Sphinx dev (#7)

* sphinx documentation quickstart

* updated autodocs

* updated documentation

* updated readme

* updated readme

* updated readme again

* more documentation updates

* updated documentation

* added docs

* updated docs

* updated opt docs

* updated read me and markdown imports

* Added installation instructions and new theme

* changes to the readme and instructions

* updates to docs and added docs for utils

INSTALL.md

@@ -0,0 +1,44 @@
+# Installation 
+
+## Dependencies
+`SOUPy` depends on [FEniCS](http://fenicsproject.org/) version 2019.1. and [hIPPYlib](https://hippylib.github.io/) version 3.0.0 or above.
+
+`FEniCS` needs to be built with the following dependencies enabled:
+
+ - `numpy`, `scipy`, `matplotlib`, `mpi4py`
+ - `PETSc` and `petsc4py` (version 3.10.0 or above)
+ - `SLEPc` and `slepc4py` (version 3.10.0 or above)
+ - PETSc dependencies: `parmetis`, `scotch`, `suitesparse`, `superlu_dist`, `ml`, `hypre`
+ - (optional): `gmsh`, `mshr`, `jupyter`
+
+## Recommended installation procedures using conda
+1. Install `FEniCS` with appropriate dependencies
+```
+conda create -n soupy -c conda-forge fenics==2019.1.0 matplotlib scipy jupyter
+```
+
+2. Clone the `hIPPYlib` [repository](https://github.com/hippylib/hippylib). 
+```
+git clone https://github.com/hippylib/hippylib.git
+```
+
+3. Clone the `SOUPy` [repository](https://github.com/hippylib/soupy/tree/main)
+```
+git clone https://github.com/hippylib/soupy.git
+```
+
+4. Set the path to the `hIPPYlib` and `SOUPy` as environment variables, e.g. 
+```
+conda activate soupy
+conda env config vars set HIPPYLIB_PATH=path/to/hippylib
+conda env config vars set SOUPY_PATH=path/to/soupy
+```
+
+Examples in the `applications` directory can now be run. We refer to the full `FEniCS` [installation instructions](https://hippylib.readthedocs.io/en/3.0.0/installation.html) from `hIPPYlib` for more detail. 
+
+## Build the SOUPy documentation using Sphinx
+
+Documentation for `SOUPy` can be built using `sphinx`, along with extensions
+`myst_parser` and `sphinx_rtd_theme`. These can be installed via `pip`.
+
+To build simply run `make html` from `doc` folder.

README.md

@@ -1,2 +1,19 @@
-# soupy
-Stochastic Optimization under Uncertainty in Python.
+# Stochastic Optimization under high-dimensional Uncertainty in Python
+
+**S**tochastic **O**ptimization under high-dimensional **U**ncertainty in **Py**thon—**SOUPy**, 
+implements scalable algorithms to solve problems of PDE-constrained optimization under uncertainty, with the computational complexity measured in terms of PDE solves independent of the uncertain parameter dimension and optimization variable dimension.
+
+`SOUPy` is built on the open-source `hIPPYlib` library, which provides state-of-the-art scalable adjoint-based methods for deterministic and Bayesian inverse problems governed by PDEs, which in turn makes use of the `FEniCS` library for high-level formulation, discretization, and scalable solution of PDEs.
+
+`SOUPy` implements algorithms for the optimization of probability/risk measures such as mean, variance, and superquantile/condition-value-at-risk, subject to PDE constraints.
+Sample based approximations of risk measures are supported in `SOUPy`, which leverages MPI for rapid parallel sampling.
+Numerical optimization algorithms can be called from `SciPy` or using the built-in optimization algorithms. 
+
+`SOUPy` has been developed and in active development to incorporate advanced approximation algorithms and capabilities, including:
+- PDE-constrained operator/tensor/matrix products,
+- symbolic differentiation (of appropriate Lagrangians) for the derivation of high order mixed derivatives (via the `FEniCS` interface),
+- randomized algorithms for matrix and high order tensor decomposition,
+- decomposition of uncertain parameter spaces by mixture models,
+- Taylor expansion-based high-dimensional control variates, and
+- product convolution approximations,
+- common interfaces for random fields, PDE models, probability/risk measures, and control/design/inversion constraints.

