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pyproject.toml
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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "cellmap-segmentation-challenge"
dynamic = ["version"]
description = "Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data."
readme = "README.md"
requires-python = ">=3.11"
license = "MIT"
keywords = ["machine learning", "deep learning", "segmentation", "cellmap"]
authors = [
{ name = "Jeff Rhoades", email = "[email protected]" },
{ name = "Emma Avetissian", email = "[email protected]" },
{ name = "Davis Vann Bennett", email = "[email protected]" },
{ name = "Marwan Zouinkhi", email = "[email protected]" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Programming Language :: Python",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
"torch",
"tensorboard",
"tensorboardX",
"cellmap-schemas==0.8.0",
"click>=8, <9",
"cellmap-data@git+https://github.com/janelia-cellmap/cellmap-data",
"tqdm",
"zarr < 3.0.0",
"xarray-ome-ngff >= 3.1.1, <=4.0.0",
"structlog",
"yarl",
"toolz",
"ml-collections",
"scipy",
"numpy",
"tensorstore",
"python-dotenv",
"universal-pathlib",
"neuroglancer",
"scikit-learn",
"scikit-image",
"boto3==1.35.81",
"pyreadline3; sys_platform == 'win32'",
]
[project.optional-dependencies]
test = ["pytest>=6.0", "pytest-cov", "mypy", "black", "pytest-dependency", "pytest-xdist"]
docs = [
"sphinx",
"sphinx-book-theme",
"sphinx_mdinclude",
]
dev = [
"ipython",
"jupyter",
"rich",
"ruff",
"snakeviz",
"twine",
"hatch",
"pdbpp",
"python-semantic-release",
"cellmap-segmentation-challenge[test,docs]",
"gunpowder",
"matplotlib",
"isort",
]
all = ["cellmap-segmentation-challenge[dev,docs,test]"]
[project.urls]
Documentation = "https://github.com/janelia-cellmap/cellmap-segmentation-challenge#readme"
Issues = "https://github.com/janelia-cellmap/cellmap-segmentation-challenge/issues"
Source = "https://github.com/janelia-cellmap/cellmap-segmentation-challenge"
[tool.hatch.metadata]
allow-direct-references=true
[tool.hatch.version]
path = "src/cellmap_segmentation_challenge/__about__.py"
[tool.hatch.envs.default]
installer = "pip"
python = "3.11"
[tool.hatch.envs.test]
dependencies = ["pytest"]
[tool.hatch.envs.types]
extra-dependencies = [
"mypy>=1.0.0",
]
[tool.hatch.envs.types.scripts]
check = "mypy --install-types --non-interactive {args:src/cellmap_segmentation_challenge tests}"
[tool.coverage.run]
source_pkgs = ["cellmap_segmentation_challenge", "tests"]
branch = true
parallel = true
omit = [
"src/cellmap_segmentation_challenge/__about__.py",
]
[tool.coverage.paths]
cellmap_segmentation_challenge = ["src/cellmap_segmentation_challenge", "*/cellmap-segmentation-challenge/src/cellmap_segmentation_challenge"]
tests = ["tests", "*/cellmap-segmentation-challenge/tests"]
[tool.coverage.report]
exclude_lines = [
"no cov",
"if __name__ == .__main__.:",
"if TYPE_CHECKING:",
]
[project.scripts]
csc = "cellmap_segmentation_challenge.cli:run"
[tool.pytest.ini_options]
"testpaths" = "tests"
markers = [
"dependency: mark tests as dependent on other tests"
]