# This file is execfile()d with the current directory set to its containing dir.
#
# 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
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import os
import sys


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

__location__ = os.path.dirname(__file__)

# 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.
sys.path.insert(0, os.path.join(__location__, "../src"))


# -- 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 = ["sphinx.ext.autodoc",
              "sphinx.ext.intersphinx",
              "sphinx.ext.todo",
              "sphinx.ext.autosummary",
              "sphinx.ext.viewcode",
              "sphinx.ext.coverage",
              "sphinx.ext.doctest",
              "sphinx.ext.ifconfig",
              "sphinx.ext.mathjax",
              "sphinx.ext.napoleon",
              "nbsphinx",
              "sphinx_gallery.load_style"]

# autodoc configuration
autodoc_typehints = "description"
autodoc_mock_imports = ["anndata",
                        "hnswlib",
                        "captum",
                        "circlify",
                        "matplotlib",
                        "networkx",
                        "numba",
                        "numcodecs",
                        "numpy",
                        "obonet",
                        "pandas",
                        "pegasusio",
                        "pytorch_lightning",
                        "scanpy",
                        "scipy",
                        "seaborn",
                        "tiledb",
                        "tqdm",
                        "torch",
                        "zarr"]

# todo configuration
todo_include_todos = True

# nbsphinx configuration
nbsphinx_thumbnails = {
    'notebooks/cell_search_tutorial_1': '_static/search_thumbnail_1.png',
    'notebooks/cell_search_tutorial_2': '_static/search_thumbnail_2.png',
    'notebooks/cell_search_tutorial_3': '_static/search_thumbnail_3.png',
    'notebooks/cell_annotation_tutorial': '_static/annotation_thumbnail.png',
    'notebooks/advanced_tutorial': '_static/advanced_thumbnail.png'
}

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

# The suffix of source filenames.
source_suffix = ".rst"

# The encoding of source files.
# source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = "index"

# General information about the project.
project = "scimilarity"
copyright = "2023, Genentech, Inc."

# 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.
#
# version: The short X.Y version.
# release: The full version, including alpha/beta/rc tags.
# If you don’t need the separation provided between version and release,
# just set them both to the same value.
try:
    from scimilarity import __version__ as version
except ImportError:
    version = ""

if not version or version.lower() == "unknown":
    version = os.getenv("READTHEDOCS_VERSION", "unknown")  # automatically set by RTD

release = version

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ''
# Else, today_fmt is used as the format for a strftime call.
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"]

# The reST default role (used for this markup: `text`) to use for all documents.
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "sphinx"

# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If this is True, todo emits a warning for each TODO entries. The default is False.
todo_emit_warnings = True


# -- 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 = {
#     "sidebar_width": "300px",
#     "page_width": "1200px"
# }

# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
# html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.
# html_short_title = None

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
# html_logo = ""

# The name of an image file (within the static path) to use as favicon of the
# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
# html_favicon = None

# 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"]

# Custom CSS
html_css_files = ['custom.css']

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
# html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
# html_additional_pages = {}

# If false, no module index is generated.
# html_domain_indices = True

# If false, no index is generated.
# html_use_index = True

# If true, the index is split into individual pages for each letter.
# html_split_index = False

# If true, links to the reST sources are added to the pages.
# html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
# html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = "scimilarity-doc"


# -- 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": "",
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
    ("index", "user_guide.tex", "scimilarity Documentation", "Graham Heimberg", "manual")
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
# latex_logo = ""

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
# latex_use_parts = False

# If true, show page references after internal links.
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
# latex_appendices = []

# If false, no module index is generated.
# latex_domain_indices = True

# -- External mapping --------------------------------------------------------
python_version = ".".join(map(str, sys.version_info[0:2]))
# intersphinx_mapping = {
#     "sphinx": ("https://www.sphinx-doc.org/en/master", None),
#     "python": ("https://docs.python.org/" + python_version, None),
#     "matplotlib": ("https://matplotlib.org", None),
#     "numpy": ("https://numpy.org/doc/stable", None),
#     "sklearn": ("https://scikit-learn.org/stable", None),
#     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
#     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
#     "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
#     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
# }

print(f"loading configurations for {project} {version} ...", file=sys.stderr)