Remerge mainline changes

CMakeLists.txt

@@ -1,57 +1,77 @@
 cmake_minimum_required(VERSION 3.3)
 project(MultiNEAT)
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+
+if(MINGW OR CYGWIN)
+    add_definitions(-O3)
+endif()
+
+#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wa,-mbig-obj")
 
 find_package(PythonLibs REQUIRED)
 include(FindPythonLibs)
+#set(Boost_Path "C:/boost/include")
+
+#set(BOOST_ROOT "C:\\Boost")
+#set(BOOSTROOT "C:\\Boost")
+
+add_definitions("-DMS_WIN64")
 
 set(Boost_USE_STATIC_LIBS       OFF) # only find static libs
 set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
-find_package(Boost COMPONENTS
-    date_time
-    system
-    filesystem
-    python3
-    serialization)
+set(Boost_USE_STATIC_RUNTIME   OFF)
+
+find_package(BOOST COMPONENTS REQUIRED
+        system
+        python
+        numpy
+        date_time
+        filesystem
+        serialization)
+
 if(Boost_FOUND)
+    message(STATUS "It works!")
     include_directories(${Boost_INCLUDE_DIRS})
+    link_directories("C:/Boost/lib")
 endif()
 
+
 include_directories(${PYTHON_INCLUDE_DIRS})
 
 add_definitions(-DUSE_BOOST_PYTHON)
+#add_definitions(-DUSE_BOOST_NUMPY)
 add_definitions(-DUSE_BOOST_RANDOM)
+#add_definitions(-DVDEBUG)
+
+
+add_executable(MultiNEAT ${PROJECT_SOURCE_DIR}/src/Assert.h
+                         ${PROJECT_SOURCE_DIR}/src/Genes.h
+                         ${PROJECT_SOURCE_DIR}/src/Genome.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Genome.h
+                         ${PROJECT_SOURCE_DIR}/src/Innovation.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Innovation.h
+                         ${PROJECT_SOURCE_DIR}/src/Main.cpp
+                         ${PROJECT_SOURCE_DIR}/src/NeuralNetwork.cpp
+                         ${PROJECT_SOURCE_DIR}/src/NeuralNetwork.h
+                         ${PROJECT_SOURCE_DIR}/src/Parameters.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Parameters.h
+                         ${PROJECT_SOURCE_DIR}/src/PhenotypeBehavior.cpp
+                         ${PROJECT_SOURCE_DIR}/src/PhenotypeBehavior.h
+                         ${PROJECT_SOURCE_DIR}/src/Population.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Population.h
+                         ${PROJECT_SOURCE_DIR}/src/PythonBindings.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Random.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Random.h
+                         ${PROJECT_SOURCE_DIR}/src/Species.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Species.h
+                         ${PROJECT_SOURCE_DIR}/src/Substrate.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Substrate.h
+                         ${PROJECT_SOURCE_DIR}/src/Utils.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Utils.h
+                         ${PROJECT_SOURCE_DIR}/src/Traits.h
+                         ${PROJECT_SOURCE_DIR}/src/Traits.cpp)
 
-set(SOURCE_FILES
-    src/Assert.h
-    src/Genes.h
-    src/Genome.cpp
-    src/Genome.h
-    src/Innovation.cpp
-    src/Innovation.h
-    src/Main.cpp
-    src/NeuralNetwork.cpp
-    src/NeuralNetwork.h
-    src/Parameters.cpp
-    src/Parameters.h
-    src/PhenotypeBehavior.cpp
-    src/PhenotypeBehavior.h
-    src/Population.cpp
-    src/Population.h
-    src/PythonBindings.cpp
-    src/Random.cpp
-    src/Random.h
-    src/Species.cpp
-    src/Species.h
-    src/Substrate.cpp
-    src/Substrate.h
-    src/Utils.cpp
-    src/Utils.h
-    src/Traits.h
-    src/Traits.cpp)
-
-
-add_executable(MultiNEAT ${SOURCE_FILES})
-target_link_libraries(MultiNEAT ${Boost_LIBRARIES} ${PYTHON_LIBRARIES} pthread)
+target_link_libraries(MultiNEAT
+        "ws2_32"
+        ${BOOST_LIBRARIES}
+        ${PYTHON_LIBRARIES})

