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

See #283

This commit introduces new dependencies: "scikit-built" and "cmake".

scikit-build is a drop-in replacement to setuptools.setup function
allowing to easily compile and package extensions (C/C++/Cython) by
bridging CMake and setuptools. See http://scikit-build.org

CMake is is an open-source, cross-platform family of tools designed
to build, test and package software. See https://cmake.org

Currently, scikit-build and cmake have to be explicitly (see [1]) installed
on the system. This could be done by simply doing:

  pip install -U scikit-build cmake

How does it work ?
------------------

In addition to simplifying setup.py, two new file have been added:

<root>
  |
  |---- CMakeLists.txt                          (1)
  .
  .
  .
  |--- ...src
  |        |--- CMakeLists.txt                  (2)
  .
  .

The first CMakeLists.txt specifies requirements for

* Python interpreter,

* the associated python libraries

* and a "PythonExtension" modules containing convenience CMake
  functions allowing to easily build extension by encapsulating
  system introspection and platform specific logic.

and include the subdirectory associated with the other CMakeLists.txt.

The second CMakeLists.txt is specific to "cmatrices" and "cshape"
extensions and it specifies:

* requirement for NumPy

Then, it declares:

* libraries for each extension, associate python extension specific properties

* and finally add an install rule specifying where in the package
  hierarchy the extension should be installed.

Et voila,

[1] Note that improvement to python packaging will be available shortly and
it will be possible to include scikit-build and cmake directly in pyproject.toml
See here for more details: https://www.python.org/dev/peps/pep-0518/

.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

@@ -26,8 +26,8 @@ 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>=28.0.0
+    - $<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
@@ -54,6 +54,7 @@ build:
 
 test:
   commands:
+    - $<RUN_ENV> pip install -e .
     - $<RUN_ENV> python setup.py test  --args="--with-xunit --logging-level=DEBUG"
 
   circleci:

setup.py

@@ -1,15 +1,21 @@
 #!/usr/bin/env python
 
-from distutils import sysconfig
+from __future__ import print_function
 
 import numpy
-
-from setuptools import Extension, setup
+import sys
+import versioneer
 
 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)
 
 with open('requirements.txt', 'r') as fp:
     requirements = list(filter(bool, (line.strip() for line in fp)))
@@ -45,13 +51,6 @@ 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',
 
@@ -64,7 +63,6 @@ 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']},