Make proper sdist and make setup.py able to boostrap numpy and cython

MANIFEST.in

@@ -1,9 +1,13 @@
 include LICENSE
 include README.md
+include Makefile
 graft tests
 graft include
 graft src
 
+global-include *.pyx
+global-include *.pxd
+
 global-exclude __pycache__/*
 global-exclude *.o
 global-exclude *.a

setup.py

@@ -2,18 +2,51 @@
 # -*- coding: utf-8 -*-
 from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext as _build_ext
-from Cython.Build import cythonize
 from subprocess import check_call
 import os.path as op
-import numpy as np
 import sys
 import os
 import re
 import io
 
+
 thisdir = op.dirname(op.realpath(__file__))
 
 
+def read(*parts, **kwargs):
+    encoding = kwargs.pop('encoding', 'utf-8')
+    filepath = op.join(op.dirname(__file__), *parts)
+    return io.open(filepath, encoding=encoding).read()
+
+
+def get_version(pkg):
+    version = re.search(
+        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
+        read(pkg, '__init__.py'),
+        re.MULTILINE).group(1)
+    return version
+
+
+class lazy_list(list):
+    '''
+    Used to delay cython import until all setup_requires have been installed.
+
+    '''
+    def __init__(self, callback):
+        self._list, self.callback = None, callback
+    def c_list(self):
+        if self._list is None:
+            self._list = self.callback()
+        return self._list
+    def __iter__(self):
+        for e in self.c_list():
+            yield e
+    def __getitem__(self, i):
+        return self.c_list()[i]
+    def __len__(self):
+        return len(self.c_list())
+
+
 # Paths to propagate to make to build libkent
 extra_library_dirs = []
 extra_include_dirs = []
@@ -45,43 +78,40 @@ def run(self):
         print("LIBRARY_PATH: " + os.environ.get("LIBRARY_PATH", ""), file=sys.stderr)
         print("C_INCLUDE_PATH: " + os.environ.get("C_INCLUDE_PATH", ""), file=sys.stderr)
         check_call(['make', 'build-c'])
-
         # Now, proceed to build extension modules
         _build_ext.run(self)
 
-
-ext_modules = [
-    Extension(
-        name='bbi.cbbi', 
-        sources=[
-            op.join(thisdir, 'bbi/cbbi.pyx')
-        ],
-        library_dirs=[
-            op.join(thisdir, 'src/x86_64'),
-        ] + extra_library_dirs,
-        libraries=[
-            'c', 'z', 'pthread', 'kent',
-        ],
-        include_dirs=[
-            np.get_include(),
-            op.join(thisdir, 'include'),
-        ] + extra_include_dirs,
-    ),
-]
-
-
-def read(*parts, **kwargs):
-    encoding = kwargs.pop('encoding', 'utf-8')
-    filepath = op.join(op.dirname(__file__), *parts)
-    return io.open(filepath, encoding=encoding).read()
-
-
-def get_version(pkg):
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        read(pkg, '__init__.py'),
-        re.MULTILINE).group(1)
-    return version
+    def finalize_options(self):
+        _build_ext.finalize_options(self)
+        # Fix to work with bootstrapped numpy installation
+        # http://stackoverflow.com/a/21621689/579416
+        # Prevent numpy from thinking it is still in its setup process:
+        __builtins__.__NUMPY_SETUP__ = False
+        import numpy
+        self.include_dirs.append(numpy.get_include())
+
+
+def get_ext_modules():
+    from Cython.Build import cythonize
+    ext_modules = [
+        Extension(
+            name='bbi.cbbi', 
+            sources=[
+                op.join(thisdir, 'bbi/cbbi.pyx')
+            ],
+            library_dirs=[
+                op.join(thisdir, 'src/x86_64'),
+            ] + extra_library_dirs,
+            libraries=[
+                'c', 'z', 'pthread', 'kent',
+            ],
+            include_dirs=[
+                #np.get_include(),
+                op.join(thisdir, 'include'),
+            ] + extra_include_dirs,
+        ),
+    ]
+    return cythonize(ext_modules)
 
 
 setup(
@@ -90,9 +120,14 @@ def get_version(pkg):
     version=get_version('bbi'),
     packages=['bbi'],
     zip_safe=False,
-    install_requires=['numpy', 'cython'],
+    setup_requires=[
+        'setuptools>=18.0',
+        'cython',
+        'numpy',
+    ],
+    install_requires=['six', 'numpy'],
     tests_require=['pytest'],
-    ext_modules=cythonize(ext_modules),
+    ext_modules=lazy_list(get_ext_modules),
     cmdclass={
         'build_ext': build_ext
     }