add a bunch of docs stuff

.readthedocs.yaml

@@ -0,0 +1,24 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  fail_on_warning: true
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+python:
+  install:
+    - requirements: requirements-dev.txt
+
+# Build all formats
+# formats:
+#   - pdf
+#   - htmlzip

Docs/Makefile

@@ -0,0 +1,23 @@
+# 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
+SPHINXAPIDOC  ?= sphinx-apidoc
+
+# 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 $(SPHINXOPTS).
+%: Makefile
+#   TODO: Revisit %SPHINXAPIDOC% and get it working adequately with readthedocs
+#	@$(SPHINXAPIDOC) -f -M -H WaterTAP -d 3 -o apidoc ../watertap "../*tests*"
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Docs/citing.rst

@@ -0,0 +1,12 @@
+Citing PARETO
+=============
+
+If you make use of PARETO software in your work, please cite the following article:
+
+* Drouven, M. G., Caldéron, A. J., Zamarripa, M. A. et al. PARETO: An open-source produced water optimization framework. Optim Eng 24, 2229-2249 (2023). https://doi.org/10.1007/s11081-022-09773-w
+
+You can also cite the latest release of PARETO software (currently 0.9.0) as follows: 
+
+* Melody Shellman, Travis Arnold, Ludovico Bianchi, Elmira Shamlou, Naresh Susarla, Philip Tominac, Michael Pesce, Sarah Poon, Keith Beattie, Miguel Zamarripa, Dan Gunter, Markus Drouven, PARETO 0.9.0 Release, 11/2/2023, https://edx.netl.doe.gov/dataset/pareto-0-9-0-release, DOI: 10.18141/2308838
+
+Citation information for previous versions of PARETO software may be found on `EDX <https://edx.netl.doe.gov/group/pareto>`_.

Docs/conf.py

@@ -0,0 +1,79 @@
+import os
+import sys
+import sphinx_rtd_theme
+
+sys.path.insert(0, os.path.abspath(".."))
+
+# -- Project information -----------------------------------------------------
+
+project = "PARETO"
+# copyright = ""
+# author = ""
+
+release = "1.0.0"
+version = "1.0.0"
+# -- 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_rtd_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.doctest",
+]
+
+mathjax3_config = {"chtml": {"displayAlign": "left", "displayIndent": "2em"}}
+
+autosectionlabel_prefix_document = True
+autodoc_warningiserror = False  # suppress warnings during autodoc
+
+# 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", "apidoc/*tests*"]
+
+# -- 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_css_files = ["custom.css"]
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+html_logo = "_static/NAWI_logo.png"
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#
+html_favicon = "_static/favicon.ico"
+
+# intersphinx mapping to idaes
+intersphinx_mapping = {
+    "pareto": ("https://idaes-pse.readthedocs.io/en/stable/", None),
+    "parameter_sweep": ("https://parameter-sweep.readthedocs.io/en/latest/", None),
+}
+
+rst_epilog = """
+.. |Binder launch button| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/watertap-org/watertap/main?labpath=tutorials%2F00-index.ipynb
+"""

Docs/copyright.rst

@@ -0,0 +1,3 @@
+.. _pareto-project-copyright:
+
+.. include:: ../COPYRIGHT.md

Docs/how_to_guides/index.rst

@@ -0,0 +1,7 @@
+How To Guides
+=============
+
+.. toctree::
+   :maxdepth: 1
+
+   how_to_use_interface

Docs/index.rst

@@ -1,19 +1,21 @@
 .. index::
    pair: pareto-user-interface;Home
 
-Welcome to PARETO UI's documentation!
-======================================
+Produced Water Application for Beneficial Reuse, Environmental Impact and Treatment Optimization (PARETO) User Interface
+=========================================================================================================
 
 Project PARETO - The Produced Water Optimization Initiative
 The National Energy Technology Laboratory (NETL), in cooperation with the Lawrence Berkeley National Laboratory (LBNL), has launched a three-year, $5 million produced water optimization initiative to develop, demonstrate and deploy a novel optimization framework.
-Refer :ref:`https://www.project-pareto.org/` for more background information.
+Refer :ref:`Projec PARETO <https://www.project-pareto.org/>`_ for more background information.
+
 
 Collaborating Institutions
 --------------------------
 
 The PARETO development team is composed of researchers from:
 
-* National Energy Technology Laboratory
+* National Energy Technology Laboratory (Lead)
+* Sandia National Laboratory
 * Lawrence Berkeley National Laboratory
 
 Content
@@ -23,8 +25,8 @@ Content
    :maxdepth: 2
 
    how_to_guides/index
-..    license
-..    copyright
+   license
+   copyright
 
 Indices and tables
 ------------------

Docs/license.rst

@@ -0,0 +1,3 @@
+.. _pareto_project-license:
+
+.. include:: ../LICENSE.md

Docs/make.bat

@@ -0,0 +1,41 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+if "%SPHINXAPIDOC%" == "" (
+    set SPHINXAPIDOC=sphinx-apidoc
+)
+
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+REM TODO: Revisit %SPHINXAPIDOC% and get it working adequately with readthedocs
+REM %SPHINXAPIDOC%  -f -M -H WaterTAP -d 3 -o apidoc ../watertap "../*tests*"
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:end
+popd

backend/requirements-dev.txt

@@ -0,0 +1,4 @@
+-r requirements.txt
+sphinx
+sphinx_rtd_theme
+nbsphinx