Initial Commit

.gitignore

@@ -1,13 +1,41 @@
+**/.DS_Store
+**/.vscode
+**/.mp4
+**/.npy
+**/.swp
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
-
-# C extensions
+*.run
 *.so
+*.pkl
+
+
+# files which are in tests
+tests/!archive/*
+tests/scratch*
+tests/!archive_tests/*
+tests/!experimental/*
+
+pymoo/cache/
+pymoo/cache/*
+
+
+benchmark/runs/*
+
+# any video or other output file
+*.mp4
+
+# pycharm folder
+.idea/
+
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -20,12 +48,9 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
-share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -40,16 +65,13 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
 .hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -58,8 +80,6 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
 # Flask stuff:
 instance/
@@ -77,38 +97,22 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# IPython
-profile_default/
-ipython_config.py
-
 # pyenv
 .python-version
 
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
+# celery beat schedule file
 celerybeat-schedule
-celerybeat.pid
 
 # SageMath parsed files
 *.sage.py
 
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
-env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 
 # Spyder project settings
 .spyderproject
@@ -122,8 +126,3 @@ venv.bak/
 
 # mypy
 .mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/

LICENSE

@@ -633,8 +633,8 @@ the "copyright" line and a pointer to where the full notice is found.
     Copyright (C) <year>  <name of author>
 
     This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU Affero General Public License as published
-    by the Free Software Foundation, either version 3 of the License, or
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
     (at your option) any later version.
 
     This program is distributed in the hope that it will be useful,

README.rst

@@ -0,0 +1,97 @@
+pysamoo - Surrogate-Assisted Multi-objective Optimization
+====================================================================
+
+
+|python| |license|
+
+
+.. |python| image:: https://img.shields.io/badge/python-3.6-blue.svg
+   :alt: python 3.6
+
+.. |license| image:: https://img.shields.io/badge/license-apache-orange.svg
+   :alt: license apache
+   :target: https://www.apache.org/licenses/LICENSE-2.0
+
+The software documentation is available here: https://anyoptimization.com/projects/pysamoo/
+
+Installation
+====================================================================
+
+The official release is always available at PyPi:
+
+.. code:: bash
+
+    pip install -U pysamoo
+
+
+
+.. _Usage:
+
+Usage
+********************************************************************************
+
+We refer here to our documentation for all the details.
+However, for instance, executing NSGA2:
+
+.. code:: python
+
+    from pymoo.optimize import minimize
+    from pymoo.problems.multi.zdt import ZDT1
+    from pymoo.visualization.scatter import Scatter
+    from pysamoo.algorithms.ssansga2 import SSANSGA2
+
+    problem = ZDT1(n_var=10)
+
+    algorithm = SSANSGA2(n_initial_doe=50,
+                         n_infills=10,
+                         surr_pop_size=100,
+                         surr_n_gen=50)
+
+    res = minimize(
+        problem,
+        algorithm,
+        ('n_evals', 200),
+        seed=1,
+        verbose=True)
+
+    plot = Scatter()
+    plot.add(problem.pareto_front(), plot_type="line", color="black", alpha=0.7)
+    plot.add(res.F, facecolor="none", edgecolor="red")
+    plot.show()
+
+
+
+.. _Citation:
+
+Citation
+********************************************************************************
+
+If you use this framework, we kindly ask you to cite the following paper:
+
+| `Julian Blank, & Kalyanmoy Deb. (2022). pysamoo: Surrogate-Assisted Multi-Objective Optimization in Python. <https://arxiv.org/abs/2204.05855>`_
+|
+| BibTex:
+
+::
+
+    @misc{pysamoo,
+      title={pysamoo: Surrogate-Assisted Multi-Objective Optimization in Python},
+      author={Julian Blank and Kalyanmoy Deb},
+      year={2022},
+      eprint={2204.05855},
+      archivePrefix={arXiv},
+      primaryClass={cs.NE}
+    }
+
+.. _Contact:
+
+Contact
+********************************************************************************
+
+Feel free to contact me if you have any questions:
+
+| `Julian Blank <http://julianblank.com>`_  (blankjul [at] msu.edu)
+| Michigan State University
+| Computational Optimization and Innovation Laboratory (COIN)
+| East Lansing, MI 48824, USA
+

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     = source
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+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

docs/source/algorithms.csv

@@ -0,0 +1,11 @@
+Algorithm,Framework,multi-objective,constrained,Description
+`SSA-NSGA-II <#SSA-NSGA-II>`_,None,yes,yes,A simple surrogate-assisted variant of the well-known NSGA-II algorithm.
+`PSAF-GA <#PSAF-GA>`_,PSAF,no,no,An implementation using genetic algorithms assisted by surrogates.
+`PSAF-DE <#PSAF-DE>`_,PSAF,no,no,An implementation of surrogate-assisted particle swarm optimization.
+`PSAF-CMAES <#PSAF-CMAES>`_,PSAF,no,no,The popular CMAES method with surrogate assistance.
+`GPSAF-GA <#PSAF-GA>`_,GPSAF,no,yes,An implementation using genetic algorithms assisted by surrogates with constrained handling
+`GPSAF-DE <#PSAF-DE>`_,GPSAF,no,yes,An implementation of surrogate-assisted particle swarm optimization with constrained handling.
+`GPSAF-CMAES <#PSAF-CMAES>`_,GPSAF,no,no,The popular CMAES method with surrogate assistance.
+`GPSAF-ISRES <#GPSAF-ISRES>`_, GPSAF,no,yes,"A surrogate-assisted variant of ISRES, a well known algorithm for constrained single-objective optimization problems"
+`GPSAF-NSGA-II <#GPSAF-NSGA-II>`_, GPSAF,yes,yes,"A surrogate-assisted variant of NSGA-II, a well known algorithm for bi-objective optimization"
+`GPSAF-NSGA-III <#GPSAF-NSGA-III>`_, GPSAF,yes,yes,An extension of GPSAF-NSGA-II for many-objective optimization problems.

docs/source/conf.py

@@ -0,0 +1,58 @@
+# 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
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pysamoo'
+copyright = '2022, Julian Blank'
+author = 'Julian Blank'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- 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 = [
+    'nbsphinx',
+    "sphinx_rtd_theme"
+]
+
+# 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 = ['**.ipynb_checkpoints']
+
+
+# -- 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"
+html_static_path = ['_static']
+html_logo = "_static/pysamoo.png"
+html_theme_options = {
+    'logo_only': True,
+    'display_version': False,
+}