scikit-learn · lesteve · Jun 6, 2017 · May 19, 2017 · May 22, 2017 · May 22, 2017
diff --git a/doc/conf.py b/doc/conf.py
@@ -236,6 +236,7 @@
 
 sphinx_gallery_conf = {
     'doc_module': 'sklearn',
+    'backreferences_dir': os.path.join('modules', 'generated'),
     'reference_url': {
         'sklearn': None,
         'matplotlib': 'http://matplotlib.org',

diff --git a/doc/sphinxext/sphinx_gallery/__init__.py b/doc/sphinxext/sphinx_gallery/__init__.py
@@ -1,11 +1,10 @@
 """
-==============
 Sphinx Gallery
 ==============
 
 """
 import os
-__version__ = '0.1.7'
+__version__ = '0.1.11'
 
 
 def glr_path_static():

diff --git a/doc/sphinxext/sphinx_gallery/_static/gallery.css b/doc/sphinxext/sphinx_gallery/_static/gallery.css
@@ -190,25 +190,3 @@ p.sphx-glr-signature a.reference.external {
   margin-left: auto;
   display: table;
 }
-
-a.sphx-glr-code-links:hover{
-    text-decoration: none;
-}
-
-a.sphx-glr-code-links[tooltip]:hover:before{
-    background: rgba(0,0,0,.8);
-    border-radius: 5px;
-    color: white;
-    content: attr(tooltip);
-    padding: 5px 15px;
-    position: absolute;
-    z-index: 98;
-    width: 16em;
-    word-break: normal;
-    white-space: normal;
-    display: inline-block;
-    text-align: center;
-    text-indent: 0;
-    margin-left: 0; /* Use zero to avoid overlapping with sidebar */
-    margin-top: 1.2em;
-}
diff --git a/doc/sphinxext/sphinx_gallery/backreferences.py b/doc/sphinxext/sphinx_gallery/backreferences.py
@@ -2,11 +2,10 @@
 # Author: Óscar Nájera
 # License: 3-clause BSD
 """
-========================
 Backreferences Generator
 ========================
 
-Reviews generated example files in order to keep track of used modules
+Parses example file code in order to keep track of used functions
 """
 
 from __future__ import print_function
@@ -97,7 +96,10 @@ def identify_names(code):
     e.HelloWorld HelloWorld d d
     """
     finder = NameFinder()
-    finder.visit(ast.parse(code))
+    try:
+        finder.visit(ast.parse(code))
+    except SyntaxError:
+        return {}
 
     example_code_obj = {}
     for name, full_name in finder.get_mapping():
@@ -133,8 +135,6 @@ def scan_used_functions(example_file, gallery_conf):
     return backrefs
 
 
-# XXX This figure:: uses a forward slash even on Windows, but the op.join's
-# elsewhere will use backslashes...
 THUMBNAIL_TEMPLATE = """
 .. raw:: html
 
@@ -162,6 +162,10 @@ def _thumbnail_div(full_dir, fname, snippet, is_backref=False):
     """Generates RST to place a thumbnail in a gallery"""
     thumb = os.path.join(full_dir, 'images', 'thumb',
                          'sphx_glr_%s_thumb.png' % fname[:-3])
+
+    # Inside rst files forward slash defines paths
+    thumb = thumb.replace(os.sep, "/")
+
     ref_name = os.path.join(full_dir, fname).replace(os.path.sep, '_')
 
