Merge pull request #418 from bwheelz36/html_docs

SPHINX based html docs

.github/workflows/build_docs.yml

@@ -0,0 +1,44 @@
+name: build docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  deploy:
+    runs-on: ubuntu-20.04
+    permissions:
+      contents: write
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Install pandoc
+        run: sudo apt-get install -y pandoc
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install sphinx
+          pip install nbsphinx
+          pip install sphinx_rtd_theme
+          pip install jupyter
+      - name: Install package
+        run: |
+          pip install -e .
+      - name: build sphinx docs
+        run: |
+          cd docsrc
+          make github
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.ref == 'refs/heads/main' }}
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs

.gitignore

@@ -28,4 +28,8 @@ venv/
 ENV/
 env.bak/
 venv.bak/
-*temp*
+*temp*
+
+docs/*
+docsrc/.ipynb_checkpoints/*
+docsrc/*.ipynb

docsrc/Makefile

@@ -0,0 +1,24 @@
+# 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      = ../docs
+
+# Put it first so that "make" without argument is like "make help".
+# help:
+# 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+github:
+	@make html
+	@cp -a ../docs/html/. ../docs
+
+# 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)

docsrc/code_docs.rst

@@ -0,0 +1,34 @@
+Code Documentation
+==================
+
+This page shows the documentation generated by sphinx automatically scanning our source code
+
+Bayesian Optimization
+---------------------
+
+.. automodule:: bayes_opt.bayesian_optimization
+   :members:
+
+Acquisition function
+--------------------
+
+.. autoclass:: bayes_opt.util.UtilityFunction
+   :members:
+
+Target Space
+------------
+
+.. autoclass:: bayes_opt.target_space.TargetSpace
+   :members:
+
+Domain reduction
+----------------
+
+.. autoclass:: bayes_opt.domain_reduction.SequentialDomainReductionTransformer
+   :members:
+
+Constraints
+-----------
+
+.. autoclass:: bayes_opt.constraint.ConstraintModel
+   :members:

docsrc/conf.py

@@ -0,0 +1,70 @@
+# 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
+import shutil
+from glob import glob
+from pathlib import Path
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('..'))
+
+# copy the latest example files:
+this_file_loc = Path(__file__).parent
+notebooks = glob(str(this_file_loc.parent / 'examples' / '*.ipynb'))
+for notebook in notebooks:
+    shutil.copy(notebook, this_file_loc)
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Bayesian Optimization'
+author = 'Fernando Nogueira'
+
+
+# -- 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.coverage',
+    'sphinx.ext.githubpages',
+    'nbsphinx',
+    'IPython.sphinxext.ipython_console_highlighting',
+    'sphinx.ext.mathjax']
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+# 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 = []
+
+
+# -- 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']

docsrc/examples.rst

@@ -0,0 +1,13 @@
+Examples
+========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Examples:
+
+   /basic-tour
+   /advanced-tour
+   /exploitation_vs_exploration
+   /visualization
+   /constraints
+   /domain_reduction

docsrc/index.rst

@@ -0,0 +1,16 @@
+Bayesian Optimization
+=====================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   /examples
+   /code_docs
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docsrc/make.bat

@@ -0,0 +1,44 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=../docs
+
+%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
+
+if "%1" == "github" (
+    %SPHINXBUILD% -M html %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+    robocopy %BUILDDIR%/html ../docs /E > nul
+    echo.Generated files copied to ../docs
+    goto end
+)
+
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docsrc/requirements.txt

@@ -0,0 +1,3 @@
+sphinx
+nbsphinx
+sphinx_rtd_theme

examples/constraints.ipynb

@@ -14,7 +14,7 @@
     "2. Expensive constraints - in other situations, you may not know whether or not a given solution violates your constraints until you have explicitly evaluate the objective function there - which is typically an expensive operation. In such situations, it is desirable to **learn** the constrained regions on the fly in order to avoid unnecessary expensive calls to the objective function. The way to handle these situations is described in **2. Advanced Constrained Optimization**\n",
     "\n",
     "\n",
-    "# 1. Simple Constrained Optimization\n",
+    "## 1. Simple Constrained Optimization\n",
     "\n",
     "In situations where you know in advance whether or not a given point violates your constraints, you can normally simply code them directly into the objective function. To demonstrate this, let's start with a standard non-constrained optimization:"
    ]
@@ -161,7 +161,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 2. Advanced Constrained Optimization"
+    "## 2. Advanced Constrained Optimization"
    ]
   },
   {

examples/visualization.ipynb

@@ -20,7 +20,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Target Function\n",
+    "# Visualization\n",
     "\n",
     "Lets create a target 1-D function with multiple local maxima to test and visualize how the [BayesianOptimization](https://github.com/fmfn/BayesianOptimization) package works. The target function we will try to maximize is the following:\n",
     "\n",
@@ -66,7 +66,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Create a BayesianOptimization Object\n",
+    "## Create a BayesianOptimization Object\n",
     "\n",
     "Enter the target function to be maximized, its variable(s) and their corresponding ranges. A minimum number of 2 initial guesses is necessary to kick start the algorithms, these can either be random or user defined."
    ]
@@ -114,7 +114,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Plotting and visualizing the algorithm at each step"
+    "## Plotting and visualizing the algorithm at each step"
    ]
   },
   {
@@ -486,7 +486,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Stopping\n",
+    "## Stopping\n",
     "\n",
     "After just a few points the algorithm was able to get pretty close to the true maximum. It is important to notice that the trade off between exploration (exploring the parameter space) and exploitation (probing points near the current known maximum) is fundamental to a succesful bayesian optimization procedure. The utility function being used here (Upper Confidence Bound - UCB) has a free parameter $\\kappa$ that allows the user to make the algorithm more or less conservative. Additionally, the larger the initial set of random points explored, the less likely the algorithm is to get stuck in local minima due to being too conservative."
    ]