We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
improve nonpar by calling mgcpy's two-sample test
the current nonpar implementation seems "correct",
meaning it seems to do what they did in the nonpar paper.
however, there is a much better way to implement it,
and we'd like to write a short paper about that.
specifically, in the current implementation, it uses the biased MMD, 
which is equivalent to the biased Dcorr.
better would be to use the unbiased MMD/Dcorr,
and even better would be to use the unbiased MGC.
possibly further better would be to use RF, though we don't have that fully implemented just yet.



--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `setup.py`
Content:
```
1 import os
2 import sys
3 from setuptools import setup, find_packages
4 from sys import platform
5 
6 PACKAGE_NAME = "graspy"
7 DESCRIPTION = "A set of python modules for graph statistics"
8 with open("README.md", "r") as f:
9     LONG_DESCRIPTION = f.read()
10 AUTHOR = ("Eric Bridgeford, Jaewon Chung, Benjamin Pedigo, Bijan Varjavand",)
11 AUTHOR_EMAIL = "j1c@jhu.edu"
12 URL = "https://github.com/neurodata/graspy"
13 MINIMUM_PYTHON_VERSION = 3, 5  # Minimum of Python 3.5
14 REQUIRED_PACKAGES = [
15     "networkx>=2.1",
16     "numpy>=1.8.1",
17     "scikit-learn>=0.19.1",
18     "scipy>=1.1.0",
19     "seaborn>=0.9.0",
20     "matplotlib>=3.0.0",
21 ]
22 
23 # Find GraSPy version.
24 PROJECT_PATH = os.path.dirname(os.path.abspath(__file__))
25 for line in open(os.path.join(PROJECT_PATH, "graspy", "__init__.py")):
26     if line.startswith("__version__ = "):
27         VERSION = line.strip().split()[2][1:-1]
28 
29 
30 def check_python_version():
31     """Exit when the Python version is too low."""
32     if sys.version_info < MINIMUM_PYTHON_VERSION:
33         sys.exit("Python {}.{}+ is required.".format(*MINIMUM_PYTHON_VERSION))
34 
35 
36 check_python_version()
37 
38 setup(
39     name=PACKAGE_NAME,
40     version=VERSION,
41     description=DESCRIPTION,
42     long_description=LONG_DESCRIPTION,
43     long_description_content_type="text/markdown",
44     author=AUTHOR,
45     author_email=AUTHOR_EMAIL,
46     install_requires=REQUIRED_PACKAGES,
47     url=URL,
48     license="Apache License 2.0",
49     classifiers=[
50         "Development Status :: 3 - Alpha",
51         "Intended Audience :: Science/Research",
52         "Topic :: Scientific/Engineering :: Mathematics",
53         "License :: OSI Approved :: Apache Software License",
54         "Programming Language :: Python :: 3",
55         "Programming Language :: Python :: 3.5",
56         "Programming Language :: Python :: 3.6",
57         "Programming Language :: Python :: 3.7",
58     ],
59     packages=find_packages(),
60     include_package_data=True,
61 )
62
```

Path: `docs/conf.py`
Content:
```
1 # -*- coding: utf-8 -*-
2 #
3 # Configuration file for the Sphinx documentation builder.
4 #
5 # This file does only contain a selection of the most common options. For a
6 # full list see the documentation:
7 # http://www.sphinx-doc.org/en/master/config
8 
9 # -- Path setup --------------------------------------------------------------
10 
11 # If extensions (or modules to document with autodoc) are in another directory,
12 # add these directories to sys.path here. If the directory is relative to the
13 # documentation root, use os.path.abspath to make it absolute, like shown here.
14 #
15 import os
16 import sys
17 
18 sys.path.insert(0, os.path.abspath(".."))
19 
20 # -- Project information -----------------------------------------------------
21 
22 project = "GraSPy"
23 copyright = "2018"
24 authors = u"NeuroData"
25 
26 # The short X.Y version
27 # Find GraSPy version.
