First version of the simplified setup.py script

setup.py

@@ -1,87 +1,122 @@
-#!/usr/bin/env python
-
+import glob
+import os
 import sys
+import re
+import subprocess
+
+from distutils.core import setup,Extension
+from distutils.sysconfig import get_python_lib
+from Cython.Build import cythonize
+
+import os.path
+from distutils import log
+from distutils.extension import Extension
+
+sys.path.append(os.path.abspath("python"))
+
+print(sys.path)
+
+def findPackage(root,base=None):
+    modules=[]
+    if base is None:
+        base=[]
+    for module in (os.path.basename(os.path.dirname(x)) 
+                   for x in glob.glob(os.path.join(root,'*','__init__.py'))):
+        modules.append('.'.join(base+[module]))
+        modules.extend(findPackage(os.path.join(root,module),base+[module]))
+    return modules
+
 
 PACKAGE     = "OBITools3"
 VERSION     = "0.0.0"
 AUTHOR      = 'Eric Coissac'
-EMAIL       = 'eric@coissac.eu'
-URL         = 'metabarcoding.org/obitools3'
-LICENSE     = 'CeCILL-V2'
-DESCRIPTION ="Scripts and library for DNA metabarcoding",
+EMAIL       = 'eric@metabarcoding.org'
+URL         = "metabarcoding.org/obitools3"
+LICENSE     = "CeCILL-V2"
+DESCRIPTION = "Tools and library for DNA metabarcoding",
+PYTHONMIN   = '3.6'
 
 SRC       = 'python'
 CSRC      = 'src'
 
+REQUIRES  = ['Cython>=0.24',
+             'Sphinx>=1.2.0',
+             'ipython>=3.0.0',
+             'breathe>=4.0.0'
+            ]
+
+os.environ['CFLAGS'] = '-O3 -Wall -I "src" -I "src/libecoPCR" -I "src/libjson"'
+
+#sys.path.append("/Users/coissac/git/obitools3/python")
+
+cython_src  = [x for x in glob.iglob('python/obitools3/**/*.pyx', 
+                                     recursive=True
+                                    )
+              ]
+
+              
+            
+#with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as f:
+#    readme = f.read()
+    
+install_clibdir_option="-DPYTHONLIB:STRING='%s'" % get_python_lib()
+
+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]]),
+                         [x],
+                         library_dirs=[get_python_lib()],
+                         include_dirs=["src","src/libecoPCR","src/libjson"],
+                         libraries=["cobitools3"],
+                         runtime_library_dirs=[get_python_lib()],
+                         extra_compile_args=['-msse2',
+                                          '-Wno-unused-function',
+                                          '-Wmissing-braces',
+                                          '-Wchar-subscripts',
+                                          '-fPIC'
+                                         ],
+                         extra_link_args=["-Wl,-rpath,"+get_python_lib(), 
+                                          "-L"+get_python_lib()
+                                         ]
+                        )
+                for x in cython_src
+              ]              
+
+
+xx = cythonize(cython_ext,
+               language_level=3,
+               annotate=True)
+
+#,              include_path=["src","src/libecoPCR","src/libjson"]
+
 classifiers=['Development Status :: 1 - Planning',
              'Environment :: Console',
              'Intended Audience :: Science/Research',
              'License :: Other/Proprietary License',
              'Operating System :: Unix',
-             'Programming Language :: Python',
              'Programming Language :: Python :: 3',
+             'Programming Language :: C',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
              'Topic :: Utilities',
              ]
 
 
-PYTHONMIN='3.4'
 
-
-sys.path.append('distutils.ext')
-sys.path.append(SRC)
-
-if __name__=="__main__":
-    
-    import sys
-    
-    print("----------------")
-    print(" ".join(sys.argv))
-    print("----------------")
-    
-    #
-    # Horrible hack
-    #
-    
-    if sys.argv[0]=="-c":
-        sys.argv[0]="setup.py"
-    
-    #
-    # End of the horrible hack
-    #
-    
-
-    
-    try:
-        from obitools3 import version
-        VERSION     = version.version
-    except ImportError:
-        pass
-
-    from obidistutils.serenity import serenity_mode
-    
-    serenity=serenity_mode(PACKAGE,VERSION)
-
-    from obidistutils.core import setup
-    from obidistutils.core import CTOOLS
-    from obidistutils.core import CEXES
-    from obidistutils.core import FILES
-    
-    # Produce annotated html files
-    import Cython.Compiler.Options
-    Cython.Compiler.Options.annotate = True
-
-    
-    setup(name=PACKAGE,
-          description=DESCRIPTION,
-          classifiers=classifiers,
-          version=VERSION,
-          author=AUTHOR,
-          author_email=EMAIL,
-          license=LICENSE,
-          url=URL,
-          python_src=SRC,
-          sse='sse2',
-          serenity=serenity,
-          pythonmin=PYTHONMIN)
+setup(name=PACKAGE,
+      description=DESCRIPTION,
+      classifiers=classifiers,
+      version=VERSION,
+      author=AUTHOR,
+      author_email=EMAIL,
+      license=LICENSE,
+      url=URL,
+      ext_modules=xx,
+      packages = findPackage('python'),
+      package_dir = {"" : "python"},
+      scripts = ['python/obi.py']
+)