nipy · matthew-brett · Sep 4, 2015 · Aug 31, 2015 · Aug 31, 2015 · Sep 2, 2015
diff --git a/.travis.yml b/.travis.yml
@@ -5,6 +5,11 @@
 # - There can't be any leading "-"s - All newlines will be removed, so use
 # ";"s
 sudo: false  # To use travis container infrastructure
+addons:
+  apt:
+    packages:
+        - libblas-dev
+        - liblapack-dev
 language: python
 cache:
   directories:
@@ -27,14 +32,17 @@ matrix:
     - python: 2.7
       env:
         - DEPENDS="numpy==1.6.0 scipy==0.7.0 sympy==0.7.0 nibabel==1.2.0"
+    # Test compiling against external lapack
+    - python: 3.4
+      env:
+        - NIPY_EXTERNAL_LAPACK=1
 before_install:
     - source tools/travis_tools.sh
     - virtualenv --python=python venv
     - source venv/bin/activate
     - python --version # just to check
     - retry pip install nose # always
     - wheelhouse_pip_install $DEPENDS
-    # - sudo apt-get install -qq libatlas-dev libatlas-base-dev gfortran libpng-dev
     - if [ "${COVERAGE}" == "1" ]; then
       pip install coverage;
       pip install coveralls;

diff --git a/nipy/algorithms/clustering/setup.py b/nipy/algorithms/clustering/setup.py
@@ -7,21 +7,6 @@ def configuration(parent_package='',top_path=None):
     config = Configuration('clustering', parent_package, top_path)
     config.add_subpackage('tests')
 
-    # We need this because libcstat.a is linked to lapack, which can
-    # be a fortran library, and the linker needs this information.
-    from numpy.distutils.system_info import get_info
-    lapack_info = get_info('lapack_opt',0)
-    if 'libraries' not in lapack_info:
-        # But on OSX that may not give us what we need, so try with 'lapack'
-        # instead.  NOTE: scipy.linalg uses lapack_opt, not 'lapack'...
-        lapack_info = get_info('lapack',0)
-
-    #config.add_extension(
-    #            '_clustering',
-    #            sources=['clustering.c'],
-    #            libraries=['cstat'],
-    #            extra_info=lapack_info,
-    #            )
     return config
 
 

diff --git a/nipy/labs/bindings/setup.py b/nipy/labs/bindings/setup.py
@@ -1,29 +1,17 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-import os, sys
 
 def configuration(parent_package='',top_path=None):
     from numpy.distutils.misc_util import Configuration
     config = Configuration('bindings', parent_package, top_path)
     config.add_subpackage('tests')
     config.add_subpackage('benchmarks')
-    # We need this because libcstat.a is linked to lapack, which can
-    # be a fortran library, and the linker needs this information.
-    from numpy.distutils.system_info import get_info
-    lapack_info = get_info('lapack_opt',0)
-    if 'libraries' not in lapack_info:
-        # But on OSX that may not give us what we need, so try with 'lapack'
-        # instead.  NOTE: scipy.linalg uses lapack_opt, not 'lapack'...
-        lapack_info = get_info('lapack',0)
     config.add_extension('linalg', sources=['linalg.pyx'],
-                            libraries=['cstat'],
-                            extra_info=lapack_info)
+                            libraries=['cstat'])
     config.add_extension('array', sources=['array.pyx'],
-                            libraries=['cstat'],
-                            extra_info=lapack_info)
+                            libraries=['cstat'])
     config.add_extension('wrapper', sources=['wrapper.pyx'],
-                            libraries=['cstat'],
-                            extra_info=lapack_info)
+                            libraries=['cstat'])
     return config
 
 

diff --git a/nipy/labs/glm/setup.py b/nipy/labs/glm/setup.py
@@ -3,22 +3,13 @@
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration
-    # We need this because libcstat.a is linked to lapack, which can
-    # be a fortran library, and the linker needs this information.
-    from numpy.distutils.system_info import get_info
-    lapack_info = get_info('lapack_opt', 0)
-    if 'libraries' not in lapack_info:
-        # But on OSX that may not give us what we need, so try with 'lapack'
-        # instead.  NOTE: scipy.linalg uses lapack_opt, not 'lapack'...
-        lapack_info = get_info('lapack', 0)
     config = Configuration('glm', parent_package, top_path)
     config.add_subpackage('tests')
     config.add_subpackage('benchmarks')
     config.add_extension(
                 'kalman',
                 sources=['kalman.pyx'],
-                libraries=['cstat'],
-                extra_info=lapack_info,
+                libraries=['cstat']
                 )
     return config
 

diff --git a/nipy/labs/group/setup.py b/nipy/labs/group/setup.py
@@ -3,33 +3,22 @@ def configuration(parent_package='',top_path=None):
     from numpy.distutils.misc_util import Configuration
     # We need this because libcstat.a is linked to lapack, which can
     # be a fortran library, and the linker needs this information.
-    from numpy.distutils.system_info import get_info
-    # First, try 'lapack_info', as that seems to provide more details on Linux
-    # (both 32 and 64 bits):
-    lapack_info = get_info('lapack_opt', 0)
-    if 'libraries' not in lapack_info:
-        # But on OSX that may not give us what we need, so try with 'lapack'
-        # instead.  NOTE: scipy.linalg uses lapack_opt, not 'lapack'...
-        lapack_info = get_info('lapack',0)
     config = Configuration('group', parent_package, top_path)
     config.add_subpackage('tests')
     config.add_extension(
         'onesample',
         sources=['onesample.pyx'],
-        libraries=['cstat'],
-        extra_info=lapack_info,
+        libraries=['cstat']
         )
     config.add_extension(
         'twosample',
         sources=['twosample.pyx'],
-        libraries=['cstat'],
-        extra_info=lapack_info,
+        libraries=['cstat']
         )
     config.add_extension(
         'glm_twolevel',
         sources=['glm_twolevel.pyx'],
-        libraries=['cstat'],
-        extra_info=lapack_info,
+        libraries=['cstat']
         )
     return config
 

diff --git a/nipy/labs/setup.py b/nipy/labs/setup.py
@@ -3,18 +3,48 @@
 import os
 from distutils import log
 
