# 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.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
import re
import os

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

project = 'cellpose'
copyright = '2020, Carsen Stringer & Marius Pachitariu'
author = 'Carsen Stringer & Marius Pachitariu'

# The full version, including alpha/beta/rc tags
release = re.sub('^v', '', os.popen('git describe --tags').read().strip())
# The short X.Y version.
version = release

# -- 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.viewcode",
    'sphinx.ext.napoleon',
    # 'sphinxcontrib.autoprogram',
    'sphinxarg.ext',
]

autodoc_mock_imports = [
    "importlib",
    "torch",
    "torchvision",
    "numpy",
    "tqdm",
    "scipy",
    "skimage",
    "cv2",
    "matplotlib",
    "scikit-image",
    "tifffile",
    "fastremap",
    "natsort",
    "numba",
    "segment_anything", 
    "fill_voids"
]

autoapi_dirs = ['../cellpose']

source_suffix = '.rst'

master_doc = 'index'

# 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 = []

# -- Options for HTML output -------------------------------------------------
html_logo = '_static/favicon.ico'
html_favicon = '_static/favicon.ico'

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
html_theme_path = [
    "_themes",
]
html_theme_options = {
    'canonical_url': '',
    'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
    'logo_only': False,
    'display_version': True,
    'prev_next_buttons_location': 'top',
    'style_external_links': False,
    'style_nav_header_background': 'black',
    # Toc options
    'collapse_navigation': True,
    'sticky_navigation': True,
    'navigation_depth': 4,
    'includehidden': True,
    'titles_only': 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']