Merge branch 'master' into bumpCMake

Author: dcwhite

.gitignore

@@ -12,9 +12,12 @@ bin*
 *.*~
 CMakeCache.txt
 CMakeFiles
-Makefile
+src/Makefile
 cmake_install.cmake
 install_manifest.txt
 CTestTestfile.cmake
 DartConfiguration.tcl
 xCode_bin*
+
+# Sphinx builds
+docs/_build/

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/css/main.css

@@ -0,0 +1,5 @@
+{% extends "!layout.html" %}
+{% block rootrellink %}
+    <li><a href="https://project.invalid/">Project Homepage</a> &raquo;</li>
+    {{ super() }}
+{% endblock %}

docs/_static/seg3d.png

@@ -0,0 +1,3 @@
+Bibliography
+============
+.. bibliography::

docs/_templates/layout.html

@@ -0,0 +1,147 @@
+# 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('.'))
+
+# from recommonmark.transform import AutoStructify
+
+# -- Project information -----------------------------------------------------
+
+project = 'Seg3D'
+copyright = '2021, The Scientific Computing and Imaging Institute at the University of Utah'
+author = 'To be Added'
+
+# The full version, including alpha/beta/rc tags
+release = '0.01'
+
+
+# -- 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.napoleon',
+#        'recommonmark',
+#        'sphinxcontrib.bibtex',
+#        'sphinx_markdown_tables'
+#]
+
+extensions = [
+        'sphinx.ext.autodoc',
+        'sphinx.ext.napoleon',
+        'myst_parser',
+        'sphinx_markdown_tables',
+        'sphinxcontrib.bibtex',
+        'notfound.extension'
+]
+
+myst_enable_extensions = [
+    "colon_fence",  # Allow code fence using ::: (see https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html#syntax-colon-fence)
+    "linkify",  # Allow automatic creation of links from URLs (it is sufficient to write https://google.com instead of <https://google.com>)
+    "substitution"
+]
+
+# 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
+
+# auto number figures
+numfig = True
+
+# Path for bibtex files
+bibtex_bibfiles = ['references.bib']
+
+# 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']
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+
+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'
+
+# the master toctree doc
+master_doc = 'index'
+
+# 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 = 'python'
+
+# -- 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 = 'furo'
+
+#html_theme = 'groundwork'
+
+# html_style = '/css/main.css'
+
+#on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+
+#if not on_rtd:  # only import and set the theme if we're building docs locally
+#    import sphinx_rtd_theme
+#    html_theme = 'sphinx_book_theme'
+#    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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/main.css']
+
+html_title = project
+
+html_logo = '_static/seg3d.png'
+
+html_theme_options = {
+    "sidebar_hide_name": True,
+    "light_css_variables": {
+        "color-brand-primary": "#ad1f1f",
+        "color-brand-content": "#ad1f1f",
+    },
+    "dark_css_variables": {
+        "color-brand-primary": "#ec9393",
+        "color-brand-content": "#ec9393",
+    },
+}
+
+autosectionlabel_prefix_document = True