setup: use scikit-build for building cmatrices and cshape C extensions

.circleci/config.yml

@@ -35,10 +35,14 @@ jobs:
  name: Install pyradiomics in Python 2 and 3
  command: |
  source activate python2
+ python -m pip install -U cmake
+ python -m pip install -U scikit-build
  python -m pip install --no-cache-dir -r requirements.txt
  python -m pip install --no-cache-dir -r requirements-dev.txt
  python setup.py install
  source activate root
+ python -m pip install -U cmake
+ python -m pip install -U scikit-build
  python -m pip install --no-cache-dir -r requirements.txt
  python -m pip install --no-cache-dir -r requirements-dev.txt
  python setup.py install

.gitignore

@@ -63,3 +63,7 @@ docs/_build/
 
 # PyBuilder
 target/
+
+# scikit-build
+_skbuild
+MANIFEST

CMakeLists.txt

@@ -0,0 +1,9 @@
+cmake_minimum_required(VERSION 3.7)
+
+project(radiomics)
+
+find_package(PythonInterp REQUIRED)
+find_package(PythonLibs REQUIRED)
+find_package(PythonExtensions REQUIRED)
+
+add_subdirectory(radiomics/src)

radiomics/src/CMakeLists.txt

@@ -0,0 +1,11 @@
+find_package(NumPy REQUIRED)
+
+add_library(_cmatrices MODULE _cmatrices.c cmatrices.c)
+python_extension_module(_cmatrices)
+target_include_directories(_cmatrices PRIVATE ${NumPy_INCLUDE_DIR})
+
+add_library(_cshape MODULE _cshape.c cshape.c)
+python_extension_module(_cshape)
+target_include_directories(_cshape PRIVATE ${NumPy_INCLUDE_DIR})
+
+install(TARGETS _cmatrices _cshape LIBRARY DESTINATION radiomics)

scikit-ci.yml

@@ -28,9 +28,8 @@ install:
  commands:
  - python --version
  - python -m pip install --disable-pip-version-check --upgrade pip
- - $<RUN_ENV> pip install wheel>=0.29.0
- - $<RUN_ENV> pip install setuptools>=38.6.0
- - $<RUN_ENV> pip install numpy>=1.9.2
+ - $<RUN_ENV> pip install -U scikit-build
+ - $<RUN_ENV> pip install -U cmake
  - $<RUN_ENV> pip install --trusted-host www.itk.org -f https://itk.org/SimpleITKDoxygen/html/PyDownloadPage.html SimpleITK>=0.9.1
  - $<RUN_ENV> python -c "import SimpleITK; print('SimpleITK Version:' + SimpleITK.Version_VersionString())"
  - $<RUN_ENV> pip install -r requirements.txt

setup.py

@@ -1,14 +1,22 @@
 #!/usr/bin/env python
 
-from distutils import sysconfig
+from __future__ import print_function
+
 import platform
 import sys
 
-import numpy
-from setuptools import Extension, setup
 from setuptools.command.test import test as TestCommand
 import versioneer
 
+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)
+
 # Check if current PyRadiomics is compatible with current python installation (> 2.6, 64 bits)
 if sys.version_info < (2, 6, 0):
  raise Exception("pyradiomics > 0.9.7 requires python 2.6 or later")
@@ -55,13 +63,6 @@ def run_tests(self):
 commands = versioneer.get_cmdclass()
 commands['test'] = NoseTestCommand
 
-incDirs = [sysconfig.get_python_inc(), numpy.get_include()]
-
-ext = [Extension("radiomics._cmatrices", ["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"],
- include_dirs=incDirs),
- Extension("radiomics._cshape", ["radiomics/src/_cshape.c", "radiomics/src/cshape.c"],
- include_dirs=incDirs)]
-
 setup(
  name='pyradiomics',
 
@@ -80,7 +81,6 @@ def run_tests(self):
  cmdclass=commands,
 
  packages=['radiomics', 'radiomics.scripts'],
- ext_modules=ext,
  zip_safe=False,
  package_data={'radiomics': ['schemas/paramSchema.yaml', 'schemas/schemaFuncs.py']},