conf.py 11.9 KB
Newer Older
Brandon Walts's avatar
Brandon Walts committed
1
# -*- coding: utf-8 -*-
2
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
nwillhoft's avatar
nwillhoft committed
3
# Copyright [2016-2021] EMBL-European Bioinformatics Institute
4
5
6
7
8
9
10
11
12
13
14
15
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
Brandon Walts's avatar
Brandon Walts committed
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
#
# ehive_user_manual documentation build configuration file, created by
# sphinx-quickstart on Thu Dec 15 12:59:35 2016.
#
# 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
import os
31
import datetime
32
import sphinx_rtd_theme
Brandon Walts's avatar
Brandon Walts committed
33
34
35
36

# 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.
37
38
sys.path.insert(0, os.path.abspath('.'))

39
from xhive import setup_if_needed
40

Brandon Walts's avatar
Brandon Walts committed
41
42
43
44
45
46
47
48
49
50
51
52

# -- 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.coverage',
53
    'sphinx.ext.imgmath',
54
    'sphinx.ext.graphviz',
55
    'sphinxcontrib.doxylink',
56
    'xhive.code_doc',
57
58
59
60
    'xhive.analysis_diagram',
    'xhive.misc',
    'xhive.pipeline',
    'xhive.sql_schema',
Brandon Walts's avatar
Brandon Walts committed
61
62
63
64
65
]

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

66

67
68
69
70
71
72
73
# Add markdown support
from recommonmark.parser import CommonMarkParser

source_parsers = {
    '.md': CommonMarkParser,
}

Matthieu Muffato's avatar
Matthieu Muffato committed
74
authors = [u'Ensembl']
75

Brandon Walts's avatar
Brandon Walts committed
76
# The suffix of source filenames.
77
source_suffix = ['.rst', '.md']
Brandon Walts's avatar
Brandon Walts committed
78
79
80
81
82
83
84
85

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

# The master toctree document.
master_doc = 'index'

# General information about the project.
86
project = u'eHive user manual'
Matthieu Muffato's avatar
Matthieu Muffato committed
87
88
project_lc = project.replace(' ', '_').lower()

89
90
91
copyright_owner = u'EMBL-European Bioinformatics Institute'
copyright_dates = u'[2016-%d]' % datetime.datetime.now().year
copyright = copyright_dates + ' ' + copyright_owner
Brandon Walts's avatar
Brandon Walts committed
92
93
94
95
96
97

# 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.
98
99
import re
version = re.sub('^(heads|remotes/origin)/', '', os.popen('git describe --all').read().strip())
Brandon Walts's avatar
Brandon Walts committed
100
# The full version, including alpha/beta/rc tags.
101
release = version + '/' + os.popen('git rev-parse --short HEAD').read().strip()
Brandon Walts's avatar
Brandon Walts committed
102

103

104
doxygen_target = setup_if_needed(release, True)
105
106
107
108
109
doxylink = {
    'doxehive': (os.path.join(doxygen_target, "ensembl-hive.tag"), 'perl/'),
}


Brandon Walts's avatar
Brandon Walts committed
110
111
112
113
114
115
116
117
# 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.
118
today_fmt = '%B %d, %Y'
Brandon Walts's avatar
Brandon Walts committed
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152

# 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 = []

# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False


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

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
Matthieu Muffato's avatar
Matthieu Muffato committed
153
html_theme = 'sphinx_rtd_theme'
Brandon Walts's avatar
Brandon Walts committed
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

# 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 = []

# 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 = None

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

# 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 = None

# 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']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
187
html_extra_path = ['_build/doxygen/', 'presentations/']
Brandon Walts's avatar
Brandon Walts committed
188
189
190
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
222
223
224
225
226
227
228
229
230

# 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.
#html_sidebars = {}

# 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 = True

# 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.
Matthieu Muffato's avatar
Matthieu Muffato committed
231
htmlhelp_basename = project_lc
Brandon Walts's avatar
Brandon Walts committed
232
233
234
235
236
237
238
239
240
241
242
243


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

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.
244
245
246
247
248
'preamble': r'''
\usepackage{pdflscape}
\usepackage{charter}
\usepackage[defaultsans]{lato}
\usepackage{inconsolata}
249
\usepackage{verbatim}
250
''',
Brandon Walts's avatar
Brandon Walts committed
251
252
253
254
255
256
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
Matthieu Muffato's avatar
Matthieu Muffato committed
257
258
  (master_doc, project_lc+'.tex', project,
   authors[0], 'manual'),
Brandon Walts's avatar
Brandon Walts committed
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
]

# 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

# 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 = [
Matthieu Muffato's avatar
Matthieu Muffato committed
287
288
    (master_doc, project_lc, project,
     authors, 1)
Brandon Walts's avatar
Brandon Walts committed
289
290
291
292
293
294
295
296
297
298
299
300
]

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


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
Matthieu Muffato's avatar
Matthieu Muffato committed
301
302
  (master_doc, project_lc, project,
   authors[0], project_lc, 'One line description of project.',
Brandon Walts's avatar
Brandon Walts committed
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
   'Miscellaneous'),
]

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

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

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False


# -- Options for Epub output ----------------------------------------------

# Bibliographic Dublin Core info.
Matthieu Muffato's avatar
Matthieu Muffato committed
322
323
epub_title = project
epub_author = authors[0]
324
epub_publisher = copyright_owner
Matthieu Muffato's avatar
Matthieu Muffato committed
325
epub_copyright = copyright
Brandon Walts's avatar
Brandon Walts committed
326
327

# The basename for the epub file. It defaults to the project name.
Matthieu Muffato's avatar
Matthieu Muffato committed
328
epub_basename = project_lc
Brandon Walts's avatar
Brandon Walts committed
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386

# The HTML theme for the epub output. Since the default themes are not optimized
# for small screen space, using the same theme for HTML and epub output is
# usually not wise. This defaults to 'epub', a theme designed to save visual
# space.
#epub_theme = 'epub'

# The language of the text. It defaults to the language option
# or en if the language is not set.
#epub_language = ''

# The scheme of the identifier. Typical schemes are ISBN or URL.
#epub_scheme = ''

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#epub_identifier = ''

# A unique identification for the text.
#epub_uid = ''

# A tuple containing the cover image and cover page html template filenames.
#epub_cover = ()

# A sequence of (type, uri, title) tuples for the guide element of content.opf.
#epub_guide = ()

# HTML files that should be inserted before the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_pre_files = []

# HTML files shat should be inserted after the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_post_files = []

# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']

# The depth of the table of contents in toc.ncx.
#epub_tocdepth = 3

# Allow duplicate toc entries.
#epub_tocdup = True

# Choose between 'default' and 'includehidden'.
#epub_tocscope = 'default'

# Fix unsupported image types using the PIL.
#epub_fix_images = False

# Scale large images.
#epub_max_image_width = 0

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#epub_show_urls = 'inline'

# If false, no index is generated.
#epub_use_index = True
387
388
389
390
391

# Add overriding stylesheets, searching in html_static_path
# (see https://github.com/rtfd/sphinx_rtd_theme/issues/117)
def setup(app):
    app.add_stylesheet("theme_overrides.css")
392