# Toil documentation build configuration file, created by
# sphinx-quickstart on Tue Aug 25 12:37:16 2015.
#
# 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.
import sys
import os
import inspect
import re
from datetime import datetime
import toil.version
import time

# This makes the modules located in docs/vendor/sphinxcontrib available to import
sphinxPath = os.path.abspath(
    os.path.join(os.path.pardir, os.path.dirname("docs/vendor/sphinxcontrib/"))
)
sys.path.append(sphinxPath)
import fulltoc


def fetch_parent_dir(filepath: str, n: int = 1):
    """
    Returns a parent directory, n places above the input filepath.

    Equivalent to something like: '/home/user/dir'.split('/')[-2] if n=2.
    """
    filepath = os.path.realpath(filepath)
    for i in range(n):
        filepath = os.path.dirname(filepath)
    return os.path.basename(filepath)


path_to_dir = os.path.dirname(os.path.abspath(__file__))

# Example of toil.version.__file__ on sphinx:
# /home/docs/checkouts/readthedocs.org/user_builds/toil/envs/3.13.0/local/lib/python2.7/site-packages/toil-3.13.0a1-py2.7.egg/toil/version.pyc
envPath = os.path.abspath(toil.version.__file__)

# Example of __file__ on sphinx:
# /home/docs/checkouts/readthedocs.org/user_builds/toil/checkouts/3.13.0/docs/conf.py
wdPath_version = fetch_parent_dir(__file__, 2)
# Expected output: 3.13.0

assert (
    wdPath_version in envPath
), "Another Toil installation seems to have precedence over this working directory."
toilVersion = toil.version.baseVersion

# -- 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.doctest",
    "sphinx.ext.autosummary",
    "autoapi.extension",
    "sphinx_autodoc_typehints",
    "sphinxcontrib.autoprogram",
    "sphinx.ext.todo",
    "sphinx.ext.coverage",
    "sphinx.ext.viewcode",
    "sphinx.ext.intersphinx",
    "fulltoc",
]

intersphinx_mapping = {
    "python": ("/usr/share/doc/python3/html", None),
    "cwltool": ("/usr/share/doc/cwltool/html", None),
}

# Link definitions available everywhere so we don't need to keep repeating ourselves.
rst_epilog = """
.. _Common Workflow Language: http://www.commonwl.org/
"""


def skip(app, what, name, obj, skip, options):
    """
    Decide what to automatically generate documentation for.
    """

    # See
    # <https://sphinx-autoapi.readthedocs.io/en/latest/reference/config.html#event-autoapi-skip-member>

    # TODO: It's not clear that the contidions used here are a good idea. Why
    # are they like this?

    # Always document __init__
    return name != "__init__" and (
        skip
        # But don't document classes
        or inspect.isclass(obj)
        # Or things starting with _ that aren't modules
        or (
            name.startswith("_")
            and not inspect.ismodule(obj)
        )
    )


def setup(app):
    app.connect("autodoc-skip-member", skip)


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

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

# The master toctree document.
master_doc = "index"

# General information about the project.
project = "Toil"
build_date = datetime.utcfromtimestamp(
    int(os.environ.get("SOURCE_DATE_EPOCH", time.time()))
)
copyright = f"2015 – {build_date.year} UCSC Computational Genomics Lab"
author = "UCSC Computational Genomics Lab"

# 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 = re.split("[A-Za-z]", toilVersion)[0]
# The full version, including alpha/beta/rc tags.
release = toilVersion

# 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 = "en"

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

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

# If true, 2do and 2doList produce output, else they produce nothing.
todo_include_todos = True

# Include doc string for __init__ method in the documentation
autoclass_content = "class"
autodoc_member_order = "bysource"

autoapi_dirs = ["../src/toil"]
autodoc_typehints = "description"
autoapi_keep_files = True
autoapi_ignore = ["*.pyi", "*/test/cwl/spec*/*.py", "*/fake_mpi_run.py", "*/tutorial_*.py", "*/example_*.py", "*/mkFile.py", "*/debugWorkflow.py",
                  "*/test/wdl/wdl-conformance-tests/*"]
autoapi_options = [
    "members",
    "undoc-members",
    "show-inheritance",
    "show-module-summary",
    "special-members",
]
always_document_param_types = 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 = "alabaster"
html_theme_options = {
    "github_banner": True,
    "github_user": "BD2KGenomics",
    "github_repo": "toil",
    "caption_font_size": "24px",
}

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

# 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 = "_static/favicon.ico"

# 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"]

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

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

# -- Options for LaTeX output ---------------------------------------------
latex_elements = {}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto, manual, or own class]).
latex_documents = [(master_doc, "Toil.tex", "Toil Documentation", author, "manual")]

# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [(master_doc, "toil", "Toil Documentation", [author], 1)]

# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author, dir menu entry, description, category)
texinfo_documents = [
    (
        master_doc,
        project,
        "Toil Documentation",
        author,
        project,
        project,
        "Miscellaneous",
    )
]