From 786cde6bdb4934e2afda3f4e8846553a21b2cd5a Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Tue, 23 Nov 2021 16:27:37 +0000
Subject: [PATCH 01/12] Remove the `traitlet-documenter` dependency, add
 `autodoc-traits`

---
 doc-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc-requirements.txt b/doc-requirements.txt
index 7e7c36ef..b3d8487e 100644
--- a/doc-requirements.txt
+++ b/doc-requirements.txt
@@ -3,4 +3,4 @@ sphinx==1.4.4
 # See https://github.com/sphinx-doc/sphinx/issues/9727
 docutils<0.18
 astor==0.8.1
-git+https://github.com/simphony/traitlet-documenter.git@v0.1.0#egg=traitlet_documenter
+autodoc-traits

From a207e7be1e9d3543f94d9bb4c249990fe3d404d4 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Tue, 23 Nov 2021 16:32:27 +0000
Subject: [PATCH 02/12] Update configuration of the Sphinx documentation

---
 doc/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/conf.py b/doc/source/conf.py
index a6f3d6c1..14617509 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -43,7 +43,7 @@
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
-    'traitlet_documenter',
+    'autodoc_traits',
     # patched autosummary for issue
     # https://github.com/sphinx-doc/sphinx/issues/1061
     '_extensions'

From 7f62b5815291855230c371f6faf0f7268f56cc2f Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 17:57:23 +0000
Subject: [PATCH 03/12] Fix missing runtime dependencies

---
 setup.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 91ab2672..98ef3582 100644
--- a/setup.py
+++ b/setup.py
@@ -59,7 +59,9 @@ def run(self):
         if not on_rtd:
             import subprocess
             subprocess.check_call(['npm', 'run', 'build'])
-        super().run()
+        # Workaround for setuptools ignoring `install_requires` when `cmdclass` is overridden
+        # See https://stackoverflow.com/q/21915469
+        super().do_egg_install()
 
 
 # main setup configuration class

From 2398f3e6772e0eeee56ce0bd9cd1425aaa9e46e6 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 17:58:23 +0000
Subject: [PATCH 04/12] Remove Sphinx version constraint to resolve issue

---
 doc-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc-requirements.txt b/doc-requirements.txt
index b3d8487e..30f66043 100644
--- a/doc-requirements.txt
+++ b/doc-requirements.txt
@@ -1,4 +1,4 @@
-sphinx==1.4.4
+sphinx
 # docutils version 0.18 is known to cause issues with Sphinx
 # See https://github.com/sphinx-doc/sphinx/issues/9727
 docutils<0.18

From d4d4d2a7812ef147da3094ebf35a71c238bdb2d9 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 17:59:01 +0000
Subject: [PATCH 05/12] Resolve Sphinx and docutils issues

---
 doc/source/_extensions/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
index 98cedd8d..ea0ea946 100644
--- a/doc/source/_extensions/__init__.py
+++ b/doc/source/_extensions/__init__.py
@@ -61,13 +61,12 @@
 from types import ModuleType
 
 from six import text_type
-from docutils.parsers.rst import directives
+from docutils.parsers.rst import Directive, directives
 from docutils.statemachine import ViewList
 from docutils import nodes
 
 import sphinx
 from sphinx import addnodes
-from sphinx.util.compat import Directive
 from sphinx.pycode import ModuleAnalyzer, PycodeError
 from sphinx.ext.autodoc import Options
 
@@ -555,7 +554,7 @@ def process_generate_options(app):
 
     from .generate import generate_autosummary_docs
 
-    ext = app.config.source_suffix[0]
+    ext = list(app.config.source_suffix)[0]
     genfiles = [genfile + (not genfile.endswith(ext) and ext or '')
                 for genfile in genfiles]
 

From e66a1fa68ba161978fa077dc0ba9f82f191fc3f0 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 18:20:13 +0000
Subject: [PATCH 06/12] Fix flake8 issue

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 98ef3582..20bfed62 100644
--- a/setup.py
+++ b/setup.py
@@ -59,8 +59,8 @@ def run(self):
         if not on_rtd:
             import subprocess
             subprocess.check_call(['npm', 'run', 'build'])
-        # Workaround for setuptools ignoring `install_requires` when `cmdclass` is overridden
-        # See https://stackoverflow.com/q/21915469
+        # Workaround for setuptools ignoring `install_requires` when
+        # `cmdclass` is overridden. See https://stackoverflow.com/q/21915469
         super().do_egg_install()
 
 

From 99cd76f4c44e35ab6612f8f8f96b5634cd1ec7e9 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 18:33:38 +0000
Subject: [PATCH 07/12] Fix `autodoc_member_order` in Sphinx config

---
 doc/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/conf.py b/doc/source/conf.py
index 14617509..f4153e9c 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -455,7 +455,7 @@
 del _config
 
 
-autodoc_member_order = 'source'
+autodoc_member_order = 'bysource'
 autoclass_content = 'both'
 autodoc_default_flags = [
     'show-inheritance', 'members', 'undoc-members']

From 49e06a15d383f3401b1cf1bc0d9bd44bc5317f0b Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 26 Nov 2021 19:30:04 +0000
Subject: [PATCH 08/12] Use app.add_autodocumenter to resolve Sphinx failure

