conf.py

#
# Sphinx configuration for aiida-mlip
#
# 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.

import os
import sys
import time

from aiida import load_profile
from aiida.storage.sqlite_temp import SqliteTempBackend

import aiida_mlip

# -- AiiDA-related setup --------------------------------------------------

# Load AiiDA profile
temp_profile = SqliteTempBackend.create_profile("temp-profile")
load_profile(temp_profile, allow_switch=True)

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

# 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.

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    "aiida.sphinxext",
    "numpydoc",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.mathjax",
    "sphinx.ext.viewcode",
    "sphinxcontrib.contentui",
]

# Add the numpydoc_show_inherited_class_members option
numpydoc_show_inherited_class_members = False

numpydoc_validation_checks = {"all", "EX01", "SA01", "ES01"}
numpydoc_validation_exclude = {r"\.__weakref__$", r"\.__repr__$"}

intersphinx_mapping = {
    "python": ("https://docs.python.org/3", None),
    "aiida": ("https://aiida.readthedocs.io/projects/aiida-core/en/latest", None),
    "ase": ("https://wiki.fysik.dtu.dk/ase/", None),
}

# 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'
master_doc = "index"

# General information about the project.
project = "aiida-mlip"
copyright_first_year = "2024"
copyright_owners = "Federica Zanca, Elliott Kasoar, Jacob Wilkins, Alin M. Elena"

current_year = str(time.localtime().tm_year)
copyright_year_string = (
    current_year
    if current_year == copyright_first_year
    else f"{copyright_first_year}-{current_year}"
)
copyright = f"{copyright_year_string}, {copyright_owners}. All rights reserved"

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

# The short X.Y version.
version = ".".join(release.split(".")[:2])

# 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"

# 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 = ['doc.rst']
# ~ exclude_patterns = ['index.rst']

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
show_authors = True

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

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

html_theme = "furo"
html_logo = "images/aiida-mlip.png"
html_title = f"aiida-mlip v{release}"
html_theme_options = {
    "source_repository": "https://github.com/stfc/aiida-mlip/",
    "source_branch": "main",
    "source_directory": "docs/",
}


# Add any paths that contain custom themes here, relative to this directory.
# ~ html_theme_path = ["."]

# 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 = "images/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']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
# html_extra_path = []

# 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 = False

# 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 = False

# 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 = "https://stfc.github.io/aiida-mlip/"

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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
html_search_language = "en"

# Warnings to ignore when using the -n (nitpicky) option
# We should ignore any python built-in exception, for instance
nitpick_ignore = [("py:class", "Logger"), ("py:class", "QbFields")]


def run_apidoc(_):
    """Runs sphinx-apidoc when building the documentation.

    Needs to be done in conf.py in order to include the APIdoc in the
    build on readthedocs.

    See also https://github.com/rtfd/readthedocs.org/issues/1139
    """
    source_dir = os.path.abspath(os.path.dirname(__file__))
    apidoc_dir = os.path.join(source_dir, "apidoc")
    package_dir = os.path.join(source_dir, os.pardir, os.pardir, "aiida_mlip")

    # In #1139, they suggest the route below, but this ended up
    # calling sphinx-build, not sphinx-apidoc
    # from sphinx.apidoc import main
    # main([None, '-e', '-o', apidoc_dir, package_dir, '--force'])

    import subprocess

    cmd_path = "sphinx-apidoc"
    if hasattr(sys, "real_prefix"):  # Check to see if we are in a virtualenv
        # If we are, assemble the path manually
        cmd_path = os.path.abspath(os.path.join(sys.prefix, "bin", "sphinx-apidoc"))

    options = [
        "-o",
        apidoc_dir,
        package_dir,
        "--private",
        "--force",
        "--no-toc",
    ]

    # See https://stackoverflow.com/a/30144019
    env = os.environ.copy()
    env["SPHINX_APIDOC_OPTIONS"] = (
        "members,special-members,private-members,undoc-members,show-inheritance"
    )
    subprocess.check_call([cmd_path] + options, env=env)


def setup(app):
    app.connect("builder-inited", run_apidoc)