conf.py 8.03 KB
Newer Older
Aaron's avatar
Aaron committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
# -*- coding: utf-8 -*-
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import sys, os

# 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('../'))
Aaron's avatar
Aaron committed
17
18
sys.path.append(os.path.abspath('sphinxext'))
sys.path.append(os.path.abspath('pyplots'))
Aaron's avatar
Aaron committed
19
20
21
22
23
24
25
26
27
28
29

# -- General configuration -----------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 
              'sphinx.ext.intersphinx', 'sphinx.ext.todo', 
              'sphinx.ext.coverage', 'sphinx.ext.pngmath', 
Aaron's avatar
Aaron committed
30
              'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
arq5x's avatar
arq5x committed
31
			        'matplotlib.sphinxext.plot_directive']
Aaron's avatar
Aaron committed
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46

# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The encoding of source files.
#source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'bedtools'
arq5x's avatar
arq5x committed
47
copyright = u'2009 - 2015, Aaron R. Quinlan & Neil Kindlon'
Aaron's avatar
Aaron committed
48
49
50
51
52
53

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
arq5x's avatar
arq5x committed
54
version = '2.24.0'
Aaron's avatar
Aaron committed
55
# The full version, including alpha/beta/rc tags.
arq5x's avatar
arq5x committed
56
release = '2.24.0'
Aaron's avatar
Aaron committed
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']

# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []


# -- Options for HTML output ---------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
html_theme = 'rtd'

# Theme options are theme-specific and customize the look and feel of a theme
# further.  For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.
html_theme_path = ["themes"]

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.
html_short_title = project + " v" + release

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
116
html_logo = 'bedtools.swiss.png'
Aaron's avatar
Aaron committed
117
118
119
120
121
122

# The name of an image file (within the static path) to use as favicon of the
# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
html_favicon = 'bedtools.png'

123
124
125
126
127
128
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_style = 'labibi.css'

Aaron's avatar
Aaron committed
129
130
131
132
133
134
135
136
137
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
Aaron's avatar
Aaron committed
138
139
140
html_sidebars = {
    'index': ['sidebar-intro.html', 'sourcelink.html', 'searchbox.html']
}
Aaron's avatar
Aaron committed
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189

# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True

# If false, no index is generated.
#html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False

# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
html_show_sphinx = False

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'bedtools-docs'

# Google analytics
#googleanalytics_id = "UA-24167610-15"

# -- Options for LaTeX output --------------------------------------------------

# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'

# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
  ('index', 'bedtools.tex', u'Bedtools Documentation', 
arq5x's avatar
arq5x committed
190
  u'Quinlan lab @ Univ. of Utah', 'manual'),
Aaron's avatar
Aaron committed
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False

# If true, show page references after internal links.
#latex_show_pagerefs = False

# If true, show URL addresses after external links.
#latex_show_urls = False

# Additional stuff for the LaTeX preamble.
#latex_preamble = ''

# Documents to append as an appendix to all manuals.
#latex_appendices = []

# If false, no module index is generated.
#latex_domain_indices = True


# -- Options for manual page output --------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
arq5x's avatar
arq5x committed
222
    ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1)
Aaron's avatar
Aaron committed
223
224
225
]

# Example configuration for intersphinx: refer to the Python standard library.
226
intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}
Aaron's avatar
Aaron committed
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243

class Mock(object):
    def __init__(self, *args, **kwargs):
        pass

    def __call__(self, *args, **kwargs):
        return Mock()

    @classmethod
    def __getattr__(cls, name):
        if name in ('__file__', '__path__'):
            return '/dev/null'
        elif name[0] == name[0].upper():
            return type(name, (), {})
        else:
            return Mock()

Aaron's avatar
Aaron committed
244
245
MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot', 
                'matplotlib.sphinxext', 'matplotlib.sphinxext.plot_directive']
Aaron's avatar
Aaron committed
246
247
for mod_name in MOCK_MODULES:
    sys.modules[mod_name] = Mock()