Merge pull request nilearn#919 from lesteve/update-numpydoc-sphinxext

[MRG] Update numpydoc sphinxext

doc/conf.py

@@ -39,7 +39,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
               'sphinx.ext.pngmath', 'sphinx.ext.intersphinx',
-              'numpy_ext.numpydoc',
+              'numpydoc.numpydoc',
               'sphinx_gallery.gen_gallery',
               ]
 
@@ -287,6 +287,12 @@
         'sklearn': 'http://scikit-learn.org/stable'}
     }
 
+# Get rid of spurious warnings due to some interaction between
+# autosummary and numpydoc. See
+# https://github.com/phn/pytpm/issues/3#issuecomment-12133978 for more
+# details
+numpydoc_show_class_members = False
+
 
 def touch_example_backreferences(app, what, name, obj, options, lines):
     # generate empty examples files, so that we don't get

doc/sphinxext/numpydoc/__init__.py

@@ -0,0 +1,3 @@
+from __future__ import division, absolute_import, print_function
+
+from .numpydoc import setup

doc/sphinxext/numpydoc/comment_eater.py

@@ -0,0 +1,169 @@
+from __future__ import division, absolute_import, print_function
+
+import sys
+if sys.version_info[0] >= 3:
+    from io import StringIO
+else:
+    from io import StringIO
+
+import compiler
+import inspect
+import textwrap
+import tokenize
+
+from .compiler_unparse import unparse
+
+
+class Comment(object):
+    """ A comment block.
+    """
+    is_comment = True
+    def __init__(self, start_lineno, end_lineno, text):
+        # int : The first line number in the block. 1-indexed.
+        self.start_lineno = start_lineno
+        # int : The last line number. Inclusive!
+        self.end_lineno = end_lineno
+        # str : The text block including '#' character but not any leading spaces.
+        self.text = text
+
+    def add(self, string, start, end, line):
+        """ Add a new comment line.
+        """
+        self.start_lineno = min(self.start_lineno, start[0])
+        self.end_lineno = max(self.end_lineno, end[0])
+        self.text += string
+
+    def __repr__(self):
+        return '%s(%r, %r, %r)' % (self.__class__.__name__, self.start_lineno,
+            self.end_lineno, self.text)
+
+
+class NonComment(object):
+    """ A non-comment block of code.
+    """
+    is_comment = False
+    def __init__(self, start_lineno, end_lineno):
+        self.start_lineno = start_lineno
+        self.end_lineno = end_lineno
+
+    def add(self, string, start, end, line):
+        """ Add lines to the block.
+        """
+        if string.strip():
+            # Only add if not entirely whitespace.
+            self.start_lineno = min(self.start_lineno, start[0])
+            self.end_lineno = max(self.end_lineno, end[0])
+
+    def __repr__(self):
+        return '%s(%r, %r)' % (self.__class__.__name__, self.start_lineno,
+            self.end_lineno)
+
+
+class CommentBlocker(object):
+    """ Pull out contiguous comment blocks.
+    """
+    def __init__(self):
+        # Start with a dummy.
+        self.current_block = NonComment(0, 0)
+
+        # All of the blocks seen so far.
+        self.blocks = []
+
+        # The index mapping lines of code to their associated comment blocks.
+        self.index = {}
+
+    def process_file(self, file):
+        """ Process a file object.
+        """
+        if sys.version_info[0] >= 3:
+            nxt = file.__next__
+        else:
+            nxt = file.next
+        for token in tokenize.generate_tokens(nxt):
+            self.process_token(*token)
+        self.make_index()
+
+    def process_token(self, kind, string, start, end, line):
+        """ Process a single token.
+        """
+        if self.current_block.is_comment:
+            if kind == tokenize.COMMENT:
+                self.current_block.add(string, start, end, line)
+            else:
+                self.new_noncomment(start[0], end[0])
+        else:
+            if kind == tokenize.COMMENT:
+                self.new_comment(string, start, end, line)
+            else:
+                self.current_block.add(string, start, end, line)
+
+    def new_noncomment(self, start_lineno, end_lineno):
+        """ We are transitioning from a noncomment to a comment.
+        """
+        block = NonComment(start_lineno, end_lineno)
+        self.blocks.append(block)
+        self.current_block = block
+
+    def new_comment(self, string, start, end, line):
+        """ Possibly add a new comment.
+
+        Only adds a new comment if this comment is the only thing on the line.
+        Otherwise, it extends the noncomment block.
+        """
+        prefix = line[:start[1]]
+        if prefix.strip():
+            # Oops! Trailing comment, not a comment block.
+            self.current_block.add(string, start, end, line)
+        else:
+            # A comment block.
+            block = Comment(start[0], end[0], string)
+            self.blocks.append(block)
+            self.current_block = block
+
+    def make_index(self):
+        """ Make the index mapping lines of actual code to their associated
+        prefix comments.
+        """
+        for prev, block in zip(self.blocks[:-1], self.blocks[1:]):
+            if not block.is_comment:
+                self.index[block.start_lineno] = prev
+
+    def search_for_comment(self, lineno, default=None):
+        """ Find the comment block just before the given line number.
+
+        Returns None (or the specified default) if there is no such block.
+        """
+        if not self.index:
+            self.make_index()
+        block = self.index.get(lineno, None)
+        text = getattr(block, 'text', default)
+        return text
+
+
+def strip_comment_marker(text):
+    """ Strip # markers at the front of a block of comment text.
+    """
+    lines = []
+    for line in text.splitlines():
+        lines.append(line.lstrip('#'))
+    text = textwrap.dedent('\n'.join(lines))
+    return text
+
+
+def get_class_traits(klass):
+    """ Yield all of the documentation for trait definitions on a class object.
+    """
+    # FIXME: gracefully handle errors here or in the caller?
+    source = inspect.getsource(klass)
+    cb = CommentBlocker()
+    cb.process_file(StringIO(source))
+    mod_ast = compiler.parse(source)
+    class_ast = mod_ast.node.nodes[0]
+    for node in class_ast.code.nodes:
+        # FIXME: handle other kinds of assignments?
+        if isinstance(node, compiler.ast.Assign):
+            name = node.nodes[0].name
+            rhs = unparse(node.expr).strip()
+            doc = strip_comment_marker(cb.search_for_comment(node.lineno, default=''))
+            yield name, rhs, doc
+