CMakeLists_MinGW64.txt

@@ -0,0 +1,84 @@
+cmake_minimum_required(VERSION 3.3)
+project(MultiNEAT)
+
+
+if(MINGW OR CYGWIN)
+    add_definitions(-O3)
+endif()
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wa,-mbig-obj")
+
+find_package(PythonLibs REQUIRED)
+include(FindPythonLibs)
+#set(Boost_Path "C:/boost/include")
+
+#set(BOOST_ROOT "C:\\Boost")
+#set(BOOSTROOT "C:\\Boost")
+
+#add_definitions("-DMS_WIN64")
+
+set(Boost_USE_STATIC_LIBS       OFF) # only find static libs
+set(Boost_USE_MULTITHREADED      ON)
+set(Boost_USE_STATIC_RUNTIME   OFF)
+
+find_package(BOOST COMPONENTS REQUIRED
+        system
+        python36
+        numpy36
+        date_time
+        filesystem
+        serialization)
+
+if(Boost_FOUND)
+    message(STATUS "It works!")
+    include_directories(${Boost_INCLUDE_DIRS})
+    link_directories("C:/Boost/lib")
+endif()
+
+
+include_directories(${PYTHON_INCLUDE_DIRS})
+
+add_definitions(-DUSE_BOOST_PYTHON)
+add_definitions(-DUSE_BOOST_NUMPY)
+add_definitions(-DUSE_BOOST_RANDOM)
+#add_definitions(-DVDEBUG)
+
+
+add_executable(MultiNEAT ${PROJECT_SOURCE_DIR}/src/Assert.h
+                         ${PROJECT_SOURCE_DIR}/src/Genes.h
+                         ${PROJECT_SOURCE_DIR}/src/Genome.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Genome.h
+                         ${PROJECT_SOURCE_DIR}/src/Innovation.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Innovation.h
+                         ${PROJECT_SOURCE_DIR}/src/Main.cpp
+                         ${PROJECT_SOURCE_DIR}/src/NeuralNetwork.cpp
+                         ${PROJECT_SOURCE_DIR}/src/NeuralNetwork.h
+                         ${PROJECT_SOURCE_DIR}/src/Parameters.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Parameters.h
+                         ${PROJECT_SOURCE_DIR}/src/PhenotypeBehavior.cpp
+                         ${PROJECT_SOURCE_DIR}/src/PhenotypeBehavior.h
+                         ${PROJECT_SOURCE_DIR}/src/Population.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Population.h
+                         ${PROJECT_SOURCE_DIR}/src/PythonBindings.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Random.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Random.h
+                         ${PROJECT_SOURCE_DIR}/src/Species.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Species.h
+                         ${PROJECT_SOURCE_DIR}/src/Substrate.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Substrate.h
+                         ${PROJECT_SOURCE_DIR}/src/Utils.cpp
+                         ${PROJECT_SOURCE_DIR}/src/Utils.h
+                         ${PROJECT_SOURCE_DIR}/src/Traits.h
+                         ${PROJECT_SOURCE_DIR}/src/Traits.cpp)
+
+target_link_libraries(MultiNEAT
+        "ws2_32"
+#        ${BOOST_LIBRARIES}
+        "boost_system-mgw81-mt-x64-1_71"
+        "boost_filesystem-mgw81-mt-x64-1_71"
+        "boost_serialization-mgw81-mt-x64-1_71"
+        "boost_date_time-mgw81-mt-x64-1_71"
+        "boost_random-mgw81-mt-x64-1_71"
+        "boost_python36-mgw81-mt-x64-1_71"
+        "boost_numpy36-mgw81-mt-x64-1_71"
+        ${PYTHON_LIBRARIES} pthread)

MultiNEAT.sln

@@ -1,7 +1,9 @@
 
-Microsoft Visual Studio Solution File, Format Version 10.00
-# Visual Studio 2008
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MultiNEAT", "MultiNEAT.vcproj", "{826B4E58-F9C4-45F1-BFE3-4E8B16D37AA6}"
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 15
+VisualStudioVersion = 15.0.28307.1082
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MultiNEAT", "MultiNEAT.vcxproj", "{826B4E58-F9C4-45F1-BFE3-4E8B16D37AA6}"
 EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
@@ -17,4 +19,7 @@ Global
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
 	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {57264A91-576A-4F26-B2AA-727EE1EAED34}
+	EndGlobalSection
 EndGlobal

MultiNEAT/__init__.py

@@ -21,17 +21,29 @@ def ZipFitness(genome_list, fitness_list):
 try:
     import networkx as nx
 
-    def Genome2NX(g):
+    def Genome2NX(g, with_inputs=False, with_weights=False):
 
         nts = g.GetNeuronTraits()
-        lts = g.GetLinkTraits()
+        lts = g.GetLinkTraits(with_weights)
         gr = nx.DiGraph()
 
         for i, tp, traits in nts:
-            gr.add_node( i, **traits)
-
-        for inp, outp, traits in lts:
-            gr.add_edge( inp, outp, **traits )
+            if with_inputs:
+                gr.add_node( i, **traits)
+            else:
+                # don't add traits on inputs
+                if tp != 'input':
+                    gr.add_node( i, **traits)
+                else:
+                    gr.add_node( i )
+
+        if not with_weights:
+            for inp, outp, traits in lts:
+                gr.add_edge( inp, outp, **traits)
+        else:
+            for inp, outp, traits, w in lts:
+                t = {**traits, 'w':w}
+                gr.add_edge( inp, outp, **t)
 
         gr.genome_traits = g.GetGenomeTraits()
 

