From 73bb2445a98eacd89471c1fe88663db321022c14 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 19 Jun 2024 15:59:54 -0400 Subject: [PATCH 1/4] ENH: Update setup.py to pyproject.toml Build with scikit-build-core. Update project.urls for repo rename. --- pyproject.toml | 108 +++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 54 ------------------------- 2 files changed, 108 insertions(+), 54 deletions(-) create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..622175c --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,108 @@ +[build-system] +requires = ["scikit-build-core"] +build-backend = "scikit_build_core.build" + +[project] +name = "itk-morphologicalcontourinterpolation" +version = "2.0.0" +description = "A morphology-based approach for interslice interpolation of anatomical slices from volumetric images." +readme = "README.md" +license = {file = "LICENSE"} +authors = [ + { name = "Dženan Zukić", email = "community@itk.org" }, +] +keywords = [ + "itk", +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "Intended Audience :: Education", + "Intended Audience :: Healthcare Industry", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Apache Software License", + "Operating System :: Android", + "Operating System :: MacOS", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX", + "Operating System :: Unix", + "Programming Language :: C++", + "Programming Language :: Python", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Information Analysis", + "Topic :: Scientific/Engineering :: Medical Science Apps.", + "Topic :: Software Development :: Libraries", +] +requires-python = ">=3.8" +dependencies = [ + "itk == 5.4.*", +] + +[project.urls] +Download = "https://github.com/KitwareMedical/ITKContourInterpolation" +Homepage = "https://github.com/KitwareMedical/ITKContourInterpolation" + +[tool.scikit-build] +# The versions of CMake to allow. If CMake is not present on the system or does +# not pass this specifier, it will be downloaded via PyPI if possible. An empty +# string will disable this check. +cmake.version = ">=3.16.3" + +# A list of args to pass to CMake when configuring the project. Setting this in +# config or envvar will override toml. See also ``cmake.define``. +cmake.args = [] + +# A table of defines to pass to CMake when configuring the project. Additive. +cmake.define = {} + +# Verbose printout when building. +cmake.verbose = true + +# The build type to use when building the project. Valid options are: "Debug", +# "Release", "RelWithDebInfo", "MinSizeRel", "", etc. +cmake.build-type = "Release" + +# The source directory to use when building the project. Currently only affects +# the native builder (not the setuptools plugin). +cmake.source-dir = "." + +# The versions of Ninja to allow. If Ninja is not present on the system or does +# not pass this specifier, it will be downloaded via PyPI if possible. An empty +# string will disable this check. +ninja.version = ">=1.11" + +# The logging level to display, "DEBUG", "INFO", "WARNING", and "ERROR" are +# possible options. +logging.level = "INFO" + +# Files to include in the SDist even if they are skipped by default. Supports +# gitignore syntax. +sdist.include = [] + +# Files to exclude from the SDist even if they are included by default. Supports +# gitignore syntax. +sdist.exclude = [] + +# A list of license files to include in the wheel. Supports glob patterns. +wheel.license-files = ["LICEN[CS]E*",] + +# Target the platlib or the purelib. If not set, the default is to target the +# platlib if wheel.cmake is true, and the purelib otherwise. +wheel.platlib = "false" + +# If CMake is less than this value, backport a copy of FindPython. Set to 0 +# disable this, or the empty string. +backport.find-python = "3.26.1" + +# Select the editable mode to use. Can be "redirect" (default) or "inplace". +editable.mode = "redirect" + +# Rebuild the project when the package is imported. The build-directory must be +# set. +editable.rebuild = false + +# If set, this will provide a method for scikit-build-core backward compatibility. +minimum-version = "0.8.2" + +# The build directory. Defaults to a temporary directory, but can be set. +build-dir = "build/{wheel_tag}" diff --git a/setup.py b/setup.py deleted file mode 100644 index 1721cd6..0000000 --- a/setup.py +++ /dev/null @@ -1,54 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import print_function -from os import sys - -try: - from skbuild import setup -except ImportError: - print('scikit-build is required to build from source.', file=sys.stderr) - print('Please run:', file=sys.stderr) - print('', file=sys.stderr) - print(' python -m pip install scikit-build') - sys.exit(1) - -setup( - name='itk-morphologicalcontourinterpolation', - version='1.1.0', - author='Dženan Zukić', - author_email='community@itk.org', - packages=['itk'], - package_dir={'itk': 'itk'}, - download_url=r'https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation', - description=r'Image morphological contour interpolation.', - long_description='itk-morphologicalcontourinterpolation provides classes ' - 'to perform image morphological contour interpolation.