Merge branch 'dev'

Author: geoffreyp

docs/examples/example_rmnk_moead.py

@@ -16,21 +16,19 @@
 ###############################
 #  Initialize the algorithm   #
 ###############################
-number_of_objective = rmnk.function_numbers
 number_of_weight = 10
 number_of_weight_neighborhood = 20
 number_of_evaluations = 1000
 # The file is available here : https://github.com/moead-framework/data/blob/master/weights/SOBOL-2objs-10wei.ws
 # Others weights files are available here : https://github.com/moead-framework/data/tree/master/weights
-weight_file = "SOBOL-" + str(number_of_objective) + "objs-" + str(number_of_weight) + "wei.ws"
+weight_file = "SOBOL-" + str(rmnk.function_numbers) + "objs-" + str(number_of_weight) + "wei.ws"
 
 
 ###############################
 #    Execute the algorithm    #
 ###############################
 moead = Moead(problem=rmnk,
               max_evaluation=number_of_evaluations,
-              number_of_objective=number_of_objective,
               number_of_weight_neighborhood=number_of_weight_neighborhood,
               weight_file=weight_file,
               aggregation_function=Tchebycheff,
@@ -42,7 +40,7 @@
 ###############################
 #       Save the result       #
 ###############################
-save_file = "moead-rmnk" + str(number_of_objective) \
+save_file = "moead-rmnk" + str(rmnk.function_numbers) \
             + "-N" + str(number_of_weight) \
             + "-T" + str(number_of_weight_neighborhood) \
             + "-iter" + str(number_of_evaluations) \

docs/html/_modules/moead_framework/algorithm/abstract_moead.html

@@ -162,7 +162,7 @@ <h1>Source code for moead_framework.algorithm.abstract_moead</h1><div class="hig
 
 <span class="k">class</span> <span class="nc">AbstractMoead</span><span class="p">:</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">problem</span><span class="p">,</span> <span class="n">max_evaluation</span><span class="p">,</span> <span class="n">number_of_objective</span><span class="p">,</span> <span class="n">number_of_weight_neighborhood</span><span class="p">,</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">problem</span><span class="p">,</span> <span class="n">max_evaluation</span><span class="p">,</span> <span class="n">number_of_weight_neighborhood</span><span class="p">,</span>
                  <span class="n">aggregation_function</span><span class="p">,</span> <span class="n">weight_file</span><span class="p">,</span>
                  <span class="n">termination_criteria</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">genetic_operator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -171,14 +171,14 @@ <h1>Source code for moead_framework.algorithm.abstract_moead</h1><div class="hig
                  <span class="n">sps_strategy</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">offspring_generator</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">number_of_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">number_of_objective</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Constructor of the algorithm.</span>
 
 <span class="sd">        :param problem: {:class:`~moead_framework.problem.Problem`} problem to optimize</span>
 <span class="sd">        :param max_evaluation: {integer} maximum number of evaluation</span>
-<span class="sd">        :param number_of_objective: {integer} number of objective in the problem</span>
-<span class="sd">        :param number_of_weight: {integer} number of weight vector used to decompose the problem</span>
+<span class="sd">        :param number_of_weight_neighborhood: {integer} size of the neighborhood.</span>
 <span class="sd">        :param aggregation_function: {:class:`~moead_framework.aggregation.functions.AggregationFunction`}</span>
 <span class="sd">        :param weight_file: {string} path of the weight file. Each line represent a weight vector, each column represent a coordinate. An exemple is available here: https://github.com/moead-framework/data/blob/master/weights/SOBOL-2objs-10wei.ws</span>
 <span class="sd">        :param termination_criteria: Optional -- {:class:`~moead_framework.core.termination_criteria.abstract_termination_criteria.TerminationCriteria`} The default component is {:class:`~moead_framework.core.termination_criteria.max_evaluation.MaxEvaluation`}</span>
@@ -187,22 +187,27 @@ <h1>Source code for moead_framework.algorithm.abstract_moead</h1><div class="hig
 <span class="sd">        :param mating_pool_selector: Optional -- {:class:`~moead_framework.core.selector.abstract_selector.MatingPoolSelector`} The default selector is {:class:`~moead_framework.core.selector.closest_neighbors_selector.ClosestNeighborsSelector`}</span>
 <span class="sd">        :param sps_strategy: Optional -- {:class:`~moead_framework.core.sps_strategy.abstract_sps.SpsStrategy`} The default strategy is {:class:`~moead_framework.core.sps_strategy.sps_all.SpsAllSubproblems`}</span>
 <span class="sd">        :param offspring_generator: Optional -- {:class:`~moead_framework.core.offspring_generator.abstract_mating.OffspringGenerator`} The default generator is {:class:`~moead_framework.core.offspring_generator.offspring_generator.OffspringGeneratorGeneric`}</span>
-<span class="sd">        :param number_of_weight_neighborhood: Deprecated -- {integer} size of the neighborhood. Deprecated, remove in the next major release.</span>
+<span class="sd">        :param number_of_weight: Deprecated -- {integer} number of weight vector used to decompose the problem. Deprecated, remove in the next major release.</span>
+<span class="sd">        :param number_of_objective: Deprecated -- {integer} number of objective in the problem. Deprecated, remove in the next major release.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">problem</span> <span class="o">=</span> <span class="n">problem</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">aggregation_function</span> <span class="o">=</span> <span class="n">aggregation_function</span><span class="p">()</span>
 