---
 doc/source/_extensions/__init__.py | 15 ++++++++++++++-
 doc/source/_extensions/generate.py | 14 --------------
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
index ea0ea946..5b76b929 100644
--- a/doc/source/_extensions/__init__.py
+++ b/doc/source/_extensions/__init__.py
@@ -68,7 +68,10 @@
 import sphinx
 from sphinx import addnodes
 from sphinx.pycode import ModuleAnalyzer, PycodeError
-from sphinx.ext.autodoc import Options
+from sphinx.ext.autodoc import Options, \
+    ModuleDocumenter, ClassDocumenter, ExceptionDocumenter, DataDocumenter, \
+    FunctionDocumenter, MethodDocumenter, AttributeDocumenter, \
+    InstanceAttributeDocumenter
 
 
 # -- autosummary_toc node ------------------------------------------------------
@@ -554,6 +557,16 @@ def process_generate_options(app):
 
     from .generate import generate_autosummary_docs
 
+    # Add documenters to AutoDirective registry
+    app.add_autodocumenter(ModuleDocumenter)
+    app.add_autodocumenter(ClassDocumenter)
+    app.add_autodocumenter(ExceptionDocumenter)
+    app.add_autodocumenter(DataDocumenter)
+    app.add_autodocumenter(FunctionDocumenter)
+    app.add_autodocumenter(MethodDocumenter)
+    app.add_autodocumenter(AttributeDocumenter)
+    app.add_autodocumenter(InstanceAttributeDocumenter)
+
     ext = list(app.config.source_suffix)[0]
     genfiles = [genfile + (not genfile.endswith(ext) and ext or '')
                 for genfile in genfiles]
diff --git a/doc/source/_extensions/generate.py b/doc/source/_extensions/generate.py
index ba511f0a..f1e596aa 100644
--- a/doc/source/_extensions/generate.py
+++ b/doc/source/_extensions/generate.py
@@ -35,20 +35,6 @@
 from sphinx.util.osutil import ensuredir
 from sphinx.util.inspect import safe_getattr
 
-# Add documenters to AutoDirective registry
-from sphinx.ext.autodoc import add_documenter, \
-    ModuleDocumenter, ClassDocumenter, ExceptionDocumenter, DataDocumenter, \
-    FunctionDocumenter, MethodDocumenter, AttributeDocumenter, \
-    InstanceAttributeDocumenter
-add_documenter(ModuleDocumenter)
-add_documenter(ClassDocumenter)
-add_documenter(ExceptionDocumenter)
-add_documenter(DataDocumenter)
-add_documenter(FunctionDocumenter)
-add_documenter(MethodDocumenter)
-add_documenter(AttributeDocumenter)
-add_documenter(InstanceAttributeDocumenter)
-
 
 def main(argv=sys.argv):
     usage = """%prog [OPTIONS] SOURCEFILE ..."""

From 4fd167bc7eebd98852f90894b97c1f59d438a559 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 3 Dec 2021 16:54:52 +0000
Subject: [PATCH 09/12] Remove duplicate documenter classes

---
 doc/source/_extensions/__init__.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
index 5b76b929..8740a929 100644
--- a/doc/source/_extensions/__init__.py
+++ b/doc/source/_extensions/__init__.py
@@ -558,13 +558,6 @@ def process_generate_options(app):
     from .generate import generate_autosummary_docs
 
     # Add documenters to AutoDirective registry
-    app.add_autodocumenter(ModuleDocumenter)
-    app.add_autodocumenter(ClassDocumenter)
-    app.add_autodocumenter(ExceptionDocumenter)
-    app.add_autodocumenter(DataDocumenter)
-    app.add_autodocumenter(FunctionDocumenter)
-    app.add_autodocumenter(MethodDocumenter)
-    app.add_autodocumenter(AttributeDocumenter)
     app.add_autodocumenter(InstanceAttributeDocumenter)
 
     ext = list(app.config.source_suffix)[0]

From 9c64a75ffeaaf473b1c8f4dae9777e00a2bac492 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Fri, 3 Dec 2021 17:08:50 +0000
Subject: [PATCH 10/12] Remove deprecated methods

---
 doc/source/_extensions/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
index 8740a929..43b2a8dc 100644
--- a/doc/source/_extensions/__init__.py
+++ b/doc/source/_extensions/__init__.py
@@ -565,8 +565,7 @@ def process_generate_options(app):
                 for genfile in genfiles]
 
     generate_autosummary_docs(genfiles, builder=app.builder,
-                              warn=app.warn, info=app.info, suffix=ext,
-                              base_path=app.srcdir)
+                              suffix=ext, base_path=app.srcdir)
 
 
 def setup(app):

From 193eda3a749ed7a04b095b81703e069137fb43d3 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Wed, 15 Dec 2021 19:26:14 +0000
Subject: [PATCH 11/12] Clean up imports

---
 doc/source/_extensions/__init__.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
index 43b2a8dc..6999da10 100644
--- a/doc/source/_extensions/__init__.py
+++ b/doc/source/_extensions/__init__.py
@@ -68,10 +68,7 @@
 import sphinx
 from sphinx import addnodes
 from sphinx.pycode import ModuleAnalyzer, PycodeError
-from sphinx.ext.autodoc import Options, \
-    ModuleDocumenter, ClassDocumenter, ExceptionDocumenter, DataDocumenter, \
-    FunctionDocumenter, MethodDocumenter, AttributeDocumenter, \
-    InstanceAttributeDocumenter
+from sphinx.ext.autodoc import Options, InstanceAttributeDocumenter
 