28 PROJECT_PATH = os.path.dirname(os.path.abspath(__file__))
29 for line in open(os.path.join(PROJECT_PATH, "..", "graspy", "__init__.py")):
30     if line.startswith("__version__ = "):
31         version = line.strip().split()[2][1:-1]
32 
33 # The full version, including alpha/beta/rc tags
34 release = "alpha"
35 
36 # -- Extension configuration -------------------------------------------------
37 extensions = [
38     "sphinx.ext.autodoc",
39     "sphinx.ext.autosummary",
40     "sphinx.ext.todo",
41     "sphinx.ext.viewcode",
42     "sphinx.ext.mathjax",
43     "numpydoc",
44     "sphinx.ext.ifconfig",
45     "sphinx.ext.githubpages",
46     "sphinxcontrib.rawfiles",
47     "nbsphinx",
48     "sphinx.ext.intersphinx",
49 ]
50 
51 # -- sphinxcontrib.rawfiles
52 rawfiles = ["CNAME"]
53 
54 # -- numpydoc
55 # Below is needed to prevent errors
56 numpydoc_show_class_members = False
57 numpydoc_attributes_as_param_list = True
58 numpydoc_use_blockquotes = True
59 
60 # -- sphinx.ext.autosummary
61 autosummary_generate = True
62 
63 # -- sphinx.ext.autodoc
64 autoclass_content = "both"
65 autodoc_default_flags = ["members", "inherited-members"]
66 autodoc_member_order = "bysource"  # default is alphabetical
67 
68 # -- sphinx.ext.intersphinx
69 intersphinx_mapping = {
70     "numpy": ("https://docs.scipy.org/doc/numpy", None),
71     "python": ("https://docs.python.org/3", None),
72     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
73     "sklearn": ("http://scikit-learn.org/dev", None),
74 }
75 
76 # -- sphinx options ----------------------------------------------------------
77 source_suffix = ".rst"
78 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
79 master_doc = "index"
80 source_encoding = "utf-8"
81 
82 # -- Options for HTML output -------------------------------------------------
83 # Add any paths that contain templates here, relative to this directory.
84 templates_path = ["_templates"]
85 html_static_path = ["_static"]
86 modindex_common_prefix = ["graspy."]
87 
88 pygments_style = "sphinx"
89 smartquotes = False
90 
91 # Use RTD Theme
92 import sphinx_rtd_theme
93 
94 html_theme = "sphinx_rtd_theme"
95 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
96 html_theme_options = {
97     #'includehidden': False,
98     "navigation_depth": 2,
99     "collapse_navigation": False,
100     "navigation_depth": 3,
101 }
102 
103 # Custom sidebar templates, must be a dictionary that maps document names
104 # to template names.
105 #
106 # The default sidebars (for documents that don't match any pattern) are
107 # defined by theme itself.  Builtin themes are using these templates by
108 # default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
109 # 'searchbox.html']``.
110 #
111 # html_sidebars = {}
112 
113 # -- Options for HTMLHelp output ---------------------------------------------
114 
115 # Output file base name for HTML help builder.
116 htmlhelp_basename = "graspydoc"
117 
118 # -- Options for LaTeX output ------------------------------------------------
119 
120 latex_elements = {
121     # The paper size ('letterpaper' or 'a4paper').
122     #
123     # 'papersize': 'letterpaper',
124     # The font size ('10pt', '11pt' or '12pt').
125     #
126     # 'pointsize': '10pt',
127     # Additional stuff for the LaTeX preamble.
128     #
129     # 'preamble': '',
130     # Latex figure (float) alignment
131     #
132     # 'figure_align': 'htbp',
133 }
134 
135 # Grouping the document tree into LaTeX files. List of tuples
136 # (source start file, target name, title,
137 #  author, documentclass [howto, manual, or own class]).
138 latex_documents = [
139     (master_doc, "graspy.tex", "GraSPy Documentation", authors, "manual")
140 ]
141 
142 # -- Options for manual page output ------------------------------------------
143 
144 # One entry per manual page. List of tuples
145 # (source start file, name, description, authors, manual section).
146 man_pages = [(master_doc, "graspy", "graspy Documentation", [authors], 1)]
147 
148 # -- Options for Texinfo output ----------------------------------------------
149 
150 # Grouping the document tree into Texinfo files. List of tuples
151 # (source start file, target name, title, author,
152 #  dir menu entry, description, category)
153 texinfo_documents = [
154     (
155         master_doc,
156         "graspy",
157         "graspy Documentation",
158         authors,
159         "graspy",
160         "One line description of project.",
161         "Miscellaneous",
162     )
163 ]
164 
165 # -- Options for Epub output -------------------------------------------------
166 
167 # Bibliographic Dublin Core info.
