We are currently solving the following issue within our repository. Here is the issue text:
--- BEGIN ISSUE ---
'make docs' falls back to an installed toil rather than the source
_From @hannes-ucsc on October 22, 2015 23:1_

Benedict ran `cd docs && make html` without having run `make develop` first. He also had installed an older version of toil. Sphinx then fell back to using that older version to generate the docs. This should not happen. The build should either produce an error or it should hardcode the path to the src directory so it doesn't fall back to an external installation.

_Copied from original issue: BD2KGenomics/cgl-docker-lib#46_

'make docs' falls back to an installed toil rather than the source
_From @hannes-ucsc on October 22, 2015 23:1_

Benedict ran `cd docs && make html` without having run `make develop` first. He also had installed an older version of toil. Sphinx then fell back to using that older version to generate the docs. This should not happen. The build should either produce an error or it should hardcode the path to the src directory so it doesn't fall back to an external installation.

_Copied from original issue: BD2KGenomics/cgl-docker-lib#46_


--- END ISSUE ---

Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
--- BEGIN FILES ---
Path: `docs/conf.py`
Content:
```
1 # -*- coding: utf-8 -*-
2 #
3 # Toil documentation build configuration file, created by
4 # sphinx-quickstart on Tue Aug 25 12:37:16 2015.
5 #
6 # This file is execfile()d with the current directory set to its
7 # containing dir.
8 #
9 # Note that not all possible configuration values are present in this
10 # autogenerated file.
11 #
12 # All configuration values have a default; values that are commented out
13 # serve to show the default.
14 
15 import sys
16 import os
17 import inspect
18 import re
19 import shlex
20 from toil.version import version as toilVersion
21 
22 # If extensions (or modules to document with autodoc) are in another directory,
23 # add these directories to sys.path here. If the directory is relative to the
24 # documentation root, use os.path.abspath to make it absolute, like shown here.
25 sys.path.insert(0, os.path.abspath('../src/toil/'))
26 
27 # -- General configuration ------------------------------------------------
28 
29 # If your documentation needs a minimal Sphinx version, state it here.
30 #needs_sphinx = '1.0'
31 
32 # Add any Sphinx extension module names here, as strings. They can be
33 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
34 # ones.
35 extensions = [
36     'sphinx.ext.autodoc',
37     'sphinx.ext.doctest',
38     'sphinx.ext.todo',
39     'sphinx.ext.coverage',
40     'sphinx.ext.viewcode',
41 ]
42 
43 def is_class(app, what, name, obj, skip, options):
44     return inspect.isclass(obj) or name.startswith('_')
45 
46 def setup(app):
47     app.connect('autodoc-skip-member', is_class)
48 
49 # Add any paths that contain templates here, relative to this directory.
50 templates_path = ['_templates']
51 
52 # The suffix(es) of source filenames.
53 # You can specify multiple suffix as a list of string:
54 # source_suffix = ['.rst', '.md']
55 source_suffix = '.rst'
56 
57 # The encoding of source files.
58 #source_encoding = 'utf-8-sig'
59 
60 # The master toctree document.
61 master_doc = 'index'
62 
63 # General information about the project.
64 project = u'Toil'
65 copyright = u'2015, UCSC Computational Genomics Lab'
66 author = u'UCSC Computational Genomics Lab'
67 
68 # The version info for the project you're documenting, acts as replacement for
69 # |version| and |release|, also used in various other places throughout the
70 # built documents.
71 #
72 # The short X.Y version.
73 version = re.split('[A-Za-z]', toilVersion)[0]
74 # The full version, including alpha/beta/rc tags.
75 release = toilVersion
76 
77 # The language for content autogenerated by Sphinx. Refer to documentation
78 # for a list of supported languages.
79 #
80 # This is also used if you do content translation via gettext catalogs.
81 # Usually you set "language" from the command line for these cases.
82 language = None
83 
84 # There are two options for replacing |today|: either, you set today to some
85 # non-false value, then it is used:
86 #today = ''
87 # Else, today_fmt is used as the format for a strftime call.