 
 # -- autosummary_toc node ------------------------------------------------------

From 991d4abe6760f58fd1ae76f249916612dc311707 Mon Sep 17 00:00:00 2001
From: Peter Zahemszky <63169891+peterzahemszky@users.noreply.github.com>
Date: Wed, 15 Dec 2021 23:24:21 +0000
Subject: [PATCH 12/12] Remove redundant code

---
 doc/source/_extensions/__init__.py | 588 -----------------------------
 doc/source/_extensions/generate.py | 334 ----------------
 doc/source/conf.py                 |   5 +-
 3 files changed, 1 insertion(+), 926 deletions(-)
 delete mode 100644 doc/source/_extensions/__init__.py
 delete mode 100644 doc/source/_extensions/generate.py

diff --git a/doc/source/_extensions/__init__.py b/doc/source/_extensions/__init__.py
deleted file mode 100644
index 6999da10..00000000
--- a/doc/source/_extensions/__init__.py
+++ /dev/null
@@ -1,588 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-    sphinx.ext.autosummary
-    ~~~~~~~~~~~~~~~~~~~~~~
-
-    Sphinx extension that adds an autosummary:: directive, which can be
-    used to generate function/method/attribute/etc. summary lists, similar
-    to those output eg. by Epydoc and other API doc generation tools.
-
-    An :autolink: role is also provided.
-
-    autosummary directive
-    ---------------------
-
-    The autosummary directive has the form::
-
-        .. autosummary::
-           :nosignatures:
-           :toctree: generated/
-
-           module.function_1
-           module.function_2
-           ...
-
-    and it generates an output table (containing signatures, optionally)
-
-        ========================  =============================================
-        module.function_1(args)   Summary line from the docstring of function_1
-        module.function_2(args)   Summary line from the docstring
-        ...
-        ========================  =============================================
-
-    If the :toctree: option is specified, files matching the function names
-    are inserted to the toctree with the given prefix:
-
-        generated/module.function_1
-        generated/module.function_2
-        ...
-
-    Note: The file names contain the module:: or currentmodule:: prefixes.
-
-    .. seealso:: autosummary_generate.py
-
-
-    autolink role
-    -------------
-
-    The autolink role functions as ``:obj:`` when the name referred can be
-    resolved to a Python object, and otherwise it becomes simple emphasis.
-    This can be used as the default role to make links 'smart'.
-
-    :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-"""
-
-import os
-import re
-import sys
-import inspect
-import posixpath
-from types import ModuleType
-
-from six import text_type
-from docutils.parsers.rst import Directive, directives
-from docutils.statemachine import ViewList
-from docutils import nodes
-
-import sphinx
-from sphinx import addnodes
-from sphinx.pycode import ModuleAnalyzer, PycodeError
-from sphinx.ext.autodoc import Options, InstanceAttributeDocumenter
-
-
-# -- autosummary_toc node ------------------------------------------------------
-
-class autosummary_toc(nodes.comment):
-    pass
-
-
-def process_autosummary_toc(app, doctree):
-    """Insert items described in autosummary:: to the TOC tree, but do
-    not generate the toctree:: list.
-    """
-    env = app.builder.env
-    crawled = {}
-
-    def crawl_toc(node, depth=1):
-        crawled[node] = True
-        for j, subnode in enumerate(node):
-            try:
-                if (isinstance(subnode, autosummary_toc) and
-                        isinstance(subnode[0], addnodes.toctree)):
-                    env.note_toctree(env.docname, subnode[0])
-                    continue
-            except IndexError:
-                continue
-            if not isinstance(subnode, nodes.section):
-                continue
-            if subnode not in crawled:
-                crawl_toc(subnode, depth+1)
-    crawl_toc(doctree)
-
-
-def autosummary_toc_visit_html(self, node):
-    """Hide autosummary toctree list in HTML output."""
-    raise nodes.SkipNode
-
-
-def autosummary_noop(self, node):
-    pass
-
-
-# -- autosummary_table node ----------------------------------------------------
-
-class autosummary_table(nodes.comment):
-    pass
-
-
-def autosummary_table_visit_html(self, node):
-    """Make the first column of the table non-breaking."""
-    try:
-        tbody = node[0][0][-1]
-        for row in tbody:
-            col1_entry = row[0]
-            par = col1_entry[0]
-            for j, subnode in enumerate(list(par)):
-                if isinstance(subnode, nodes.Text):
-                    new_text = text_type(subnode.astext())
-                    new_text = new_text.replace(u" ", u"\u00a0")
-                    par[j] = nodes.Text(new_text)
-    except IndexError:
-        pass
-
-
-# -- autodoc integration -------------------------------------------------------
-
-class FakeDirective:
-    env = {}
-    genopt = Options()
-
-
-def get_documenter(obj, parent):
-    """Get an autodoc.Documenter class suitable for documenting the given
-    object.
-
-    *obj* is the Python object to be documented, and *parent* is an
-    another Python object (e.g. a module or a class) to which *obj*
-    belongs to.
-    """
-    from sphinx.ext.autodoc import AutoDirective, DataDocumenter, \
-        ModuleDocumenter
-
-    if inspect.ismodule(obj):
-        # ModuleDocumenter.can_document_member always returns False
-        return ModuleDocumenter
-
-    # Construct a fake documenter for *parent*
-    if parent is not None:
-        parent_doc_cls = get_documenter(parent, None)
