followed cython docs to build extensions from pyx or c files based on…

… whether or not cython is installed

requirements.txt

@@ -1,5 +1,4 @@
 coloredlogs
-Cython>=0.28.4
 inicheck>=0.9.0,<0.10.0
 netCDF4>=1.2.9
 numpy>=1.14.0

requirements_dev.txt

@@ -1,4 +1,5 @@
 -r requirements.txt
+Cython
 coveralls>=1.3.0
 tox>=3.14.0
 flake8>=3.5.0

setup.py

@@ -6,6 +6,17 @@
 from setuptools import Extension, find_packages, setup
 from setuptools.command.build_ext import build_ext as _build_ext
 
+# Test if compiling with cython or using the C source
+try:
+    from Cython.Distutils import build_ext as _build_ext
+except ImportError:
+    USE_CYTHON = False
+else:
+    USE_CYTHON = True
+
+print('Using Cython {}'.format(USE_CYTHON))
+ext = '.pyx' if USE_CYTHON else '.c'
+
 
 def c_name_from_path(location, name):
     return os.path.join(location, name).replace('/', '.')
@@ -22,10 +33,8 @@ def finalize_options(self):
 
 # Give user option to specify his local compiler name
 if "CC" not in os.environ:
-    # force the compiler to use gcc
     os.environ["CC"] = "gcc"
 
-
 ext_modules = []
 extension_params = dict(
     extra_compile_args=['-fopenmp', '-O3'],
@@ -38,7 +47,7 @@ def finalize_options(self):
     Extension(
         c_name_from_path(source_folder, 'detrended_kriging'),
         sources=[os.path.join(source_folder, val) for val in [
-            "detrended_kriging.pyx",
+            "detrended_kriging" + ext,
             "krige.c",
             "lusolv.c",
             "array.c"
@@ -53,7 +62,7 @@ def finalize_options(self):
     Extension(
         c_name_from_path(source_folder, 'envphys_c'),
         sources=[os.path.join(source_folder, val) for val in [
-            "envphys_c.pyx",
+            "envphys_c" + ext,
             "topotherm.c",
             "dewpt.c",
             "iwbt.c"
@@ -68,14 +77,18 @@ def finalize_options(self):
     Extension(
         c_name_from_path(source_folder, 'wind_c'),
         sources=[os.path.join(source_folder, val) for val in [
-            "wind_c.pyx",
+            "wind_c" + ext,
             "breshen.c",
             "calc_wind.c"
         ]],
         **extension_params
     ),
 ]
 
+cmdclass = {}
+if USE_CYTHON:
+    cmdclass = {'build_ext': build_ext}
+
 with open('requirements.txt') as requirements_file:
     requirements = requirements_file.read()
 
@@ -117,9 +130,7 @@ def finalize_options(self):
     ],
     test_suite='smrf.tests',
     # tests_require=test_requirements,
-    cmdclass={
-        'build_ext': build_ext
-    },
+    cmdclass=cmdclass,
     ext_modules=ext_modules,
     scripts=[
         'scripts/update_configs',

smrf/envphys/core/envphys_c.pyx

@@ -1,4 +1,5 @@
 # cython: embedsignature=True
+# cython: language_level=3
 """
 C implementation of some radiation functions
 """

smrf/spatial/dk/detrended_kriging.pyx

@@ -1,4 +1,5 @@
 # cython: embedsignature=True
+# cython: language_level=3
 '''
 Compiling dk's kriging function
 

smrf/utils/wind/wind_c.pyx

@@ -1,3 +1,4 @@
+# cython: language_level=3
 """
 Cython wrapper to the underlying C code