88 #today_fmt = '%B %d, %Y'
89 
90 # List of patterns, relative to source directory, that match files and
91 # directories to ignore when looking for source files.
92 exclude_patterns = ['_build']
93 
94 # The reST default role (used for this markup: `text`) to use for all
95 # documents.
96 #default_role = None
97 
98 # If true, '()' will be appended to :func: etc. cross-reference text.
99 #add_function_parentheses = True
100 
101 # If true, the current module name will be prepended to all description
102 # unit titles (such as .. function::).
103 #add_module_names = True
104 
105 # If true, sectionauthor and moduleauthor directives will be shown in the
106 # output. They are ignored by default.
107 #show_authors = False
108 
109 # The name of the Pygments (syntax highlighting) style to use.
110 pygments_style = 'sphinx'
111 
112 # A list of ignored prefixes for module index sorting.
113 #modindex_common_prefix = []
114 
115 # If true, keep warnings as "system message" paragraphs in the built documents.
116 #keep_warnings = False
117 
118 # If true, `todo` and `todoList` produce output, else they produce nothing.
119 todo_include_todos = True
120 
121 # Include doc string for __init__ method in the documentation
122 autoclass_content = 'both'
123 
124 # -- Options for HTML output ----------------------------------------------
125 
126 # The theme to use for HTML and HTML Help pages.  See the documentation for
127 # a list of builtin themes.
128 html_theme = 'alabaster'
129 
130 # Theme options are theme-specific and customize the look and feel of a theme
131 # further.  For a list of options available for each theme, see the
132 # documentation.
133 #html_theme_options = {}
134 
135 # Add any paths that contain custom themes here, relative to this directory.
136 #html_theme_path = []
137 
138 # The name for this set of Sphinx documents.  If None, it defaults to
139 # "<project> v<release> documentation".
140 #html_title = None
141 
142 # A shorter title for the navigation bar.  Default is the same as html_title.
143 #html_short_title = None
144 
145 # The name of an image file (relative to this directory) to place at the top
146 # of the sidebar.
147 #html_logo = None
148 
149 # The name of an image file (within the static path) to use as favicon of the
150 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
151 # pixels large.
152 #html_favicon = None
153 
154 # Add any paths that contain custom static files (such as style sheets) here,
155 # relative to this directory. They are copied after the builtin static files,
156 # so a file named "default.css" will overwrite the builtin "default.css".
157 html_static_path = ['_static']
158 
159 # Add any extra paths that contain custom files (such as robots.txt or
160 # .htaccess) here, relative to this directory. These files are copied
161 # directly to the root of the documentation.
162 #html_extra_path = []
163 
164 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
165 # using the given strftime format.
166 #html_last_updated_fmt = '%b %d, %Y'
167 
168 # If true, SmartyPants will be used to convert quotes and dashes to
169 # typographically correct entities.
170 #html_use_smartypants = True
171 
172 # Custom sidebar templates, maps document names to template names.
173 #html_sidebars = {}
174 
175 # Additional templates that should be rendered to pages, maps page names to
176 # template names.
177 #html_additional_pages = {}
178 
179 # If false, no module index is generated.
180 #html_domain_indices = True
181 
182 # If false, no index is generated.
183 #html_use_index = True
184 
185 # If true, the index is split into individual pages for each letter.
186 #html_split_index = False
187 
188 # If true, links to the reST sources are added to the pages.
189 #html_show_sourcelink = True
190 
191 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
192 #html_show_sphinx = True
193 
194 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
195 #html_show_copyright = True
196 
197 # If true, an OpenSearch description file will be output, and all pages will
198 # contain a <link> tag referring to it.  The value of this option must be the
199 # base URL from which the finished HTML is served.
200 #html_use_opensearch = ''
201 
202 # This is the file name suffix for HTML files (e.g. ".xhtml").
203 #html_file_suffix = None
204 
205 # Language to be used for generating the HTML full-text search index.