\n' - 'Please refer to:\n' - 'Zukić Dž., Vicory J., McCormick M., Wisse L., Gerig G., Yushkevich P., Aylward S. ' - '"nD Morphological Contour Interpolation", ' - 'Insight Journal, January-December 2016, https://hdl.handle.net/10380/3563.', - classifiers=[ - "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python", - "Programming Language :: C++", - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "Intended Audience :: Education", - "Intended Audience :: Healthcare Industry", - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Medical Science Apps.", - "Topic :: Scientific/Engineering :: Information Analysis", - "Topic :: Software Development :: Libraries", - "Operating System :: Android", - "Operating System :: Microsoft :: Windows", - "Operating System :: POSIX", - "Operating System :: Unix", - "Operating System :: MacOS" - ], - license='Apache', - keywords='ITK InsightToolkit Segmentation Interpolation-methods', - url=r'https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation', - install_requires=[ - r'itk>=5.4rc2' - ] - ) From 65b00649853f83bdc246c25a7681b786ad2db1e1 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 19 Jun 2024 16:00:45 -0400 Subject: [PATCH 2/4] DOC: Remove README.rst Duplicate of README.md, outdated. --- README.rst | 65 ------------------------------------------------------ 1 file changed, 65 deletions(-) delete mode 100644 README.rst diff --git a/README.rst b/README.rst deleted file mode 100644 index 2b95f30..0000000 --- a/README.rst +++ /dev/null @@ -1,65 +0,0 @@ -ITKMorphologicalContourInterpolation -==================================== - -.. image:: https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation/workflows/Build,%20test,%20package/badge.svg - -.. image:: https://img.shields.io/pypi/v/itk-morphologicalcontourinterpolation.svg - :target: https://pypi.python.org/pypi/itk-morphologicalcontourinterpolation - :alt: PyPI - -.. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg - :target: https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation/blob/master/LICENSE) - :alt: License - -Overview --------- - -An `ITK `_-based implementation of morphological contour -interpolation based off the paper: - - Albu AB1, Beugeling T, Laurendeau D. - "A morphology-based approach for interslice interpolation of anatomical slices from volumetric images." - IEEE Trans Biomed Eng. - 2008 Aug;55(8):2022-38. - doi: 10.1109/TBME.2008.921158. - -Documentation can be found in the `Insight Journal article -`_:: - - Zukić D., Vicory J., McCormick M., Wisse L., Gerig G., Yushkevich P., Aylward S. - "ND Morphological Contour Interpolation", - The Insight Journal. January-December, 2016. - https://hdl.handle.net/10380/3563 - https://insight-journal.org/browse/publication/977 - -Installation ------------- - -Since ITK 4.11.0, this module is available in the ITK source tree as a remote -module. To enable it, set:: - - Module_MorphologicalContourInterpolation:BOOL=ON - -in ITK's CMake build configuration. - -Python -^^^^^^ - -To install the Python packages:: - - python -m pip install --upgrade pip - python -m pip install itk-morphologicalcontourinterpolation - - -License -------- - -This software is distributed under the Apache 2.0 license. Please see -the *LICENSE* file for details. - - -Acknowledgements ----------------- - -This work is supported by NIH grant R01 EB014346, "Continued development and -maintenance of the ITK-SNAP 3D image segmentation software." From deef52c69a7a6988d11e6324e806fbd89562164a Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Mon, 24 Jun 2024 11:06:06 -0400 Subject: [PATCH 3/4] BUG: Add RLEImage to CXX CI module deps Closes #123 --- .github/workflows/build-test-package.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-test-package.yml b/.github/workflows/build-test-package.yml index 1685f5b..a0b564d 100644 --- a/.github/workflows/build-test-package.yml +++ b/.github/workflows/build-test-package.yml @@ -7,6 +7,7 @@ jobs: uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.0 with: itk-cmake-options: '-DModule_MorphologicalContourInterpolation_BUILD_EXAMPLES:BOOL=ON' + itk-module-deps: 'RLEImage@v1.0.1' python-build-workflow: uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.0 From f926250c6ba9c8ae7956f16024611c98fb3e6f37 Mon Sep 17 00:00:00 2001 From: Matt McCormick Date: Wed, 26 Jun 2024 15:11:56 -0400 Subject: [PATCH 4/4] DOC: Remove Android from pyproject.toml Future support anticipated via ITK-Wasm. --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 622175c..75164cf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,6 @@ classifiers = [ "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", - "Operating System :: Android", "Operating System :: MacOS", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX",