Add option to build C++ extensions

README.md

@@ -64,6 +64,12 @@ Then install with:
     cd LSMTool
     python setup.py install
 
+If you have a C++11-compliant compiler, you can build a faster
+version of the mean shift grouping algorithm with:
+
+    cd LSMTool
+    python setup.py install --build_c_extentions
+
 ### Testing
 
 You can test that the installation worked with:

meanshift.cpp → lsmtool/operations/_grouper.cpp

@@ -158,7 +158,7 @@ void Grouper::group(py::list l){
   }
 }
 
-PYBIND11_MODULE(grouper, m)    
+PYBIND11_MODULE(_grouper, m)
 {
   py::class_<Grouper>(m, "Grouper")
     .def(py::init<>())

lsmtool/operations/_meanshiftc.py

@@ -18,7 +18,7 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 import numpy as np
-import grouper
+from . import _grouper
 import logging
 log = logging.getLogger('LSMTool.Group')
 
@@ -52,7 +52,7 @@ class Grouper(object):
         self.grouping_distance = grouping_distance
         self.past_coords = [np.copy(self.coords)]
         self.clusters = []
-        self.g = grouper.Grouper()
+        self.g = _grouper.Grouper()
         self.g.readCoordinates(self.coords, self.fluxes)
         self.g.setKernelSize(self.kernel_size)
         self.g.setNumberOfIterations(self.n_iterations)

lsmtool/operations/group.py

@@ -150,6 +150,9 @@ def group(LSM, algorithm, targetFlux=None, weightBySize=False, numClusters=100,
     from . import _tessellate
     from . import _cluster
     from . import _threshold
+    try:
+        from . import _meanshiftc as _meanshift
+    except ImportError:
         from . import _meanshift
     import numpy as np
     import os

setup.py

 from __future__ import print_function
-from setuptools import setup, Command
-import os
+from setuptools import setup, Command, Extension, Distribution
+from setuptools.command.build_ext import build_ext
 import sys
 import lsmtool._version
 
 
+# Flag that determines whether to build the optional (but faster) C++
+# extensions. Set to False to install only the pure Python versions.
+if "--build_c_extentions" in sys.argv:
+    build_c_extentions = True
+    sys.argv.remove("--build_c_extentions")
+else:
+    build_c_extentions = False
+
+# Handle Python 3-only dependencies
+if sys.version_info < (3, 0):
+    reqlist = ['numpy', 'astropy >= 0.4, <3.0']
+else:
+    reqlist = ['numpy', 'astropy >= 0.4']
+if build_c_extentions:
+    reqlist.append('pybind11>=2.2.0')
+    ext_modules = [Extension('lsmtool.operations._grouper',
+                             ['lsmtool/operations/_grouper.cpp'],
+                             language='c++')]
+else:
+    ext_modules = []
+
+
 class PyTest(Command):
     user_options = []
+
     def initialize_options(self):
         pass
 
@@ -14,15 +37,36 @@ class PyTest(Command):
         pass
 
     def run(self):
-        import sys,subprocess
+        import sys
+        import subprocess
         errno = subprocess.call([sys.executable, 'runtests.py'])
         raise SystemExit(errno)
 
-# Handle Python 3-only dependencies
-if sys.version_info < (3, 0):
-    reqlist = ['numpy','astropy >= 0.4, <3.0']
-else:
-    reqlist = ['numpy','astropy >= 0.4']
+
+class LSMToolDistribution(Distribution):
+
+    def is_pure(self):
+        if self.pure:
+            return True
+
+    def has_ext_modules(self):
+        return not self.pure
+
+    global_options = Distribution.global_options + [
+        ('pure', None, "use pure Python code instead of C++ extensions")]
+    pure = False
+
+
+class BuildExt(build_ext):
+
+    def build_extensions(self):
+        opts = ['-std=c++11']
+        if sys.platform == 'darwin':
+            opts += ['-stdlib=libc++']
+        for ext in self.extensions:
+            ext.extra_compile_args = opts
+        build_ext.build_extensions(self)
+
 
 setup(
     name='lsmtool',
@@ -41,6 +85,9 @@ setup(
         ],
     install_requires=reqlist,
     scripts=['bin/lsmtool'],
+    ext_modules=ext_modules,
+    cmdclass={'build_ext': BuildExt},
+    distclass=LSMToolDistribution,
     packages=['lsmtool', 'lsmtool.operations'],
     setup_requires=['pytest-runner'],
     tests_require=['pytest']