conf.py

# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# 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

SCIPION_HOME = os.environ.get("SCIPION_HOME")
sys.path.insert(0, os.path.join(SCIPION_HOME, 'software/em/xmipp/bindings/python/'))
sys.path.insert(0, os.path.join(SCIPION_HOME, 'software/em/xmipp/lib/'))
sys.path.insert(0, os.path.join(SCIPION_HOME, 'scipion-em/'))
sys.path.insert(0, os.path.join(SCIPION_HOME, 'scipion-pyworkflow/'))
sys.path.insert(0, os.path.join(SCIPION_HOME, 'scipion-em/pwem/'))
sys.path.insert(0, os.path.join(SCIPION_HOME, 'scipion-pyworkflow/pyworkflow/'))
sys.path.insert(0, os.path.join(SCIPION_HOME))



# -- Project information -----------------------------------------------------

project = u'Scipion'
copyright = u'2022, Scipion team'
author = u'Scipion team'

# The short X.Y version
version = u''
# The full version, including alpha/beta/rc tags
release = u'3.0.0'


# -- 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.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.coverage',
    'sphinx.ext.imgmath',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosectionlabel',
    'sphinxcontrib.bibtex',
    'sphinx_multiversion',
]
bibtex_bibfiles = ['em.bib']
bibtex_reference_style = u'author_year'
autosectionlabel_prefix_document = True

napoleon_google_docstring = False
napoleon_use_param = False
napoleon_use_ivar = True

autodoc_mock_imports = ["psycopg2"]
autoclass_content = "both"

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


# **************************** VERSIONING WITH sphinx-multiversion ***************************************
# Versioning side bar, from https://holzhaus.github.io/sphinx-multiversion/master/templates.html#templates

# Whitelist pattern for tags (set to None to ignore all tags)
smv_tag_whitelist = None

# Whitelist pattern for branches (set to None to ignore all branches)
smv_branch_whitelist = 'release-3.0.0'

# Whitelist pattern for remotes (set to None to use local branches only)
smv_remote_whitelist = None

# Pattern for released versions
smv_released_pattern = r'^tags/.*$'

# Format for versioned output directories inside the build directory
smv_outputdir_format = '{ref.name}'

# Determines whether remote or local git branches/tags are preferred if their output dirs conflict
smv_prefer_remote_refs = False

# ******************************** END OF VERSIONING ******************************************************

# 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'

# add file with custom css
def setup(app):
    app.add_css_file('custom.css')

# use :numref: for references (instead of :ref:)
numfig = True
numfig_format = {'figure': 'Fig. %s', 'table': 'Tab. %s', 'code-block': 'Code %s'}

# 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 = "en"

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = [
    u'build',
    'Thumbs.db',
    '.DS_Store',
    'docs/developer/scipion-web*',
    'docs/developer/introduction-scipion-web.rst',
]

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None


# -- 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 = 'sphinx_rtd_theme'

# 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 = {
    'display_version': True,
    'style_external_links': True,
}

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# 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', '_static/pdfs']

# Style


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

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


# -- 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, 'Scipion.tex', u'Scipion Documentation',
     u'Scipion team', '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, 'scipion', u'Scipion 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, 'Scipion', u'Scipion Documentation',
     author, 'Scipion', 'One line description of project.',
     'Miscellaneous'),
]


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

# Bibliographic Dublin Core info.
epub_title = project

# 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']


# -- Extension configuration -------------------------------------------------

# -- Options for intersphinx extension ---------------------------------------

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

# -- Options for todo extension ----------------------------------------------

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