First version compiling the code correctly

setup.py

@@ -11,6 +11,7 @@ from Cython.Build import cythonize
 import os.path
 from distutils import log
 from distutils.extension import Extension
+from pip._internal.cli.cmdoptions import build_dir
 
 sys.path.append(os.path.abspath("python"))
 
@@ -65,9 +66,10 @@ subprocess.call(['cmake', install_clibdir_option, 'src'])
 subprocess.call(['make', '-C', 'src','install'])
 
 
-cython_ext  = [Extension('.'.join(["obitools3",
-                                   os.path.basename(os.path.dirname(x)),
-                                   os.path.splitext(os.path.basename(x))[0]]),
+
+
+cython_ext  = [Extension('.'.join([os.path.dirname(x).replace("python/",""),
+                                   os.path.splitext(os.path.basename(x))[0]]).replace('/','.'),
                          [x],
                          library_dirs=[get_python_lib()],
                          include_dirs=["src","src/libecoPCR","src/libjson"],
@@ -89,7 +91,8 @@ cython_ext  = [Extension('.'.join(["obitools3",
 
 xx = cythonize(cython_ext,
                language_level=3,
-               annotate=True)
+               annotate=True,
+               build_dir="build")
 
 #,              include_path=["src","src/libecoPCR","src/libjson"]