VERSION 0.3.2

liaoweiduo · Oct 21, 2019 · 373bd57 · 373bd57
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Showing 102 changed files with 4,105 additions and 422 deletions.
diff --git a/README.rst b/README.rst
@@ -78,7 +78,7 @@ However, for instance executing NSGA2:
 
     problem = get_problem("zdt2")
 
-    algorithm = NSGA2(pop_size=100, elimate_duplicates=True)
+    algorithm = NSGA2(pop_size=100, eliminate_duplicates=True)
 
     res = minimize(problem,
                    algorithm,

diff --git a/benchmark/benchmark_nelder_mead.py b/benchmark/benchmark_nelder_mead.py
@@ -4,10 +4,9 @@
 import os
 import pickle
 
-from pymoo.algorithms.so_genetic_algorithm import ga
-from pymoo.algorithms.so_nelder_mead import nelder_mead
-from pymoo.factory import get_problem, get_termination
-from pymoo.operators.crossover.nelder_mead_crossover import NelderMeadCrossover
+from pymoo.algorithms.so_nelder_mead import NelderMead
+
+from pymoo.factory import get_problem
 
 setup = [
     "go-amgm",
@@ -222,7 +221,7 @@ def add_with_variables(D, problem, n_vars):
     prefix = "runs"
 
     # name of the experiment
-    name = "nelder-mead-0.3.1"
+    name = "nelder-mead-0.3.2"
 
     # number of runs to execute
     n_runs = 10
@@ -234,7 +233,7 @@ def add_with_variables(D, problem, n_vars):
 
         problem = get_problem(_problem)
 
-        method = nelder_mead(n_max_restarts=100)
+        method = NelderMead(n_max_local_restarts=2)
 
         for run in range(1, n_runs + 1):
             fname = "%s_%s.run" % (_problem, run)

diff --git a/benchmark/benchmark_nsga2.py b/benchmark/benchmark_nsga2.py
@@ -4,7 +4,8 @@
 import os
 import pickle
 
-from pymoo.algorithms.nsga2 import nsga2
+from pymoo.algorithms.nsga2 import NSGA2
+
 from pymoo.factory import get_sampling, get_crossover, get_mutation, get_problem
 from pymoo.operators.crossover.simulated_binary_crossover import SimulatedBinaryCrossover
 from pymoo.operators.mutation.polynomial_mutation import PolynomialMutation
@@ -90,7 +91,7 @@
     prefix = "runs"
 
     # name of the experiment
-    name = "pynsga2-0.3.1"
+    name = "pynsga2-0.3.2"
 
     # number of runs to execute
     n_runs = 100
@@ -107,7 +108,7 @@
         s = setup[_problem]
         problem = s['problem']
 
-        method = nsga2(
+        method = NSGA2(
             pop_size=s['pop_size'],
             crossover=s['crossover'],
             mutation=s['mutation'],

diff --git a/benchmark/benchmark_nsga3.py b/benchmark/benchmark_nsga3.py
@@ -1,7 +1,7 @@
 import os
 import pickle
 
-from pymoo.algorithms.nsga3 import nsga3
+from pymoo.algorithms.nsga3 import NSGA3
 from pymoo.factory import get_problem, get_reference_directions
 from pymoo.operators.crossover.simulated_binary_crossover import SimulatedBinaryCrossover
 from pymoo.operators.mutation.polynomial_mutation import PolynomialMutation
@@ -206,7 +206,7 @@ def get_setup(n_obj):
     prefix = "runs"
 
     # name of the experiment
-    name = "pynsga3-0.3.1"
+    name = "pynsga3-0.3.2"
 
     # number of runs to execute
     n_runs = 50
@@ -222,7 +222,7 @@ def get_setup(n_obj):
         s = setup[_problem]
         problem = s['problem']
 