-    else:
-        parent_doc_cls = ModuleDocumenter
-
-    if hasattr(parent, '__name__'):
-        parent_doc = parent_doc_cls(FakeDirective(), parent.__name__)
-    else:
-        parent_doc = parent_doc_cls(FakeDirective(), "")
-
-    # Get the corrent documenter class for *obj*
-    classes = [cls for cls in AutoDirective._registry.values()
-               if cls.can_document_member(obj, '', False, parent_doc)]
-    if classes:
-        classes.sort(key=lambda cls: cls.priority)
-        return classes[-1]
-    else:
-        return DataDocumenter
-
-
-# -- .. autosummary:: ----------------------------------------------------------
-
-class Autosummary(Directive):
-    """
-    Pretty table containing short signatures and summaries of functions etc.
-
-    autosummary can also optionally generate a hidden toctree:: node.
-    """
-
-    required_arguments = 0
-    optional_arguments = 0
-    final_argument_whitespace = False
-    has_content = True
-    option_spec = {
-        'toctree': directives.unchanged,
-        'nosignatures': directives.flag,
-        'template': directives.unchanged,
-    }
-
-    def warn(self, msg):
-        self.warnings.append(self.state.document.reporter.warning(
-            msg, line=self.lineno))
-
-    def run(self):
-        self.env = env = self.state.document.settings.env
-        self.genopt = Options()
-        self.warnings = []
-        self.result = ViewList()
-
-        names = [x.strip().split()[0] for x in self.content
-                 if x.strip() and re.search(r'^[~a-zA-Z_]', x.strip()[0])]
-        items = self.get_items(names)
-        nodes = self.get_table(items)
-
-        if 'toctree' in self.options:
-            dirname = posixpath.dirname(env.docname)
-
-            tree_prefix = self.options['toctree'].strip()
-            docnames = []
-            for name, sig, summary, real_name in items:
-                docname = posixpath.join(tree_prefix, real_name)
-                docname = posixpath.normpath(posixpath.join(dirname, docname))
-                if docname not in env.found_docs:
-                    self.warn('toctree references unknown document %r'
-                              % docname)
-                docnames.append(docname)
-
-            tocnode = addnodes.toctree()
-            tocnode['includefiles'] = docnames
-            tocnode['entries'] = [(None, docn) for docn in docnames]
-            tocnode['maxdepth'] = -1
-            tocnode['glob'] = None
-
-            tocnode = autosummary_toc('', '', tocnode)
-            nodes.append(tocnode)
-
-        return self.warnings + nodes
-
-    def get_items(self, names):
-        """Try to import the given names, and return a list of
-        ``[(name, signature, summary_string, real_name), ...]``.
-        """
-        env = self.state.document.settings.env
-
-        prefixes = get_import_prefixes_from_env(env)
-
-        items = []
-
-        max_item_chars = 50
-
-        for name in names:
-            display_name = name
-            if name.startswith('~'):
-                name = name[1:]
-                display_name = name.split('.')[-1]
-
-            try:
-                real_name, obj, parent, modname = import_by_name(name, prefixes=prefixes)
-            except ImportError:
-                self.warn('failed to import %s' % name)
-                items.append((name, '', '', name))
-                continue
-
-            self.result = ViewList()  # initialize for each documenter
-            full_name = real_name
-            if not isinstance(obj, ModuleType):
-                # give explicitly separated module name, so that members
-                # of inner classes can be documented
-                full_name = modname + '::' + full_name[len(modname)+1:]
-            # NB. using full_name here is important, since Documenters
-            #     handle module prefixes slightly differently
-            documenter = get_documenter(obj, parent)(self, full_name)
-            if not documenter.parse_name():
-                self.warn('failed to parse name %s' % real_name)
-                items.append((display_name, '', '', real_name))
-                continue
-            if not documenter.import_object():
-                self.warn('failed to import object %s' % real_name)
-                items.append((display_name, '', '', real_name))
-                continue
-            if documenter.options.members and not documenter.check_module():
-                continue
-
-            # try to also get a source code analyzer for attribute docs
-            try:
-                documenter.analyzer = ModuleAnalyzer.for_module(
-                    documenter.get_real_modname())
-                # parse right now, to get PycodeErrors on parsing (results will
-                # be cached anyway)
-                documenter.analyzer.find_attr_docs()
-            except PycodeError as err:
-                documenter.env.app.debug(
-                    '[autodoc] module analyzer failed: %s', err)
-                # no source file -- e.g. for builtin and C modules
-                documenter.analyzer = None
-
-            # -- Grab the signature
-
-            sig = documenter.format_signature()
-            if not sig:
-                sig = ''
-            else:
-                max_chars = max(10, max_item_chars - len(display_name))
-                sig = mangle_signature(sig, max_chars=max_chars)
-                sig = sig.replace('*', r'\*')
-
-            # -- Grab the summary
-
-            documenter.add_content(None)
