conf.py

#!/usr/bin/env python3
#
# PlasmaPy documentation build configuration file, created by
# sphinx-quickstart on Wed May 31 18:16:46 2017.
#
# 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

from datetime import datetime
from pkg_resources import parse_version
from sphinx.application import Sphinx

sys.path.insert(0, os.path.abspath(".."))
sys.path.insert(0, os.path.abspath("."))

from plasmapy import __version__ as release  # noqa

# -- General configuration ------------------------------------------------
autosummary_generate = True
automodapi_custom_groups = {
    "aliases": {
        "title": "Aliases",
        "description": (
            "PlasmaPy provides short-named (alias) versions of the most "
            "common plasma functionality.  These aliases are only given to "
            "functionality where there is a common lexicon in the community, "
            "for example `~plasmapy.formulary.frequencies.plasma_frequency` "
            " has the alias `~plasmapy.formulary.frequencies.wp_`.  All aliases "
            "in PlasmaPy are denoted with a trailing underscore ``_``."
        ),
        "dunder": "__aliases__",
    },
    "lite-functions": {
        "title": "Lite-Functions",
        "description": (
            """
            Much of PlasmaPy's functionality incorporates `Astropy units
            <https://docs.astropy.org/en/stable/units/>`_ for user convenience and
            to mitigate calculation errors from inappropriate units, but this
            comes at the sacrifice of speed.  While this penalty is not significant
            for typical use, it can become substantial during intensive numerical
            calculations. **Lite-functions** are introduced for the specific case
            where speed matters, but **[USER NOTICE]** this comes with the
            reduction of safeguards so a user needs to know what they are doing!
            For additional details look to the glossary entry for
            :term:`lite-function`.
            """
        ),
        "dunder": "__lite_funcs__",
    },
}
automodapi_group_order = (
    "modules",
    "classes",
    "exceptions",
    "warnings",
    "functions",
    "aliases",
    "lite-functions",
    "variables",
)

# If your documentation needs a minimal Sphinx version, state it here.

needs_sphinx = "4.4"

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones. When extensions are removed or added, please update the section
# in docs/doc_guide.rst on Sphinx extensions.

extensions = [
    "sphinx.ext.autodoc",
    "sphinx.ext.extlinks",
    "sphinx.ext.graphviz",
    "sphinx.ext.intersphinx",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.todo",
    "nbsphinx",
    "sphinxcontrib.bibtex",
    "sphinx_copybutton",
    "sphinx_gallery.load_style",
    "IPython.sphinxext.ipython_console_highlighting",
    "sphinx_changelog",
    "hoverxref.extension",
    "notfound.extension",
    "sphinx_issues",
    "sphinx_reredirects",
    "plasmapy_sphinx",
]

# Configure sphinxcontrib-bibtex

bibtex_bibfiles = ["bibliography.bib"]
bibtex_default_style = "plain"
bibtex_reference_style = "author_year"
bibtex_cite_id = "{key}"

# Intersphinx generates automatic links to the documentation of objects
# in other packages. When mappings are removed or added, please update
# the section in docs/doc_guide.rst on references to other packages.

intersphinx_mapping = {
    "readthedocs": ("https://docs.readthedocs.io/en/stable/", None),
    "python": ("https://docs.python.org/3/", None),
    "numpy": ("https://numpy.org/doc/stable/", None),
    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
    "astropy": ("https://docs.astropy.org/en/stable/", None),
    "pytest": ("https://docs.pytest.org/en/stable/", None),
    "sphinx_automodapi": (
        "https://sphinx-automodapi.readthedocs.io/en/latest/",
        None,
    ),
    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
    "numba": ("https://numba.readthedocs.io/en/stable/", None),
    "lmfit": ("https://lmfit.github.io/lmfit-py/", None),
}

hoverxref_intersphinx = [
    "readthedocs",
    "python",
    "numpy",
    "scipy",
    "pandas",
    "astropy",
    "pytest",
    "sphinx_automodapi",
    "sphinx",
    "numba",
    "lmfit",
]

autoclass_content = "both"
autodoc_typehints_format = "short"

# Configure sphinx-issues

issues_github_path = "PlasmaPy/PlasmaPy"

# 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 root toctree document.
root_doc = "index"

# General information about the project.
project = "PlasmaPy"
author = "PlasmaPy Community"
copyright = f"2015–{datetime.utcnow().year}, {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 full version, including alpha/beta/rc tags.
#  Note: If plasmapy.__version__ can not be defined then it is set to 'unknown'.
#        However, release needs to be a semantic style version number, so set
#        the 'unknown' case to ''.
release = "" if release == "unknown" else release
pv = parse_version(release)
release = pv.public
version = ".".join(release.split(".")[:2])  # short X.Y version
revision = pv.local[1:] if pv.local is not None else ""

# This is added to the end of RST files — a good place to put substitutions to
# be used globally.
rst_epilog = ""
with open("common_links.rst") as cl:
    rst_epilog += cl.read()

