Targeting the posterior thalamic hub: hemispheric-specific encoding of pain-depression comorbidity after hemorrhagic stroke.

1. # -*- coding: utf-8 -*-
2. #
3. # scikit-learn documentation build configuration file, created by
4. # sphinx-quickstart on Fri Jan 8 09:13:42 2010.
5. #
6. # This file is execfile()d with the current directory set to its containing
7. # 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.
15. import sys
16. import os
18. # If extensions (or modules to document with autodoc) are in another
19. # directory, add these directories to sys.path here. If the directory
20. # is relative to the documentation root, use os.path.abspath to make it
21. # absolute, like shown here.
22. # sys.path.insert(0, os.path.abspath('sphinxext'))
23. sourcepath = os.path.abspath('..')
24. sys.path.insert(1, sourcepath)
26. # -- General configuration ---------------------------------------------------
28. # Try to override the matplotlib configuration as early as possible
29. # try:
30. # import gen_rst
31. # except:
32. # pass
34. # Add any Sphinx extension module names here, as strings. They can be
35. # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
36. extensions = [
37. # 'gen_rst',
38. 'sphinx.ext.autodoc', 'sphinx.ext.autosummary',
39. 'sphinx.ext.imgmath', 'numpydoc',
40. 'sphinx.ext.todo', 'sphinx.ext.viewcode',
41. 'sphinx.ext.inheritance_diagram'
42. ]
44. autosummary_generate = True
46. autodoc_default_flags = ['members', 'show-inheritance']
48. autodoc_member_order = 'bysource'
50. # Add any paths that contain templates here, relative to this directory.
51. templates_path = ['templates']
53. # generate autosummary even if no references
54. autosummary_generate = True
56. # The suffix of source filenames.
57. source_suffix = '.rst'
59. # The encoding of source files.
60. source_encoding = 'utf-8'
62. # Generate the plots for the gallery
63. plot_gallery = True
65. # The master toctree document.
66. master_doc = 'index'
68. # General information about the project.
69. project = u'WMQL'
70. copyright = u'2013, Demian Wassermann (Modified BSD License)'
72. # The version info for the project you're documenting, acts as replacement for
73. # |version| and |release|, also used in various other places throughout the
74. # built documents.
75. #
76. # The short X.Y version.
77. version = '0.1'
78. # The full version, including alpha/beta/rc tags.
79. import tract_querier
80. release = str(tract_querier.__version__)
82. # The language for content autogenerated by Sphinx. Refer to documentation
83. # for a list of supported languages.
84. #language = None
86. # There are two options for replacing |today|: either, you set today to some
87. # non-false value, then it is used:
88. #today = ''
89. # Else, today_fmt is used as the format for a strftime call.
90. #today_fmt = '%B %d, %Y'
92. # List of documents that shouldn't be included in the build.
93. #unused_docs = []
95. # List of directories, relative to source directory, that shouldn't be
96. # searched for source files.
97. exclude_trees = ['_build', 'templates', 'includes']
99. # List of patterns, relative to source directory, that match files and
100. # directories to ignore when looking for source files.
101. exclude_patterns = ['test', 'lbgfsb']
104. # The reST default role (used for this markup: `text`) to use for all
105. # documents.
106. #default_role = None
108. # If true, '()' will be appended to :func: etc. cross-reference text.
109. add_function_parentheses = False
111. # If true, the current module name will be prepended to all description
112. # unit titles (such as .. function::).
113. #add_module_names = True
115. # If true, sectionauthor and moduleauthor directives will be shown in the
116. # output. They are ignored by default.
117. #show_authors = False
119. # The name of the Pygments (syntax highlighting) style to use.
120. pygments_style = 'sphinx'
122. # A list of ignored prefixes for module index sorting.
123. #modindex_common_prefix = []
126. # -- Options for HTML output -------------------------------------------------
128. # The theme to use for HTML and HTML Help pages. Major themes that come with
129. # Sphinx are currently 'default' and 'sphinxdoc'.
130. html_theme = 'sphinxdoc'
132. # Theme options are theme-specific and customize the look and feel of a theme
133. # further. For a list of options available for each theme, see the
134. # documentation.
135. # html_theme_options = {'oldversion': False, 'collapsiblesidebar': True,
136. # 'google_analytics': True
137. # }
139. # Add any paths that contain custom themes here, relative to this directory.
