brainiak · mihaic · Jul 13, 2016 · Jul 12, 2016 · Jul 13, 2016 · xiazhu
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,7 @@
 *.o
 
 brainiak.egg-info
+build
 .cache
 .coverage
 coverage.xml

diff --git a/README.rst b/README.rst
@@ -104,21 +104,12 @@ steps::
     pip install .
 
 
-Building documentation
-----------------------
+Documentation
+-------------
 
-The documentation will soon be available online. Until then, you can build it
-yourself after installing the required tools::
+The documentation is available at::
 
-    pip3 install -U sphinx sphinx_rtd_theme
-
-Then, assuming you're already in the ``brainiak`` folder, do::
-
-    cd docs
-    make
-
-This will generate HTML documentation in the ``_build/html`` folder within the
-``docs`` folder. ``_build/html/index.html`` is the starting page.
+    https://pythonhosted.org/brainiak
 
 
 Contribute

diff --git a/brainiak/factor_analysis/tfa.py b/brainiak/factor_analysis/tfa.py
@@ -35,7 +35,7 @@
 from scipy.optimize import linear_sum_assignment
 from scipy.spatial import distance
 from ..utils.utils import from_tri_2_sym, from_sym_2_tri
-import tfa_extension
+from . import tfa_extension
 import numpy as np
 import math
 import gc

diff --git a/examples/download-data.sh → ...les/functional_alignment/download-data.sh b/examples/download-data.sh → ...les/functional_alignment/download-data.sh
diff --git a/examples/functional_alignment/requirements.txt b/examples/functional_alignment/requirements.txt
@@ -0,0 +1,2 @@
+matplotlib
+notebook
diff --git a/examples/srm_image_prediction_example.ipynb → ...gnment/srm_image_prediction_example.ipynb b/examples/srm_image_prediction_example.ipynb → ...gnment/srm_image_prediction_example.ipynb
diff --git a/examples/srm_image_prediction_example.py → ...alignment/srm_image_prediction_example.py b/examples/srm_image_prediction_example.py → ...alignment/srm_image_prediction_example.py
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,6 +1,5 @@
 flake8
 flake8-print
-notebook
 pytest
 pytest-cov
 restructuredtext-lint

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,3 @@
-[aliases]
-test = pytest
-
 [pytest]
 addopts =
     --junitxml=junit-results.xml

diff --git a/setup.py b/setup.py
@@ -4,7 +4,7 @@
 import sys
 import setuptools
 
-__version__ = '0.0.1'
+__version__ = '0.1'
 
 assert sys.version_info >= (3, 4), (
     "Please use Python version 3.4 or higher, "
@@ -35,14 +35,13 @@ def __str__(self):
 
 ext_modules = [
     Extension(
-        'tfa_extension',
+        'brainiak.factor_analysis.tfa_extension',
         ['brainiak/factor_analysis/tfa_extension.cpp'],
            include_dirs=[
             # Path to pybind11 headers
             get_pybind_include(),
             get_pybind_include(user=True)
         ],
-        language='c++'
     ),
 ]
 
@@ -80,7 +79,7 @@ def cpp_flag(compiler):
 class BuildExt(build_ext):
     """A custom build extension for adding compiler-specific options."""
     c_opts = {
-        'unix': ['-std=c++11'],
+        'unix': ['-g0', '-fopenmp'],
     }
 
     if sys.platform == 'darwin':
@@ -91,12 +90,14 @@ def build_extensions(self):
         ct = self.compiler.compiler_type
         opts = self.c_opts.get(ct, [])
         if ct == 'unix':
-            opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
+            opts.append('-DVERSION_INFO="%s"' %
+                        self.distribution.get_version())
             opts.append(cpp_flag(self.compiler))
             if has_flag(self.compiler, '-fvisibility=hidden'):
                 opts.append('-fvisibility=hidden')
         for ext in self.extensions:
             ext.extra_compile_args = opts
+            ext.extra_link_args = opts
         build_ext.build_extensions(self)
 
 setup(
@@ -112,12 +113,12 @@ def build_extensions(self):
     author='Princeton Neuroscience Institute and Intel Corporation',
     author_email='bryn.keller@intel.com',
     url='https://github.com/IntelPNI/brainiak',
-    description='Scalable algorithms for advanced fMRI analysis',
+    description='Brain Imaging Analysis Kit',
     license='Apache 2',
     keywords='neuroscience, algorithm, fMRI, distributed, scalable',
     long_description=long_description,
     ext_modules=ext_modules,
     cmdclass={'build_ext': BuildExt},
-    packages=find_packages(exclude=['doc', 'test']),
+    packages=find_packages(),
     zip_safe=False,
 )
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,6 +7,7 @@ @@
     *.o
     brainiak.egg-info
+    build
     .cache
     .coverage
     coverage.xml
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		matplotlib
Copy link Contributor xiazhu Jul 13, 2016 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. notebook will also be needed for this example. Copy link Member Author mihaic Jul 13, 2016 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. Done. Anything else?
		notebook