##!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# cassiopeia documentation build configuration file, created by
# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

# 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 sys
from pathlib import Path

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

import cassiopeia  # noqa


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

# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = "3.4"  # Nicer param docs

# 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.viewcode",
    "nbsphinx",
    "nbsphinx_link",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "sphinx.ext.autosummary",
    "scanpydoc.elegant_typehints",
    "scanpydoc.definition_list_typed_field",
    "scanpydoc.autosummary_generate_imported",
    *[p.stem for p in (HERE / "extensions").glob("*.py")],
    "sphinx_gallery.load_style",
]

# nbsphinx specific settings
exclude_patterns = ["_build", "**.ipynb_checkpoints"]
nbsphinx_execute = "never"

autodoc_mock_imports = ["gurobipy"]


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

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = ".rst"

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
napoleon_google_docstring = True  # for pytorch lightning
napoleon_numpy_docstring = False
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

# The master toctree document.
master_doc = "index"


intersphinx_mapping = dict(
    matplotlib=("https://matplotlib.org/", None),
    numpy=("https://docs.scipy.org/doc/numpy/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
    python=("https://docs.python.org/3", None),
)

# General information about the project.
project = "cassiopeia"
copyright = "2022, Yosef Lab, UC Berkeley"
author = "Matthew G Jones, Richard Zhang, Sebastian Prillo, Joseph Min, Jeffrey J Quinn, Alex Khodaverdian"

# 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.
#
# The short X.Y version.
version = cassiopeia.__version__
# The full version, including alpha/beta/rc tags.
release = cassiopeia.__version__

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None

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

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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False


# -- 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 = {}

# html_logo = "_static/logo3.png"
html_logo = "_static/logo.png"

html_theme_options = {
    "github_url": "https://github.com/YosefLab/Cassiopeia",
    "twitter_url": "https://twitter.com/YosefLab",
    # "use_edit_page_button": True,
}
html_context = dict(
    display_github=True,  # Integrate GitHub
    github_user="YosefLab",  # Username
    github_repo="Cassiopeia",  # Repo name
    github_version="master",  # Version
    doc_path="docs/",  # Path in the checkout to the docs root
)
# 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/override.css", "css/sphinx_gallery.css"]
html_show_sphinx = False

nbsphinx_thumbnails = {
    "notebooks/preprocess": "_static/tutorials/preprocess.png",
    "notebooks/benchmark": "_static/tutorials/benchmark.png",
    "notebooks/reconstruct": "_static/tutorials/reconstruct.png",
    "notebooks/local_plotting": "_static/tutorials/local_plotting.png",
}


# -- Options for HTMLHelp output ---------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = "cassiopeiadoc"

mathjax_config = {
    "extensions": ["tex2jax.js"],
    "jax": ["input/TeX", "output/HTML-CSS"],
    "tex2jax": {
        "inlineMath": [["$", "$"], ["\\(", "\\)"]],
        "displayMath": [["$$", "$$"], ["\\[", "\\]"]],
        "processEscapes": True,
    },
}


from sphinx.ext.autosummary import Autosummary
from sphinx.ext.autosummary import get_documenter
from docutils.parsers.rst import directives
from sphinx.util.inspect import safe_getattr
import re

# Code for creating autosummaries for class methods / attributes
# Taken originally from Pandas documentation
class AutoAutoSummary(Autosummary):

    option_spec = {
        "methods": directives.unchanged,
        "attributes": directives.unchanged,
        "toctree": directives.unchanged,
    }

    required_arguments = 1

    @staticmethod
    def get_members(obj, typ, include_public=None):
        if not include_public:
            include_public = []
        items = []
        for name in dir(obj):
            try:
                documenter = get_documenter(safe_getattr(obj, name), obj)
            except AttributeError:
                continue
            if documenter.objtype == typ:
                items.append(name)
        public = [x for x in items if x in include_public or not x.startswith("_")]
        return public, items

    def run(self):
        clazz = str(self.arguments[0])
        try:
            (module_name, class_name) = clazz.rsplit(".", 1)
            m = __import__(module_name, globals(), locals(), [class_name])
            c = getattr(m, class_name)
            if "methods" in self.options:
                _, methods = self.get_members(c, "method", ["__init__"])

                self.content = [
                    "~%s.%s" % (clazz, method)
                    for method in methods
                    if not method.startswith("_")
                ]
            if "attributes" in self.options:
                _, attribs = self.get_members(c, "attribute")
                self.content = [
                    "~%s.%s" % (clazz, attrib)
                    for attrib in attribs
                    if not attrib.startswith("_")
                ]
        finally:
            return super(AutoAutoSummary, self).run()


def setup(app):
    app.add_directive("autoautosummary", AutoAutoSummary)