-        <span class="k">if</span> <span class="n">number_of_weight_neighborhood</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">number_of_weight</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="kn">import</span> <span class="nn">warnings</span>
-            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;deprecated&quot;</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;The attribute number_of_weight is deprecated&quot;</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">number_of_objective</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="kn">import</span> <span class="nn">warnings</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;The attribute number_of_objective is deprecated&quot;</span><span class="p">,</span> <span class="ne">DeprecationWarning</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">termination_criteria</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">termination_criteria</span> <span class="o">=</span> <span class="n">MaxEvaluation</span><span class="p">(</span><span class="n">algorithm_instance</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">termination_criteria</span> <span class="o">=</span> <span class="n">termination_criteria</span><span class="p">(</span><span class="n">algorithm_instance</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">max_evaluation</span> <span class="o">=</span> <span class="n">max_evaluation</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">number_of_objective</span> <span class="o">=</span> <span class="n">number_of_objective</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">number_of_objective</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">problem</span><span class="o">.</span><span class="n">number_of_objective</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">t</span> <span class="o">=</span> <span class="n">number_of_weight_neighborhood</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">ep</span> <span class="o">=</span> <span class="p">[]</span>
 

docs/html/_modules/moead_framework/algorithm/combinatorial/moead.html

@@ -161,10 +161,10 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead</h1><div class
 
 <div class="viewcode-block" id="Moead.__init__"><a class="viewcode-back" href="../../../../moead_framework/moead_framework.algorithm.combinatorial.moead.Moead.html#moead_framework.algorithm.combinatorial.moead.Moead.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">problem</span><span class="p">,</span>
                  <span class="n">max_evaluation</span><span class="p">,</span>
-                 <span class="n">number_of_objective</span><span class="p">,</span>
                  <span class="n">number_of_weight_neighborhood</span><span class="p">,</span>
                  <span class="n">aggregation_function</span><span class="p">,</span>
                  <span class="n">weight_file</span><span class="p">,</span>
+                 <span class="n">number_of_objective</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">termination_criteria</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">number_of_crossover_points</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
                  <span class="n">mutation_probability</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
@@ -180,8 +180,6 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead</h1><div class
 
 <span class="sd">        :param problem: {:class:`~moead_framework.problem.Problem`} problem to optimize</span>
 <span class="sd">        :param max_evaluation: {integer} maximum number of evaluation</span>
-<span class="sd">        :param number_of_objective: {integer} number of objective in the problem</span>
-<span class="sd">        :param number_of_weight: {integer} number of weight vector used to decompose the problem</span>
 <span class="sd">        :param aggregation_function: {:class:`~moead_framework.aggregation.functions.AggregationFunction`}</span>
 <span class="sd">        :param weight_file: {string} path of the weight file. Each line represent a weight vector, each column represent a coordinate. An exemple is available here: https://github.com/moead-framework/data/blob/master/weights/SOBOL-2objs-10wei.ws</span>
 <span class="sd">        :param termination_criteria: Optional -- {:class:`~moead_framework.core.termination_criteria.abstract_termination_criteria.TerminationCriteria`} The default component is {:class:`~moead_framework.core.termination_criteria.max_evaluation.MaxEvaluation`}</span>
@@ -190,12 +188,14 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead</h1><div class
 <span class="sd">        :param mating_pool_selector: Optional -- {:class:`~moead_framework.core.selector.abstract_selector.MatingPoolSelector`} The default selector is {:class:`~moead_framework.core.selector.closest_neighbors_selector.ClosestNeighborsSelector`}</span>
 <span class="sd">        :param sps_strategy: Optional -- {:class:`~moead_framework.core.sps_strategy.abstract_sps.SpsStrategy`} The default strategy is {:class:`~moead_framework.core.sps_strategy.sps_all.SpsAllSubproblems`}</span>
 <span class="sd">        :param offspring_generator: Optional -- {:class:`~moead_framework.core.offspring_generator.abstract_mating.OffspringGenerator`} The default generator is {:class:`~moead_framework.core.offspring_generator.offspring_generator.OffspringGeneratorGeneric`}</span>
+<span class="sd">        :param number_of_weight: Deprecated -- {integer} number of weight vector used to decompose the problem. Deprecated, remove in the next major release.</span>
+<span class="sd">        :param number_of_objective: Deprecated -- {integer} number of objective in the problem. Deprecated, remove in the next major release.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
 