168 epub_title = project
169 
170 # The unique identifier of the text. This can be a ISBN number
171 # or the project homepage.
172 #
173 # epub_identifier = ''
174 
175 # A unique identification for the text.
176 #
177 # epub_uid = ''
178 
179 # A list of files that should not be packed into the epub file.
180 epub_exclude_files = ["search.html"]
181
```
--- END FILES ---

Please first localize the bug based on the issue statement, and then generate a patch according to the `git diff` format fenced by three backticks.

Here is an example:

```diff
diff --git a/examples/server_async.py b/examples/server_async.py
--- a/examples/server_async.py
+++ b/examples/server_async.py
@@ -313,4 +313,4 @@
 
 
 if __name__ == "__main__":
-    asyncio.run(run_async_server("."), debug=True)
+    asyncio.run(run_async_server(), debug=True)
diff --git a/examples/server_sync.py b/examples/server_sync.py
--- a/examples/server_sync.py
+++ b/examples/server_sync.py
@@ -313,5 +313,5 @@
 
 
 if __name__ == "__main__":
-    server = run_sync_server(".")
+    server = run_sync_server()
     server.shutdown()

```

diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -71,6 +71,7 @@
     "python": ("https://docs.python.org/3", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
     "sklearn": ("http://scikit-learn.org/dev", None),
+    "hyppo": ("https://hyppo.neurodata.io", None),
 }
 
 # -- sphinx options ----------------------------------------------------------
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -18,8 +18,10 @@
     "scipy>=1.1.0",
     "seaborn>=0.9.0",
     "matplotlib>=3.0.0",
+    "hyppo>=0.1.2",
 ]
 
+
 # Find GraSPy version.
 PROJECT_PATH = os.path.dirname(os.path.abspath(__file__))
 for line in open(os.path.join(PROJECT_PATH, "graspy", "__init__.py")):

{"golden_diff": "diff --git a/docs/conf.py b/docs/conf.py\n--- a/docs/conf.py\n+++ b/docs/conf.py\n@@ -71,6 +71,7 @@\n     \"python\": (\"https://docs.python.org/3\", None),\n     \"scipy\": (\"https://docs.scipy.org/doc/scipy/reference\", None),\n     \"sklearn\": (\"http://scikit-learn.org/dev\", None),\n+    \"hyppo\": (\"https://hyppo.neurodata.io\", None),\n }\n \n # -- sphinx options ----------------------------------------------------------\ndiff --git a/setup.py b/setup.py\n--- a/setup.py\n+++ b/setup.py\n@@ -18,8 +18,10 @@\n     \"scipy>=1.1.0\",\n     \"seaborn>=0.9.0\",\n     \"matplotlib>=3.0.0\",\n+    \"hyppo>=0.1.2\",\n ]\n \n+\n # Find GraSPy version.\n PROJECT_PATH = os.path.dirname(os.path.abspath(__file__))\n for line in open(os.path.join(PROJECT_PATH, \"graspy\", \"__init__.py\")):\n", "issue": "improve nonpar by calling mgcpy's two-sample test\nthe current nonpar implementation seems \"correct\",\r\nmeaning it seems to do what they did in the nonpar paper.\r\nhowever, there is a much better way to implement it,\r\nand we'd like to write a short paper about that.\r\nspecifically, in the current implementation, it uses the biased MMD, \r\nwhich is equivalent to the biased Dcorr.\r\nbetter would be to use the unbiased MMD/Dcorr,\r\nand even better would be to use the unbiased MGC.\r\npossibly further better would be to use RF, though we don't have that fully implemented just yet.\r\n\r\n\n", "before_files": [{"content": "import os\nimport sys\nfrom setuptools import setup, find_packages\nfrom sys import platform\n\nPACKAGE_NAME = \"graspy\"\nDESCRIPTION = \"A set of python modules for graph statistics\"\nwith open(\"README.md\", \"r\") as f:\n    LONG_DESCRIPTION = f.read()\nAUTHOR = (\"Eric Bridgeford, Jaewon Chung, Benjamin Pedigo, Bijan Varjavand\",)\nAUTHOR_EMAIL = \"j1c@jhu.edu\"\nURL = \"https://github.com/neurodata/graspy\"\nMINIMUM_PYTHON_VERSION = 3, 5  # Minimum of Python 3.5\nREQUIRED_PACKAGES = [\n    \"networkx>=2.1\",\n    \"numpy>=1.8.1\",\n    \"scikit-learn>=0.19.1\",\n    \"scipy>=1.1.0\",\n    \"seaborn>=0.9.0\",\n    \"matplotlib>=3.0.0\",\n]\n\n# Find GraSPy version.