Fixed Cython deployment issues

pystencils/boundaries/createindexlist.py

@@ -3,17 +3,25 @@ import itertools
 import warnings
 
 try:
-    import pyximport
-
-    pyximport.install(language_level=3)
+    # Try to import right away - assume compiled code is available
+    # compile with: python setup.py build_ext --inplace --use-cython
     from pystencils.boundaries.createindexlistcython import create_boundary_neighbor_index_list_2d, \
         create_boundary_neighbor_index_list_3d, create_boundary_cell_index_list_2d, create_boundary_cell_index_list_3d
 
     cython_funcs_available = True
-except Exception:
-    cython_funcs_available = False
-    create_boundary_index_list_2d = None
-    create_boundary_index_list_3d = None
+except ImportError:
+    try:
+        # If not, try development mode and import via pyximport
+        import pyximport
+
+        pyximport.install(language_level=3)
+        cython_funcs_available = True
+    except ImportError:
+        cython_funcs_available = False
+    if cython_funcs_available:
+        from pystencils.boundaries.createindexlistcython import create_boundary_neighbor_index_list_2d, \
+            create_boundary_neighbor_index_list_3d, create_boundary_cell_index_list_2d, \
+            create_boundary_cell_index_list_3d
 
 boundary_index_array_coordinate_names = ["x", "y", "z"]
 direction_member_name = "dir"

pystencils/boundaries/createindexlistcython.pyx

+# distutils: language=c
 # Workaround for cython bug
 # see https://stackoverflow.com/questions/8024805/cython-compiled-c-extension-importerror-dynamic-module-does-not-define-init-fu
 WORKAROUND = "Something"

setup.py

@@ -3,11 +3,18 @@ import sys
 import io
 from setuptools import setup, find_packages
 import distutils
+from distutils.extension import Extension
 from contextlib import redirect_stdout
 from importlib import import_module
 sys.path.insert(0, os.path.abspath('doc'))
 from version_from_git import version_number_from_git
 
+if '--use-cython' in sys.argv:
+    USE_CYTHON = True
+    sys.argv.remove('--use-cython')
+else:
+    USE_CYTHON = False
+
 
 quick_tests = [
     'test_datahandling.test_kernel',
@@ -52,6 +59,15 @@ def readme():
         return f.read()
 
 
+def cython_extensions(*extensions):
+    ext = '.pyx' if USE_CYTHON else '.c'
+    result = [Extension(e, [e.replace('.', '/') + ext]) for e in extensions]
+    if USE_CYTHON:
+        from Cython.Build import cythonize
+        result = cythonize(result, language_level=3)
+    return result
+
+
 setup(name='pystencils',
       version=version_number_from_git(),
       description='Speeding up stencil computations on CPUs and GPUs',
@@ -64,6 +80,7 @@ setup(name='pystencils',
       packages=['pystencils'] + ['pystencils.' + s for s in find_packages('pystencils')],
       install_requires=['sympy>=1.1', 'numpy', 'appdirs', 'joblib'],
       package_data={'pystencils': ['include/*.h']},
+      ext_modules = cython_extensions("pystencils.boundaries.createindexlistcython"),
       classifiers=[
           'Development Status :: 4 - Beta',
           'Framework :: Jupyter',