conf.py

# 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

import os
import subprocess
import sys
import warnings

# -- 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.
#
sys.path.insert(0, os.path.abspath(".."))

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

project = "libpetab-python"
copyright = "2018-2024, the PEtab developers"
author = "PEtab developers"

# The full version, including alpha/beta/rc tags
release = "latest"

# -- Custom pre-build --------------------------------------------------------


subprocess.run([sys.executable, "md2rst.py"])  # noqa: S603

# -- 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.napoleon",
    "sphinx.ext.autodoc",
    "sphinx.ext.autosummary",
    "sphinx.ext.intersphinx",
    "sphinx.ext.viewcode",
    "sphinx_markdown_tables",
    "myst_nb",
]

intersphinx_mapping = {
    "petab": ("https://petab.readthedocs.io/en/latest/", None),
    "pandas": ("https://pandas.pydata.org/docs/", None),
    "numpy": ("https://numpy.org/devdocs/", None),
    "sympy": ("https://docs.sympy.org/latest/", None),
    "python": ("https://docs.python.org/3", None),
}

# 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 = [
    "build/doctrees",
    "build/html",
    "build/jupyter_execute",
    "**.ipynb_checkpoints",
    "logo/LICENSE.md",
]

master_doc = "index"

autosummary_generate = True

autodoc_default_options = {
    "members": True,
    "imported-members": ["petab"],
    "show-inheritance": True,
    "undoc-members": True,
}

# For some reason causes sphinx import errors otherwise
autodoc_mock_imports = ["yaml"]

# myst_nb options
#  https://myst-nb.readthedocs.io/en/latest/configuration.html
nb_execution_mode = "force"
nb_execution_raise_on_error = True
nb_execution_show_tb = True
nb_execution_timeout = 90  # max. seconds/cell

source_suffix = {
    ".rst": "restructuredtext",
    ".txt": "restructuredtext",
}

# ignore numpy warnings
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ufunc size changed")

# -- 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 = "sphinx_rtd_theme"

# 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_context = {
    "display_github": True,
    "github_user": "petab-dev",
    "github_repo": "libpetab-python",
    "github_version": "develop",
    "conf_py_path": "/doc",
}

html_logo = "logo/PEtab.png"


def skip_some_objects(app, what, name, obj, skip, options):
    """Exclude some objects from the documentation"""
    if getattr(obj, "__module__", None) == "collections":
        return True


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