Merge pull request #418 from bwheelz36/html_docs

SPHINX based html docs

Author: bwheelz36

.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"
    ]
   },
   {