\nPROJECT_PATH = os.path.dirname(os.path.abspath(__file__))\nfor line in open(os.path.join(PROJECT_PATH, \"graspy\", \"__init__.py\")):\n    if line.startswith(\"__version__ = \"):\n        VERSION = line.strip().split()[2][1:-1]\n\n\ndef check_python_version():\n    \"\"\"Exit when the Python version is too low.\"\"\"\n    if sys.version_info < MINIMUM_PYTHON_VERSION:\n        sys.exit(\"Python {}.{}+ is required.\".format(*MINIMUM_PYTHON_VERSION))\n\n\ncheck_python_version()\n\nsetup(\n    name=PACKAGE_NAME,\n    version=VERSION,\n    description=DESCRIPTION,\n    long_description=LONG_DESCRIPTION,\n    long_description_content_type=\"text/markdown\",\n    author=AUTHOR,\n    author_email=AUTHOR_EMAIL,\n    install_requires=REQUIRED_PACKAGES,\n    url=URL,\n    license=\"Apache License 2.0\",\n    classifiers=[\n        \"Development Status :: 3 - Alpha\",\n        \"Intended Audience :: Science/Research\",\n        \"Topic :: Scientific/Engineering :: Mathematics\",\n        \"License :: OSI Approved :: Apache Software License\",\n        \"Programming Language :: Python :: 3\",\n        \"Programming Language :: Python :: 3.5\",\n        \"Programming Language :: Python :: 3.6\",\n        \"Programming Language :: Python :: 3.7\",\n    ],\n    packages=find_packages(),\n    include_package_data=True,\n)\n", "path": "setup.py"}, {"content": "# -*- coding: utf-8 -*-\n#\n# Configuration file for the Sphinx documentation builder.\n#\n# This file does only contain a selection of the most common options. For a\n# full list see the documentation:\n# http://www.sphinx-doc.org/en/master/config\n\n# -- Path setup --------------------------------------------------------------\n\n# If extensions (or modules to document with autodoc) are in another directory,\n# add these directories to sys.path here. If the directory is relative to the\n# documentation root, use os.path.abspath to make it absolute, like shown here.\n#\nimport os\nimport sys\n\nsys.path.insert(0, os.path.abspath(\"..\"))\n\n# -- Project information -----------------------------------------------------\n\nproject = \"GraSPy\"\ncopyright = \"2018\"\nauthors = u\"NeuroData\"\n\n# The short X.Y version\n# Find GraSPy version.\nPROJECT_PATH = os.path.dirname(os.path.abspath(__file__))\nfor line in open(os.path.join(PROJECT_PATH, \"..\", \"graspy\", \"__init__.py\")):\n    if line.startswith(\"__version__ = \"):\n        version = line.strip().split()[2][1:-1]\n\n# The full version, including alpha/beta/rc tags\nrelease = \"alpha\"\n\n# -- Extension configuration -------------------------------------------------\nextensions = [\n    \"sphinx.ext.autodoc\",\n    \"sphinx.ext.autosummary\",\n    \"sphinx.ext.todo\",\n    \"sphinx.ext.viewcode\",\n    \"sphinx.ext.mathjax\",\n    \"numpydoc\",\n    \"sphinx.ext.ifconfig\",\n    \"sphinx.ext.githubpages\",\n    \"sphinxcontrib.rawfiles\",\n    \"nbsphinx\",\n    \"sphinx.ext.intersphinx\",\n]\n\n# -- sphinxcontrib.rawfiles\nrawfiles = [\"CNAME\"]\n\n# -- numpydoc\n# Below is needed to prevent errors\nnumpydoc_show_class_members = False\nnumpydoc_attributes_as_param_list = True\nnumpydoc_use_blockquotes = True\n\n# -- sphinx.ext.autosummary\nautosummary_generate = True\n\n# -- sphinx.ext.autodoc\nautoclass_content = \"both\"\nautodoc_default_flags = [\"members\", \"inherited-members\"]\nautodoc_member_order = \"bysource\"  # default is alphabetical\n\n# -- sphinx.ext.intersphinx\nintersphinx_mapping = {\n    \"numpy\": (\"https://docs.scipy.org/doc/numpy\", None),\n    \"python\": (\"https://docs.python.org/3\", None),\n    \"scipy\": (\"https://docs.scipy.org/doc/scipy/reference\", None),\n    \"sklearn\": (\"http://scikit-learn.org/dev\", None),\n}\n\n# -- sphinx options ----------------------------------------------------------\nsource_suffix = \".rst\"\nexclude_patterns = [\"_build\", \"Thumbs.db\", \".DS_Store\", \"**.ipynb_checkpoints\"]\nmaster_doc = \"index\"\nsource_encoding = \"utf-8\"\n\n# -- Options for HTML output -------------------------------------------------\n# Add any paths that contain templates here, relative to this directory.