pyproject.toml

[project]
name = "conflunet"
version = "0.2.1"
requires-python = ">=3.9"
description = "ConfLUNet is a code repo for instance segmentation of multiple sclerosis lesions on brain MRI scans."
readme = "README.md"
license = { file = "LICENSE" }
authors = [
    { name = "Maxence Wynen", email = "maxence.wynen@uclouvain.be" },
]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Image Recognition",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]
keywords = [
    'deep learning',
    'image segmentation',
    'instance segmentation',
    'medical image analysis',
    'medical image segmentation',
    'ConfLUNet',
    'conflunet',
    'multiple sclerosis',
    'mri'
]
dependencies = [
    "torch>=2.1.2",
    "acvl-utils>=0.2,<0.3",  # 0.3 may bring breaking changes. Careful!
    "dynamic-network-architectures>=0.3.1,<0.4",  # 0.3.1 and lower are supported, 0.4 may have breaking changes. Let's be careful here
    "tqdm>=4.64.0",
    "dicom2nifti",
    "scipy>=1.10.1",
    "batchgenerators>=0.25",
    "numpy>=1.26.4,<2.0.0",
    "scikit-learn>=1.3.0",
    "scikit-image>=0.22.0",
    "SimpleITK>=2.2.1",
    "pandas>=1.5.3",
    "graphviz",
    'tifffile',
    'requests==2.31.0',
    "nibabel>=4.0.1",
    "matplotlib",
    "seaborn",
    "imagecodecs",
    "yacs",
    "batchgeneratorsv2>=0.2",
    "einops",
    "joblib==1.3.1",
    "monai==0.9.1",
    "nnunetv2==2.5.1",
    "wandb>=0.15.5",
    "seaborn"
]

[project.urls]
homepage = "https://github.com/maxencewynen/ConfLUNet"
repository = "https://github.com/maxencewynen/ConfLUNet"

[project.scripts]
conflunet_plan_and_preprocess = "conflunet.preprocessing.plan_and_preprocess_entrypoints:plan_and_preprocess_entry"
conflunet_extract_fingerprint = "conflunet.preprocessing.plan_and_preprocess_entrypoints:extract_fingerprint_entry"
conflunet_plan_experiment = "conflunet.preprocessing.plan_and_preprocess_entrypoints:plan_experiment_entry"
conflunet_preprocess = "conflunet.preprocessing.plan_and_preprocess_entrypoints:preprocess_entry"
conflunet_train = "conflunet.training.run_training:run_training_entry"
conflunet_predict = "conflunet.inference.predict_from_raw_input:predict_entry_point"
conflunet_predict_folds = "conflunet.inference.predict_folds:predict_folds_entry_point"
conflunet_evaluate = "conflunet.evaluation.run_evaluation:evaluate_entry_point"
conflunet_export_model_to_zip = "conflunet.model_sharing.export_model:export_pretrained_model_entry"
conflunet_install_pretrained_model_from_zip = "conflunet.model_sharing.import_model:import_pretrained_model_entry"

[build-system]
requires = ["setuptools>=67.8.0"]
build-backend = "setuptools.build_meta"

[tool.codespell]
skip = '.git,*.pdf,*.svg'