-            doc = list(documenter.process_doc([self.result.data]))
-
-            while doc and not doc[0].strip():
-                doc.pop(0)
-
-            # If there's a blank line, then we can assume the first sentence /
-            # paragraph has ended, so anything after shouldn't be part of the
-            # summary
-            for i, piece in enumerate(doc):
-                if not piece.strip():
-                    doc = doc[:i]
-                    break
-
-            # Try to find the "first sentence", which may span multiple lines
-            m = re.search(r"^([A-Z].*?\.)(?:\s|$)", " ".join(doc).strip())
-            if m:
-                summary = m.group(1).strip()
-            elif doc:
-                summary = doc[0].strip()
-            else:
-                summary = ''
-
-            items.append((display_name, sig, summary, real_name))
-
-        return items
-
-    def get_table(self, items):
-        """Generate a proper list of table nodes for autosummary:: directive.
-
-        *items* is a list produced by :meth:`get_items`.
-        """
-        table_spec = addnodes.tabular_col_spec()
-        table_spec['spec'] = 'p{0.5\linewidth}p{0.5\linewidth}'
-
-        table = autosummary_table('')
-        real_table = nodes.table('', classes=['longtable'])
-        table.append(real_table)
-        group = nodes.tgroup('', cols=2)
-        real_table.append(group)
-        group.append(nodes.colspec('', colwidth=10))
-        group.append(nodes.colspec('', colwidth=90))
-        body = nodes.tbody('')
-        group.append(body)
-
-        def append_row(*column_texts):
-            row = nodes.row('')
-            for text in column_texts:
-                node = nodes.paragraph('')
-                vl = ViewList()
-                vl.append(text, '<autosummary>')
-                self.state.nested_parse(vl, 0, node)
-                try:
-                    if isinstance(node[0], nodes.paragraph):
-                        node = node[0]
-                except IndexError:
-                    pass
-                row.append(nodes.entry('', node))
-            body.append(row)
-
-        for name, sig, summary, real_name in items:
-            qualifier = 'obj'
-            if 'nosignatures' not in self.options:
-                col1 = ':%s:`%s <%s>`\ %s' % (qualifier, name, real_name, sig)
-            else:
-                col1 = ':%s:`%s <%s>`' % (qualifier, name, real_name)
-            col2 = summary
-            append_row(col1, col2)
-
-        return [table_spec, table]
-
-
-def mangle_signature(sig, max_chars=30):
-    """Reformat a function signature to a more compact form."""
-    s = re.sub(r"^\((.*)\)$", r"\1", sig).strip()
-
-    # Strip strings (which can contain things that confuse the code below)
-    s = re.sub(r"\\\\", "", s)
-    s = re.sub(r"\\'", "", s)
-    s = re.sub(r"'[^']*'", "", s)
-
-    # Parse the signature to arguments + options
-    args = []
-    opts = []
-
-    opt_re = re.compile(r"^(.*, |)([a-zA-Z0-9_*]+)=")
-    while s:
-        m = opt_re.search(s)
-        if not m:
-            # The rest are arguments
-            args = s.split(', ')
-            break
-
-        opts.insert(0, m.group(2))
-        s = m.group(1)[:-2]
-
-    # Produce a more compact signature
-    sig = limited_join(", ", args, max_chars=max_chars-2)
-    if opts:
-        if not sig:
-            sig = "[%s]" % limited_join(", ", opts, max_chars=max_chars-4)
-        elif len(sig) < max_chars - 4 - 2 - 3:
-            sig += "[, %s]" % limited_join(", ", opts,
-                                           max_chars=max_chars-len(sig)-4-2)
-
-    return u"(%s)" % sig
-
-
-def limited_join(sep, items, max_chars=30, overflow_marker="..."):
-    """Join a number of strings to one, limiting the length to *max_chars*.
-
-    If the string overflows this limit, replace the last fitting item by
-    *overflow_marker*.
-
-    Returns: joined_string
-    """
-    full_str = sep.join(items)
-    if len(full_str) < max_chars:
-        return full_str
-
-    n_chars = 0
-    n_items = 0
-    for j, item in enumerate(items):
-        n_chars += len(item) + len(sep)
-        if n_chars < max_chars - len(overflow_marker):
-            n_items += 1
-        else:
-            break
-
-    return sep.join(list(items[:n_items]) + [overflow_marker])
-
-
-# -- Importing items -----------------------------------------------------------
-
-def get_import_prefixes_from_env(env):
-    """
-    Obtain current Python import prefixes (for `import_by_name`)
-    from ``document.env``
-    """
-    prefixes = [None]
-
-    currmodule = env.ref_context.get('py:module')
-    if currmodule:
-        prefixes.insert(0, currmodule)
-
-    currclass = env.ref_context.get('py:class')
-    if currclass:
-        if currmodule:
-            prefixes.insert(0, currmodule + "." + currclass)
-        else:
-            prefixes.insert(0, currclass)
-
-    return prefixes
-
-
-def import_by_name(name, prefixes=[None]):
-    """Import a Python object that has the given *name*, under one of the
-    *prefixes*.  The first name that succeeds is used.
-    """
-    tried = []
-    for prefix in prefixes:
-        try:
-            if prefix:
-                prefixed_name = '.'.join([prefix, name])
-            else:
-                prefixed_name = name
-            obj, parent, modname = _import_by_name(prefixed_name)
-            return prefixed_name, obj, parent, modname
-        except ImportError:
-            tried.append(prefixed_name)
-    raise ImportError('no module named %s' % ' or '.join(tried))
-
-
-def _import_by_name(name):
