#!/usr/bin/env python

# mypy: ignore-errors

import sys

from datetime import datetime

from importlib.metadata import metadata

from pathlib import Path

HERE = Path(__file__).parent

sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]

needs_sphinx = "4.3"

info = metadata("ehrapy")

project_name = info["Name"]

author = info["Author"]

copyright = f"{datetime.now():%Y}, {author}."

version = info["Version"]

urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))

repository_url = urls["Source"]

release = info["Version"]

github_repo = "ehrapy"

extensions = [

    "myst_parser",

    "sphinx.ext.autodoc",

    "sphinx.ext.intersphinx",

    "sphinx.ext.viewcode",

    "nbsphinx",

    "nbsphinx_link",

    "sphinx.ext.mathjax",

    "sphinx.ext.napoleon",

    "sphinx_autodoc_typehints",  # needs to be after napoleon

    "sphinx.ext.autosummary",

    "sphinx_copybutton",

    "sphinx_gallery.load_style",

    "sphinx_remove_toctrees",

    "sphinx_design",

]

# remove_from_toctrees = ["tutorials/notebooks/*", "api/reference/*"]

# for sharing urls with nice info

ogp_site_url = "https://ehrapy.readthedocs.io/en/latest/"

ogp_image = "https://ehrapy.readthedocs.io/en/latest//_static/logo.png"

# nbsphinx specific settings

exclude_patterns = [

    "_build",

    "Thumbs.db",

    ".DS_Store",

    "auto_*/**.ipynb",

    "auto_*/**.md5",

    "auto_*/**.py",

    "**.ipynb_checkpoints",

]

nbsphinx_execute = "never"

templates_path = ["_templates"]

# source_suffix = ".md"

autosummary_generate = True

autodoc_member_order = "bysource"

napoleon_google_docstring = True  # for pytorch lightning

napoleon_numpy_docstring = True

napoleon_include_init_with_doc = False

napoleon_use_rtype = True  # having a separate entry generally helps readability

napoleon_use_param = True

napoleon_custom_sections = [("Params", "Parameters")]

todo_include_todos = False

numpydoc_show_class_members = False

annotate_defaults = True  # scanpydoc option, look into why we need this

myst_enable_extensions = [

    "colon_fence",

    "dollarmath",

    "amsmath",

]

master_doc = "index"

intersphinx_mapping = {

    "anndata": ("https://anndata.readthedocs.io/en/stable/", None),

    "ipython": ("https://ipython.readthedocs.io/en/stable/", None),

    "matplotlib": ("https://matplotlib.org/", None),

    "numpy": ("https://numpy.org/doc/stable/", None),

    "pandas": ("https://pandas.pydata.org/docs/", None),

    "python": ("https://docs.python.org/3", None),

    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),

    "pynndescent": ("https://pynndescent.readthedocs.io/en/latest/", None),

    "sklearn": ("https://scikit-learn.org/stable/", None),

    "torch": ("https://pytorch.org/docs/master/", None),

    "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),

    "pytorch_lightning": ("https://pytorch-lightning.readthedocs.io/en/stable/", None),

    "pyro": ("http://docs.pyro.ai/en/stable/", None),

    "pymde": ("https://pymde.org/", None),

    "flax": ("https://flax.readthedocs.io/en/latest/", None),

    "jax": ("https://jax.readthedocs.io/en/latest/", None),

    "lamin": ("https://lamin.ai/docs", None),

    "lifelines": ("https://lifelines.readthedocs.io/en/latest/", None),

}

language = "en"

typehints_defaults = "comma"

pygments_style = "default"

pygments_dark_style = "native"

# html_show_sourcelink = True

html_theme = "furo"

html_title = "ehrapy"

html_logo = "_static/ehrapy_logos/ehrapy_pure.png"

html_theme_options = {

    "sidebar_hide_name": True,

    "light_css_variables": {

        "color-brand-primary": "#003262",

        "color-brand-content": "#003262",

        "admonition-font-size": "var(--font-size-normal)",

        "admonition-title-font-size": "var(--font-size-normal)",

        "code-font-size": "var(--font-size--small)",

    },

}

html_static_path = ["_static"]

html_css_files = ["css/overwrite.css", "css/sphinx_gallery.css"]

html_show_sphinx = False

nbsphinx_prolog = r"""

.. raw:: html

{{% set docname = env.doc2path(env.docname, base=None).split("/")[-1] %}}

.. raw:: html

    <style>

        p {{

            margin-bottom: 0.5rem;

        }}

        /* Main index page overview cards */

        /* https://github.com/spatialaudio/nbsphinx/pull/635/files */

        .jp-RenderedHTMLCommon table,

        div.rendered_html table {{

        border: none;

        border-collapse: collapse;

        border-spacing: 0;

        font-size: 12px;

        table-layout: fixed;

        color: inherit;

        }}

        body:not([data-theme=light]) .jp-RenderedHTMLCommon tbody tr:nth-child(odd),

        body:not([data-theme=light]) div.rendered_html tbody tr:nth-child(odd) {{

        background: rgba(255, 255, 255, .1);

        }}

    </style>

.. raw:: html

    <div class="admonition note">

        <p class="admonition-title">Note</p>

        <p>

        This page was generated from

        <a class="reference external" href="https://github.com/theislab/ehrapy/tree/{version}/">{docname}</a>.

        Some tutorial content may look better in light mode.

        </p>

    </div>

""".format(version=version, docname="{{ docname|e }}")

nbsphinx_thumbnails = {

    "tutorials/notebooks/ehrapy_introduction": "_static/ehrapy_logos/ehrapy_pure.png",

    "tutorials/notebooks/mimic_2_introduction": "_static/tutorials/catheter.png",

    "tutorials/notebooks/mimic_2_fate": "_static/tutorials/fate.png",

    "tutorials/notebooks/mimic_2_survival_analysis": "_static/tutorials/survival.png",

    "tutorials/notebooks/mimic_2_effect_estimation": "_static/tutorials/effect_estimation.png",

    "tutorials/notebooks/mimic_2_causal_inference": "_static/tutorials/causal_inference.png",

    "tutorials/notebooks/medcat": "_static/tutorials/nlp.png",

    "tutorials/notebooks/ml_usecases": "_static/tutorials/machine_learning.png",

    "tutorials/notebooks/ontology_mapping": "_static/tutorials/ontology.png",

    "tutorials/notebooks/fhir": "_static/tutorials/fhir.png",

    "tutorials/notebooks/cohort_tracking": "_static/tutorials/cohort_tracking.png",

    "tutorials/notebooks/bias": "_static/tutorials/bias.png",

    "tutorials/notebooks/out_of_core": "_static/tutorials/out_of_core.png",

    "tutorials/notebooks/patient_trajectory": "_static/tutorials/patient_trajectory.png",

}