lipase/doc/sphinx/source/conf.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# lipase documentation build configuration file, created by
# sphinx-quickstart on Tue Apr 14 10:32:30 2020.
#
# 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.

# 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.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../../../src'))


# use mock mechanism for modules that sphinx cannot find (eg ij, which is only available in jython)
#import mock   # sudo apt install python3-mock

#MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot']
MOCK_MODULES = ['ij', 'ij.process', 'ij.plugin', 'ncsa', 'jarray']
autodoc_mock_imports = MOCK_MODULES
#for mod_name in MOCK_MODULES:
#    sys.modules[mod_name] = mock.Mock()


def skip(app, what, name, obj, would_skip, options):
    if name == "__init__":
        return False
    return would_skip

def setup(app):
    app.connect("autodoc-skip-member", skip)

# -- 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.napoleon',
    'sphinx.ext.doctest',
    'sphinx.ext.todo',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages']


# enable automatic translation of google style comments to rest comments as google style comments are less wordy (see https://brendanhasz.github.io/2019/01/05/sphinx.html#napoleon-extension)
napoleon_google_docstring = True
napoleon_numpy_docstring = True


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

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = 'lipase'
copyright = '2020, Guillaume Raffy'
author = 'Guillaume Raffy'

# 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.
version = '1.00'
# The full version, including alpha/beta/rc tags.
release = '1.00'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []

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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True


# -- 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 = 'classic'

# 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 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']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
html_sidebars = {
    '**': [
        'relations.html',  # needs 'show_related': True theme option to display
        'searchbox.html',
    ]
}


# -- Options for HTMLHelp output ------------------------------------------

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


# -- 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.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# 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 = [
    (master_doc, 'lipase.tex', 'lipase Documentation',
     'Guillaume Raffy', 'manual'),
]


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

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'lipase', 'lipase Documentation',
     [author], 1)
]


# -- 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 = [
    (master_doc, 'lipase', 'lipase Documentation',
     author, 'lipase', 'One line description of project.',
     'Miscellaneous'),
]



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

# Bibliographic Dublin Core info.
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright

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