setup.py improvements

- resolve numpy header location using numpy.get_include()
- a hack to install cython, numpy before calling setup()
  (needed for cythonize() and get_include()) if necessary
- use named lists to reduce repetitions
- remove gslcblas from linker dependencies
- remove some old, commented out stuff

setup.py

@@ -1,6 +1,16 @@
-from setuptools import setup#, Extension
+from setuptools import setup, dist#, Extension
-from Cython.Build import cythonize, build_ext
 from distutils.extension import Extension
+
+# We need to have numpy and cython imported before calling cythonize
+# cf. https://luminousmen.com/post/resolve-cython-and-numpy-dependencies
+# and https://github.com/pypa/pip/issues/5761
+
+dist.Distribution().fetch_build_eggs(['Cython>=0.28', 'numpy>=1.2'])
+
+from Cython.Build import cythonize, build_ext
+import numpy
+numpy_includes=numpy.get_include()
+
 # setuptools DWIM monkey-patch madness
 # http://mail.python.org/pipermail/distutils-sig/2007-September/thread.html#8204
 #import sys
@@ -82,19 +92,24 @@ libqpms_sources = [
             ]
 '''
 
+common_libs=['qpms', 'gsl', 'lapacke', 'blas', 'pthread',]
+
 cycommon = Extension('qpms.cycommon',
         sources = ['qpms/cycommon.pyx'],
         #extra_link_args=['qpms/libqpms.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cytmatrices = Extension('qpms.cytmatrices',
         sources = ['qpms/cytmatrices.pyx'],
         #extra_link_args=['qpms/libqpms.a', 'amos/libamos.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cywaves = Extension('qpms.cywaves',
         sources = ['qpms/cywaves.pyx'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cytranslations = Extension('qpms.cytranslations',
         sources = ['qpms/cytranslations.pyx',
@@ -104,51 +119,49 @@ cytranslations = Extension('qpms.cytranslations',
             '-DQPMS_COMPILE_PYTHON_EXTENSIONS', # This is needed to enable it in translations.h
             ],
         #extra_link_args=['qpms/libqpms.a', 'amos/libamos.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cybspec = Extension('qpms.cybspec',
         sources = ['qpms/cybspec.pyx'],
         #extra_link_args=['qpms/libqpms.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cymaterials = Extension('qpms.cymaterials',
         sources = ['qpms/cymaterials.pyx'],
         #extra_link_args=['qpms/libqpms.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cyquaternions = Extension('qpms.cyquaternions',
         sources = ['qpms/cyquaternions.pyx'],
         #extra_link_args=['amos/libamos.a', 'qpms/libqpms.a'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 cyewaldtest = Extension('qpms.cyewaldtest',
         sources = ['qpms/cyewaldtest.pyx'],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
+        libraries = common_libs,
+        include_dirs = [numpy_includes], 
         )
 
 qpms_c = Extension('qpms.qpms_c',
-        sources = [
+        sources = ['qpms/qpms_c.pyx',],
-            'qpms/qpms_c.pyx',
+        libraries = common_libs,
-        ],
+        include_dirs=['amos', 'qpms', numpy_includes],
-        libraries=['qpms', 'gsl', 'lapacke', 'blas', 'gslcblas', 'pthread', #'omp'
-            #('amos', dict(sources=amos_sources) ),
-	],
-        include_dirs=['amos', 'qpms'],
         extra_link_args=['-fopenmp'],
         extra_compile_args=['-fopenmp'],
-        #extra_link_args=[ 'qpms/libqpms.a','amos/libamos.a', ],
-        #runtime_library_dirs=os.environ['LD_LIBRARY_PATH'].split(':') if 'LD_LIBRARY_PATH' in os.environ else [],
-        #extra_objects = ['amos/libamos.a'], # FIXME apparently, I would like to eliminate the need to cmake/make first
         )
 
 setup(name='qpms',
         version = "0.2.996",
         packages=['qpms'],
 #        libraries = [('amos', {'sources': amos_sources} )],
-        setup_requires=['cython>=0.28',],
+        setup_requires=['cython>=0.28','numpy>=1.2','setuptools>=18.0'],
         install_requires=['cython>=0.28',
             #'quaternion','spherical_functions',
-            'scipy>=0.18.0', 'sympy>=1.2'],
+            'scipy>=0.18.0', 'sympy>=1.2', 'numpy>=1.2'],
         #dependency_links=['https://github.com/moble/quaternion/archive/v2.0.tar.gz','https://github.com/moble/spherical_functions/archive/master.zip'],
         ext_modules=cythonize([qpms_c, cywaves, cytranslations, cytmatrices, cycommon, cyquaternions, cybspec, cymaterials, cyewaldtest], include_path=['qpms', 'amos'], gdb_debug=True),
         cmdclass = {'build_ext': build_ext},