206 # Sphinx supports the following languages:
207 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
208 #   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
209 #html_search_language = 'en'
210 
211 # A dictionary with options for the search language support, empty by default.
212 # Now only 'ja' uses this config value
213 #html_search_options = {'type': 'default'}
214 
215 # The name of a javascript file (relative to the configuration directory) that
216 # implements a search results scorer. If empty, the default will be used.
217 #html_search_scorer = 'scorer.js'
218 
219 # Output file base name for HTML help builder.
220 htmlhelp_basename = 'Toildoc'
221 
222 # -- Options for LaTeX output ---------------------------------------------
223 
224 latex_elements = {
225 # The paper size ('letterpaper' or 'a4paper').
226 #'papersize': 'letterpaper',
227 
228 # The font size ('10pt', '11pt' or '12pt').
229 #'pointsize': '10pt',
230 
231 # Additional stuff for the LaTeX preamble.
232 #'preamble': '',
233 
234 # Latex figure (float) alignment
235 #'figure_align': 'htbp',
236 }
237 
238 # Grouping the document tree into LaTeX files. List of tuples
239 # (source start file, target name, title,
240 #  author, documentclass [howto, manual, or own class]).
241 latex_documents = [
242   (master_doc, 'Toil.tex', u'Toil Documentation',
243    u'UCSC Computational Genomics Lab', 'manual'),
244 ]
245 
246 # The name of an image file (relative to this directory) to place at the top of
247 # the title page.
248 #latex_logo = None
249 
250 # For "manual" documents, if this is true, then toplevel headings are parts,
251 # not chapters.
252 #latex_use_parts = False
253 
254 # If true, show page references after internal links.
255 #latex_show_pagerefs = False
256 
257 # If true, show URL addresses after external links.
258 #latex_show_urls = False
259 
260 # Documents to append as an appendix to all manuals.
261 #latex_appendices = []
262 
263 # If false, no module index is generated.
264 #latex_domain_indices = True
265 
266 
267 # -- Options for manual page output ---------------------------------------
268 
269 # One entry per manual page. List of tuples
270 # (source start file, name, description, authors, manual section).
271 man_pages = [
272     (master_doc, 'toil', u'Toil Documentation',
273      [author], 1)
274 ]
275 
276 # If true, show URL addresses after external links.
277 #man_show_urls = False
278 
279 
280 # -- Options for Texinfo output -------------------------------------------
281 
282 # Grouping the document tree into Texinfo files. List of tuples
283 # (source start file, target name, title, author,
284 #  dir menu entry, description, category)
285 texinfo_documents = [
286   (master_doc, 'Toil', u'Toil Documentation',
287    author, 'Toil', 'One line description of project.',
288    'Miscellaneous'),
289 ]
290 
291 # Documents to append as an appendix to all manuals.
292 #texinfo_appendices = []
293 
294 # If false, no module index is generated.
295 #texinfo_domain_indices = True
296 
297 # How to display URL addresses: 'footnote', 'no', or 'inline'.
298 #texinfo_show_urls = 'footnote'
299 
300 # If true, do not generate a @detailmenu in the "Top" node's menu.
301 #texinfo_no_detailmenu = False
302
```
--- 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
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Toil documentation build configuration file, created by
 # sphinx-quickstart on Tue Aug 25 12:37:16 2015.
@@ -16,13 +15,26 @@
 import os
 import inspect
 import re
-import shlex
-from toil.version import version as toilVersion
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../src/toil/'))
+sys.path.insert(0, os.path.abspath('../src'))
+
+import toil.version
+
+
+def real_dir_name(p, n=1):
+    p = os.path.realpath(p)
+    for i in range(n):
+        p = os.path.dirname(p)
+    print p
+    return p
+
+
+assert real_dir_name(__file__, 2) == real_dir_name(toil.version.__file__, 3), \
+    "Another Toil installation seems to have precedence over this working directory."