     template = BACKREF_THUMBNAIL_TEMPLATE if is_backref else THUMBNAIL_TEMPLATE
@@ -172,17 +176,22 @@ def write_backreferences(seen_backrefs, gallery_conf,
                          target_dir, fname, snippet):
     """Writes down back reference files, which include a thumbnail list
     of examples using a certain module"""
+    if gallery_conf['backreferences_dir'] is None:
+        return
+
     example_file = os.path.join(target_dir, fname)
+    build_target_dir = os.path.relpath(target_dir, gallery_conf['src_dir'])
     backrefs = scan_used_functions(example_file, gallery_conf)
     for backref in backrefs:
-        include_path = os.path.join(gallery_conf['mod_example_dir'],
+        include_path = os.path.join(gallery_conf['src_dir'],
+                                    gallery_conf['backreferences_dir'],
                                     '%s.examples' % backref)
         seen = backref in seen_backrefs
         with open(include_path, 'a' if seen else 'w') as ex_file:
             if not seen:
                 heading = '\n\nExamples using ``%s``' % backref
                 ex_file.write(heading + '\n')
                 ex_file.write('^' * len(heading) + '\n')
-            ex_file.write(_thumbnail_div(target_dir, fname, snippet,
+            ex_file.write(_thumbnail_div(build_target_dir, fname, snippet,
                                          is_backref=True))
             seen_backrefs.add(backref)
diff --git a/doc/sphinxext/sphinx_gallery/docs_resolv.py b/doc/sphinxext/sphinx_gallery/docs_resolv.py
@@ -1,8 +1,10 @@
 # -*- coding: utf-8 -*-
 # Author: Óscar Nájera
 # License: 3-clause BSD
-###############################################################################
-# Documentation link resolver objects
+"""
+Link resolver objects
+=====================
+"""
 from __future__ import print_function
 import gzip
 import os
@@ -11,6 +13,8 @@
 import shelve
 import sys
 
+from sphinx.util.console import fuchsia
+
 # Try Python 2 first, otherwise load from Python 3
 try:
     import cPickle as pickle
@@ -291,7 +295,7 @@ def resolve(self, cobj, this_url):
         cobj : dict
             Dict with information about the "code object" for which we are
             resolving a link.
-            cobi['name'] : function or class name (str)
+            cobj['name'] : function or class name (str)
             cobj['module_short'] : shortened module name (str)
             cobj['module'] : module name (str)
         this_url: str
@@ -331,16 +335,17 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
     # Add resolvers for the packages for which we want to show links
     doc_resolvers = {}
 
+    src_gallery_dir = os.path.join(app.builder.srcdir, gallery_dir)
     for this_module, url in gallery_conf['reference_url'].items():
         try:
             if url is None:
                 doc_resolvers[this_module] = SphinxDocLinkResolver(
                     app.builder.outdir,
-                    gallery_dir,
+                    src_gallery_dir,
                     relative=True)
             else:
                 doc_resolvers[this_module] = SphinxDocLinkResolver(url,
-                                                                   gallery_dir)
+                                                                   src_gallery_dir)
 
         except HTTPError as e:
             print("The following HTTP Error has occurred:\n")
@@ -357,72 +362,74 @@ def _embed_code_links(app, gallery_conf, gallery_dir):
                                                     gallery_dir))
 
     # patterns for replacement
-    link_pattern = ('<a href="%s" class="sphx-glr-code-links" '
-       'tooltip="Link to documentation for %s">%s</a>')
+    link_pattern = ('<a href="%s" title="View documentation for %s">%s</a>')
     orig_pattern = '<span class="n">%s</span>'
     period = '<span class="o">.</span>'
 
