conf.py

"""
pymatgen documentation build configuration file, created by
sphinx-quickstart on Tue Nov 15 00:13:52 2011.

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.
"""

from __future__ import annotations

import os
import sys

from pymatgen.core import __author__, __file__, __version__

# 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.
sys.path.insert(0, os.path.abspath("."))
sys.path.insert(0, os.path.dirname(".."))
sys.path.insert(0, os.path.dirname("../pymatgen"))
sys.path.insert(0, os.path.dirname("../.."))


# -- 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.linkcode", "sphinx.ext.mathjax"]
exclude_patterns = ["../**/tests*"]
exclude_dirnames = ["../**/tests*"]
autoclass_content = "both"

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

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

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

# The master toctree document.
master_doc = "index"

# General information about the project.
project = "pymatgen"
copyright = "2011, " + __author__

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

# 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.
# today_fmt = '%B %d, %Y'

# 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 = False

# 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 = []


# -- 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 = {}

# 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 = "favicon.ico"

# 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_css_files = [
    "css/custom.css",
]

# 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.
htmlhelp_basename = "pymatgendoc"

html_theme_options = {
    "canonical_url": "https://pymatgen.org",
    "logo_only": True,
    "display_version": True,
    "prev_next_buttons_location": None,
    "style_external_links": True,
    "style_nav_header_background": "linear-gradient(0deg, rgba(23,63,162,1) 0%, rgba(0,70,192,1) 100%)",
    "collapse_navigation": True,
    "sticky_navigation": True,
    "navigation_depth": 4,
    "includehidden": True,
    "titles_only": False,
}

html_context = {
    "display_github": True,
    "github_user": "materialsproject",
    "github_repo": "pymatgen",
    "github_version": "master",
    "conf_py_path": "/docs_rst/",
}

# -- 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': '',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
    ("index", "pymatgen.tex", "pymatgen Documentation", __author__, "manual"),
]

# 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 = [("index", "pymatgen", "pymatgen Documentation", [__author__], 1)]

# 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 = [
    (
        "index",
        "pymatgen",
        "pymatgen Documentation",
        __author__,
        "pymatgen",
        "One line description of project.",
        "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'


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

# Bibliographic Dublin Core info.
epub_title = "pymatgen"
epub_author = __author__
epub_publisher = "Pymatgen Development Team"
epub_copyright = copyright

# 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 = ()

# 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 = []

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

# Allow duplicate toc entries.
# epub_tocdup = True


def linkcode_resolve(domain, info):
    """Resolve function for the linkcode extension.
    Thanks to https://github.com/Lasagne/Lasagne/blob/master/docs/conf.py.
    """

    def find_source():
        # try to find the file and line number, based on code from numpy:
        # https://github.com/numpy/numpy/blob/master/doc/source/conf.py#L286
        obj = sys.modules[info["module"]]
        for part in info["fullname"].split("."):
            obj = getattr(obj, part)
        import inspect
        import os

        fn = inspect.getsourcefile(obj)
        fn = os.path.relpath(fn, start=os.path.dirname(__file__))
        source, lineno = inspect.getsourcelines(obj)
        return fn, lineno, lineno + len(source) - 1

    if domain != "py" or not info["module"]:
        return None

    try:
        rel_path, line_start, line_end = find_source()
        # __file__ is imported from pymatgen.core
        filename = f"pymatgen/core/{rel_path}#L{line_start}-L{line_end}"
    except Exception:
        # no need to be relative to core here as module includes full path.
        filename = info["module"].replace(".", "/") + ".py"

    return f"https://github.com/materialsproject/pymatgen/blob/v{__version__}/{filename}"