+toilVersion = toil.version.version
 
 # -- General configuration ------------------------------------------------

{"golden_diff": "diff --git a/docs/conf.py b/docs/conf.py\n--- a/docs/conf.py\n+++ b/docs/conf.py\n@@ -1,4 +1,3 @@\n-# -*- coding: utf-8 -*-\n #\n # Toil documentation build configuration file, created by\n # sphinx-quickstart on Tue Aug 25 12:37:16 2015.\n@@ -16,13 +15,26 @@\n import os\n import inspect\n import re\n-import shlex\n-from toil.version import version as toilVersion\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-sys.path.insert(0, os.path.abspath('../src/toil/'))\n+sys.path.insert(0, os.path.abspath('../src'))\n+\n+import toil.version\n+\n+\n+def real_dir_name(p, n=1):\n+    p = os.path.realpath(p)\n+    for i in range(n):\n+        p = os.path.dirname(p)\n+    print p\n+    return p\n+\n+\n+assert real_dir_name(__file__, 2) == real_dir_name(toil.version.__file__, 3), \\\n+    \"Another Toil installation seems to have precedence over this working directory.\"\n+toilVersion = toil.version.version\n \n # -- General configuration ------------------------------------------------\n", "issue": "'make docs' falls back to an installed toil rather than the source\n_From @hannes-ucsc on October 22, 2015 23:1_\n\nBenedict ran `cd docs && make html` without having run `make develop` first. He also had installed an older version of toil. Sphinx then fell back to using that older version to generate the docs. This should not happen. The build should either produce an error or it should hardcode the path to the src directory so it doesn't fall back to an external installation.\n\n_Copied from original issue: BD2KGenomics/cgl-docker-lib#46_\n\n'make docs' falls back to an installed toil rather than the source\n_From @hannes-ucsc on October 22, 2015 23:1_\n\nBenedict ran `cd docs && make html` without having run `make develop` first. He also had installed an older version of toil. Sphinx then fell back to using that older version to generate the docs. This should not happen. The build should either produce an error or it should hardcode the path to the src directory so it doesn't fall back to an external installation.\n\n_Copied from original issue: BD2KGenomics/cgl-docker-lib#46_\n\n", "before_files": [{"content": "# -*- coding: utf-8 -*-\n#\n# Toil documentation build configuration file, created by\n# sphinx-quickstart on Tue Aug 25 12:37:16 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\n# Note that not all possible configuration values are present in this\n# autogenerated file.\n#\n# All configuration values have a default; values that are commented out\n# serve to show the default.\n\nimport sys\nimport os\nimport inspect\nimport re\nimport shlex\nfrom toil.version import version as toilVersion\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.\nsys.path.insert(0, os.path.abspath('../src/toil/'))\n\n# -- General configuration ------------------------------------------------\n\n# If your documentation needs a minimal Sphinx version, state it here.\n#needs_sphinx = '1.0'\n\n# Add any Sphinx extension module names here, as strings. They can be\n# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom\n# ones.\nextensions = [\n    'sphinx.ext.autodoc',\n    'sphinx.ext.doctest',\n    'sphinx.ext.todo',\n    'sphinx.ext.coverage',\n    'sphinx.ext.viewcode',\n]\n\ndef is_class(app, what, name, obj, skip, options):\n    return inspect.isclass(obj) or name.startswith('_')\n\ndef setup(app):\n    app.connect('autodoc-skip-member', is_class)\n\n# Add any paths that contain templates here, relative to this directory.\ntemplates_path = ['_templates']\n\n# The suffix(es) of source filenames.\n# You can specify multiple suffix as a list of string:\n# source_suffix = ['.rst', '.md']\nsource_suffix = '.rst'\n\n# The encoding of source files.\n#source_encoding = 'utf-8-sig'\n\n# The master toctree document.\nmaster_doc = 'index'\n\n# General information about the project.\nproject = u'Toil'\ncopyright = u'2015, UCSC Computational Genomics Lab'\nauthor = u'UCSC Computational Genomics Lab'\n\n# The version info for the project you're documenting, acts as replacement for\n# |version| and |release|, also used in various other places throughout the\n# built documents.