-        method = nsga3(
+        method = NSGA3(
             s['ref_dirs'],
             pop_size=s['pop_size'],
             crossover=s['crossover'],

diff --git a/doc/source/_theme/custom_theme/layout.html b/doc/source/_theme/custom_theme/layout.html
@@ -29,13 +29,13 @@
     <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css">
     <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css">
     <link rel="stylesheet" href="https://unpkg.com/[email protected]/build/pure-min.css" integrity="sha384-nn4HPE8lTHyVtfCBi5yW9d20FjT8BJwUXyWZT9InLYax14RDjBj46LmSztkmNP9w" crossorigin="anonymous">
-    
+
     {%- for cssfile in css_files %}
         <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css">
     {%- endfor %}
 
 
-    
+
     <!--
     ---------------------------------------
     JavaScript
@@ -59,18 +59,17 @@
 
     <script type="text/javascript" src="{{ pathto('_static/js/custom.js', 1) }}"></script>
     {%- for scriptfile in script_files %}
+     {% if pathto(scriptfile, 1) %}
         <script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
+      {%endif %}
     {%- endfor %}
-
-    {%- if favicon %}
-        <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}">
-    {%- endif %}
+
+    <link rel="icon" type="image/png" href="{{ pathto('_static/img/favicon.ico', 1) }}">
 
     <meta charset="{{ encoding }}">
     {{ metatags }}
 
 
-
 	<title>pymoo</title>
 
 
@@ -91,7 +90,7 @@
     <div class="container">
         <div class="top-scipy-org-logo-header">
             <a href="{{ pathto('index') }}">
-                <img style="border: 0;" alt="pymoo" src="{{ pathto('_static/img/pymoo.svg', 1) }}"></a>
+                <img style="border: 0;" alt="pymoo" src="{{ pathto('_static/img/pymoo.jpg', 1) }}"></a>
         </div>
     </div>
     {% endblock %}
@@ -148,7 +147,7 @@
                     {%- block document %}
                     <div class="bodywrapper">
                         <div class="body" id="spc-section-body">
-                            {% block body %} 
+                            {% block body %}
                             {% endblock %}
                         </div>
                     </div>

diff --git a/doc/source/_theme/custom_theme/static/img/favicon.ico b/doc/source/_theme/custom_theme/static/img/favicon.ico
diff --git a/doc/source/_theme/custom_theme/static/img/pymoo.jpg b/doc/source/_theme/custom_theme/static/img/pymoo.jpg
diff --git a/doc/source/algorithms/differential_evolution.ipynb b/doc/source/algorithms/differential_evolution.ipynb
@@ -65,9 +65,10 @@
      "output_type": "stream",
      "text": [
       "Best solution found: \n",
-      "X = [-0.00055292 -0.00016638 -0.00024617  0.00021267 -0.0003819  -0.00024424\n",
-      " -0.0004285   0.00022352 -0.00025735  0.00014052]\n",
-      "F = [0.00124724]\n"
+      "X = [-1.72696533e-05  4.11624478e-06  7.02351801e-06  6.20937154e-05\n",
+      "  7.70382670e-05 -2.80596809e-05 -4.42434414e-06 -5.74272367e-06\n",
+      " -1.24745030e-06 -4.59264431e-05]\n",
+      "F = [0.00014488]\n"
      ]
     }
    ],
@@ -92,8 +93,8 @@
     "\n",
     "res = minimize(problem,\n",
     "               algorithm,\n",
-    "               termination=('n_gen', 250),\n",
-    "               seed=1)\n",
+    "               seed=1,\n",
+    "               verbose=False)\n",
     "\n",
     "print(\"Best solution found: \\nX = %s\\nF = %s\" % (res.X, res.F))"
    ]