-    """Import a Python object given its full name."""
-    try:
-        name_parts = name.split('.')
-
-        # try first interpret `name` as MODNAME.OBJ
-        modname = '.'.join(name_parts[:-1])
-        if modname:
-            try:
-                __import__(modname)
-                mod = sys.modules[modname]
-                return getattr(mod, name_parts[-1]), mod, modname
-            except (ImportError, IndexError, AttributeError):
-                pass
-
-        # ... then as MODNAME, MODNAME.OBJ1, MODNAME.OBJ1.OBJ2, ...
-        last_j = 0
-        modname = None
-        for j in reversed(range(1, len(name_parts)+1)):
-            last_j = j
-            modname = '.'.join(name_parts[:j])
-            try:
-                __import__(modname)
-            except ImportError:
-                continue
-            if modname in sys.modules:
-                break
-
-        if last_j < len(name_parts):
-            parent = None
-            obj = sys.modules[modname]
-            for obj_name in name_parts[last_j:]:
-                parent = obj
-                obj = getattr(obj, obj_name)
-            return obj, parent, modname
-        else:
-            return sys.modules[modname], None, modname
-    except (ValueError, ImportError, AttributeError, KeyError) as e:
-        raise ImportError(*e.args)
-
-
-# -- :autolink: (smart default role) -------------------------------------------
-
-def autolink_role(typ, rawtext, etext, lineno, inliner,
-                  options={}, content=[]):
-    """Smart linking role.
-
-    Expands to ':obj:`text`' if `text` is an object that can be imported;
-    otherwise expands to '*text*'.
-    """
-    env = inliner.document.settings.env
-    r = env.get_domain('py').role('obj')(
-        'obj', rawtext, etext, lineno, inliner, options, content)
-    pnode = r[0][0]
-
-    prefixes = get_import_prefixes_from_env(env)
-    try:
-        name, obj, parent, modname = import_by_name(pnode['reftarget'], prefixes)
-    except ImportError:
-        content = pnode[0]
-        r[0][0] = nodes.emphasis(rawtext, content[0].astext(),
-                                 classes=content['classes'])
-    return r
-
-
-def process_generate_options(app):
-    genfiles = app.config.autosummary_generate
-
-    if genfiles and not hasattr(genfiles, '__len__'):
-        env = app.builder.env
-        genfiles = [env.doc2path(x, base=None) for x in env.found_docs
-                    if os.path.isfile(env.doc2path(x))]
-
-    if not genfiles:
-        return
-
-    from .generate import generate_autosummary_docs
-
-    # Add documenters to AutoDirective registry
-    app.add_autodocumenter(InstanceAttributeDocumenter)
-
-    ext = list(app.config.source_suffix)[0]
-    genfiles = [genfile + (not genfile.endswith(ext) and ext or '')
-                for genfile in genfiles]
-
-    generate_autosummary_docs(genfiles, builder=app.builder,
-                              suffix=ext, base_path=app.srcdir)
-
-
-def setup(app):
-    # I need autodoc
-    app.setup_extension('sphinx.ext.autodoc')
-    app.add_node(autosummary_toc,
-                 html=(autosummary_toc_visit_html, autosummary_noop),
-                 latex=(autosummary_noop, autosummary_noop),
-                 text=(autosummary_noop, autosummary_noop),
-                 man=(autosummary_noop, autosummary_noop),
-                 texinfo=(autosummary_noop, autosummary_noop))
-    app.add_node(autosummary_table,
-                 html=(autosummary_table_visit_html, autosummary_noop),
-                 latex=(autosummary_noop, autosummary_noop),
-                 text=(autosummary_noop, autosummary_noop),
-                 man=(autosummary_noop, autosummary_noop),
-                 texinfo=(autosummary_noop, autosummary_noop))
-    app.add_directive('autosummary', Autosummary)
-    app.add_role('autolink', autolink_role)
-    app.connect('doctree-read', process_autosummary_toc)
-    app.connect('builder-inited', process_generate_options)
-    app.add_config_value('autosummary_generate', [], True, [bool])
-    return {'version': sphinx.__display_version__, 'parallel_read_safe': True}
diff --git a/doc/source/_extensions/generate.py b/doc/source/_extensions/generate.py
deleted file mode 100644
index f1e596aa..00000000
--- a/doc/source/_extensions/generate.py
+++ /dev/null
@@ -1,334 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-    sphinx.ext.autosummary.generate
-    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-    Usable as a library or script to generate automatic RST source files for
-    items referred to in autosummary:: directives.
-
-    Each generated RST file contains a single auto*:: directive which
-    extracts the docstring of the referred item.
-
-    Example Makefile rule::
-
-       generate:
-               sphinx-autogen -o source/generated source/*.rst
-
-    :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-"""
-from __future__ import print_function
-
-import os
-import re
-import sys
-import pydoc
-import optparse
-import codecs
-
-from jinja2 import FileSystemLoader, TemplateNotFound
-from jinja2.sandbox import SandboxedEnvironment
-
-from sphinx import package_dir
-from . import import_by_name, get_documenter
-from sphinx.jinja2glue import BuiltinTemplateLoader
-from sphinx.util.osutil import ensuredir
-from sphinx.util.inspect import safe_getattr
-
-
-def main(argv=sys.argv):
-    usage = """%prog [OPTIONS] SOURCEFILE ..."""
-    p = optparse.OptionParser(usage.strip())
-    p.add_option("-o", "--output-dir", action="store", type="string",
-                 dest="output_dir", default=None,
-                 help="Directory to place all output in")
-    p.add_option("-s", "--suffix", action="store", type="string",
-                 dest="suffix", default="rst",
-                 help="Default suffix for files (default: %default)")
-    p.add_option("-t", "--templates", action="store", type="string",
-                 dest="templates", default=None,
-                 help="Custom template directory (default: %default)")
-    options, args = p.parse_args(argv[1:])
-
-    if len(args) < 1:
-        p.error('no input files given')
-
-    generate_autosummary_docs(args, options.output_dir,
-                              "." + options.suffix,
-                              template_dir=options.templates)
-
-
-def _simple_info(msg):
-    print(msg)
-
-
-def _simple_warn(msg):
-    print('WARNING: ' + msg, file=sys.stderr)
-
-
-# -- Generating output ---------------------------------------------------------
-
-def generate_autosummary_docs(sources, output_dir=None, suffix='.rst',
-                              warn=_simple_warn, info=_simple_info,
-                              base_path=None, builder=None, template_dir=None):
-
-    showed_sources = list(sorted(sources))
-    if len(showed_sources) > 20:
-        showed_sources = showed_sources[:10] + ['...'] + showed_sources[-10:]
-    info('[autosummary] generating autosummary for: %s' %
-         ', '.join(showed_sources))
-
-    if output_dir:
-        info('[autosummary] writing to %s' % output_dir)
-
-    if base_path is not None:
-        sources = [os.path.join(base_path, filename) for filename in sources]
-
-    # create our own templating environment
-    template_dirs = [os.path.join(package_dir, 'ext',
-                                  'autosummary', 'templates')]
-    if builder is not None:
-        # allow the user to override the templates
-        template_loader = BuiltinTemplateLoader()
-        template_loader.init(builder, dirs=template_dirs)
-    else:
-        if template_dir:
-            template_dirs.insert(0, template_dir)
-        template_loader = FileSystemLoader(template_dirs)
-    template_env = SandboxedEnvironment(loader=template_loader)
-
-    # read
-    items = find_autosummary_in_files(sources)
-
-    # keep track of new files
-    new_files = []
-
-    # write
-    for name, path, template_name in sorted(set(items), key=str):
-        if path is None:
-            # The corresponding autosummary:: directive did not have
-            # a :toctree: option
-            continue
-
-        path = output_dir or os.path.abspath(path)
-        ensuredir(path)
-
-        try:
-            name, obj, parent, mod_name = import_by_name(name)
-        except ImportError as e:
-            warn('[autosummary] failed to import %r: %s' % (name, e))
-            continue
-
-        fn = os.path.join(path, name + suffix)
-
-        # skip it if it exists
-        if os.path.isfile(fn):
-            continue
-
-        new_files.append(fn)
-
-        with open(fn, 'w') as f:
-            doc = get_documenter(obj, parent)
-
-            if template_name is not None:
-                template = template_env.get_template(template_name)
-            else:
-                try:
-                    template = template_env.get_template('autosummary/%s.rst'
-                                                         % doc.objtype)
-                except TemplateNotFound:
-                    template = template_env.get_template('autosummary/base.rst')
-
-            # Patched get_members according to
-            # http://stackoverflow.com/questions/25405110/sphinx-autosummary-with-toctree-also-lists-imported-members/25460763#25460763
-            def get_members(obj, typ, include_public=[], imported=False):
-                items = []
-                for name in dir(obj):
-                    try:
-                        obj_name = safe_getattr(obj, name)
-                        documenter = get_documenter(obj_name, obj)
-                    except AttributeError:
-                        continue
-                    if documenter.objtype == typ:
-                        try:
-                            cond = (
-                                imported or
-                                obj_name.__module__ == obj.__name__
-                                )
-                        except AttributeError:
-                            cond = True
-                        if cond:
-                            items.append(name)
-                public = [x for x in items
-                          if x in include_public or not x.startswith('_')]
-                return public, items
-
-            ns = {}
-
-            if doc.objtype == 'module':
-                ns['members'] = dir(obj)
-                ns['functions'], ns['all_functions'] = \
-                    get_members(obj, 'function')
-                ns['classes'], ns['all_classes'] = \
-                    get_members(obj, 'class')
-                ns['exceptions'], ns['all_exceptions'] = \
-                    get_members(obj, 'exception')
-            elif doc.objtype == 'class':
-                ns['members'] = dir(obj)
-                ns['methods'], ns['all_methods'] = \
-                    get_members(obj, 'method', ['__init__'])
-                ns['attributes'], ns['all_attributes'] = \
-                    get_members(obj, 'attribute')
-
-            parts = name.split('.')
-            if doc.objtype in ('method', 'attribute'):
-                mod_name = '.'.join(parts[:-2])
-                cls_name = parts[-2]
-                obj_name = '.'.join(parts[-2:])
-                ns['class'] = cls_name
-            else:
-                mod_name, obj_name = '.'.join(parts[:-1]), parts[-1]
-
-            ns['fullname'] = name
-            ns['module'] = mod_name
-            ns['objname'] = obj_name
-            ns['name'] = parts[-1]
-
-            ns['objtype'] = doc.objtype
-            ns['underline'] = len(name) * '='
-
-            rendered = template.render(**ns)
-            f.write(rendered)
-
-    # descend recursively to new files
-    if new_files:
-        generate_autosummary_docs(new_files, output_dir=output_dir,
-                                  suffix=suffix, warn=warn, info=info,
-                                  base_path=base_path, builder=builder,
-                                  template_dir=template_dir)
-
-
-# -- Finding documented entries in files ---------------------------------------
-
-def find_autosummary_in_files(filenames):
-    """Find out what items are documented in source/*.rst.
-
-    See `find_autosummary_in_lines`.
-    """
-    documented = []
-    for filename in filenames:
-        with codecs.open(filename, 'r', encoding='utf-8',
-                         errors='ignore') as f:
-            lines = f.read().splitlines()
-            documented.extend(find_autosummary_in_lines(lines,
-                                                        filename=filename))
-    return documented
-
-
-def find_autosummary_in_docstring(name, module=None, filename=None):
-    """Find out what items are documented in the given object's docstring.
-
-    See `find_autosummary_in_lines`.
-    """
-    try:
-        real_name, obj, parent, modname = import_by_name(name)
-        lines = pydoc.getdoc(obj).splitlines()
-        return find_autosummary_in_lines(lines, module=name, filename=filename)
-    except AttributeError:
-        pass
-    except ImportError as e:
-        print("Failed to import '%s': %s" % (name, e))
-    except SystemExit as e:
-        print("Failed to import '%s'; the module executes module level "
-              "statement and it might call sys.exit()." % name)
-    return []
-
-
-def find_autosummary_in_lines(lines, module=None, filename=None):
-    """Find out what items appear in autosummary:: directives in the
-    given lines.
-
-    Returns a list of (name, toctree, template) where *name* is a name
-    of an object and *toctree* the :toctree: path of the corresponding
-    autosummary directive (relative to the root of the file name), and
-    *template* the value of the :template: option. *toctree* and
-    *template* ``None`` if the directive does not have the
-    corresponding options set.
-    """
-    autosummary_re = re.compile(r'^(\s*)\.\.\s+autosummary::\s*')
-    automodule_re = re.compile(
-        r'^\s*\.\.\s+automodule::\s*([A-Za-z0-9_.]+)\s*$')
-    module_re = re.compile(
-        r'^\s*\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
-    autosummary_item_re = re.compile(r'^\s+(~?[_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')
-    toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
-    template_arg_re = re.compile(r'^\s+:template:\s*(.*?)\s*$')
-
-    documented = []
-
-    toctree = None
-    template = None
-    current_module = module
-    in_autosummary = False
-    base_indent = ""
-
-    for line in lines:
-        if in_autosummary:
-            m = toctree_arg_re.match(line)
-            if m:
-                toctree = m.group(1)
-                if filename:
-                    toctree = os.path.join(os.path.dirname(filename),
-                                           toctree)
-                continue
-
-            m = template_arg_re.match(line)
-            if m:
-                template = m.group(1).strip()
-                continue
-
-            if line.strip().startswith(':'):
-                continue  # skip options
-
-            m = autosummary_item_re.match(line)
-            if m:
-                name = m.group(1).strip()
-                if name.startswith('~'):
-                    name = name[1:]
-                if current_module and \
-                   not name.startswith(current_module + '.'):
-                    name = "%s.%s" % (current_module, name)
-                documented.append((name, toctree, template))
-                continue
-
-            if not line.strip() or line.startswith(base_indent + " "):
-                continue
-
-            in_autosummary = False
-
-        m = autosummary_re.match(line)
-        if m:
-            in_autosummary = True
-            base_indent = m.group(1)
-            toctree = None
-            template = None
-            continue
-
-        m = automodule_re.search(line)
-        if m:
-            current_module = m.group(1).strip()
-            # recurse into the automodule docstring
-            documented.extend(find_autosummary_in_docstring(
-                current_module, filename=filename))
-            continue
-
-        m = module_re.match(line)
-        if m:
-            current_module = m.group(2)
-            continue
-
-    return documented
-
-
-if __name__ == '__main__':
-    main()
diff --git a/doc/source/conf.py b/doc/source/conf.py
index f4153e9c..e0aa9ea4 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -44,10 +44,7 @@
     'sphinx.ext.coverage',
     'sphinx.ext.viewcode',
     'autodoc_traits',
-    # patched autosummary for issue
-    # https://github.com/sphinx-doc/sphinx/issues/1061
-    '_extensions'
-    #'sphinx.ext.autosummary'
+    'sphinx.ext.autosummary',
 ]
 
 # Add any paths that contain templates here, relative to this directory.