Merge pull request #3 from agramfort/sphx_gallery

first attempt to support sphinx-gallery

Author: rflamary

docs/source/conf.py

@@ -15,23 +15,25 @@
 import sys
 import os
 import re
+import sphinx_gallery
+
 #try:
-from unittest.mock import MagicMock
+# from unittest.mock import MagicMock
 #except ImportError:
 #    from mock import MagicMock
 
-sys.path.insert(0, os.path.abspath("../.."))
+# sys.path.insert(0, os.path.abspath("../.."))
 #sys.setrecursionlimit(1500)
 
 
 
-class Mock(MagicMock):
-    @classmethod
-    def __getattr__(cls, name):
-        return Mock()
+# class Mock(MagicMock):
+#     @classmethod
+#     def __getattr__(cls, name):
+#         return Mock()
 
-MOCK_MODULES = [ 'emd','ot.lp.emd']
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+# MOCK_MODULES = [ 'emd','ot.lp.emd']
+# sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -54,7 +56,9 @@ def __getattr__(cls, name):
     'sphinx.ext.coverage',
     'sphinx.ext.mathjax',
     'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode', 'sphinx.ext.napoleon'
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx_gallery.gen_gallery',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -316,3 +320,11 @@ def __getattr__(cls, name):
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'https://docs.python.org/': None}
+
+sphinx_gallery_conf = {
+    'examples_dirs': '../../examples',
+    'gallery_dirs': 'auto_examples',
+    'reference_url': {
+        'numpy': 'http://docs.scipy.org/doc/numpy-1.9.1',
+        'scipy': 'http://docs.scipy.org/doc/scipy-0.17.0/reference'}
+}

docs/source/index.rst

@@ -14,7 +14,7 @@ Contents
 
    self
    all
-   examples
+   auto_examples
 
 .. include:: readme.rst
     :start-line: 6

examples/demo_OTDA_2D.py examples/plot_OTDA_2D.pyexamples/demo_OTDA_2D.py renamed to examples/plot_OTDA_2D.py

@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 """
+===============================================
 demo of Optimal transport for domain adaptation
+===============================================
+
 """
 
 import numpy as np

examples/demo_OTDA_classes.py examples/plot_OTDA_classes.pyexamples/demo_OTDA_classes.py renamed to examples/plot_OTDA_classes.py

@@ -1,6 +1,9 @@
 # -*- coding: utf-8 -*-
 """
+===============================================
 demo of Optimal transport for domain adaptation
+===============================================
+
 """
 
 import matplotlib.pylab as pl

examples/demo_OTDA_color_images.py examples/plot_OTDA_color_images.pyexamples/demo_OTDA_color_images.py renamed to examples/plot_OTDA_color_images.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 """
+=====================================================================================
 Demo of Optimal transport for domain adaptation with image color adaptation as in [6]
+=====================================================================================
 
 [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014). Regularized discrete optimal transport. SIAM Journal on Imaging Sciences, 7(3), 1853-1882.
 """

examples/demo_OTDA_mapping.py examples/plot_OTDA_mapping.pyexamples/demo_OTDA_mapping.py renamed to examples/plot_OTDA_mapping.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 """
+=======================================================
 Demo of OT mapping estimation for domain adaptation [8]
+=======================================================
 
 [8] M. Perrot, N. Courty, R. Flamary, A. Habrard, "Mapping estimation for
     discrete optimal transport", Neural Information Processing Systems (NIPS), 2016.
@@ -106,8 +108,3 @@
 pl.scatter(xt[:,0],xt[:,1],c=yt,marker='o',label='Target samples',alpha=.2)
 pl.scatter(xst_kernel[:,0],xst_kernel[:,1],c=ys,marker='+',label='Learned mapping')
 pl.title("Estim. mapping (kernel)")
-
-
-
-
-

…amples/demo_OTDA_mapping_color_images.py …amples/plot_OTDA_mapping_color_images.pyexamples/demo_OTDA_mapping_color_images.py renamed to examples/plot_OTDA_mapping_color_images.py examples/demo_OTDA_mapping_color_images.py renamed to examples/plot_OTDA_mapping_color_images.py

@@ -1,13 +1,14 @@
 # -*- coding: utf-8 -*-
 """
+======================================================================================================================
 Demo of Optimal transport for domain adaptation with image color adaptation as in [6] with mapping estimation from [8]
+======================================================================================================================
 
 [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014). Regularized
     discrete optimal transport. SIAM Journal on Imaging Sciences, 7(3), 1853-1882.
 [8] M. Perrot, N. Courty, R. Flamary, A. Habrard, "Mapping estimation for
     discrete optimal transport", Neural Information Processing Systems (NIPS), 2016.
 
-
 """
 
 import numpy as np

examples/demo_OT_1D.py examples/plot_OT_1D.pyexamples/demo_OT_1D.py renamed to examples/plot_OT_1D.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 """
+=============================
 Demo for 1D optimal transport
+=============================
 
 @author: rflamary
 """

examples/demo_OT_2D_samples.py examples/plot_OT_2D_samples.pyexamples/demo_OT_2D_samples.py renamed to examples/plot_OT_2D_samples.py

@@ -74,5 +74,3 @@
 pl.plot(xt[:,0],xt[:,1],'xr',label='Target samples')
 pl.legend(loc=0)
 pl.title('OT matrix Sinkhorn with samples')
-
-