\ntemplates_path = [\"_templates\"]\nhtml_static_path = [\"_static\"]\nmodindex_common_prefix = [\"graspy.\"]\n\npygments_style = \"sphinx\"\nsmartquotes = False\n\n# Use RTD Theme\nimport sphinx_rtd_theme\n\nhtml_theme = \"sphinx_rtd_theme\"\nhtml_theme_path = [sphinx_rtd_theme.get_html_theme_path()]\nhtml_theme_options = {\n    #'includehidden': False,\n    \"navigation_depth\": 2,\n    \"collapse_navigation\": False,\n    \"navigation_depth\": 3,\n}\n\n# Custom sidebar templates, must be a dictionary that maps document names\n# to template names.\n#\n# The default sidebars (for documents that don't match any pattern) are\n# defined by theme itself.  Builtin themes are using these templates by\n# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',\n# 'searchbox.html']``.\n#\n# html_sidebars = {}\n\n# -- Options for HTMLHelp output ---------------------------------------------\n\n# Output file base name for HTML help builder.\nhtmlhelp_basename = \"graspydoc\"\n\n# -- Options for LaTeX output ------------------------------------------------\n\nlatex_elements = {\n    # The paper size ('letterpaper' or 'a4paper').\n    #\n    # 'papersize': 'letterpaper',\n    # The font size ('10pt', '11pt' or '12pt').\n    #\n    # 'pointsize': '10pt',\n    # Additional stuff for the LaTeX preamble.\n    #\n    # 'preamble': '',\n    # Latex figure (float) alignment\n    #\n    # 'figure_align': 'htbp',\n}\n\n# Grouping the document tree into LaTeX files. List of tuples\n# (source start file, target name, title,\n#  author, documentclass [howto, manual, or own class]).\nlatex_documents = [\n    (master_doc, \"graspy.tex\", \"GraSPy Documentation\", authors, \"manual\")\n]\n\n# -- Options for manual page output ------------------------------------------\n\n# One entry per manual page. List of tuples\n# (source start file, name, description, authors, manual section).\nman_pages = [(master_doc, \"graspy\", \"graspy Documentation\", [authors], 1)]\n\n# -- Options for Texinfo output ----------------------------------------------\n\n# Grouping the document tree into Texinfo files. List of tuples\n# (source start file, target name, title, author,\n#  dir menu entry, description, category)\ntexinfo_documents = [\n    (\n        master_doc,\n        \"graspy\",\n        \"graspy Documentation\",\n        authors,\n        \"graspy\",\n        \"One line description of project.\",\n        \"Miscellaneous\",\n    )\n]\n\n# -- Options for Epub output -------------------------------------------------\n\n# Bibliographic Dublin Core info.\nepub_title = project\n\n# The unique identifier of the text. This can be a ISBN number\n# or the project homepage.\n#\n# epub_identifier = ''\n\n# A unique identification for the text.\n#\n# epub_uid = ''\n\n# A list of files that should not be packed into the epub file.