Merge pull request #33 from samuelstjean/apple_veclib_fix

the big refactor release

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## [0.5] - unreleased
+## [0.5] - 2016-08-30
 
 - Heavy refactor of the library. There is now a single script named nlsam_denoising
 to replace both stabilizer and nlsam in one go.
@@ -13,6 +13,8 @@ nlsam_denoising input output N bvals bvecs n_angular_neighbors
 - There is also new cool command line options (such as logging) to discover with nlsam_denoising -h
 - Some code from the previous scripts was moved in the library part of nlsam,
 so now it is easier to hook in with other python projects.
+- (Un)Official python 3 support. You will also need to grab an
+[unofficial spams build](https://github.com/samuelstjean/spams-python/releases) which has been patched for python 3 support.
 
 ## [0.3.1] - 2016-07-11
 

scripts/nlsam_denoising

@@ -3,10 +3,15 @@
 from __future__ import division, print_function
 
 import os
+
 # Fix openblas threading bug with openmp before loading numpy
 # Spams has openmp support already, and openblas conflicts with python multiprocessing.
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 
+# Mac OSX has it's own blas/lapack, but like openblas it causes conflict for
+# python 2.7 and before python 3.4 in multiprocessing, so disable it.
+os.environ['VECLIB_MAXIMUM_THREADS'] = '1'
+
 import argparse
 import logging
 from multiprocessing import cpu_count, freeze_support

setup.py

@@ -8,7 +8,7 @@
 params['author'] = 'Samuel St-Jean'
 params['author_email'] = 'samuel@isi.uu.nl'
 params['url'] = 'https://github.com/samuelstjean/nlsam'
-params['version'] = '0.3.1'
+params['version'] = '0.5'
 params['requires'] = ['cythongsl>=0.2.1',
                       'numpy>=1.10.4',
                       'cython>=0.21']