7.2. Documentation

7.2.1. Overview

The documentation should contain information about the project, its usage as well as implementation and programming details. All should be presented as easily navigable webpage which includes figures, equations and code snippets.

To allow for a simple and up-to-date code reference the process should be automatic, by generating it from typing hints and docstrings.

7.2.2. Workflow

The gen_docs.yml action compiles the documentation and publishes it in the gh-pages branch. In the future, this content will be published on a webpage.

Internally the workflow executes the docs environment for tox (see the tox file), which builds the documentation with the help of Sphinx. The steps also include an automatic generation of a changelog and a source file toctree.

7.2.3. Documentation Generation

The documentation is created with Sphinx, which uses reStructuredText as markup language. The html builder of Sphinx compiles a webpage including the self-written documentation, automatically generated code information, as well as indices for searching.

The following extensions are used:

doctest	automatic testing of documentation code examples
autodoc	automatic source code documentation generation
intersphinx	linking to the documentation of external packages
mathjax	LaTeX equations
sphinxcontrib.bibtex	bibliography management
Shibuya Sphinx Theme	A modern looking theme
Sphinx Sitemap	Generate sitemaps while building the documentation
Sphinx Mathjax Offline	Provides the mathjax js and font files without having to rely on an external CDN

Additionally, a custom css (docs/source/_static/css/custom.css) adapts the formatting to our needs.

Documentation source files can be found under docs/source/ The Sphinx configuration can be found below.

Content of docs/source/conf.py

# Configuration file for the Sphinx documentation builder.
#

# -- Path setup --------------------------------------------------------------

# 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
import datetime

sys.path.insert(0, os.path.abspath('..'))
sys.path.insert(0, os.path.abspath(os.path.join('..', '..')))


# -- Project information -----------------------------------------------------

# load package information
metadata = {}
path = os.path.join("..", "..", "optrace", "metadata.py")
with open(path, "r") as f:
    exec(f.read(), metadata)

# assign metadata
project = metadata["name"]
release = metadata["version"]
author = metadata["author"]
copyright = f"{datetime.date.today().year}, {author}"
language = "en"

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

# 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.intersphinx',
        'sphinx.ext.mathjax',
        'sphinx.ext.doctest',
        'sphinxcontrib.bibtex',
        'sphinx_sitemap',
        'sphinx-mathjax-offline',
]

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

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []

bibtex_bibfiles = ['bib.bib']
bibtex_default_style = 'unsrt'

# -- 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 = "shibuya"

# 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']
html_baseurl = metadata["documentation"]

html_theme_options = {
    "nav_links": [
        {
            "title": "Examples",
            "url": "./examples"
        },
        {
            "title": "Installation",
            "url": "./installation"
        },
        {
            "title": "User Guide",
            "url": "./usage/index"
        },
        {
            "title": "GitHub Repo",
            "url": "https://github.com/drocheam/optrace"
        }
    ],
    "accent_color": "cyan",
    "color_mode": "dark",
}

html_context = {
   "default_mode": "dark"
}

numfig = True
math_numfig = True
math_number_all = True

# lazy load equations
# improves loading speed of details/ pages significantly
mathjax3_config = {
    'loader': {'load': ['ui/lazy']},
    'options': {
        'lazyMargin': '400px',
        'lazyAlwaysTypeset': None,
    },
}

# links to libraries
intersphinx_mapping = {'python': ('http://docs.python.org/3', None),
                       'coverage': ('https://coverage.readthedocs.io/en/latest', None),
                       'numpy': ('http://numpy.org/doc/stable', None),
                       'pytest': ('https://docs.pytest.org/en/stable', None),
                       'scipy': ('http://docs.scipy.org/doc/scipy/', None),
                       'traits': ('https://docs.enthought.com/traits/', None),
                       'matplotlib': ('http://matplotlib.org/stable', None),
                       'mayavi': ('https://docs.enthought.com/mayavi/mayavi', None)}

autodoc_default_options = {
	'members': True,
    'undoc-members': True,
    'special-members' : '__call__, __eq__, __ne__',
    'exclude-members': '__weakref__'
}

autodoc_member_order = 'groupwise'

# move docstring from __init__ to class
autoclass_content = "init"

# move typehints from header to description
autodoc_typehints = "description"

# settings for sitemap generation
sitemap_locales = [None]
sitemap_url_scheme = "{link}"
sitemap_excludes = [
    "development/notes.html",
    "development/changelog.html",
    "development/packaging.html",
    "development/documentation.html",
    "development/testing.html",
    "development/index.html",
    "search.html",
    "impressum.html",
    "genindex.html",
    "py-modindex.html",
]

# -- Misc Options -------------------------------------------------

# ignore links that seemingly only work in a browser and not in automated tests
linkcheck_ignore = [
    'https://doi.org/10.1002/9783527648962.app1',
    'https://www.publicdomainpictures.net/en/view-image.php',
    'https://www.pexels.com/photo/sliced-fruits-on-tray-1132047/',
    'https://www.pexels.com/photo/photo-of-people-standing-near-blackboard-3184393/',
    'https://www.pexels.com/photo/green-island-in-the-middle-of-the-lake-during-daytime-724963/',
    'https://www.pexels.com/photo/green-2-seat-sofa-1918291/',
    'https://www.pexels.com/photo/documents-on-wooden-surface-95916/',
    'https://www.pexels.com/photo/cars-on-street-during-night-time-3158562/',
    'https://stackoverflow.com/questions/40065321/how-to-include-git-dependencies-in-setup-py-for-pip-installation',
    'https://www.edmundoptics.com/knowledge-center/tech-tools/focal-length/',
    'https://doi.org/10.1080/713818864',
    'https://doi.org/10.1167/8.2.13',
    'https://doi.org/10.1080/10867651.1997.10487479',
    'https://stackoverflow.com/questions/68073819/pypi-install-requires-direct-links',
    'https://eyewiki.org/Lens_Material_Properties',
]

linkcheck_timeout = 15
linkcheck_workers = 3
linkcheck_rate_limit_timeout = 15

# only check doctest blocks
doctest_test_doctest_blocks = ""