From a11f4fea260a63df9f88ebffb2f6fd07fea63feb Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Thu, 26 Oct 2023 18:14:22 +0200 Subject: [PATCH 1/2] - migrate pyproject file to poetry --- pyproject.toml | 86 ++++++++++++++++++++++++-------------------------- 1 file changed, 41 insertions(+), 45 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d2860be..7e4389f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,59 +1,55 @@ -[build-system] -requires = ["setuptools>=61.0", "setuptools_scm[toml]>=6.2"] - -[tool.setuptools] -packages = ["brats_toolkit"] - -[tool.setuptools.dynamic] -#version = {attr = "my_package.VERSION"} -readme = {file = "README.md"} - -[tool.setuptools_scm] -write_to = "brats_toolkit/_version.py" - -[project] +[tool.poetry] name = "BraTS-Toolkit" -dynamic = ["version"] +version = "1.0.7" # TODO: make version dynamic? +description = "BraTS Toolkit is a holistic approach to brain tumor segmentation allowing to build modular pipeliens for preprocessing, segmentation and fusion of segmentations." +license = "AGPL-3.0" + authors = [ - {name="Florian Kofler", email="florian.kofler@tum.de"}, - {name="Christoph Berger", email="c.berger@tum.de"}, - {name="Isra Mekki", email="isra.mekki@helmholtz-muenchen.de"}, - {name="Mahyar Valizadeh", email="mahyar.valizadeh@helmholtz-muenchen.de"}, + "Florian Kofler ", + "Christoph Berger ", + "Isra Mekki ", + "Mahyar Valizadeh ", + "Marcel Rosier ", ] + maintainers = [ - {name="Florian Kofler", email="florian.kofler@tum.de"}, - {name="Isra Mekki", email="isra.mekki@helmholtz-muenchen.de"}, - {name="Mahyar Valizadeh", email="mahyar.valizadeh@helmholtz-muenchen.de"}, + "Florian Kofler ", + "Isra Mekki ", + "Mahyar Valizadeh ", + "Marcel Rosier ", ] -description = "BraTS Toolkit is a holistic approach to brain tumor segmentation allowing to build modular pipeliens for preprocessing, segmentation and fusion of segmentations." -keywords = ["brain tumor", "glioma", "BraTS", "segmentation", "fusion", "skullstripping", "brain extraction"] + readme = "README.md" -# requires-python = "==3.10" +repository = "https://github.com/neuronflow/BraTS-Toolkit" +documentation = "https://brats-toolkit.readthedocs.io/en/latest/" + +keywords = ["brain tumor", "glioma", "BraTS", "segmentation", "fusion", "skullstripping", "brain extraction"] classifiers = [ "Programming Language :: Python :: 3", "License :: OSI Approved :: GNU Affero General Public License v3", "Operating System :: OS Independent", ] -dependencies = [ - 'SimpleITK==2.1.1.2', - 'numpy==1.22.0', - 'python-engineio==3.14.2', - 'python-socketio==4.6.1', - 'requests==2.24.0', - 'rich==13.6.0' -] -[project.optional-dependencies] -dev = [ - "pytest", -] +[tool.poetry.dependencies] +python = "^3.10" -[project.scripts] -brats-segment = "brats_toolkit.cli:segmentation" -brats-fuse = "brats_toolkit.cli:fusion" -brats-batch-preprocess = "brats_toolkit.cli:batchpreprocess" -brats-preprocess = "brats_toolkit.cli:singlepreprocess" +# core +SimpleITK = "2.1.1.2" +numpy = "^1.23.0" +python-engineio = "3.14.2" +python-socketio = "4.6.1" +requests = "^2.24.0" + +# pretty citation reminder +rich = "^13.6.0" + + +[tool.poetry.dev-dependencies] +pytest = "^6.2" + +[tool.poetry.scripts] +brats-segment = 'brats_toolkit.cli:segmentation' +brats-fuse = 'brats_toolkit.cli:fusion' +brats-batch-preprocess = 'brats_toolkit.cli:batchpreprocess' +brats-preprocess = 'brats_toolkit.cli:singlepreprocess' -[project.urls] -# documentation = "TODO" -repository = "https://github.com/neuronflow/BraTS-Toolkit" From 67131b1dd21e391a9c5ac76c271c1d029266ca6a Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Tue, 31 Oct 2023 13:46:57 +0100 Subject: [PATCH 2/2] - 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