Merge branch 'linking_arrayfuncs'

Conflicts:
	setup.py
	sklearn/__init__.py

setup.py

@@ -9,6 +9,16 @@
 import os
 import shutil
 
+if sys.version_info[0] < 3:
+    import __builtin__ as builtins
+else:
+    import builtins
+
+# This is a bit (!) hackish: we are setting a global variable so that the main
+# sklearn __init__ can detect if it is being loaded by the setup routine, to
+# avoid attempting to load components that aren't built yet.
+builtins.__SKLEARN_SETUP__ = True
+
 DISTNAME = 'scikit-learn'
 DESCRIPTION = 'A set of python modules for machine learning and data mining'
 LONG_DESCRIPTION = open('README.rst').read()
@@ -17,7 +27,11 @@
 URL = 'http://scikit-learn.sourceforge.net'
 LICENSE = 'new BSD'
 DOWNLOAD_URL = 'http://sourceforge.net/projects/scikit-learn/files/'
-VERSION = '0.12-git'
+
+# We can actually import a restricted version of sklearn that
+# does not need the compiled code
+import sklearn
+VERSION = sklearn.__version__
 
 from numpy.distutils.core import setup
 

sklearn/__init__.py

@@ -12,51 +12,63 @@
 
 See http://scikit-learn.sourceforge.net for complete documentation.
 """
-
-from . import __check_build
-from .base import clone
-
+import sys
+__version__ = '0.12-git'
 
 try:
-    from numpy.testing import nosetester
-
-    class _NoseTester(nosetester.NoseTester):
-        """ Subclass numpy's NoseTester to add doctests by default
-        """
-
-        def test(self, label='fast', verbose=1, extra_argv=['--exe'],
-                        doctests=True, coverage=False):
-            """Run the full test suite
-
-            Examples
-            --------
-            This will run the test suite and stop at the first failing
-            example
-            >>> from sklearn import test
-            >>> test(extra_argv=['--exe', '-sx']) #doctest: +SKIP
-            """
-            return super(_NoseTester, self).test(label=label, verbose=verbose,
-                                    extra_argv=extra_argv,
-                                    doctests=doctests, coverage=coverage)
+    # This variable is injected in the __builtins__ by the build
+    # process. It used to enable importing subpackages of sklearn when
+    # the binaries are not built
+    __SKLEARN_SETUP__
+except NameError:
+    __SKLEARN_SETUP__ = False
+
+if __SKLEARN_SETUP__:
+    sys.stderr.write('Partial import of sklearn during the build process.\n')
+    # We are not importing the rest of the scikit during the build
+    # process, as it may not be compiled yet
+else:
+    from . import __check_build
+    from .base import clone
 
     try:
-        test = _NoseTester(raise_warnings="release").test
-    except TypeError:
-        # Older versions of numpy do not have a raise_warnings argument
-        test = _NoseTester().test
-    del nosetester
-except:
-    pass
+        from numpy.testing import nosetester
 
+        class _NoseTester(nosetester.NoseTester):
+            """ Subclass numpy's NoseTester to add doctests by default
+            """
 
-__all__ = ['cross_validation', 'cluster', 'covariance',
-           'datasets', 'decomposition', 'feature_extraction',
-           'feature_selection', 'semi_supervised',
-           'gaussian_process', 'grid_search', 'hmm', 'lda', 'linear_model',
-           'metrics', 'mixture', 'naive_bayes', 'neighbors', 'pipeline',
-           'preprocessing', 'qda', 'svm', 'test', 'clone', 'pls']
+            def test(self, label='fast', verbose=1, extra_argv=['--exe'],
+                            doctests=True, coverage=False):
+                """Run the full test suite
+
+                Examples
+                --------
+                This will run the test suite and stop at the first failing
+                example
+                >>> from sklearn import test
+                >>> test(extra_argv=['--exe', '-sx']) #doctest: +SKIP
+                """
+                return super(_NoseTester, self).test(label=label, verbose=verbose,
+                                        extra_argv=extra_argv,
+                                        doctests=doctests, coverage=coverage)
+
+        try:
+            test = _NoseTester(raise_warnings="release").test
+        except TypeError:
+            # Older versions of numpy do not have a raise_warnings argument
+            test = _NoseTester().test
+        del nosetester
+    except:
+        pass
+
+    __all__ = ['cross_validation', 'cluster', 'covariance',
+               'datasets', 'decomposition', 'feature_extraction',
+               'feature_selection', 'semi_supervised',
+               'gaussian_process', 'grid_search', 'hmm', 'lda', 'linear_model',
+               'metrics', 'mixture', 'naive_bayes', 'neighbors', 'pipeline',
+               'preprocessing', 'qda', 'svm', 'test', 'clone', 'pls']
 