+try:
+    from configparser import ConfigParser, NoSectionError, NoOptionError
+except ImportError:
+    from ConfigParser import ConfigParser, NoSectionError, NoOptionError
+
 # Global variables
 LIBS = os.path.realpath('lib')
 
-# The following variable disables linking with Lapack by default. So
-# far, the only way to attempt at linking with Lapack is to edit this
-# file and set WANT_LAPACK_LINKING=True. We might later want to pass
-# in this variable as an optional argument of `python setup.py build`.
-WANT_LAPACK_LINKING = False
+# Stuff for reading setup file
+SETUP_FILE = 'setup.cfg'
+SECTION = 'lapack'
+KEY = 'external'
+EXTERNAL_LAPACK_VAR = 'NIPY_EXTERNAL_LAPACK'
+
+def get_link_external():
+    """ Return True if we should link to system BLAS / LAPACK
+
+    If True, attempt to link to system BLAS / LAPACK.  Otherwise, compile
+    lapack_lite, and link to that.
+
+    First check ``setup.cfg`` file for section ``[lapack]`` key ``external``.
+
+    If this value undefined, then get string from environment variable
+    NIPY_EXTERNAL_LAPACK.
+
+    If value from ``setup.cfg`` or environment variable is not 'False' or '0',
+    then return True.
+    """
+    config = ConfigParser()
+    try:
+        config.read(SETUP_FILE)
+        external_link = config.get(SECTION, KEY)
+    except (IOError, KeyError, NoOptionError, NoSectionError):
+        external_link = os.environ.get(EXTERNAL_LAPACK_VAR)
+    if external_link is None:
+        return False
+    return external_link.lower() not in ('0', 'false')
+
 
 def configuration(parent_package='',top_path=None):
     from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
-    from numpy.distutils.system_info import get_info, system_info
+    from numpy.distutils.system_info import get_info
 
     config = Configuration('labs', parent_package, top_path)
 
@@ -50,16 +80,20 @@ def configuration(parent_package='',top_path=None):
     # If lapack linking not required or no lapack install is found, we
     # use the rescue lapack lite distribution included in the package
     # (sources have been translated to C using f2c)
-    if not WANT_LAPACK_LINKING or not lapack_info:
-        if WANT_LAPACK_LINKING:
-            log.warn('Lapack not found')
-        log.warn('Building Lapack lite distribution')
+    want_lapack_link = get_link_external()
+    if not want_lapack_link:
+        log.warn('Building with (slow) Lapack lite distribution: '
+                 'set {0} environment variable or use setup.cfg '
+                 'to enable link to optimized BLAS / LAPACK'.format(
+                        EXTERNAL_LAPACK_VAR)
+                 )
         sources.append(os.path.join(LIBS,'lapack_lite','*.c'))
         library_dirs = []
         libraries = []
-
-    # Best-case scenario: lapack found 
-    else:
+    else: # Best-case scenario: external lapack found
+        if not lapack_info:
+            raise RuntimeError('Specified external lapack linking but '
+                               'numpy does not report external lapack')
         log.warn('Linking with system Lapack')
         library_dirs = lapack_info['library_dirs']
         libraries = lapack_info['libraries']

diff --git a/nipy/labs/utils/setup.py b/nipy/labs/utils/setup.py
@@ -3,22 +3,12 @@
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration
-    # We need this because libcstat.a is linked to lapack, which can
-    # be a fortran library, and the linker needs this information.
-    from numpy.distutils.system_info import get_info
-    lapack_info = get_info('lapack_opt', 0)
-    if 'libraries' not in lapack_info:
-        # But on OSX that may not give us what we need, so try with 'lapack'
-        # instead.  NOTE: scipy.linalg uses lapack_opt, not 'lapack'...
-        lapack_info = get_info('lapack', 0)
-
     config = Configuration('utils', parent_package, top_path)
     config.add_subpackage('tests')
     config.add_extension(
                 'routines',
                 sources=['routines.pyx'],
-                libraries=['cstat'],
-                extra_info=lapack_info,
+                libraries=['cstat']
                 )
 
     return config

diff --git a/setup.cfg b/setup.cfg
@@ -19,3 +19,11 @@ cover-package = nipy
 #with-doctest=1
 doctest-extension=rst
 
+# In this section specify if you want to link to external BLAS / LAPACK
+[lapack]
+# Value of 0 or False implies compile of, link to lapack_lite
+# Value of 1 or True will cause setup to try and link to external BLAS /
+# LAPACK as identified with the numpy configuration.  Default is False.
+# The value in this file overrides the equivalent setting in the environment
+# variable NIPY_EXTERNAL_LAPACK.
+#external = False