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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "segger"
version = "0.1.0"
description = "Fast and accurate cell segmentation for single-molecule spatial omics"
authors = [
{ name = "Elyas Heidari", email = "[email protected]" }
]
license = { text = "MIT" }
readme = "README.md"
requires-python = ">=3.10"
keywords = ["segmentation", "deep learning", "pytorch", "geometric deep learning"]
dependencies = [
"torch>=2.0.0",
"dask-cuda>=23.10.0",
"distributed>=2023.10.0",
"numpy>=1.21.0",
"pandas>=1.3.0",
"scipy>=1.7.0",
"matplotlib>=3.4.0",
"seaborn>=0.11.0",
"tqdm>=4.61.0",
"torchvision>=0.10.0",
"lightning>=1.9.0",
"torchmetrics>=0.5.0",
"scanpy>=1.9.3",
"squidpy==1.2.0",
"adjustText>=0.8",
"scikit-learn>=0.24.0",
"geopandas>=0.9.0",
"shapely>=1.7.0",
"path>=17.0.0",
"pyarrow>=16.1.0,<16.2.0",
"dask_geopandas>=0.4.0",
"torch-geometric>=2.2.0",
"pqdm>=0.2.0"
]
[project.optional-dependencies]
faiss = [
"faiss-cpu>=1.7.0",
"faiss-gpu>=1.7.0"
]
rapids11 = [
"cupy-cuda11x",
"cuvs-cu11==24.4.*",
]
rapids12 = [
"cupy-cuda12x",
"cuvs-cu12==24.4.*",
]
multiprocessing = ["multiprocessing"]
dev = [
"pytest",
"black",
"flake8",
"pre-commit",
"twine>=4.0.2"
]
docs = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4.1",
"sphinx-book-theme>=1.0.0",
"myst-nb",
"myst-parser",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
"sphinx_rtd_theme",
"sphinxext-opengraph",
"sphinx-copybutton",
"sphinx-design",
"sphinx-hoverxref",
"ipykernel",
"ipython",
"pandas"
]
tests = [
"pytest",
"coverage"
]
[project.urls]
bug_tracker = "https://github.com/EliHei2/segger_dev/issues"
documentation = "https://EliHei2.github.io/segger_dev"
source_code = "https://github.com/EliHei2/segger_dev"
homepage = "https://EliHei2.github.io/segger_dev"
repository = "https://github.com/EliHei2/segger_dev"
[tool.setuptools]
packages = ["segger"]
package-dir = {"" = "src"}
[tool.black]
line-length = 120
target-version = ['py39']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''