Merge from dev

.gitignore

@@ -1,36 +1,29 @@
-.DS_Store
+**/.DS_Store
+**/.vscode
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
-
-*.c
-*.cpp
+*.run
 *.so
 
-pymoo/experimental
-
-
-README.html
-
-pymoo/cython/*html
 
-experiments/runs
+# files which are in tests
+tests/!archive/*
+tests/!archive_tests/*
+tests/!experimental/*
 
+benchmark/runs/*
 
-tests/resources/*
-
+# any video or other output file
 *.mp4
 *.out
 *.dat
 
-pymoo/.DS_Store
-
+# pycharm folder
 .idea/
 
-# C extensions
-*.so
 
 # Distribution / packaging
 .Python

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include . *.py *.pyx *.pxd
-recursive-exclude . *.so
-recursive-exclude pymoo/experimental *.py
-include LICENSE
+recursive-include pymoo *.py *.cpp
+recursive-exclude pymoo *.so *.pyx *.pxd
+
+include LICENSE Makefile

Makefile

@@ -0,0 +1,21 @@
+clean:
+	rm -rf build dist pymoo.egg-info
+
+clean-ext:
+	rm -f pymoo/cython/*.c
+	rm -f pymoo/cython/*.so
+	rm -f pymoo/cython/*.cpp
+	rm -f pymoo/cython/*.html
+
+compile:
+	python setup.py build_ext --inplace
+
+compile-with-cython:
+	python setup.py build_ext --inplace --cythonize
+
+dist:
+	python setup.py sdist
+
+install:
+	python setup.py install
+

README.rst

@@ -41,7 +41,7 @@ The official release is always available at PyPi:
 
 .. code:: bash
 
-    pip install Cython>=0.29 numpy>=1.15 pymoo
+    pip install -U pymoo
 
 
 For the current developer version:
@@ -52,6 +52,7 @@ For the current developer version:
     cd pymoo
     pip install .
 
+
 Since for speedup some of the modules are also available compiled you can double check
 if the compilation worked. When executing the command be sure not already being in the local pymoo
 directory because otherwise not the in site-packages installed version will be used.
@@ -61,7 +62,6 @@ directory because otherwise not the in site-packages installed version will be u
     python -c "from pymoo.cython.function_loader import is_compiled;print('Compiled Extensions: ', is_compiled())"
 
 
-
 Usage
 ==================================
 
@@ -70,38 +70,36 @@ However, for instance executing NSGA2:
 
 .. code:: python
 
-   from pymoo.optimize import minimize
-   from pymoo.algorithms.nsga2 import nsga2
-   from pymoo.util import plotting
-   from pymop.factory import get_problem
-
-   # load a test or define your own problem
-   problem = get_problem("zdt1")
+    
+    from pymoo.algorithms.nsga2 import NSGA2
+    from pymoo.factory import get_problem
+    from pymoo.optimize import minimize
+    from pymoo.visualization.scatter import Scatter
 
-   # get the optimal solution of the problem for the purpose of comparison
-   pf = problem.pareto_front()
+    problem = get_problem("zdt3")
+    pf = problem.pareto_front(n_points=200, flatten=False, use_cache=False)
 
-   # create the algorithm object
-   method = nsga2(pop_size=100, elimate_duplicates=True)
+    algorithm = NSGA2(pop_size=100, elimate_duplicates=True)
 
-   # execute the optimization
-   res = minimize(problem,
-                  method,
-                  termination=('n_gen', 200),
-                  pf=pf,
-                  disp=True)
+    res = minimize(problem,
+                   algorithm,
+                   ('n_gen', 200),
+                   seed=1,
+                   verbose=False)
 
-   # plot the results as a scatter plot
-   plotting.plot(pf, res.F, labels=["Pareto-Front", "F"])
+    plot = Scatter()
+    plot.add(pf, plot_type="line", color="black", alpha=0.7)
+    plot.add(res.F, color="red")
+    plot.show()
 
 
 
