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update doc
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@cokelaer
cokelaer committed Jan 27, 2025
1 parent d8633cc commit 26dd535
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153 changes: 75 additions & 78 deletions doc/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@
# All configuration values have a default; values that are commented out
# serve to show the default.

import sys, os
import sphinx

sys.path.insert(0, os.path.abspath('sphinxext'))
import os
import sys

import sphinx
import sphinx_gallery

# 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.
Expand All @@ -25,13 +25,14 @@

# This is for ReadTheDoc
import matplotlib
matplotlib.use('Agg')

on_rtd = os.environ.get("READTHEDOCS", None) == "True"
matplotlib.use("Agg")

on_rtd = os.environ.get("READTHEDOCS", None) == "True"


import pkg_resources

version = pkg_resources.require(pkg_name)[0].version
release = version
author = "Thomas Cokelaer, Lea M. Harder, Jordi Serra-Musach, \nDennis Pultz"
Expand All @@ -42,48 +43,49 @@
import easydev
from easydev import get_path_sphinx_themes


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

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# 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.imgmath' # only available for sphinx >= 1.4
if sphinx.version_info[:2] >= (1, 4)
else 'sphinx.ext.pngmath'),
'sphinx.ext.coverage',
'sphinx.ext.doctest',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
"sphinx.ext.autodoc",
(
"sphinx.ext.imgmath" # only available for sphinx >= 1.4
if sphinx.version_info[:2] >= (1, 4)
else "sphinx.ext.pngmath"
),
"sphinx.ext.coverage",
"sphinx.ext.doctest",
"sphinx.ext.intersphinx",
"sphinx.ext.todo",
"sphinx.ext.ifconfig",
"sphinx.ext.viewcode",
"numpydoc.numpydoc",
'matplotlib.sphinxext.plot_directive',
'sphinx.ext.autosummary',
'sphinx_gallery.gen_gallery',
]
"matplotlib.sphinxext.plot_directive",
"sphinx.ext.autosummary",
"sphinx_gallery.gen_gallery",
]
# note that the numpy directives is buggy. Example: class and init are not recognised as two entities for the autoclass_content=both here below


todo_include_todos=True
autoclass_content = 'both'
todo_include_todos = True
autoclass_content = "both"

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

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

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

# The master toctree document.
master_doc = 'index'
master_doc = "index"

# General information about the project.
project = project
Expand All @@ -94,34 +96,34 @@
# built documents.
#
# The short X.Y version.
version = 'Current version: ' + str(version)
version = "Current version: " + str(version)
# The full version, including alpha/beta/rc tags.
release = release

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

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

# List of documents that shouldn't be included in the build.
#unused_docs = []
# unused_docs = []


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

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

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

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
Expand All @@ -132,7 +134,7 @@
show_authors = True

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

# A list of ignored prefixes for module index sorting.
modindex_common_prefix = ["bioservices."]
Expand All @@ -143,14 +145,14 @@
# to force their creation. Note that it requires singularity or dot to be
# installed. Fixes https://github.com/biokit/bioconvert/issues/153

plot_gallery = True
plot_gallery = "True"

#sphinx_gallery_conf = {
# sphinx_gallery_conf = {
# "doc_module": "bioservices",
# 'backreferences_dir': os.path.join("modules", "generated"),
# #"examples_dirs": "examples",
# #"gallery_dirs": "auto_examples",
#}
# }

# Get rid of spurious warnings due to some interaction between
# autosummary and numpydoc. See
Expand All @@ -163,23 +165,23 @@
def touch_example_backreferences(app, what, name, obj, options, lines):
# generate empty examples files, so that we don't get
# inclusion errors if there are no examples for a class / module
examples_path = os.path.join(app.srcdir, "modules", "generated",
"%s.examples" % name)
examples_path = os.path.join(app.srcdir, "modules", "generated", "%s.examples" % name)
if not os.path.exists(examples_path):
# touch file
os.makedirs(os.path.dirname(examples_path), exist_ok=True)
open(examples_path, 'w').close()
open(examples_path, "w").close()


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

# The theme to use for HTML and HTML Help pages. Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = 'standard'
html_theme = "standard"
on_rtd = os.environ.get("READTHEDOCS", None) == True
if not on_rtd:
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'

html_theme = "sphinx_rtd_theme"
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
else:
html_theme = "default"
Expand All @@ -188,18 +190,17 @@ def touch_example_backreferences(app, what, name, obj, options, lines):
# further. For a list of options available for each theme, see the
# documentation.
# the user theme contains the otpions 'homepage', which is populated here
#html_theme_options = {'homepage': init_sphinx.url}
# html_theme_options = {'homepage': init_sphinx.url}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = [get_path_sphinx_themes()]

# html_theme_path = [get_path_sphinx_themes()]


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

# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
Expand All @@ -208,34 +209,34 @@ def touch_example_backreferences(app, what, name, obj, options, lines):
# 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
# 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".

# the copybutton.js must be copied there:
html_static_path = ['_static']
html_static_path = ["_static"]

# 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'
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
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
html_index = 'index.html'
html_index = "index.html"

#Custom sidebar templates, maps page names to templates.
# Custom sidebar templates, maps page names to templates.
html_sidebars = {
'index': [ 'indexsidebar.html'],
'contents':'indexsidebar.html',
"index": ["indexsidebar.html"],
"contents": "indexsidebar.html",
}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = { 'index': 'index.html'}
# html_additional_pages = { 'index': 'index.html'}


# If false, no module index is generated.
Expand All @@ -255,18 +256,18 @@ def touch_example_backreferences(app, what, name, obj, options, lines):
html_show_sphinx = True

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

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

# Output file base name for HTML help builder.
htmlhelp_basename = 'doc'
htmlhelp_basename = "doc"


# -- Options for LaTeX output --------------------------------------------------
Expand All @@ -275,48 +276,44 @@ def touch_example_backreferences(app, what, name, obj, options, lines):
pngmath_use_preview = True

# The font size ('10pt', '11pt' or '12pt').
latex_font_size = '10pt'
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', 'main.tex', title,
author, 'manual'),
("index", "main.tex", title, author, "manual"),
]

latex_elements = { 'inputenc': '\\usepackage[utf8]{inputenc}' }
#latex_elements["latex_paper_size"] = "a4"
latex_elements = {"inputenc": "\\usepackage[utf8]{inputenc}"}
# latex_elements["latex_paper_size"] = "a4"
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# 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
# latex_show_pagerefs = False

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


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

# If false, no module index is generated.
#latex_domain_indices = True
# 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 = [
('index', project, project,
[author], 1)
]
man_pages = [("index", project, project, [author], 1)]


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'http://docs.python.org/': None}
# intersphinx_mapping = {'http://docs.python.org/': None}
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