diff --git a/doc/source/algorithms/genetic_algorithm.ipynb b/doc/source/algorithms/genetic_algorithm.ipynb
@@ -65,10 +65,10 @@
      "output_type": "stream",
      "text": [
       "Best solution found: \n",
-      "X = [0.99303414 0.99782661 0.99754116 0.99912976 0.99483    0.99544777\n",
-      " 0.98882008 0.97191879 0.9899395  2.9192581  2.80936782 2.33122498\n",
-      " 0.9894118 ]\n",
-      "F = [-13.92817742]\n"
+      "X = [0.99846487 0.99896452 0.99227818 0.98115003 0.97598486 0.93133579\n",
+      " 0.9989595  0.99283295 0.93527323 2.74333764 2.73101357 2.83238454\n",
+      " 0.99763872]\n",
+      "F = [-13.99514066]\n"
      ]
     }
    ],
@@ -86,6 +86,7 @@
     "res = minimize(problem,\n",
     "               algorithm,\n",
     "               termination=('n_gen', 50),\n",
+    "               seed=1,\n",
     "               verbose=False)\n",
     "\n",
     "print(\"Best solution found: \\nX = %s\\nF = %s\" % (res.X, res.F))\n",

diff --git a/doc/source/algorithms/index.ipynb b/doc/source/algorithms/index.ipynb
@@ -21,6 +21,7 @@
     "\n",
     "   differential_evolution\n",
     "   genetic_algorithm\n",
+    "   nelder_mead\n",
     "   nsga2\n",
     "   rnsga2\n",
     "   nsga3\n",
@@ -42,25 +43,24 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "|Name|Convenience|\n",
-    "|---|---|\n",
-    "|[Differential Evolution](differential_evolution.ipynb)|\"de\"|\n",
-    "|[Genetic Algorithm](genetic_algorithm.ipynb)|\"ga\"|\n",
-    "|[NSGA-II](nsga2.ipynb)|\"nsga2\"|\n",
-    "|[RNSGA-II](rnsga2.ipynb)|\"rnsga2\"|\n",
-    "|[NSGA-III](nsga3.ipynb)|\"nsga3\"|\n",
-    "|[UNSGA-III](unsga3.ipynb)|\"unsga3\"|\n",
-    "|[RNSGA-III](rnsga3.ipynb)|\"rnsga3\"|\n",
-    "|[MOEA/D](moead.ipynb)|\"moead\"|\n"
+    "|Name|Class|Convenience|\n",
+    "|---|---|---|\n",
+    "|[Differential Evolution](differential_evolution.ipynb)|\"DE\"|\"de\"\n",
+    "|[Genetic Algorithm](genetic_algorithm.ipynb)|\"GA\"|\"ga\"\n",
+    "|[Nelder Mead](nelder_mead.ipynb)|\"NelderMead\"|\"nelder-mead\"\n",
+    "|[NSGA-II](nsga2.ipynb)|\"NSGA2\"|\"nsga2\"\n",
+    "|[RNSGA-II](rnsga2.ipynb)|\"RNSGA2\"|\"rnsga2\"\n",
+    "|[NSGA-III](nsga3.ipynb)|\"NSGA3\"|\"nsga3\"\n",
+    "|[UNSGA-III](unsga3.ipynb)|\"UNSGA3\"|\"unsga3\"\n",
+    "|[RNSGA-III](rnsga3.ipynb)|\"RNSGA3\"|\"rnsga3\"\n",
+    "|[MOEA/D](moead.ipynb)|\"MOEAD\"|\"moead\"\n"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Each of them is implemented in a class which can be used directly. However, it might\n",
-    "be more comfortable to either use the factory or convenience function.\n",
-    "For example for scatter plots the following initiates the same object:"
+    "Each of them is implemented in a class which can be used directly and the constructor takes parameter of the algorithm."
    ]
   },
   {
@@ -69,8 +69,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pymoo.algorithms.nsga2 import nsga2\n",
-    "algorithm = nsga2()\n",
+    "from pymoo.algorithms.nsga2 import NSGA2\n",
+    "algorithm = NSGA2()\n",
     "\n",
     "from pymoo.factory import get_algorithm\n",
     "algorithm = get_algorithm(\"nsga2\")"