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">problem</span><span class="p">,</span>
                          <span class="n">max_evaluation</span><span class="p">,</span>
-                         <span class="n">number_of_objective</span><span class="p">,</span>
                          <span class="n">number_of_weight_neighborhood</span><span class="p">,</span>
+                         <span class="n">number_of_objective</span><span class="o">=</span><span class="n">number_of_objective</span><span class="p">,</span>
                          <span class="n">termination_criteria</span><span class="o">=</span><span class="n">termination_criteria</span><span class="p">,</span>
                          <span class="n">aggregation_function</span><span class="o">=</span><span class="n">aggregation_function</span><span class="p">,</span>
                          <span class="n">genetic_operator</span><span class="o">=</span><span class="n">genetic_operator</span><span class="p">,</span>

docs/html/_modules/moead_framework/algorithm/combinatorial/moead_delta_nr.html

@@ -181,7 +181,6 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead_delta_nr</h1><
 
 <span class="sd">        :param problem: {:class:`~moead_framework.problem.Problem`} problem to optimize</span>
 <span class="sd">        :param max_evaluation: {integer} maximum number of evaluation</span>
-<span class="sd">        :param number_of_objective: {integer} number of objective in the problem</span>
 <span class="sd">        :param number_of_weight_neighborhood: {integer} size of the neighborhood</span>
 <span class="sd">        :param delta: {float} probability to use all the population as neighborhood</span>
 <span class="sd">        :param number_of_replacement: {integer} maximum number of solutions replaced in the population for each new offspring generated</span>
@@ -191,6 +190,7 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead_delta_nr</h1><
 <span class="sd">        :param sps_strategy: Optional -- {:class:`~moead_framework.core.sps_strategy.abstract_sps.SpsStrategy`} The default strategy is {:class:`~moead_framework.core.sps_strategy.sps_all.SpsAllSubproblems`}</span>
 <span class="sd">        :param number_of_crossover_points: {integer} number of crossover point</span>
 <span class="sd">        :param mutation_probability: {integer} probability of mutation used by the genetic operator</span>
+<span class="sd">        :param number_of_objective: Deprecated -- {integer} number of objective in the problem. Deprecated, remove in the next major release.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
 
         <span class="n">mating_pool_selector</span> <span class="o">=</span> <span class="n">DeltaSelector</span>

docs/html/_modules/moead_framework/algorithm/combinatorial/moead_dra.html

@@ -164,12 +164,12 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead_dra</h1><div c
 
 <div class="viewcode-block" id="MoeadDRA.__init__"><a class="viewcode-back" href="../../../../moead_framework/moead_framework.algorithm.combinatorial.moead_dra.MoeadDRA.html#moead_framework.algorithm.combinatorial.moead_dra.MoeadDRA.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">problem</span><span class="p">,</span>
                  <span class="n">max_evaluation</span><span class="p">,</span>
-                 <span class="n">number_of_objective</span><span class="p">,</span>
                  <span class="n">number_of_weight_neighborhood</span><span class="p">,</span>
                  <span class="n">delta</span><span class="p">,</span>
                  <span class="n">number_of_replacement</span><span class="p">,</span>
                  <span class="n">aggregation_function</span><span class="p">,</span>
                  <span class="n">weight_file</span><span class="p">,</span>
+                 <span class="n">number_of_objective</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
                  <span class="n">number_of_crossover_points</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
                  <span class="n">threshold_before_evaluate_subproblem_utility</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span>
                  <span class="n">delta_threshold</span><span class="o">=</span><span class="mf">0.001</span><span class="p">,</span>
@@ -179,7 +179,6 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead_dra</h1><div c
 
 <span class="sd">        :param problem: {:class:`~moead_framework.problem.Problem`} problem to optimize</span>
 <span class="sd">        :param max_evaluation: {integer} maximum number of evaluation</span>
-<span class="sd">        :param number_of_objective: {integer} number of objective in the problem</span>
 <span class="sd">        :param number_of_weight_neighborhood: {integer} size of the neighborhood</span>
 <span class="sd">        :param delta: {float} probability to use all the population as neighborhood</span>
 <span class="sd">        :param number_of_replacement: {integer} maximum number of solutions replaced in the population for each new offspring generated</span>
@@ -188,6 +187,7 @@ <h1>Source code for moead_framework.algorithm.combinatorial.moead_dra</h1><div c
 <span class="sd">        :param number_of_crossover_points: {integer} number of crossover point</span>
 <span class="sd">        :param threshold_before_evaluate_subproblem_utility: Optional -- Threshold before evaluate the subproblem utility. The default value is 50</span>
 <span class="sd">        :param delta_threshold: Optional -- reset the utility if the relative decrease delta_i is under this treshold. The default value is 0.001</span>
+<span class="sd">        :param number_of_objective: Deprecated -- {integer} number of objective in the problem. Deprecated, remove in the next major release.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
 
         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">problem</span><span class="o">=</span><span class="n">problem</span><span class="p">,</span>