Set up Sphinx.

- Add GitHub workflow.
- Simplify doc build workflow and add requirements.
- Remove currently unused extensions in `conf.py`.
- Add a few documentation pages.

.github/workflows/build_docs.yaml

@@ -0,0 +1,26 @@
+name: Build and deploy documentation
+on:
+  push:
+    branches:
+      - docs
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+          python -m pip install sphinx sphinx_design sphinx-rtd-theme sphinxcontrib-bibtex numpydoc
+      - name: Build docs
+        run: cd doc && make html
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.gitignore

@@ -1,2 +1,5 @@
 /data_sources/HAZUS_MH_4.2_HU/output/
 /data_sources/HAZUS_MH_4.2_HU/session.dill
+/doc/build/
+*.pyc
+/.ropeproject/

doc/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     = source
+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)

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/source/_static/css/custom.css

@@ -0,0 +1,33 @@
+wy-nav-content {
+    max-width: none;
+}
+
+
+.math {
+    text-align: left;
+}
+
+.eqno {
+    float: right;
+}
+
+
+#div.wy-side-scroll{
+#	background:#cb463f;
+#}
+
+div.wy-menu.wy-menu-vertical > .caption {
+	 color: #cb463f;
+}
+
+# LIGHT BLUE  background:#0099ff
+# BLUE: background:#0B619C
+# ADAM RED: background:#cb463f;
+
+span.caption.caption-text{
+	color: #000000;
+}
+
+td{
+	white-space: normal !important;
+}

doc/source/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

doc/source/_templates/custom-module-template.rst

@@ -0,0 +1,63 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

doc/source/about/about.rst

@@ -0,0 +1,11 @@
+.. _about:
+
+.. admonition:: Coming soon
+
+   This section is under construction.
+
+*******
+ About
+*******
+
+About the damage and loss model library.

doc/source/conf.py

@@ -0,0 +1,95 @@
+"""Damage and Loss Model Library Sphinx configuration."""
+
+# 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.
+#
+from datetime import datetime
+
+# -- Project information -----------------------------------------------------
+project = 'Damage and Loss Model Library'
+copyright = (
+    f'{datetime.now().year}, Leland Stanford Junior '
+    f'University and The Regents of the University of California'
+)
+
+# -- 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 = [
+    'numpydoc',
+    'sphinx_design',
+    'sphinxcontrib.bibtex',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.doctest',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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/custom.css']
+
+# 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 = []
+
+# Extension configuration
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
+}
+
+numpydoc_show_class_members = False  # TODO(JVM): remove and extend docstrings
+
+nbsphinx_custom_formats = {
+    '.pct.py': ['jupytext.reads', {'fmt': 'py:percent'}],
+}
+
+# -- 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_options = {
+    'analytics_id': None,  # TODO (AZ): Add analytics ID.
+    'logo_only': True,
+    'collapse_navigation': False,
+    'prev_next_buttons_location': None,
+    'navigation_depth': 2,
+    'style_nav_header_background': '#F2F2F2',
+}
+html_show_sphinx = False  # Removes "Built with Sphinx using a theme [...]"
+html_show_sourcelink = (
+    False  # Remove 'view source code' from top of page (for html, not python)
+)
+numfig = True
+bibtex_bibfiles = ['references.bib']
+bibtex_style = 'plain'

doc/source/index.rst

@@ -0,0 +1,18 @@
+:notoc:
+
+===============================
+ Damage and Loss Model Library
+===============================
+
+.. warning::
+
+   Development Preview Only.
+   This documentation is intended for internal review and demonstration purposes.
+   It is not finalized or ready for public use.
+
+.. toctree::
+   :caption: About
+   :maxdepth: 1
+
+   about/about.rst
+   release_notes/index.rst

doc/source/release_notes/index.rst

@@ -0,0 +1,16 @@
+.. _release_notes:
+
+*************
+Release Notes
+*************
+
+The following sections document the notable changes of each release.
+The sequence of all changes is available in the `commit logs <https://github.com/NHERI-SimCenter/DamageAndLossModelLibrary/commits/>`_.
+
+Version 1
+-----------
+
+.. toctree::
+   :maxdepth: 2
+
+   v1.0

doc/source/release_notes/v1.0.rst

@@ -0,0 +1,10 @@
+.. _changes_v1_0:
+
+==========================
+Version 1.0 (May 19, 2023)
+==========================
+
+Initial Release.
+
+- FEMA P-58 2nd edition.
+- Hazus Earthquake Model for Buildings.