conf.py

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#!/usr/bin/env python3
#
# 3D Slicer documentation build configuration file, created by
# sphinx-quickstart on Tue Mar 21 03:07:30 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 lxml.etree as ET
import os
import re
import sys
from datetime import date
 
sys.path.insert(0, os.path.abspath("../Base/Python"))
sys.path.insert(0, os.path.abspath("./_ext"))
 
# -- 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",
    "myst_parser",
    "sphinx_markdown_tables",
    "notfound.extension",  # Show a better 404 page when an invalid address is entered
    "sphinx_rtd_theme",
    "sphinx-jsonschema",
    "github_alerts",
    "sphinx_reredirects",  # Handle page redirects
]
 
# Redirect renamed/moved pages for keeping external links working
redirects = {
    "user_guide/extensions_manager.html": "extensions.html#extensions-manager",
}
 
suppress_warnings = [
    # Since we split the "script_repository.md" into smaller documents combined using
    # the "include" directive, we ignore warnings like "Document headings start at H2, not H1"
    "myst.header",
]
 
autodoc_mock_imports = [
    "ctk",
    "qt",
    "vtk",
]
 
myst_enable_extensions = [
    "attrs_inline",  # Enable parsing of inline attributes (see https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#inline-attributes)
    "colon_fence",  # Allow code fence using ::: (see https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html#syntax-colon-fence)
    "dollarmath",  # Support syntax for inline and block math using `$...$` and `$$...$$`
    # (see https://myst-parser.readthedocs.io/en/latest/syntax/optional.html#dollar-delimited-math)
    "linkify",  # Allow automatic creation of links from URLs (it is sufficient to write https://google.com instead of <https://google.com>)
]
 
# Auto-generate header anchors up to level 6, so that it can be referenced like [](file.md#header-anchor).
# (see https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html#auto-generated-header-anchors)
myst_heading_anchors = 6
 
# Allow display (block) math with equation label syntax
myst_dmath_allow_labels = True
 
 
def _extract_slicer_xy_version(slicer_src_dir):
    """
    Given a Slicer source director, extract <major>.<minor> version
    from top-level `CMakeLists.txt`.
 
    Return a dictionary containing `major` and `minor` version components as strings
    """
    slicer_src_dir = os.path.abspath(slicer_src_dir)
    version_patterns = {
        part: re.compile(rf'set\‍(Slicer_VERSION_{part.upper()} "(\d+)"\‍)')
        for part in ["major", "minor"]
    }
    version_parts = {}
 
    # Parse the CMakeLists.txt file to extract version components.
    cmakelists_path = os.path.join(slicer_src_dir, "CMakeLists.txt")
    with open(cmakelists_path) as cmake_file:
        for line in cmake_file:
            for part, pattern in version_patterns.items():
                match = pattern.match(line.strip())
                if match is not None:
                    version_parts[part] = match.group(1)
            if len(version_parts) == len(version_patterns ):
                break
 
    if len(version_parts) != len(version_patterns):
        raise ValueError(f"Failed to extract version from {cmakelists_path}")
 
    return version_parts
 
 
def _get_apidocs_doxygen_version():
    """
    Determine the Doxygen documentation version to use based on the Slicer version.
 
    Return Doxygen version identifier (`v<major>.<minor>` for Stable, `main` for Preview)
    """
 
    slicer_repo_dir = os.path.dirname(os.path.dirname(__file__))
    version_parts = _extract_slicer_xy_version(slicer_repo_dir)
 
    # Determine the documentation branch based on the minor version parity.
    is_even = int(version_parts["minor"]) % 2 == 0
    return "v{major}.{minor}".format(**version_parts) if is_even else "main"
 
 
# Construct the custom URL scheme for Slicer Doxygen documentation links.
slicerapidocs_url_scheme = "https://apidocs.slicer.org/" + _get_apidocs_doxygen_version() + "/{{path}}#{{fragment}}"
print(f"Slicer API documentation URL scheme: {slicerapidocs_url_scheme}")
 
 
# Register custom URL schemes for Markdown processing.
# These schemes allow linking to external and Slicer-specific resources dynamically.
myst_url_schemes = {
    "http": None,
    "https": None,
    "mailto": None,
    "ftp": None,
    "slicerapidocs": slicerapidocs_url_scheme,
}
 
#
# 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"]
 
# The master toctree document.
master_doc = "index"
 
# General information about the project.
project = "3D Slicer"
copyright = f"{date.today().year}, Slicer Community"
author = "Slicer Community"
 
# 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 = ""
# The full version, including alpha/beta/rc tags.
release = ""
 
# 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", "_moduledescriptions"]
 
# Set EXCLUDE_DEVELOPER_GUIDE=True environment variable to exclude developer guide.
# It is useful for quicker documentation generation while eiditing user manual.
if os.environ.get("EXCLUDE_API_REFERENCE", "False") == "True":
    print("API reference is excluded from documentation.")
    exclude_patterns.append("developer_guide/vtkTeem.rst")
    exclude_patterns.append("developer_guide/vtkAddon.rst")
    exclude_patterns.append("developer_guide/vtkITK.rst")
    exclude_patterns.append("developer_guide/slicer.rst")
    exclude_patterns.append("developer_guide/mrml.rst")
 
