Add Sphinx docs and enable ReadTheDocs build (#13)

* Remove WaterTAP-specific how-to pages

* Move existing files

* Add core files for Sphinx docs

* Add minimal installation instructions

* Add ReadTheDocs config file

* Reformat with Black

* Add basic GHA check for docs build

* Try resolving failures for Python 3.8

* Try fixing Codecov upload error

* Try fixing workflow syntax error

* Try with space

* Try downgrading Codecov CLI due to codecov/codecov-action#1487

.github/workflows/checks.yml

@@ -132,13 +132,24 @@ jobs:
       - uses: actions/download-artifact@v4
         with:
           pattern: coverage-report-*
-      - name: Upload coverage report to Codecov
+      - name: Upload coverage report to Codecov (token)
         uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
           verbose: true
-          # NOTE: secrets are not available for pull_request workflows
-          # However, as of 2024-02-10, Codecov is still allowing tokenless upload from PRs
-          # but does require token for other workflows e.g. merge to `main`
-          # see https://github.com/codecov/codecov-action/issues/1274#issuecomment-1934437359
           token: ${{ secrets.CODECOV_TOKEN }}
+          # downgrading after v0.7.0 broke tokenless upload
+          # see codecov/codecov-action#1487
+          version: v0.6.0
+
+  build-docs:
+    name: Build docs (Sphinx)
+    needs: [code-formatting]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - run: pip install -r requirements-dev.txt
+      - run: make -C docs html

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# .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-22.04
+  tools:
+    python: "3.10"
+
+python:
+  install:
+   - requirements: requirements-dev.txt

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/conf.py

@@ -0,0 +1,68 @@
+from importlib import metadata
+
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "Parameter Sweep"
+copyright = "2024, WaterTAP"
+author = "WaterTAP"
+
+release = version = metadata.version("parameter-sweep")
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx_rtd_theme",
+    "sphinx.ext.doctest",
+    "sphinx.ext.napoleon",
+    "autoapi.extension",
+    "sphinx.ext.intersphinx",
+]
+suppress_warnings = []
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# see https://sphinx-autoapi.readthedocs.io/en/latest/reference/config.html
+autoapi_dirs = ["../src"]
+autoapi_root = "technical_reference"
+autoapi_options = [
+    "members",
+    "undoc-members",
+    "show-module-summary",
+]
+# set to True to save the autogenerated
+autoapi_keep_files = False
+autoapi_ignore = [
+    "*conftest.py",
+    "*test_*.py",
+    "*tests/*.py",
+]
+# the warnings come from parameter_sweep._compat
+suppress_warnings += ["autoapi.python_import_resolution"]
+
+intersphinx_mapping = {
+    "pyomo": ("https://pyomo.readthedocs.org/en/stable", None),
+    "numpy": ("https://numpy.org/doc/1.26", None),
+}
+
+
+def _skip_tests(app, what: str, name: str, obj, skip, options):
+    return skip
+
+
+def setup(sphinx):
+    sphinx.connect("autoapi-skip-member", _skip_tests)
+
+
+# -- 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 = ["_static"]

docs/getting_started/index.rst

@@ -0,0 +1,9 @@
+Getting started
+===============
+
+.. toctree::
+   :maxdepth: 1
+
+   installation
+   parameter_sweep
+   parallel_manager

docs/getting_started/installation.rst

@@ -0,0 +1,6 @@
+Installation
+------------
+
+.. code-block:: bash
+
+   pip install parameter-sweep

docs/technical_reference/tools/parallel_manager.rst → docs/getting_started/parallel_manager.rst

@@ -1,10 +1,5 @@
 Parallel Manager
-====================
-
-.. index::
-    pair: parameter_sweep.parallel.parallel_manager;parallel_manager
-
-.. currentmodule:: parameter_sweep.parallel.parallel_manager
+================
 
 Overview
 --------
@@ -66,11 +61,11 @@ following statement.
 