-    for dirpath, _, filenames in os.walk(html_gallery_dir):
-        for fname in filenames:
-            print('\tprocessing: %s' % fname)
-            full_fname = os.path.join(html_gallery_dir, dirpath, fname)
-            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:
-                    example_code_obj = pickle.load(fid)
-                fid.close()
-                str_repl = {}
-                # 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
-
-                    try:
-                        link = doc_resolvers[this_module].resolve(cobj,
-                                                                  full_fname)
-                    except (HTTPError, URLError) as e:
-                        if isinstance(e, HTTPError):
-                            extra = e.code
-                        else:
-                            extra = e.reason
-                        print("\t\tError resolving %s.%s: %r (%s)"
-                              % (cobj['module'], cobj['name'], e, extra))
-                        continue
-
-                    if link is not None:
-                        parts = name.split('.')
-                        name_html = period.join(orig_pattern % part
-                                                for part in parts)
-                        full_function_name = '%s.%s' % (
-                            cobj['module'], cobj['name'])
-                        str_repl[name_html] = link_pattern % (
-                            link, full_function_name, name_html)
-                # do the replacement in the html file
-
-                # ensure greediness
-                names = sorted(str_repl, key=len, reverse=True)
-                expr = re.compile(r'(?<!\.)\b' +  # don't follow . or word
-                                  '|'.join(re.escape(name)
-                                           for name in names))
-
-                def substitute_link(match):
-                    return str_repl[match.group()]
-
-                if len(str_repl) > 0:
-                    with open(full_fname, 'rb') as fid:
-                        lines_in = fid.readlines()
-                    with open(full_fname, 'wb') as fid:
-                        for line in lines_in:
-                            line = line.decode('utf-8')
-                            line = expr.sub(substitute_link, line)
-                            fid.write(line.encode('utf-8'))
-    print('[done]')
+    # This could be turned into a generator if necessary, but should be okay
+    flat = [[dirpath, filename]
+            for dirpath, _, filenames in os.walk(html_gallery_dir)
+            for filename in filenames]
+    iterator = app.status_iterator(
+        flat, os.path.basename(html_gallery_dir), colorfunc=fuchsia,
+        length=len(flat), stringify_func=lambda x: os.path.basename(x[1]))
+    for dirpath, fname in iterator:
+        full_fname = os.path.join(html_gallery_dir, dirpath, fname)
+        subpath = dirpath[len(html_gallery_dir) + 1:]
+        pickle_fname = os.path.join(src_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:
+                example_code_obj = pickle.load(fid)
+            fid.close()
+            str_repl = {}
+            # 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
+
+                try:
+                    link = doc_resolvers[this_module].resolve(cobj,
+                                                              full_fname)
+                except (HTTPError, URLError) as e:
+                    if isinstance(e, HTTPError):
+                        extra = e.code
+                    else:
+                        extra = e.reason
+                    print("\n\t\tError resolving %s.%s: %r (%s)"
+                          % (cobj['module'], cobj['name'], e, extra))
+                    continue
+
+                if link is not None:
+                    parts = name.split('.')
+                    name_html = period.join(orig_pattern % part
+                                            for part in parts)
+                    full_function_name = '%s.%s' % (
+                        cobj['module'], cobj['name'])
+                    str_repl[name_html] = link_pattern % (
+                        link, full_function_name, name_html)
+            # do the replacement in the html file
+
+            # ensure greediness
+            names = sorted(str_repl, key=len, reverse=True)
+            regex_str = '|'.join(re.escape(name) for name in names)
+            regex = re.compile(regex_str)
+
+            def substitute_link(match):
+                return str_repl[match.group()]
+
+            if len(str_repl) > 0:
+                with open(full_fname, 'rb') as fid:
+                    lines_in = fid.readlines()
+                with open(full_fname, 'wb') as fid:
+                    for line in lines_in:
+                        line = line.decode('utf-8')
+                        line = regex.sub(substitute_link, line)
+                        fid.write(line.encode('utf-8'))
 
 
 def embed_code_links(app, exception):

diff --git a/doc/sphinxext/sphinx_gallery/downloads.py b/doc/sphinxext/sphinx_gallery/downloads.py
@@ -55,14 +55,14 @@ def python_zip(file_list, gallery_path, extension='.py'):
         zip file name, written as `target_dir_{python,jupyter}.zip`
         depending on the extension
     """
-    zipname = gallery_path.replace(os.path.sep, '_')
+    zipname = os.path.basename(gallery_path)
     zipname += '_python' if extension == '.py' else '_jupyter'
     zipname = os.path.join(gallery_path, zipname + '.zip')
 
     zipf = zipfile.ZipFile(zipname, mode='w')
     for fname in file_list:
         file_src = os.path.splitext(fname)[0] + extension
-        zipf.write(file_src)
+        zipf.write(file_src, os.path.relpath(file_src, gallery_path))
     zipf.close()
 
     return zipname
@@ -110,8 +110,11 @@ def generate_zipfiles(gallery_dir):
     py_zipfile = python_zip(listdir, gallery_dir)
     jy_zipfile = python_zip(listdir, gallery_dir, ".ipynb")
 
+    def rst_path(filepath):
+        return filepath.replace(os.sep, '/')
+
     dw_rst = CODE_ZIP_DOWNLOAD.format(os.path.basename(py_zipfile),
-                                      py_zipfile,
+                                      rst_path(py_zipfile),
                                       os.path.basename(jy_zipfile),
-                                      jy_zipfile)
+                                      rst_path(jy_zipfile))
     return dw_rst