Links to API in examples

doc/ext/sphinx_gallery/docs_resolv.py

@@ -58,7 +58,11 @@ def get_data(url, gallery_dir):
     if sys.version_info[0] == 2 and isinstance(url, unicode):
         url = url.encode('utf-8')
 
-    cached_file = os.path.join(gallery_dir, 'searchindex')
+    cwd = os.getcwd()
+    if 'source' in cwd:
+        cached_file = os.path.join(gallery_dir, 'searchindex')
+    else:
+        cached_file = os.path.join('source', gallery_dir, 'searchindex')
     search_index = shelve.open(cached_file)
     if url in search_index:
         data = search_index[url]
@@ -318,7 +322,6 @@ class SphinxDocLinkResolver(object):
 def _embed_code_links(app, gallery_conf, gallery_dir):
     # Add resolvers for the packages for which we want to show links
     doc_resolvers = {}
-
     for this_module, url in gallery_conf['reference_url'].items():
         try:
             if url is None:
@@ -341,9 +344,10 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
                   "Error:\n".format(this_module))
             print(e.args)
 
+    working_dir = os.getcwd()
+    os.chdir(app.builder.srcdir)
     html_gallery_dir = os.path.abspath(os.path.join(app.builder.outdir,
                                                     gallery_dir))
-
     # patterns for replacement
     link_pattern = '<a href="%s">%s</a>'
     orig_pattern = '<span class="n">%s</span>'
@@ -356,7 +360,6 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
             subpath = dirpath[len(html_gallery_dir) + 1:]
             pickle_fname = os.path.join(gallery_dir, subpath,
                                         fname[:-5] + '_codeobj.pickle')
-
             if os.path.exists(pickle_fname):
                 # we have a pickle file with the objects to embed links for
                 with open(pickle_fname, 'rb') as fid:
@@ -366,7 +369,6 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
                 # generate replacement strings with the links
                 for name, cobj in example_code_obj.items():
                     this_module = cobj['module'].split('.')[0]
-
                     if this_module not in doc_resolvers:
                         continue
 
@@ -403,6 +405,7 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
                             line = expr.sub(substitute_link, line)
                             fid.write(line.encode('utf-8'))
     print('[done]')
+    os.chdir(working_dir)
 
 
 def embed_code_links(app, exception):

doc/ext/sphinx_gallery/gen_gallery.py

@@ -73,15 +73,16 @@ def generate_gallery_rst(app):
     if not isinstance(gallery_dirs, list):
         gallery_dirs = [gallery_dirs]
 
+    # cd to the appropriate directory regardless of sphinx configuration
+    working_dir = os.getcwd()
+    os.chdir(app.builder.srcdir)
+
     mod_examples_dir = os.path.relpath(gallery_conf['mod_example_dir'],
                                        app.builder.srcdir)
     seen_backrefs = set()
 
     computation_times = []
 
-    # cd to the appropriate directory regardless of sphinx configuration
-    working_dir = os.getcwd()
-    os.chdir(app.builder.srcdir)
     for examples_dir, gallery_dir in zip(examples_dirs, gallery_dirs):
         examples_dir = os.path.relpath(examples_dir,
                                        app.builder.srcdir)
@@ -100,7 +101,6 @@ def generate_gallery_rst(app):
                              seen_backrefs)
 
         computation_times += this_computation_times
-
         fhindex.write(this_fhindex)
         for directory in sorted(os.listdir(examples_dir)):
             if os.path.isdir(os.path.join(examples_dir, directory)):
@@ -113,7 +113,6 @@ def generate_gallery_rst(app):
                 computation_times += this_computation_times
 
         fhindex.flush()
-
     # Back to initial directory
     os.chdir(working_dir)
 

doc/source/conf.py

@@ -31,7 +31,7 @@ extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.imgmath',
               'numpydoc',
               'sphinx.ext.autosummary',
-              'plot2rst',
+              #'plot2rst',
               'sphinx.ext.intersphinx',
               'sphinx.ext.linkcode',
               'sphinx_gallery.gen_gallery'
@@ -44,11 +44,17 @@ autosummary_generate = True
 #------------------------------------------------------------------------
 
 sphinx_gallery_conf = {
-    # 'doc_module'        : 'skimage',
+    'doc_module'        : 'skimage',
     # path to your examples scripts
     'examples_dirs' : '../examples',
     # path where to save gallery generated examples
     'gallery_dirs'  : 'auto_examples',
+    'mod_example_dir': 'api',
+    'reference_url'     : {
+            'skimage': None,
+            'matplotlib': 'http://matplotlib.org',
+            'numpy': 'http://docs.scipy.org/doc/numpy-1.6.0',
+            'scipy': 'http://docs.scipy.org/doc/scipy-0.11.0/reference',}
     }
 
 # Determine if the matplotlib has a recent enough version of the