\n#\n# The short X.Y version.\nversion = re.split('[A-Za-z]', toilVersion)[0]\n# The full version, including alpha/beta/rc tags.\nrelease = toilVersion\n\n# The language for content autogenerated by Sphinx. Refer to documentation\n# for a list of supported languages.\n#\n# This is also used if you do content translation via gettext catalogs.\n# Usually you set \"language\" from the command line for these cases.\nlanguage = None\n\n# There are two options for replacing |today|: either, you set today to some\n# non-false value, then it is used:\n#today = ''\n# Else, today_fmt is used as the format for a strftime call.\n#today_fmt = '%B %d, %Y'\n\n# List of patterns, relative to source directory, that match files and\n# directories to ignore when looking for source files.\nexclude_patterns = ['_build']\n\n# The reST default role (used for this markup: `text`) to use for all\n# documents.\n#default_role = None\n\n# If true, '()' will be appended to :func: etc. cross-reference text.\n#add_function_parentheses = True\n\n# If true, the current module name will be prepended to all description\n# unit titles (such as .. function::).\n#add_module_names = True\n\n# If true, sectionauthor and moduleauthor directives will be shown in the\n# output. They are ignored by default.\n#show_authors = False\n\n# The name of the Pygments (syntax highlighting) style to use.\npygments_style = 'sphinx'\n\n# A list of ignored prefixes for module index sorting.\n#modindex_common_prefix = []\n\n# If true, keep warnings as \"system message\" paragraphs in the built documents.\n#keep_warnings = False\n\n# If true, `todo` and `todoList` produce output, else they produce nothing.\ntodo_include_todos = True\n\n# Include doc string for __init__ method in the documentation\nautoclass_content = 'both'\n\n# -- Options for HTML output ----------------------------------------------\n\n# The theme to use for HTML and HTML Help pages.  See the documentation for\n# a list of builtin themes.\nhtml_theme = 'alabaster'\n\n# Theme options are theme-specific and customize the look and feel of a theme\n# further.  For a list of options available for each theme, see the\n# documentation.\n#html_theme_options = {}\n\n# Add any paths that contain custom themes here, relative to this directory.\n#html_theme_path = []\n\n# The name for this set of Sphinx documents.  If None, it defaults to\n# \"<project> v<release> documentation\".\n#html_title = None\n\n# A shorter title for the navigation bar.  Default is the same as html_title.\n#html_short_title = None\n\n# The name of an image file (relative to this directory) to place at the top\n# of the sidebar.\n#html_logo = None\n\n# The name of an image file (within the static path) to use as favicon of the\n# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32\n# pixels large.\n#html_favicon = None\n\n# Add any paths that contain custom static files (such as style sheets) here,\n# relative to this directory. They are copied after the builtin static files,\n# so a file named \"default.css\" will overwrite the builtin \"default.css\".\nhtml_static_path = ['_static']\n\n# Add any extra paths that contain custom files (such as robots.txt or\n# .htaccess) here, relative to this directory. These files are copied\n# directly to the root of the documentation.\n#html_extra_path = []\n\n# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,\n# using the given strftime format.\n#html_last_updated_fmt = '%b %d, %Y'\n\n# If true, SmartyPants will be used to convert quotes and dashes to\n# typographically correct entities.\n#html_use_smartypants = True\n\n# Custom sidebar templates, maps document names to template names.\n#html_sidebars = {}\n\n# Additional templates that should be rendered to pages, maps page names to\n# template names.\n#html_additional_pages = {}\n\n# If false, no module index is generated.\n#html_domain_indices = True\n\n# If false, no index is generated.\n#html_use_index = True\n\n# If true, the index is split into individual pages for each letter.\n#html_split_index = False\n\n# If true, links to the reST sources are added to the pages.