diff --git a/doc/source/algorithms/moead.ipynb b/doc/source/algorithms/moead.ipynb
diff --git a/doc/source/algorithms/nelder_mead.ipynb b/doc/source/algorithms/nelder_mead.ipynb
@@ -0,0 +1,97 @@
+{
+ "cells": [
+  {
+   "cell_type": "raw",
+   "metadata": {
+    "raw_mimetype": "text/restructuredtext"
+   },
+   "source": [
+    ".. _nb_nelder_mead:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Nelder Mead\n",
+    "\n",
+    "\n",
+    "This algorithm is implemented based on <cite data-cite=\"NelderMead65\"></cite>. In addition to other implementations, a boundary check is included. This ensures that the search considers the box constraints of the given optimization problem. If no boundaries are provided the algorithm falls back to a search without any constraints. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "code": "algorithms/usage_so_nelder_mead.py"
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[0.49955771 0.49951863 0.50041486 0.49977682 0.50047266 0.50000158\n",
+      " 0.50030921 0.50048091 0.49992482 0.49986138]\n",
+      "[1.22442015e-06]\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pymoo.algorithms.so_nelder_mead import NelderMead\n",
+    "from pymoo.factory import get_problem\n",
+    "from pymoo.optimize import minimize\n",
+    "\n",
+    "problem = get_problem(\"sphere\")\n",
+    "\n",
+    "algorithm = NelderMead(n_max_restarts=10)\n",
+    "\n",
+    "res = minimize(problem,\n",
+    "               algorithm,\n",
+    "               seed=1,\n",
+    "               verbose=False)\n",
+    "\n",
+    "print(res.X)\n",
+    "print(res.F)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### API"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "metadata": {
+    "raw_mimetype": "text/restructuredtext"
+   },
+   "source": [
+    ".. autoclass:: pymoo.algorithms.so_nelder_mead.NelderMead\n",
+    "    :noindex:"
+   ]
+  }
+ ],
+ "metadata": {
+  "celltoolbar": "Raw Cell Format",
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/doc/source/algorithms/nsga2.ipynb b/doc/source/algorithms/nsga2.ipynb
diff --git a/doc/source/algorithms/nsga3.ipynb b/doc/source/algorithms/nsga3.ipynb
diff --git a/doc/source/algorithms/rnsga2.ipynb b/doc/source/algorithms/rnsga2.ipynb
diff --git a/doc/source/algorithms/rnsga3.ipynb b/doc/source/algorithms/rnsga3.ipynb
diff --git a/doc/source/api/algorithms.rst b/doc/source/api/algorithms.rst
@@ -1,19 +1,19 @@
 Algorithms
 ==============================================================================
 
-.. autofunction:: pymoo.algorithms.so_genetic_algorithm.ga
+.. autoclass:: pymoo.algorithms.so_genetic_algorithm.GA
 
-.. autofunction:: pymoo.algorithms.so_de.de
+.. autoclass:: pymoo.algorithms.so_de.DE
 
-.. autofunction:: pymoo.algorithms.nsga2.nsga2
+.. autoclass:: pymoo.algorithms.nsga2.NSGA2
 
-.. autofunction:: pymoo.algorithms.rnsga2.rnsga2
+.. autoclass:: pymoo.algorithms.rnsga2.RNSGA2
 
-.. autofunction:: pymoo.algorithms.nsga3.nsga3
+.. autoclass:: pymoo.algorithms.nsga3.NSGA3
 
-.. autofunction:: pymoo.algorithms.unsga3.unsga3
+.. autoclass:: pymoo.algorithms.unsga3.UNSGA3
 
-.. autofunction:: pymoo.algorithms.rnsga3.rnsga3
+.. autoclass:: pymoo.algorithms.rnsga3.RNSGA3
 
-.. autofunction:: pymoo.algorithms.moead.moead
+.. autoclass:: pymoo.algorithms.moead.MOEAD
 
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -156,13 +156,13 @@
 links_local = [
     ("http://localhost:8001", "pymoo.org"),
     ("https://github.com/msu-coinlab/pymoo", "GitHub"),
-    ("/api/simulation.html", "API")
+    ("api/index.html", "API")
 ]
 
 links_remote = [
     ("http://pymoo.org/", "pymoo.org"),
     ("https://github.com/msu-coinlab/pymoo", "GitHub"),
-    ("/api/simulation.html", "API")
+    ("api/index.html", "API")
 ]
 
 html_theme_options = {