# 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 patterns also effect to html_static_path and html_extra_path
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "notebooks/langmuir_samples",
    "**.ipynb_checkpoints",
    "plasmapy_sphinx",
    "common_links.rst",
    "**Untitled*",
]

html_extra_path = ["robots.txt"]

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

default_role = "py:obj"

# Customizations for make linkcheck using regular expressions

linkcheck_allowed_redirects = {
    r"https://doi\.org/.+": r"https://.+",  # DOI links are more persistent
    r"https://docs.+\.org": r"https://docs.+\.org/en/.+",
    r"https://docs.+\.io": r"https://docs.+\.io/en/.+",
    r"https://docs.+\.com": r"https://docs.+\.com/en/.+",
    r"https://docs.+\.dev": r"https://docs.+\.dev/en/.+",
    r"https://en.wikipedia.org/wiki.+": "https://en.wikipedia.org/wiki.+",
    r"https://.+\.readthedocs\.io": r"https://.+\.readthedocs\.io/en/.+",
    r"https://www\.sphinx-doc\.org": r"https://www\.sphinx-doc\.org/en/.+",
    r"https://.+/github\.io": r"https://.+/github\.io/en/.+",
    r"https://.+": r".+(google|github).+[lL]ogin.+",  # some links require logins
    r"https://jinja\.palletsprojects\.com": r"https://jinja\.palletsprojects\.com/.+",
    r"https://pip\.pypa\.io": r"https://pip\.pypa\.io/en/.+",
    r"https://www.python.org/dev/peps/pep.+": "https://peps.python.org/pep.+",
}

linkcheck_anchors = True
linkcheck_anchors_ignore = [
    "/room",
    r".+openastronomy.+",
    "L[0-9].+",
    "!forum/plasmapy",
]

redirects = {
    "development": "../contributing/",
    "development/index": "../contributing/index.html",
    "development/changelog_guide": "../contributing/changelog_guide.html",
    "development/code_guide": "../contributing/code_guide.html",
    "development/doc_guide": "../contributing/doc_guide.html",
    "development/install_dev": "../contributing/install_dev.html",
    "development/release_guide": "../contributing/release_guide.html",
    "development/testing_guide": "../contributing/testing_guide.html",
}

# Use a code highlighting style that meets the WCAG AA contrast standard
pygments_style = "default"

# adapted from sphinx-hoverxref conf.py
if os.environ.get("READTHEDOCS"):
    # Building on Read the Docs
    hoverxref_api_host = "https://readthedocs.org"

    if os.environ.get("PROXIED_API_ENDPOINT"):
        # Use the proxied API endpoint
        # - A RTD thing to avoid a CSRF block when docs are using a
        #   custom domain
        hoverxref_api_host = "/_"

hoverxref_tooltip_maxwidth = 600  # RTD main window is 696px
hoverxref_auto_ref = True
hoverxref_mathjax = True
hoverxref_sphinxtabs = True

# hoverxref has to be applied to these
hoverxref_domains = ["py", "cite"]
hoverxref_roles = ["confval", "term"]

hoverxref_role_types = {
    # roles with cite domain
    "p": "tooltip",
    "t": "tooltip",
    #
    # roles with py domain
    "attr": "tooltip",
    "class": "tooltip",
    "const": "tooltip",
    "data": "tooltip",
    "exc": "tooltip",
    "func": "tooltip",
    "meth": "tooltip",
    "mod": "tooltip",
    "obj": "tooltip",
    #
    # roles with std domain
    "confval": "tooltip",
    "hoverxref": "tooltip",
    "ref": "tooltip",
    "term": "tooltip",
}

# Using sphinx.ext.extlinks lets us simplify the process of creating
# links to commonly used external sites. The key of the extlink becomes
# a new role, and the corresponding tuple contains the base url and the
# caption. For example, we can now do :orcid:`0000-0000-0000-0000` and
# have a link create to the corresponding ORCID page. New roles should
# be added to rst-roles in setup.cfg to avoid being caught by
# flake8-rst-docstrings.

extlinks = {
    "orcid": ("https://orcid.org/%s", "%s"),
    "wikipedia": ("https://en.wikipedia.org/wiki/%s", "%s"),
}

# Specify patterns to ignore when doing a nitpicky documentation build.
# These may include common expressions like "real number" as well as
# workarounds for nested inline literals as defined in docs/common_links.py

python_role = "py:.*"

