conf.py

# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

# -- 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.

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

project = 'CLASTER'
copyright = '2022, Marc Pielies Avelli'
author = 'Marc Pielies Avelli'
version = '2024.05.29'
release = '2024.05.29'

# -- 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.autodoc.typehints',
    'sphinx.ext.viewcode',
    'sphinx.ext.intersphinx',
    'myst_nb',
    'sphinx.ext.napoleon',
    # 'sphinx_new_tab_link',
]

#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
nb_execution_mode = "off"

myst_enable_extensions = ["dollarmath", "amsmath"]

# Plolty support through require javascript library
# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
# html_js_files = ["https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"]

# https://myst-nb.readthedocs.io/en/latest/configuration.html
# Execution
nb_execution_raise_on_error = True
# Rendering
nb_merge_streams = True

# 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 = ['_build', 'Thumbs.db', 'jupyter_execute','.DS_Store']


# Intersphinx options
intersphinx_mapping = {
    "python": ("https://docs.python.org/3", None),
    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
    "scikit-learn": ("https://scikit-learn.org/stable/", None),
    "matplotlib": ("https://matplotlib.org/stable/", None),
}

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

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
# See:
# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
html_title = "CLASTER"
html_theme = "sphinx_book_theme"
# html_logo = "_static/logo-wide.svg"
# html_favicon = "_static/logo-square.svg"
html_theme_options = {
    "github_url": "https://github.com/RasmussenLab/CLASTER",
    "repository_url": "https://github.com/RasmussenLab/CLASTER",
    "repository_branch": "master",
    "home_page_in_toc": True,
    # "path_to_docs": "",
    "show_navbar_depth": 1,
    "use_edit_page_button": True,
    "use_repository_button": True,
    "use_download_button": True,
    "launch_buttons": {
        "colab_url": "https://colab.research.google.com"
        #     "binderhub_url": "https://mybinder.org",
        #     "notebook_interface": "jupyterlab",
    },
    "navigation_with_keys": 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"]