# -*- coding: utf-8 -*-
# The Procrustes library provides a set of functions for transforming
# a matrix to make it as similar as possible to a target matrix.
#
# Copyright (C) 2017-2024 The QC-Devs Community
#
# This file is part of Procrustes.
#
# Procrustes is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# Procrustes is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
# --

# Procrustes documentation build configuration file, created by
# sphinx-quickstart on Wed Apr 11 19:35:53 2018.
#
# 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('../'))
# sys.path.append(os.path.abspath('sphinxext'))


# -- 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.todo',
    'sphinx.ext.mathjax',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
    'numpydoc',
    # 'sphinx.ext.autosummary',
    'sphinx.ext.doctest',
    'sphinx.ext.inheritance_diagram',
    'IPython.sphinxext.ipython_console_highlighting',
    # for adding “copy to clipboard” buttons to all text/code boxes
    'sphinx_copybutton',
    # 'IPython.sphinxext.ipython_directive',
    'autoapi.extension',
    'nbsphinx',
    'sphinxcontrib.bibtex']

# List of arguments to be passed to the kernel that executes the notebooks:
nbsphinx_execute_arguments = [
    "--InlineBackend.figure_formats={'svg', 'pdf'}",
    "--InlineBackend.rc=figure.dpi=200",
]
# nbsphinx_input_prompt = 'In [%s]:'
# nbsphinx_output_prompt = 'Out[%s]:'
# explicitly dis-/enabling notebook execution
nbsphinx_execute = 'never'

# Don't add .txt suffix to source files:
html_sourcelink_suffix = ''

# This is processed by Jinja2 and inserted before each notebook

# nbsphinx_prolog = r"""
nbsphinx_epilog = r"""
{% set docname = env.docname.split("/")[-1] %}

.. raw:: html

.. role:: raw-html(raw)
 :format: html
.. nbinfo::
 The corresponding file can be obtained from:

 - Jupyter Notebook: :download:`{{docname+".ipynb"}}`
 - Interactive Jupyter Notebook: :raw-html:`<a href="https://mybinder.org/v2/gh/theochem/procrustes/master?filepath=doc%2Fnotebooks%2F/{{ docname }}.ipynb"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>`    """

autoapi_type = 'python'
autoapi_dirs = ['../procrustes']
autoapi_generate_api_docs = False

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

mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"

# mathjax configuration
mathjax_config = {
    'TeX': {'equationNumbers': {'autoNumber': 'AMS', 'useLabelIds': True}},
}

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

# The master toctree document.
master_doc = 'index'

# number the figures
numfig = True

# General information about the project.
project = 'Procrustes'
copyright = "2017-2024, The QC-Devs Community"
author = 'The QC-Devs Community'

# 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 = "1.1.0"
# The full version, including alpha/beta/rc tags.
release = "1.1.0alpha"

# 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 = 'python'

# 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 = ['_build', 'Thumbs.db', '_themes/*', '.DS_Store']

# 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 = 'alabaster'
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 = {}

# 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_static_path = []

# 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 = 'Procrustesdoc'

# -- 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, 'Procrustes.tex', 'Procrustes Documentation',
     'The QC-Devs Community', '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, 'procrustes', 'Procrustes 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, 'Procrustes', 'Procrustes Documentation',
     author, 'Procrustes', 'One line description of project.',
     'Miscellaneous'),
]

# -- Custom Procrustes-specific settings -------------------------------------------

# Put class docstring and the __init__ docstring together in the documentation
# for your class when you use the autoclass directive.
autoclass_content = 'both'
autodoc_member_order = 'bysource'

# autodoc_default_options = {'members': True,
#                            'undoc-members': None,
#                            'inherited-members': None,
#                            'special-members': None,
#                            'show-inheritance': None}

# Specify the location of .bib file(s)
bibtex_bibfiles = ["zreference.bib"]