nitpick_ignore_regex = [
    (python_role, "and"),
    (python_role, "array .*"),
    (python_role, "array_like"),
    (python_role, "callable"),
    (python_role, "dictionary.*"),
    (python_role, "function"),
    (python_role, ".*integer.*"),
    (python_role, "iterable"),
    (python_role, "key"),
    (python_role, "keyword-only"),
    (python_role, ".* object"),
    (python_role, "optional"),
    (python_role, "or"),
    (python_role, "Real"),
    (python_role, ".*real number.*"),
    (python_role, ".*representation.*"),
    (python_role, "shape.*"),
    (python_role, r"u\..*"),
    (python_role, ".*Unit.*"),
    # pytest helpers
    (python_role, "_pytest.*"),
    (python_role, "Failed"),
    # charged_particle_radiography
    (python_role, "2 ints"),
    (python_role, "a single int"),
    (python_role, "Tuple of 1"),
    # thomson
    (python_role, "Ne"),
    (python_role, "Ni"),
    # for reST workarounds defined in docs/common_links.rst
    (python_role, "h5py"),
    (python_role, "IPython.sphinxext.ipython_console_highlighting"),
    (python_role, "lmfit"),
    (python_role, "mpmath"),
    (python_role, "nbsphinx"),
    (python_role, "numba"),
    (python_role, "xarray"),
    # plasmapy_sphinx
    (python_role, "automod.*"),
    (python_role, "Builder"),
    (python_role, "docutils.*"),
    (python_role, "level"),
    (python_role, ".*member.*"),
    (python_role, "OptionSpec"),
    (python_role, "py"),
    (python_role, "[Ss]phinx.*"),  # also for reST workarounds in docs/common_links.rst
    # The following patterns still need to be fixed.
    (python_role, "json.decoder.JSONDecoder"),
    (python_role, "plasmapy.analysis.swept_langmuir.find_floating_potential"),
    (python_role, "plasmapy.particles.particle_collections"),
    (python_role, "plasmapy.utils.decorators.lite_func"),
]

# -- 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 = 'traditional'
# html_theme = 'agogo'
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_logo = "./_static/with-text-light-190px.png"
html_theme_options = {
    "logo_only": True,
    #
    # TOC options
    #   https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#theme-options
    "includehidden": False,
}

# 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"]

# A list of prefixes that are ignored for sorting the Python module
# index (e.g., if this is set to ['foo.'], then foo.bar is shown under
# B, not F).
modindex_common_prefix = ["plasmapy."]

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

# Output file base name for HTML help builder.
htmlhelp_basename = "PlasmaPydoc"

# -- 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 = [
    (
        root_doc,
        "PlasmaPy.tex",
        "PlasmaPy Documentation",
        "PlasmaPy 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 = [(root_doc, "plasmapy", "PlasmaPy 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 = [
    (
        root_doc,
        "PlasmaPy",
        "PlasmaPy Documentation",
        author,
        "PlasmaPy",
        "Python package for plasma physics",
        "Miscellaneous",
    )
]

html_favicon = "./_static/icon.ico"

# -- NBSphinx options

nbsphinx_thumbnails = {
    "notebooks/*": "_static/graphic-circular.png",
    "notebooks/*/*": "_static/graphic-circular.png",
    "notebooks/diagnostics/langmuir_analysis": (
        "_static/notebook_images/langmuir_analysis.png"
    ),
    "notebooks/formulary/magnetosphere": (
        "_static/notebook_images/mms.png"
    ),  # public domain
    "notebooks/getting_started/units": (
        "_static/notebook_images/astropy_logo_notext.png"
    ),  # CC BY-SA
    "notebooks/formulary/solar_plasma_beta": "_static/notebook_images/coronal_loops.png",
    "notebooks/plasma/grids_cartesian": (
        "_static/notebook_images/uniform_grid_thumbnail.png"
    ),
    "notebooks/plasma/grids_nonuniform": (
        "_static/notebook_images/nonuniform_grid_thumbnail.png"
    ),
}

# adapted from
# https://github.com/spatialaudio/nbsphinx/blob/58b8034dd9d7349c1b4ac3e7a7d6baa87ab2a6a9/doc/conf.py

# This is processed by Jinja2 and inserted before each notebook
nbsphinx_prolog = r"""
{% set docname = 'docs/' + env.doc2path(env.docname, base=None) %}
{% set nb_base = 'tree' if env.config.revision else 'blob' %}
{% set nb_where = env.config.revision if env.config.revision else 'main' %}

.. raw:: html

    <div class="admonition note">
      <p style="margin-bottom:0px">
        This page was generated by
        <a href="https://nbsphinx.readthedocs.io/">nbsphinx</a> from
        <a class="reference external" href="https://github.com/PlasmaPy/PlasmaPy/{{ nb_base|e }}/{{ nb_where|e }}/{{ docname|e }}">{{ docname|e }}</a>.
        <br>
        Interactive online version:
        <a href="https://mybinder.org/v2/gh/PlasmaPy/PlasmaPy/{{ nb_where|e }}/?filepath={{ docname|e }}"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>.
      </p>
    </div>

.. raw:: latex

    \nbsphinxstartnotebook{\scriptsize\noindent\strut
    \textcolor{gray}{The following section was generated from
    \sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
"""


def setup(app: Sphinx) -> None:
    app.add_config_value("revision", "", True)
    app.add_css_file("css/admonition_color_contrast.css")
    app.add_css_file("css/plasmapy.css", priority=600)