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conf.py
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conf.py
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# 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
# -- 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.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- Project information -----------------------------------------------------
project = 'QuPath'
copyright = '2019-2024, QuPath docs authors'
author = 'QuPath authors'
# -- 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 = [
'myst_parser',
'sphinx_rtd_theme',
'sphinx_design',
'sphinx.ext.autosectionlabel'
]
# 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', 'Thumbs.db', '.DS_Store']
# -- 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'
# html_theme = 'alabaster'
# 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_theme_options = {
'style_nav_header_background': '#343131'
}
html_css_files = [
'css/custom.css',
]
master_doc = 'index'
rst_prolog = """
.. |br| raw:: html
<br/>
.. |vertical_ellipsis| unicode:: 0x22EE
.. |copyright| unicode:: 0xA9
"""
myst_enable_extensions = [
"amsmath",
"colon_fence",
"deflist",
"dollarmath",
"fieldlist",
"html_admonition",
"html_image",
# "linkify",
"replacements",
"smartquotes",
"strikethrough",
"substitution",
"tasklist",
]
highlight_language = 'groovy'
html_logo = 'docs/images/qupath_128.png'
html_favicon = 'docs/images/QuPath.ico'
# Variables for current QuPath version
release = '0.6.0-rc3'
version = '0.6'
java_version = '21'
# myst_heading_anchors = 2
myst_substitutions = {
"java_version": java_version,
"rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" />',
"icon_rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" class="inline-icon" />',
"tool_rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" class="tool-icon" />',
"ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" />',
"icon_ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" class="inline-icon" />',
"tool_ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" class="tool-icon" />',
"line": '<img src="../images/icons/LINE_TOOL.png" />',
"icon_line": '<img src="../images/icons/LINE_TOOL.png" class="inline-icon" />',
"tool_line": '<img src="../images/icons/LINE_TOOL.png" class="tool-icon" />',
"polygon": '<img src="../images/icons/POLYGON_TOOL.png" />',
"icon_polygon": '<img src="../images/icons/POLYGON_TOOL.png" class="inline-icon" />',
"tool_polygon": '<img src="../images/icons/POLYGON_TOOL.png" class="tool-icon" />',
"polyline": '<img src="../images/icons/POLYLINE_TOOL.png" />',
"icon_polyline": '<img src="../images/icons/POLYLINE_TOOL.png" class="inline-icon" />',
"tool_polyline": '<img src="../images/icons/POLYLINE_TOOL.png" class="tool-icon" />',
"brush": '<img src="../images/icons/BRUSH_TOOL.png" />',
"icon_brush": '<img src="../images/icons/BRUSH_TOOL.png" class="inline-icon" />',
"tool_brush": '<img src="../images/icons/BRUSH_TOOL.png" class="tool-icon" />',
"wand": '<img src="../images/icons/WAND_TOOL.png" />',
"icon_wand": '<img src="../images/icons/WAND_TOOL.png" class="inline-icon" />',
"tool_wand": '<img src="../images/icons/WAND_TOOL.png" class="tool-icon" />',
"points": '<img src="../images/icons/POINTS_TOOL.png" />',
"icon_points": '<img src="../images/icons/POINTS_TOOL.png" class="inline-icon" />',
"tool_points": '<img src="../images/icons/POINTS_TOOL.png" class="tool-icon" />',
"move": '<img src="../images/icons/MOVE_TOOL.png" />',
"icon_move": '<img src="../images/icons/MOVE_TOOL.png" class="inline-icon" />',
"tool_move": '<img src="../images/icons/MOVE_TOOL.png" class="tool-icon" />',
"selection_mode": '<img src="../images/icons/SELECTION_MODE.png" />',
"icon_selection_mode": '<img src="../images/icons/SELECTION_MODE.png" class="inline-icon" />',
"tool_selection_mode": '<img src="../images/icons/SELECTION_MODE.png" class="tool-icon" />',
"help": '<img src="../images/icons/HELP.png" />',
"icon_help": '<img src="../images/icons/HELP.png" class="inline-icon" />',
"tool_help": '<img src="../images/icons/HELP.png" class="tool-icon" />',
"log": '<img src="../images/icons/LOG_VIEWER.png" />',
"icon_log": '<img src="../images/icons/LOG_VIEWER.png" class="inline-icon" />',
"tool_log": '<img src="../images/icons/LOG_VIEWER.png" class="tool-icon" />',
"grid": '<img src="../images/icons/GRID.png" />',
"icon_grid": '<img src="../images/icons/GRID.png" class="inline-icon" />',
"measure": '<img src="../images/icons/MEASURE.png" />',
"icon_measure": '<img src="../images/icons/MEASURE.png" class="inline-icon" />',
"table": '<img src="../images/icons/TABLE.png" />',
"icon_table": '<img src="../images/icons/TABLE.png" class="inline-icon" />',
"cog": '<img src="../images/icons/COG.png" />',
"icon_cog": '<img src="../images/icons/COG.png" class="inline-icon" />',
"annotations": '<img src="../images/icons/ANNOTATIONS.png" />',
"icon_annotations": '<img src="../images/icons/ANNOTATIONS.png" class="inline-icon" />',
"detections": '<img src="../images/icons/DETECTIONS.png" />',
"icon_detections": '<img src="../images/icons/DETECTIONS.png" class="inline-icon" />',
"annotations_fill": '<img src="../images/icons/ANNOTATIONS_FILL.png" />',
"icon_annotations_fill": '<img src="../images/icons/ANNOTATIONS_FILL.png" class="inline-icon" />',
"detections_fill": '<img src="../images/icons/DETECTIONS_FILL.png" />',
"icon_detections_fill": '<img src="../images/icons/DETECTIONS_FILL.png" class="inline-icon" />',
"tma_grid": '<img src="../images/icons/TMA_GRID.png" />',
"icon_tma_grid": '<img src="../images/icons/TMA_GRID.png" class="inline-icon" />',
"screenshot": '<img src="../images/icons/SCREENSHOT.png" />',
"icon_screenshot": '<img src="../images/icons/SCREENSHOT.png" class="inline-icon" />',
"extract_image": '<img src="../images/icons/EXTRACT_REGION.png" />',
"icon_extract_image": '<img src="../images/icons/EXTRACT_REGION.png" class="inline-icon" />',
"contrast": '<img src="../images/icons/CONTRAST.png" />',
"icon_contrast": '<img src="../images/icons/CONTRAST.png" class="inline-icon" />',
"play": '<img src="../images/icons/PLAYBACK_PLAY.png" />',
"icon_play": '<img src="../images/icons/PLAYBACK_PLAY.png" class="inline-icon" />',
"stop": '<img src="../images/icons/TRACKING_STOP.png" />',
"icon_stop": '<img src="../images/icons/TRACKING_STOP.png" class="inline-icon" />',
"record": '<img src="../images/icons/TRACKING_RECORD.png" />',
"icon_record": '<img src="../images/icons/TRACKING_RECORD.png" class="inline-icon" />',
}