conf.py

# -*- coding: utf-8 -*-
#
# pyOpenMS documentation build configuration file, created by
# sphinx-quickstart on Fri Jun  1 15:50:55 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 subprocess
import glob
import shutil
import urllib.request
import contextlib
import sys
from datetime import date

sys.path.append(os.path.abspath("./_ext"))

from platform import python_version_tuple
from sys import platform

# -- 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 = [
    'glossary_warnings',
    'sphinx_copybutton', 'sphinx.ext.autodoc',
    'sphinx.ext.autosummary', 'sphinx.ext.mathjax',
    'sphinx_remove_toctrees',
    'chemrole',
]

## warn about invalid references (e.g. invalid class names)
nitpicky = True              
nitpick_ignore = []

autosummary_generate = True
autosummary_imported_members = True
remove_from_toctrees = [
    "apidocs/_autosummary/pyopenms/pyopenms.*.rst",
    "apidocs/_autosummary/pyopenmssubmodules/pyopenms.Constants.*.rst",
    "apidocs/_autosummary/pyopenmssubmodules/pyopenms.plotting.*.rst"]
autodoc_docstring_signature = True

# 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 master toctree document.
master_doc = 'index'

# General information about the project.
project = u'pyOpenMS'
copyright = f'{date.today().year}, OpenMS Inc'
author = u'OpenMS Team'

# 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 = u'3.5.0'
# The full version, including alpha/beta/rc tags.
release = version
rtd_branch = os.environ.get('READTHEDOCS_GIT_IDENTIFIER', '')

# if the variable is not set (e.g., when building locally and not on RTD)
if not rtd_branch:
    release += 'local'

# if not built from release branch or tag
elif not rtd_branch.startswith('release') and not rtd_branch.startswith('Release'):
    release += 'dev'

# 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 = []

# 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 = False

# -- 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 = 'pydata_sphinx_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 = {
    "switcher": {
        "json_url": "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master/docs/source/_static/switcher.json",
        "version_match": release
    },
    "navbar_end": ["navbar-run-binder", "navbar-icon-links", "version-switcher"],
    "navbar_persistent": [], # default: ["search-button"] but we don't need it since we use the search bar in the sidebar
    "use_edit_page_button": True,
    "logo": {
        "alt_text": "pyOpenMS Documentation - Home",
    },
    "icon_links": [
        {
            # Label for this link
            "name": "GitHub",
            # URL where the link will redirect
            "url": "https://github.com/OpenMS/OpenMS",  # required
            # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
            "icon": "fa-brands fa-github",
            # The type of image to be used (see below for details)
            "type": "fontawesome",
        },
        {
            "name": "Discord",
            "url": "https://discord.com/invite/4TAGhqJ7s5",
            "icon": "fa-brands fa-discord",
        },
        {
            "name": "PyPI",
            "url": "https://pypi.org/project/pyopenms",
            "icon": "pypi", # defined in our custom.css
        },
        {
            "name": "OpenMS project",
            "url": "https://www.openms.de",
            "icon": "_static/OpenMS.svg",
            "type": "local",
            "attributes": {"target": "_blank"},
        },
    ],
    "show_nav_level": 1
}

html_context = {
    # "github_url": "https://github.com", # or your GitHub Enterprise site
    "github_user": "OpenMS",
    "github_repo": "pyopenms-docs",
    "github_version": "master",
    "doc_path": "docs/source/",
}

html_sidebars = {
    "**": ["search-field.html", "sidebar-nav-bs.html"]
}

html_favicon = 'img/pyOpenMSlogo_color.svg'
html_logo = 'img/pyOpenMSlogo_color.svg'

# 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 = ["custom.css"]
# adding custom icons probably only possible with newest pydata theme version
html_js_files = ["piwik.js", "matomo.js", "custom.js"]

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

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

# -- 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, 'pyOpenMS.tex', u'pyOpenMS Documentation',
     u'OpenMS 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, 'pyopenms', u'pyOpenMS 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, 'pyOpenMS', u'pyOpenMS Documentation',
     author, 'pyOpenMS', 'One line description of project.',
     'Miscellaneous'),
]


def env_get_outdated(app, env, added, changed, removed):
    return ['index']


def setup(app):
    app.connect('env-get-outdated', env_get_outdated)