 Contact
 ====================================================================
+
 Feel free to contact me if you have any question:
 
 | Julian Blank (blankjul [at] egr.msu.edu)
 | Michigan State University
 | Computational Optimization and Innovation Laboratory (COIN)
 | East Lansing, MI 48824, USA
-

TODO

@@ -0,0 +1,45 @@
+
+# TODO
+
+
+- Write test suite for all algorithms (many problems just run once - no crash should occur)
+- Add global tests of all optimization methods
+- Elementwise function evaluation gradient is not working yet
+- Report None of infeasible or feasible
+
+
+
+
+####################################################################
+
+# DONE
+- NSGA3 - add non-dom check finally (factor out the algorithm method and reuse)
+- !!! NDS and crowding cast to np.float
+- !!! Rewrite integer operation with a wrapper - check if casting is working for different types
+- copy of algorithm object when minimize is called
+- Add sidebar to homepage
+- Decision Making (Pseudo Weight, ...)
+- Termination Criteria in x space and fspace - xtol and ftol
+- PCP values do have different ranges
+- Add ZDT5 and show it for NSGA2
+- 0.9 prob for crossover in general
+- add normalization to radar - externalize from pcp
+- Performance check nsga3
+- Deliver just .c files for pip to make the build independent from Cython
+- Compilation issue with MacOSX Macoave
+- NSGA3 worst swap of arguments
+
+
+####################################################################
+
+# Future
+
+- Add mixed variable possibility
+- PCX as crossover
+- Remove image file from git history
+- (mu,lambda) and (mu+lambda) difference
+- Add NoCrossover and NoMutation
+- Statistics of Survival and more attributes for individuals
+- ask and tell interface Documentation
+- maybe include CMA-ES: https://github.com/CMA-ES/pycma
+- Implement an async version of algorithms

benchmark/README

@@ -0,0 +1,42 @@
+-------------------------------------------------------------------------------------------------
+Benchmark
+-------------------------------------------------------------------------------------------------
+
+This folder contains an example benchmark setup for algorithms. It is constructed to be executed
+on a single-machine with many cores. Since most of the algorithm execute pretty fast we did
+not setup a distributed system for our benchmarking yet.
+
+
+1. Run the corresponding benchmark file which will create the configuration into the
+pymoo/benchmark/runs folder. You will find for a run a persisted configuration and a batch file
+run.bat that contains a line to run each configuration.
+
+2. The framework must be available where you execute the benchmark. Either you use the globally
+installed pymoo through pip or if you are developing a new algorithm you need to import the
+local project. To do so, open pymoo/benchmark/execute.py and make sure that the folder to
+pymoo is imported correctly. E.g.
+
+sys.path.insert(0, "/home/blankjul/workspace/pymoo/")
+
+
+
+Serialized
+========================
+
+In order to run all algorithms serialized you can now simply execute:
+
+cd pymoo/benchmark
+sh runs/<algorithm>/run.bat
+
+This will run all algorithms in a row. Be careful to be in the benchmark folder.
+
+
+Multi Processes
+========================
+
+For parallelization you can use the runner.py by provided the path to the run.bat and the number
+processes to be used.
+
+python runner.py runs/<algorithm>/run.bat 32
+
+To run it on 32 processes.

experiments/experiment_moead.py → benchmark/benchmark_moead.py

@@ -1,7 +1,7 @@
 import os
 import pickle
 
-from experiments.experiment_nsga3 import setup
+from benchmark.benchmark_nsga3 import setup
 from pymoo.algorithms.moead import moead
 
 if __name__ == '__main__':
@@ -18,7 +18,7 @@
     # number of runs to execute
     n_runs = 50
 
-    # problems to be investigated
+    # single to be investigated
     problems = setup.keys()
 
     # path were the files for this experiment are saved
@@ -33,7 +33,7 @@
             s['ref_dirs'],
             n_neighbors=20,
             decomposition='auto',
-            prob_neighbor_mating=0.7,
+            prob_neighbor_mating=0.9,
             eliminate_duplicates=True
         )