140. html_theme_path = ['themes']
143. # The name for this set of Sphinx documents. If None, it defaults to
144. # "<project> v<release> documentation".
145. #html_title = None
147. # A shorter title for the navigation bar. Default is the same as html_title.
148. html_short_title = 'WMQL'
150. # The name of an image file (relative to this directory) to place at the top
151. # of the sidebar.
152. #html_logo = 'logos/scikit-learn-logo-small.png'
154. # The name of an image file (within the static path) to use as favicon of the
155. # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
156. # pixels large.
157. #html_favicon = 'logos/favicon.ico'
159. # Add any paths that contain custom static files (such as style sheets) here,
160. # relative to this directory. They are copied after the builtin static files,
161. # so a file named "default.css" will overwrite the builtin "default.css".
162. html_static_path = ['documents', 'images']
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'
168. # If true, SmartyPants will be used to convert quotes and dashes to
169. # typographically correct entities.
170. #html_use_smartypants = True
172. # Custom sidebar templates, maps document names to template names.
173. #html_sidebars = {}
175. # Additional templates that should be rendered to pages, maps page names to
176. # template names.
177. #html_additional_pages = {}
179. # If false, no module index is generated.
180. html_use_modindex = True
182. # If false, no index is generated.
183. html_use_index = True
185. # If true, the index is split into individual pages for each letter.
186. #html_split_index = False
188. # If true, links to the reST sources are added to the pages.
189. #html_show_sourcelink = True
191. # If true, an OpenSearch description file will be output, and all pages will
192. # contain a <link> tag referring to it. The value of this option must be the
193. # base URL from which the finished HTML is served.
194. #html_use_opensearch = ''
196. # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
197. #html_file_suffix = ''
199. # Output file base name for HTML help builder.
200. htmlhelp_basename = 'tract_querierdoc'
203. # -- Options for LaTeX output ------------------------------------------------
205. # The paper size ('letter' or 'a4').
206. #latex_paper_size = 'letter'
208. # The font size ('10pt', '11pt' or '12pt').
209. #latex_font_size = '10pt'
211. # Grouping the document tree into LaTeX files. List of tuples
212. # (source start file, target name, title, author, documentclass
213. # [howto/manual]).
214. latex_documents = [('index', 'user_guide.tex', u'tract_querier user guide',
215. u'tract_querier developers', 'manual'), ]
217. # The name of an image file (relative to this directory) to place at the top of
218. # the title page.
219. # latex_logo = "logos/tract_querier-logo.png"
221. # For "manual" documents, if this is true, then toplevel headings are parts,
222. # not chapters.
223. #latex_use_parts = False
225. # Additional stuff for the LaTeX preamble.
226. latex_preamble = r"""
227. \usepackage{amsmath}\usepackage{amsfonts}\usepackage{bm}\usepackage{morefloats}
228. \usepackage{enumitem} \setlistdepth{10} \renewcommand{\Re}{\ensuremath{\mathbb R}}
229. """
231. pngmath_latex_preamble = r"""
232. \usepackage{amsmath}\usepackage{amsfonts}\usepackage{bm}\usepackage{morefloats}
233. \usepackage{enumitem}
234. \renewcommand{\Re}{\ensuremath{\mathbb R}}
235. """
237. # Documents to append as an appendix to all manuals.
238. #latex_appendices = []
240. # If false, no module index is generated.
241. #latex_use_modindex = True
243. trim_doctests_flags = True
246. def setup(app):
247. from pygments.lexers import PythonLexer
248. from pygments.token import Name, Keyword
250. class WMQLLexer(PythonLexer):
251. EXTRA_KEYWORDS = (
252. [pos + '_of' for pos in ['anterior', 'posterior', 'inferior', 'superior']] +
253. ['endpoints_in']
254. )
256. def get_tokens_unprocessed(self, text):
257. for index, token, value in PythonLexer.get_tokens_unprocessed(self, text):
258. if token is Name and value in self.EXTRA_KEYWORDS:
259. yield index, Keyword.Pseudo, value
260. else:
261. yield index, token, value
262. app.add_lexer('wmql', WMQLLexer)

conf.py at commit 5c69c59, under BSD-3-Clause · at the source