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     = .
+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/conf.py

@@ -0,0 +1,50 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, 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
+basedir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+sys.path.insert(0, basedir)
+
+autodoc_mock_imports = ["dolfin", "matplotlib", "ffc", "ufl", 
+        "petsc4py", "mpi4py", "scipy", "numpy", "hippylib"]
+autodoc_default_flags = ['members', 'private-members', 'undoc-members']
+autoclass_content = 'both'
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'SOUPy'
+copyright = "2023, Peng Chen, Dingcheng Luo, Thomas O'Leary-Roseberry, Umberto Villa"
+author = "Peng Chen, Dingcheng Luo, Thomas O'Leary-Roseberry, Umberto Villa"
+release = '0.1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 
+              'sphinx.ext.napoleon', 'myst_parser', 'sphinx.ext.autosummary']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+source_suffix = ['.rst', '.md']
+master_doc = 'index'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = []
+# html_theme_options = {
+    # "nosidebar": True
+# }
+# html_theme_options = {
+#     "nosidebar": False, "sidebarwidth": "40em"
+# }

doc/index.rst

@@ -0,0 +1,19 @@
+.. SOUPy documentation master file, created by
+   sphinx-quickstart on Thu Jul  6 18:03:26 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SOUPy's documentation!
+=================================
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
+
+Documentation
+---------------------
+
+.. toctree::
+   :titlesonly:
+   :maxdepth: 1
+
+   install
+   Complete API reference <soupy>

doc/install.rst

@@ -0,0 +1,2 @@
+.. include:: ../INSTALL.md
+   :parser: myst_parser.sphinx_

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=.
+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/soupy.collectives.rst

@@ -0,0 +1,10 @@
+soupy.collectives 
+==========================
+
+soupy.collectives.collective
+-----------------------------------
+
+.. automodule:: soupy.collectives.collective
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/soupy.modeling.rst

@@ -0,0 +1,87 @@
+soupy.modeling 
+=========================
+
+soupy.modeling.PDEControlProblem 
+---------------------------------------
+
+.. automodule:: soupy.modeling.PDEControlProblem
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+soupy.modeling.controlModel 
+---------------------------------------
+
+.. automodule:: soupy.modeling.controlModel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+soupy.modeling.controlQoI
+---------------------------------------
+
+.. automodule:: soupy.modeling.controlQoI
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+
+soupy.modeling.controlCostFunctional
+---------------------------------------
+
+.. automodule:: soupy.modeling.controlCostFunctional
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.modeling.meanVarRiskMeasure
+---------------------------------------
+
+.. automodule:: soupy.modeling.meanVarRiskMeasure
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.modeling.meanVarRiskMeasureSAA
+---------------------------------------
+
+.. automodule:: soupy.modeling.meanVarRiskMeasureSAA
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.modeling.variables
+-------------------------------------------
+
+.. automodule:: soupy.modeling.variables
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.modeling.augmentedVector
+-------------------------------------------
+
+.. automodule:: soupy.modeling.augmentedVector
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.modeling.superquantileRiskMeasureSAA
+-------------------------------------------
+
+.. automodule:: soupy.modeling.superquantileRiskMeasureSAA
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+soupy.modeling.penalization
+---------------------------------------
+
+.. automodule:: soupy.modeling.penalization
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/soupy.optimization.rst

@@ -0,0 +1,34 @@
+soupy.optimization 
+==========================
+
+soupy.optimization.bfgs 
+-----------------------------------
+
+.. automodule:: soupy.optimization.bfgs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.optimization.projectableConstraint 
+-----------------------------------------
+
+.. automodule:: soupy.optimization.projectableConstraint
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.optimization.steepestDescent 
+-----------------------------------
+
+.. automodule:: soupy.optimization.steepestDescent
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.optimization.sgd 
+-----------------------------------
+
+.. automodule:: soupy.optimization.sgd
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/soupy.rst

@@ -0,0 +1,21 @@
+soupy package
+================
+
+Submodules
+-----------
+
+.. toctree::
+
+    soupy.modeling
+    soupy.optimization
+    soupy.collectives
+    soupy.utils
+
+Module contents
+---------------
+
+.. automodule:: soupy
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

doc/soupy.utils.rst

@@ -0,0 +1,36 @@
+soupy.utils module
+=========================
+
+soupy.utils.penalizationFiniteDifference 
+-----------------------------------------------
+
+.. automodule:: soupy.utils.penalizationFiniteDifference
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+soupy.utils.qoiFiniteDifference 
+-----------------------------------------------
+
+.. automodule:: soupy.utils.qoiFiniteDifference
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+soupy.utils.stochasticCostFiniteDifference 
+-----------------------------------------------
+
+.. automodule:: soupy.utils.stochasticCostFiniteDifference
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+soupy.utils.scipyCostWrapper module
+---------------------------------------
+
+.. automodule:: soupy.utils.scipyCostWrapper
+    :members:
+    :undoc-members:
+    :show-inheritance: