = ["setuptools>=82.0.0"]

[tool.hatch.envs.default.scripts]
build = "hatch build && chmod -R 777 dist/*"

[tool.hatch.envs.test]
dependencies = [
    "pytest",
    "pytest-cov",
    "coverage[toml]>=6.2",
    "setuptools>=82.0.0",
]
[tool.hatch.envs.test.scripts]
test = "pytest {args:tests}"
cov = "pytest --cov=src --cov-report=term-missing --cov-report=xml {args:tests}"

[tool.hatch.envs.lint]
dependencies = ["ruff>=0.4.0", "setuptools>=82.0.0"]
[tool.hatch.envs.lint.scripts]
check = "ruff check src tests"
format = "ruff format src tests"
format-check = "ruff format src tests --check"
fix = "ruff check --fix src tests"
all = ["format", "fix", "check"]

[tool.hatch.envs.types]
dependencies = ["mypy>=1.0.0", "setuptools>=82.0.0"]
[tool.hatch.envs.types.scripts]
check = "mypy --install-types --non-interactive {args:src/shell tests}"

[tool.hatch.envs.docs]
dependencies = [
    "mkdocs",
    "mkdocstrings[python]",
    "mkdocs-material",
    "mkdocs-autorefs",
    "mkdocs-minify-plugin",
    "mkdocs-material-extensions",
    "mkdocs-git-revision-date-localized-plugin",
    "setuptools>=82.0.0",
]
[tool.hatch.envs.docs.scripts]
build-docs = "mkdocs build"
serve-docs = "mkdocs serve"

[[tool.hatch.envs.all.matrix]]
python = ["3.10", "3.11", "3.12"]

[tool.coverage.run]
source_pkgs = ["shell", "tests"]
branch = true
parallel = true
omit = ["src/shell/__about__.py"]

[tool.coverage.paths]
shell = ["src/shell", "*/shell/src/shell"]
tests = ["tests", "*/shell/tests"]

[tool.coverage.report]
exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]

[tool.ruff]
target-version = "py310"
line-length = 88
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    "F",   # pyflakes
    "E",
    "W",   # pycodestyle
    "I",   # isort
    "N",   # pep8-naming
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "A",   # flake8-builtins
    "C4",  # flake8-comprehensions
    "DTZ", # flake8-datetimez
    "T20", # flake8-print (catches stray prints in library code)
    "RUF", # ruff-specific rules
]
ignore = []

[tool.ruff.lint.per-file-ignores]
"tests/**/*" = ["T20"]
"src/shell/cli.py" = ["T20"]
"src/shell/benchmark.py" = ["T20"]
# Scientific code uses uppercase variable names (Io, W, H) and import aliases
# (F as torch.nn.functional, BlitzGateway as _BG) that violate pep8-naming.
"src/shell/preprocessing.py" = ["N803", "N806"]
"src/shell/inference.py" = ["N812"]
"src/shell/infer_omero_wsi.py" = ["N814", "F401"]

[tool.ruff.lint.isort]
known-first-party = ["shell"]

[tool.ruff.format]
docstring-code-format = true

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = ["-ra", "--strict-markers", "--strict-config"]
xfail_strict = true