 The above code return 1 of 5 parallel manager classes. There are currently 5 parallel manager classes:
 
-    #. ``SingleProcessParallelManager`` : To enable serial implementation
-    #. ``MPIParallelManager`` : For MPI
-    #. ``ConcurrentFuturesParallelManager`` : For python concurrent futures
-    #. ``MultiprocessingParallelManager`` : For more advanced python multiprocessing
-    #. ``RayIoParallelManager`` : For using Ray
+    #. :class:`SingleProcessParallelManager` : To enable serial implementation
+    #. :class:`MPIParallelManager` : For MPI
+    #. :class:`ConcurrentFuturesParallelManager` : For python concurrent futures
+    #. :class:`MultiprocessingParallelManager` : For more advanced python multiprocessing
+    #. :class:`RayIoParallelManager` : For using Ray
 
 Alternatively, the user can specify the parameter sweep class directly, for example
 

docs/getting_started/parameter_sweep.rst

@@ -0,0 +1,76 @@
+
+Parameter Sweep
+===============
+
+.. currentmodule:: parameter_sweep.parameter_sweep
+
+Overview
+--------
+
+The parameter sweep tool systematically fixes variables or modifies
+mutable parameters on a flowsheet (or Pyomo :class:`~pyomo.environ.ConcreteModel`), optimizes
+the flowsheet, and reports user-specified results.
+The parameter sweep tool can be operated in one of two ways: sweeping a
+fixed set of parameters, or allowing for random samples from a distribution.
+While different fixed or random sampling types can be combined, in a single
+parameter sweep the user must use either all fixed or all random sampling types.
+(This implementation detail may be relaxed in future releases.)
+
+For the "fixed" sampling type, :class:`LinearSample`, the parameter sweep tool will evaluate the
+cross product of all the specified parameters, whereas with the "random" sampling
+types :class:`UniformSample` and :class:`NormalSample` the parameter sweep tool will evaluate
+a fixed number of samples specified in :const:`num_samples`. With either sampling type,
+the values of the Pyomo objects (:class:`~pyomo.environ.Var` s, :class:`~pyomo.environ.NamedExpression` s, etc.), that the user specifies
+in `outputs`.
+
+For each item the user wants to change, they specify a `sweep_params` dictionary.
+The keys are "short" names, and the values are one of the included :class:`Sample` objects.
+In all cases the :class:`Sample` objects are instantiated with the Pyomo object to be changed,
+with additional arguements depending on the sampling type. For example, for the fixed
+:class:`LinearSample` the user would also specify a lower limit, an upper limit, and the number
+of elements to be sampled for this parameter between the lower limit and upper limit.
+Each item should be sampled at least twice to capture the upper and lower
+limit. The random :class:`UniformSample` requires a lower limit and upper limit, and the
+:class:`NormalSample` requires a mean and standard deviation.
+
+In addition to the parameters to sweep and the values to track for output,
+the user must provide an :const:`optimize_function`, which takes the :const:`model` as an
+attribute calls an optimization routine to solve it for the updated parameters.
+Should the call to :const:`optimize_function` fail, and a :const:`reinitialize_function` is not
+specified, the outputs will be reported as ``NaN`` for that parameter set.
+
+The user can optionally specify a :const:`reinitialize_function` in case any piece
+of the :const:`optimize_function` fails -- after the call to :const:`reinitialize_function`
+the model should be in a state ready to optimize again. If the :const:`reinitialize_function`
+or the second call to the :const:`optimize_function` fail for any reason, the outputs will
+be reported as ``NaN`` for that parameter set.
+
+The parameter sweep tool maintains the state of the flowsheet / Pyomo model between
+calls to :const:`optimize_function` to take advantage of initializations provided by
+earlier solutions. If this behavior is undesirable, the user should re-initialize
+their flowsheet as part of their :const:`optimize_function`.
+
+Finally, the user can specify a :const:`csv_results_file_name` and/or an :const:`h5_results_file_name`,
+which will write the outputs to disk in a CSV and/or H5 format, respectively.
+In the CSV results
+file, each column specifies a fixed parameter or the associated output, and each row
+is a single run with the specified parameters and resulting outputs. The H5 file
+contains the parameter sweep inputs and the outputs stored in a dictionary-like format.
+Additionally, when an H5 file is written, a companion text file is created with the name
+:const:`h5_results_file_name` + ``".txt"``. This text file contains the metadata of the H5 results
+file.
+
+Parallel Usage
+--------------
+
+The parameter sweep tool can optionally utilize ``mpi4py`` to split the parameter
+sweep over multiple processors. If ``mpi4py`` is installed in the user's conda environment,
+a script utilizing the parameter sweep tool can be run in parallel, in this example
+using two threads.
+
+.. code:: bash
+
+   mpiexec -n 2 python parameter_sweep_script.py
+
+For advanced users, the parameter sweep tool can optionally take a MPI communicator
+as an argument.