\n#html_show_sourcelink = True\n\n# If true, \"Created using Sphinx\" is shown in the HTML footer. Default is True.\n#html_show_sphinx = True\n\n# If true, \"(C) Copyright ...\" is shown in the HTML footer. Default is True.\n#html_show_copyright = True\n\n# If true, an OpenSearch description file will be output, and all pages will\n# contain a <link> tag referring to it.  The value of this option must be the\n# base URL from which the finished HTML is served.\n#html_use_opensearch = ''\n\n# This is the file name suffix for HTML files (e.g. \".xhtml\").\n#html_file_suffix = None\n\n# Language to be used for generating the HTML full-text search index.\n# Sphinx supports the following languages:\n#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'\n#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'\n#html_search_language = 'en'\n\n# A dictionary with options for the search language support, empty by default.\n# Now only 'ja' uses this config value\n#html_search_options = {'type': 'default'}\n\n# The name of a javascript file (relative to the configuration directory) that\n# implements a search results scorer. If empty, the default will be used.\n#html_search_scorer = 'scorer.js'\n\n# Output file base name for HTML help builder.\nhtmlhelp_basename = 'Toildoc'\n\n# -- Options for LaTeX output ---------------------------------------------\n\nlatex_elements = {\n# The paper size ('letterpaper' or 'a4paper').\n#'papersize': 'letterpaper',\n\n# The font size ('10pt', '11pt' or '12pt').\n#'pointsize': '10pt',\n\n# Additional stuff for the LaTeX preamble.\n#'preamble': '',\n\n# Latex figure (float) alignment\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, 'Toil.tex', u'Toil Documentation',\n   u'UCSC Computational Genomics Lab', 'manual'),\n]\n\n# The name of an image file (relative to this directory) to place at the top of\n# the title page.\n#latex_logo = None\n\n# For \"manual\" documents, if this is true, then toplevel headings are parts,\n# not chapters.\n#latex_use_parts = False\n\n# If true, show page references after internal links.\n#latex_show_pagerefs = False\n\n# If true, show URL addresses after external links.\n#latex_show_urls = False\n\n# Documents to append as an appendix to all manuals.\n#latex_appendices = []\n\n# If false, no module index is generated.\n#latex_domain_indices = True\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 = [\n    (master_doc, 'toil', u'Toil Documentation',\n     [author], 1)\n]\n\n# If true, show URL addresses after external links.\n#man_show_urls = False\n\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  (master_doc, 'Toil', u'Toil Documentation',\n   author, 'Toil', 'One line description of project.',\n   'Miscellaneous'),\n]\n\n# Documents to append as an appendix to all manuals.\n#texinfo_appendices = []\n\n# If false, no module index is generated.\n#texinfo_domain_indices = True\n\n# How to display URL addresses: 'footnote', 'no', or 'inline'.\n#texinfo_show_urls = 'footnote'\n\n# If true, do not generate a @detailmenu in the \"Top\" node's menu.\n#texinfo_no_detailmenu = False\n", "path": "docs/conf.py"}], "after_files": [{"content": "#\n# Toil documentation build configuration file, created by\n# sphinx-quickstart on Tue Aug 25 12:37:16 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\n# Note that not all possible configuration values are present in this\n# autogenerated file.\n#\n# All configuration values have a default; values that are commented out\n# serve to show the default.\n\nimport sys\nimport os\nimport inspect\nimport re\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.\nsys.path.insert(0, os.path.abspath('../src'))\n\nimport toil.version\n\n\ndef real_dir_name(p, n=1):\n    p = os.path.realpath(p)\n    for i in range(n):\n        p = os.path.dirname(p)\n    print p\n    return p\n\n\nassert real_dir_name(__file__, 2) == real_dir_name(toil.version.__file__, 3), \\\n    \"Another Toil installation seems to have precedence over this working directory.\"\ntoilVersion = toil.version.version\n\n# -- General configuration ------------------------------------------------\n\n# If your documentation needs a minimal Sphinx version, state it here.