# sphinx-notfound-page
# https://github.com/readthedocs/sphinx-notfound-page
notfound_context = {
    "title": "Page Not Found",
    "body": """
<h1>Page Not Found</h1>
<p>Sorry, we couldn't find that page.</p>
<p>Try using the search box or go to the homepage.</p>
""",
}
 
# 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
 
# A string of reStructuredText that will be included at the beginning of every source file that is read.
rst_prolog = open("global.rst.in").read()
 
# If given, this must be the name of an image file (path relative to the configuration directory) that is the logo of the docs.
# It is placed at the top of the sidebar; its width should therefore not exceed 200 pixels
html_logo = "_static/images/3D-Slicer-Mark.png"
 
# -- 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"
 
# 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 = {
    # Toc options
    "includehidden": False,
}
 
html_context = {
    # Enable the "Edit in GitHub link within the header of each page.
    "display_github": True,
    # Set the following variables to generate the resulting github URL for each page.
    # Format Template: https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}
    #   /blob/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}
    "github_user": "slicer",
    "github_repo": "slicer",
    "github_version": "main",
    "conf_py_path": "/Docs/",
}
 
# 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"]
 
# These paths are either relative to html_static_path
# or fully qualified paths (eg. https://...)
html_css_files = [
    "css/custom.css",
]
 
# -- Options for HTMLHelp output ------------------------------------------
 
# Output file base name for HTML help builder.
htmlhelp_basename = "3DSlicerdoc"
 
 
# -- 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': '',
    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}
 
# 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, "3DSlicer.tex", "3D Slicer Documentation",
     "Slicer Community", "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, "3Dslicer", "3D Slicer 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, "3DSlicer", "3D Slicer Documentation",
     author, "3DSlicer", "One line description of project.",
     "Miscellaneous"),
]
 
# -- Convert CLI module descriptions into markdown files ----------------
 
# Each CLI module descriptor XML file is converted to two markdown files
# in _moduledescriptions subfolder: *Overview.md and *Parameters.md.
# Overview file contains the module title and description.
# Parameters file contains detailed description of module inputs and
# outputs, contributors, and acknowledgements.
#
# These md files are included at the top and bottom of each CLI module
# documentation file (user_guide\modules\*.md). Custom content, such as
# tutorials, screenshots, etc. can be added in between these includes.
#
# A copy of all CLI module descriptor XML files for modules that are
# not part of the Slicer repository (e.g., BRAINS toolkit) are stored in
# _extracli subfolder. Content of this folder must be updated manually
# whenever they are updated in the original location. The process could
# be automated with some effort, but since these bundled libraries do
# not change frequently, manual update takes less work overall.
 
 
# Documentation root folder (folder of this script).
docsfolder = os.path.dirname(__file__)
 
# List of folders that contain CLI module descriptor XML files.
inputpaths = [
    os.path.join(docsfolder, "../Modules/CLI"),
    os.path.join(docsfolder, "_extracli"),
]
 
# List of modules to be excluded from documentation generation
# (for example, testing modules only).
excludenames = [
    "CLIROITest.xml",
    "TestGridTransformRegistration.xml",
    "DiffusionTensorTest.xml",
]
 
# Output folder that contains all generated markdown files.
outpath = os.path.join(docsfolder, "_moduledescriptions")
os.makedirs(outpath, exist_ok=True)
with open(os.path.join(outpath, "_readme_.txt"), "w") as descriptionfile:
    descriptionfile.write("Content of this folder is automatically generated by Docs/conf.py from CLI module descriptor XML files\n")
    descriptionfile.write("during documentation build. The folder can be deleted because it is automatically regenerated when needed.")
 
 
def _generatemd(dom, docsfolder, outpath, xslt, suffix):
    """Helper function to create markdown file from CLI module description XML file using XSLT"""
    xsltpath = os.path.join(docsfolder, xslt)
    transform = ET.XSLT(ET.parse(xsltpath))
    content = str(transform(dom))
    with open(os.path.join(outpath, os.path.splitext(name)[0] + suffix + ".md"), "w", encoding="utf8") as outfile:
        outfile.write(content)
 
 
for inputpath in inputpaths:
    for root, dirs, files in os.walk(inputpath):
        for name in files:
            if name in excludenames:
                continue
            if name.endswith(".xml"):
                print(f"Generating CLI module documentation from {name}")
                dom = ET.parse(os.path.join(root, name))
                _generatemd(dom, docsfolder, outpath, "cli_module_overview_to_md.xsl", "Overview")
                _generatemd(dom, docsfolder, outpath, "cli_module_parameters_to_md.xsl", "Parameters")