-__version__ = '0.12-git'
 
 def setup_module(module):
     """Fixture for the tests to assure globally controllable seeding of RNGs

sklearn/_build_utils.py

@@ -0,0 +1,31 @@
+"""
+Utilities useful during the build.
+"""
+# author: Andy Mueller, Gael Varoquaux
+# license: BSD
+
+from numpy.distutils.system_info import get_info
+
+def get_blas_info():
+
+    def atlas_not_found(blas_info_):
+        def_macros = blas_info.get('define_macros', [])
+        for x in def_macros:
+            if x[0] == "NO_ATLAS_INFO":
+                # if x[1] != 1 we should have lapack
+                # how do we do that now?
+                return True
+            if x[0] == "ATLAS_INFO":
+                if "None" in x[1]:
+                    # this one turned up on FreeBSD
+                    return True
+        return False
+
+    blas_info = get_info('blas_opt', 0)
+    if (not blas_info) or atlas_not_found(blas_info):
+        cblas_libs = ['cblas']
+        blas_info.pop('libraries', None)
+    else:
+        cblas_libs = blas_info.pop('libraries', [])
+
+    return cblas_libs, blas_info

sklearn/cluster/setup.py

@@ -5,18 +5,13 @@
 
 import numpy
 
+from sklearn._build_utils import get_blas_info
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration
-    from numpy.distutils.system_info import get_info
-
-    blas_info = get_info('blas_opt', 0)
-    if (not blas_info) or (
-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
-        cblas_libs = ['cblas']
-        blas_info.pop('libraries', None)
-    else:
-        cblas_libs = blas_info.pop('libraries', [])
+
+    cblas_libs, blas_info = get_blas_info()
+
     libraries = []
     if os.name == 'posix':
         cblas_libs.append('m')

sklearn/linear_model/setup.py

@@ -3,20 +3,15 @@
 
 import numpy
 
+from sklearn._build_utils import get_blas_info
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration
-    from numpy.distutils.system_info import get_info
+
     config = Configuration('linear_model', parent_package, top_path)
 
-    # cd fast needs CBLAS
-    blas_info = get_info('blas_opt', 0)
-    if (not blas_info) or (
-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
-        cblas_libs = ['cblas']
-        blas_info.pop('libraries', None)
-    else:
-        cblas_libs = blas_info.pop('libraries', [])
+    cblas_libs, blas_info = get_blas_info()
+
     libraries = []
     if os.name == 'posix':
         cblas_libs.append('m')

sklearn/utils/setup.py

@@ -1,25 +1,16 @@
 import os
 from os.path import join
 
-from numpy.distutils.system_info import get_info
-
+from sklearn._build_utils import get_blas_info
 
 def configuration(parent_package='', top_path=None):
     import numpy
     from numpy.distutils.misc_util import Configuration
 
     config = Configuration('utils', parent_package, top_path)
-
     config.add_subpackage('sparsetools')
 
-    # cd fast needs CBLAS
-    blas_info = get_info('blas_opt', 0)
-    if (not blas_info) or (
-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
-        cblas_libs = ['cblas']
-        blas_info.pop('libraries', None)
-    else:
-        cblas_libs = blas_info.pop('libraries', [])
+    cblas_libs, blas_info = get_blas_info()
 
     libraries = []
     if os.name == 'posix':