\n#needs_sphinx = '1.0'\n\n# Add any Sphinx extension module names here, as strings. They can be\n# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom\n# ones.\nextensions = [\n    'sphinx.ext.autodoc',\n    'sphinx.ext.doctest',\n    'sphinx.ext.todo',\n    'sphinx.ext.coverage',\n    'sphinx.ext.viewcode',\n]\n\ndef is_class(app, what, name, obj, skip, options):\n    return inspect.isclass(obj) or name.startswith('_')\n\ndef setup(app):\n    app.connect('autodoc-skip-member', is_class)\n\n# Add any paths that contain templates here, relative to this directory.\ntemplates_path = ['_templates']\n\n# The suffix(es) of source filenames.\n# You can specify multiple suffix as a list of string:\n# source_suffix = ['.rst', '.md']\nsource_suffix = '.rst'\n\n# The encoding of source files.\n#source_encoding = 'utf-8-sig'\n\n# The master toctree document.\nmaster_doc = 'index'\n\n# General information about the project.\nproject = u'Toil'\ncopyright = u'2015, UCSC Computational Genomics Lab'\nauthor = u'UCSC Computational Genomics Lab'\n\n# The version info for the project you're documenting, acts as replacement for\n# |version| and |release|, also used in various other places throughout the\n# built documents.\n#\n# The short X.Y version.\nversion = re.split('[A-Za-z]', toilVersion)[0]\n# The full version, including alpha/beta/rc tags.\nrelease = toilVersion\n\n# The language for content autogenerated by Sphinx. Refer to documentation\n# for a list of supported languages.\n#\n# This is also used if you do content translation via gettext catalogs.\n# Usually you set \"language\" from the command line for these cases.\nlanguage = None\n\n# There are two options for replacing |today|: either, you set today to some\n# non-false value, then it is used:\n#today = ''\n# Else, today_fmt is used as the format for a strftime call.\n#today_fmt = '%B %d, %Y'\n\n# List of patterns, relative to source directory, that match files and\n# directories to ignore when looking for source files.\nexclude_patterns = ['_build']\n\n# The reST default role (used for this markup: `text`) to use for all\n# documents.\n#default_role = None\n\n# If true, '()' will be appended to :func: etc. cross-reference text.\n#add_function_parentheses = True\n\n# If true, the current module name will be prepended to all description\n# unit titles (such as .. function::).\n#add_module_names = True\n\n# If true, sectionauthor and moduleauthor directives will be shown in the\n# output. They are ignored by default.\n#show_authors = False\n\n# The name of the Pygments (syntax highlighting) style to use.\npygments_style = 'sphinx'\n\n# A list of ignored prefixes for module index sorting.\n#modindex_common_prefix = []\n\n# If true, keep warnings as \"system message\" paragraphs in the built documents.\n#keep_warnings = False\n\n# If true, `todo` and `todoList` produce output, else they produce nothing.\ntodo_include_todos = True\n\n# Include doc string for __init__ method in the documentation\nautoclass_content = 'both'\n\n# -- Options for HTML output ----------------------------------------------\n\n# The theme to use for HTML and HTML Help pages.  See the documentation for\n# a list of builtin themes.\nhtml_theme = 'alabaster'\n\n# Theme options are theme-specific and customize the look and feel of a theme\n# further.  For a list of options available for each theme, see the\n# documentation.\n#html_theme_options = {}\n\n# Add any paths that contain custom themes here, relative to this directory.\n#html_theme_path = []\n\n# The name for this set of Sphinx documents.  If None, it defaults to\n# \"<project> v<release> documentation\".\n#html_title = None\n\n# A shorter title for the navigation bar.  Default is the same as html_title.\n#html_short_title = None\n\n# The name of an image file (relative to this directory) to place at the top\n# of the sidebar.\n#html_logo = None\n\n# The name of an image file (within the static path) to use as favicon of the\n# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32\n# pixels large.\n#html_favicon = None\n\n# Add any paths that contain custom static files (such as style sheets) here,\n# relative to this directory. They are copied after the builtin static files,\n# so a file named \"default.css\" will overwrite the builtin \"default.css\".\nhtml_static_path = ['_static']\n\n# Add any extra paths that contain custom files (such as robots.txt or\n# .htaccess) here, relative to this directory. These files are copied\n# directly to the root of the documentation.\n#html_extra_path = []\n\n# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,\n# using the given strftime format.\n#html_last_updated_fmt = '%b %d, %Y'\n\n# If true, SmartyPants will be used to convert quotes and dashes to\n# typographically correct entities.\n#html_use_smartypants = True\n\n# Custom sidebar templates, maps document names to template names.\n#html_sidebars = {}\n\n# Additional templates that should be rendered to pages, maps page names to\n# template names.\n#html_additional_pages = {}\n\n# If false, no module index is generated.\n#html_domain_indices = True\n\n# If false, no index is generated.\n#html_use_index = True\n\n# If true, the index is split into individual pages for each letter.\n#html_split_index = False\n\n# If true, links to the reST sources are added to the pages.\n#html_show_sourcelink = True\n\n# If true, \"Created using Sphinx\" is shown in the HTML footer. Default is True.\n#html_show_sphinx = True\n\n# If true, \"(C) Copyright ...\" is shown in the HTML footer. Default is True.\n#html_show_copyright = True\n\n# If true, an OpenSearch description file will be output, and all pages will\n# contain a <link> tag referring to it.  The value of this option must be the\n# base URL from which the finished HTML is served.\n#html_use_opensearch = ''\n\n# This is the file name suffix for HTML files (e.g. \".xhtml\").\n#html_file_suffix = None\n\n# Language to be used for generating the HTML full-text search index.\n# Sphinx supports the following languages:\n#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'\n#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'\n#html_search_language = 'en'\n\n# A dictionary with options for the search language support, empty by default.\n# Now only 'ja' uses this config value\n#html_search_options = {'type': 'default'}\n\n# The name of a javascript file (relative to the configuration directory) that\n# implements a search results scorer. If empty, the default will be used.\n#html_search_scorer = 'scorer.js'\n\n# Output file base name for HTML help builder.\nhtmlhelp_basename = 'Toildoc'\n\n# -- Options for LaTeX output ---------------------------------------------\n\nlatex_elements = {\n# The paper size ('letterpaper' or 'a4paper').\n#'papersize': 'letterpaper',\n\n# The font size ('10pt', '11pt' or '12pt').\n#'pointsize': '10pt',\n\n# Additional stuff for the LaTeX preamble.\n#'preamble': '',\n\n# Latex figure (float) alignment\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, 'Toil.tex', u'Toil Documentation',\n   u'UCSC Computational Genomics Lab', 'manual'),\n]\n\n# The name of an image file (relative to this directory) to place at the top of\n# the title page.\n#latex_logo = None\n\n# For \"manual\" documents, if this is true, then toplevel headings are parts,\n# not chapters.\n#latex_use_parts = False\n\n# If true, show page references after internal links.\n#latex_show_pagerefs = False\n\n# If true, show URL addresses after external links.\n#latex_show_urls = False\n\n# Documents to append as an appendix to all manuals.\n#latex_appendices = []\n\n# If false, no module index is generated.\n#latex_domain_indices = True\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 = [\n    (master_doc, 'toil', u'Toil Documentation',\n     [author], 1)\n]\n\n# If true, show URL addresses after external links.\n#man_show_urls = False\n\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  (master_doc, 'Toil', u'Toil Documentation',\n   author, 'Toil', 'One line description of project.',\n   'Miscellaneous'),\n]\n\n# Documents to append as an appendix to all manuals.\n#texinfo_appendices = []\n\n# If false, no module index is generated.\n#texinfo_domain_indices = True\n\n# How to display URL addresses: 'footnote', 'no', or 'inline'.\n#texinfo_show_urls = 'footnote'\n\n# If true, do not generate a @detailmenu in the \"Top\" node's menu.\n#texinfo_no_detailmenu = False\n", "path": "docs/conf.py"}]}