\nepub_exclude_files = [\"search.html\"]\n", "path": "docs/conf.py"}], "after_files": [{"content": "import os\nimport sys\nfrom setuptools import setup, find_packages\nfrom sys import platform\n\nPACKAGE_NAME = \"graspy\"\nDESCRIPTION = \"A set of python modules for graph statistics\"\nwith open(\"README.md\", \"r\") as f:\n    LONG_DESCRIPTION = f.read()\nAUTHOR = (\"Eric Bridgeford, Jaewon Chung, Benjamin Pedigo, Bijan Varjavand\",)\nAUTHOR_EMAIL = \"j1c@jhu.edu\"\nURL = \"https://github.com/neurodata/graspy\"\nMINIMUM_PYTHON_VERSION = 3, 5  # Minimum of Python 3.5\nREQUIRED_PACKAGES = [\n    \"networkx>=2.1\",\n    \"numpy>=1.8.1\",\n    \"scikit-learn>=0.19.1\",\n    \"scipy>=1.1.0\",\n    \"seaborn>=0.9.0\",\n    \"matplotlib>=3.0.0\",\n    \"hyppo>=0.1.2\",\n]\n\n\n# Find GraSPy version.\nPROJECT_PATH = os.path.dirname(os.path.abspath(__file__))\nfor line in open(os.path.join(PROJECT_PATH, \"graspy\", \"__init__.py\")):\n    if line.startswith(\"__version__ = \"):\n        VERSION = line.strip().split()[2][1:-1]\n\n\ndef check_python_version():\n    \"\"\"Exit when the Python version is too low.\"\"\"\n    if sys.version_info < MINIMUM_PYTHON_VERSION:\n        sys.exit(\"Python {}.{}+ is required.\".format(*MINIMUM_PYTHON_VERSION))\n\n\ncheck_python_version()\n\nsetup(\n    name=PACKAGE_NAME,\n    version=VERSION,\n    description=DESCRIPTION,\n    long_description=LONG_DESCRIPTION,\n    long_description_content_type=\"text/markdown\",\n    author=AUTHOR,\n    author_email=AUTHOR_EMAIL,\n    install_requires=REQUIRED_PACKAGES,\n    url=URL,\n    license=\"Apache License 2.0\",\n    classifiers=[\n        \"Development Status :: 3 - Alpha\",\n        \"Intended Audience :: Science/Research\",\n        \"Topic :: Scientific/Engineering :: Mathematics\",\n        \"License :: OSI Approved :: Apache Software License\",\n        \"Programming Language :: Python :: 3\",\n        \"Programming Language :: Python :: 3.5\",\n        \"Programming Language :: Python :: 3.6\",\n        \"Programming Language :: Python :: 3.7\",\n    ],\n    packages=find_packages(),\n    include_package_data=True,\n)\n", "path": "setup.py"}, {"content": "# -*- coding: utf-8 -*-\n#\n# Configuration file for the Sphinx documentation builder.\n#\n# This file does only contain a selection of the most common options. For a\n# full list see the documentation:\n# http://www.sphinx-doc.org/en/master/config\n\n# -- Path setup --------------------------------------------------------------\n\n# If extensions (or modules to document with autodoc) are in another directory,\n# add these directories to sys.path here. If the directory is relative to the\n# documentation root, use os.path.abspath to make it absolute, like shown here.\n#\nimport os\nimport sys\n\nsys.path.insert(0, os.path.abspath(\"..\"))\n\n# -- Project information -----------------------------------------------------\n\nproject = \"GraSPy\"\ncopyright = \"2018\"\nauthors = u\"NeuroData\"\n\n# The short X.Y version\n# Find GraSPy version.\nPROJECT_PATH = os.path.dirname(os.path.abspath(__file__))\nfor line in open(os.path.join(PROJECT_PATH, \"..\", \"graspy\", \"__init__.py\")):\n    if line.startswith(\"__version__ = \"):\n        version = line.strip().split()[2][1:-1]\n\n# The full version, including alpha/beta/rc tags\nrelease = \"alpha\"\n\n# -- Extension configuration -------------------------------------------------\nextensions = [\n    \"sphinx.ext.autodoc\",\n    \"sphinx.ext.autosummary\",\n    \"sphinx.ext.todo\",\n    \"sphinx.ext.viewcode\",\n    \"sphinx.ext.mathjax\",\n    \"numpydoc\",\n    \"sphinx.ext.ifconfig\",\n    \"sphinx.ext.githubpages\",\n    \"sphinxcontrib.rawfiles\",\n    \"nbsphinx\",\n    \"sphinx.ext.intersphinx\",\n]\n\n# -- sphinxcontrib.rawfiles\nrawfiles = [\"CNAME\"]\n\n# -- numpydoc\n# Below is needed to prevent errors\nnumpydoc_show_class_members = False\nnumpydoc_attributes_as_param_list = True\nnumpydoc_use_blockquotes = True\n\n# -- sphinx.ext.autosummary\nautosummary_generate = True\n\n# -- sphinx.ext.autodoc\nautoclass_content = \"both\"\nautodoc_default_flags = [\"members\", \"inherited-members\"]\nautodoc_member_order = \"bysource\"  # default is alphabetical\n\n# -- sphinx.ext.intersphinx\nintersphinx_mapping = {\n    \"numpy\": (\"https://docs.scipy.org/doc/numpy\", None),\n    \"python\": (\"https://docs.python.org/3\", None),\n    \"scipy\": (\"https://docs.scipy.org/doc/scipy/reference\", None),\n    \"sklearn\": (\"http://scikit-learn.org/dev\", None),\n    \"hyppo\": (\"https://hyppo.neurodata.io\", None),\n}\n\n# -- sphinx options ----------------------------------------------------------\nsource_suffix = \".rst\"\nexclude_patterns = [\"_build\", \"Thumbs.db\", \".DS_Store\", \"**.ipynb_checkpoints\"]\nmaster_doc = \"index\"\nsource_encoding = \"utf-8\"\n\n# -- Options for HTML output -------------------------------------------------\n# Add any paths that contain templates here, relative to this directory.\ntemplates_path = [\"_templates\"]\nhtml_static_path = [\"_static\"]\nmodindex_common_prefix = [\"graspy.\"]\n\npygments_style = \"sphinx\"\nsmartquotes = False\n\n# Use RTD Theme\nimport sphinx_rtd_theme\n\nhtml_theme = \"sphinx_rtd_theme\"\nhtml_theme_path = [sphinx_rtd_theme.get_html_theme_path()]\nhtml_theme_options = {\n    #'includehidden': False,\n    \"navigation_depth\": 2,\n    \"collapse_navigation\": False,\n    \"navigation_depth\": 3,\n}\n\n# Custom sidebar templates, must be a dictionary that maps document names\n# to template names.\n#\n# The default sidebars (for documents that don't match any pattern) are\n# defined by theme itself.  Builtin themes are using these templates by\n# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',\n# 'searchbox.html']``.\n#\n# html_sidebars = {}\n\n# -- Options for HTMLHelp output ---------------------------------------------\n\n# Output file base name for HTML help builder.\nhtmlhelp_basename = \"graspydoc\"\n\n# -- Options for LaTeX output ------------------------------------------------\n\nlatex_elements = {\n    # The paper size ('letterpaper' or 'a4paper').\n    #\n    # 'papersize': 'letterpaper',\n    # The font size ('10pt', '11pt' or '12pt').\n    #\n    # 'pointsize': '10pt',\n    # Additional stuff for the LaTeX preamble.\n    #\n    # 'preamble': '',\n    # Latex figure (float) alignment\n    #\n    # 'figure_align': 'htbp',\n}\n\n# Grouping the document tree into LaTeX files. List of tuples\n# (source start file, target name, title,\n#  author, documentclass [howto, manual, or own class]).\nlatex_documents = [\n    (master_doc, \"graspy.tex\", \"GraSPy Documentation\", authors, \"manual\")\n]\n\n# -- Options for manual page output ------------------------------------------\n\n# One entry per manual page. List of tuples\n# (source start file, name, description, authors, manual section).\nman_pages = [(master_doc, \"graspy\", \"graspy Documentation\", [authors], 1)]\n\n# -- Options for Texinfo output ----------------------------------------------\n\n# Grouping the document tree into Texinfo files. List of tuples\n# (source start file, target name, title, author,\n#  dir menu entry, description, category)\ntexinfo_documents = [\n    (\n        master_doc,\n        \"graspy\",\n        \"graspy Documentation\",\n        authors,\n        \"graspy\",\n        \"One line description of project.\",\n        \"Miscellaneous\",\n    )\n]\n\n# -- Options for Epub output -------------------------------------------------\n\n# Bibliographic Dublin Core info.\nepub_title = project\n\n# The unique identifier of the text. This can be a ISBN number\n# or the project homepage.\n#\n# epub_identifier = ''\n\n# A unique identification for the text.\n#\n# epub_uid = ''\n\n# A list of files that should not be packed into the epub file.\nepub_exclude_files = [\"search.html\"]\n", "path": "docs/conf.py"}]}