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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "prismtoolbox"
homepage = "https://gustaveroussy.github.io/prismtoolbox"
documentation = "https://gustaveroussy.github.io/prismtoolbox"
repository = "https://github.com/gustaveroussy/prismtoolbox"
version = "0.1.2"
description = "Toolbox for histopathology image analysis"
authors = ["Loïc Le Bescond <[email protected]>"]
packages = [
{ include = "prismtoolbox", from = "src"},
]
license = "BSD-3-Clause"
readme = "README.md"
[tool.poetry.dependencies]
python = ">=3.9,<3.13"
openslide-python = "^1.3.1"
tiffslide = "^2.3.0"
opencv-python = "^4.8.1.78"
scipy = "^1.12.0"
h5py = "^3.10.0"
shapely = "^2.0.3"
matplotlib = "^3.8.3"
uuid = "^1.30"
pandas = "^2.2.1"
numpy = "^1.26.4"
geopandas = "^1.0.1"
torch = { version = "^2.2.2", optional = true }
torchvision = { version = "^0.17.2", optional = true }
tqdm = { version = "^4.66.2", optional = true }
transformers = { version = "^4.38.2", optional = true }
timm = { version = "^0.9.16", optional = true }
scikit-learn = "^1.4.1.post1"
huggingface-hub = { version = "^0.22.1", optional = true }
umap-learn = { version = "^0.5.5", optional = true }
cellpose = { version = "^3.0.7", optional = true }
dask = { extras = ["dataframe"], version = "^2024.3.1", optional = true }
ipywidgets = { version = "^8.1.2", optional = true }
scikit-image = { version ="^0.24.0", optional = true}
[tool.poetry.group.dev.dependencies]
black = "^22.8.0"
isort = "^5.10.1"
pytest = "^7.1.3"
mkdocs-material = "^8.5.6"
mkdocstrings = {extras = ["python"], version = "^0.24.3"}
setuptools = "^69.2.0"
mkdocs-gen-files = "^0.5.0"
mkdocs-literate-nav = "^0.6.1"
mkdocs-section-index = "^0.3.8"
mkdocs-autorefs = "^1.0.1"
pyment = "^0.3.3"
pytest-subtests = "^0.12.1"
[tool.poetry.extras]
emb = ["torch", "torchvision", "tqdm", "transformers", "timm", "scikit-learn",
"huggingface-hub", "umap-learn", "dask", "scikit-image"]
seg = ["torch", "torchvision", "cellpose", "ipywidgets"]
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
python_files = "test_*.py"
[tool.black]
line-length = 90
include = '\.pyi?$'
exclude = '''
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
'''
[tool.isort]
profile = "black"
skip_glob = ["*/__init__.py"]