MultiNEAT/viz.py

@@ -30,15 +30,12 @@ def AlmostEqual(a, b, margin):
 except:
     print('Install NumPy for visualization')
 
-
 try:
     import cv2
     cvnumpy_installed = True
 except:
     print ('Tip: install the OpenCV computer vision library (2.0+) with '
-           'Python bindings')
-    print ('     to get convenient neural network visualization to NumPy '
-           'arrays')
+           'Python bindings to get convenient neural network visualization to NumPy arrays.')
     cvnumpy_installed = False
 
 try:

_MultiNEAT.pyx

@@ -920,8 +920,8 @@ cdef class Genome:
     def BuildHyperNEATPhenotype(self, NeuralNetwork net, Substrate subst):
         self.thisptr.BuildHyperNEATPhenotype(deref(net.thisptr), deref(subst.thisptr))
 
-    def BuildESHyperNEATPhenotype(Genome self, NeuralNetwork a_net, Substrate subst, Parameters params):
-        self.thisptr.BuildESHyperNEATPhenotype(deref(a_net.thisptr), deref(subst.thisptr), deref(params.thisptr))
+    #def BuildESHyperNEATPhenotype(Genome self, NeuralNetwork a_net, Substrate subst, Parameters params):
+    #    self.thisptr.BuildESHyperNEATPhenotype(deref(a_net.thisptr), deref(subst.thisptr), deref(params.thisptr))
 
     def Save(self, str a_filename):
         self.thisptr.Save(a_filename)

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: multineat
-  version: 0.5  # Update version in setup.py as well
+  version: 0.6  # Update version in setup.py as well
 
 build:
   number: 

examples/TestNEAT_xor.py

@@ -104,27 +104,29 @@ def evaluate(genome):
 params.AllowClones = True
 
 def getbest(i):
-    g = NEAT.Genome(0, 3, 0, 1, False, NEAT.ActivationFunction.UNSIGNED_SIGMOID,
-                    NEAT.ActivationFunction.UNSIGNED_SIGMOID, 0, params, 0)
+    gi = NEAT.GenomeInitStruct()
+    gi.NumInputs = 3
+    g = NEAT.Genome(params, gi)
     pop = NEAT.Population(g, params, True, 1.0, i)
-    pop.RNG.Seed(int(time.clock()*100))
+    pop.RNG.Seed(int(time.perf_counter()*100))
 
     generations = 0
-    for generation in range(1000):
+    for generation in range(300):
         genome_list = NEAT.GetGenomeList(pop)
         fitness_list = EvaluateGenomeList_Serial(genome_list, evaluate, display=False)
         NEAT.ZipFitness(genome_list, fitness_list)
         pop.Epoch()
         generations = generation
         best = max(fitness_list)
+        print('gen:', generation, 'best:',best)
         if best > 15.0:
             break
 
     return generations
 
 
 gens = []
-for run in range(100):
+for run in range(1000):
     gen = getbest(run)
     gens += [gen]
     print('Run:', run, 'Generations to solve XOR:', gen)

examples/TestTraits.py

@@ -104,8 +104,9 @@ def custom_constraint(genome):
 params.CustomConstraints = custom_constraint
 
 # the seed genome and test population
-g = NEAT.Genome(0, 3, 0, 1, False, NEAT.ActivationFunction.UNSIGNED_SIGMOID,
-                NEAT.ActivationFunction.UNSIGNED_SIGMOID, 0, params, 0)
+gi = NEAT.GenomeInitStruct()
+gi.NumInputs = 3
+g = NEAT.Genome(params, gi)
 pop = NEAT.Population(g, params, True, 1.0, rnd.randint(0, 100))
 pop.RNG.Seed(int(time.clock()*100))
 

examples/ball_keeper.py

@@ -298,7 +298,7 @@ def main():
 
 
     g = NEAT.Genome(0, 6, 0, 2, False, 
-                    NEAT.ActivationFunction.TANH, NEAT.ActivationFunction.UNSIGNED_SIGMOID, 0, params, 0)
+                    NEAT.ActivationFunction.TANH, NEAT.ActivationFunction.UNSIGNED_SIGMOID, 0, params, 0, 1)
     pop = NEAT.Population(g, params, True, 1.0, rnd.randint(0, 1000))
 
     best_genome_ever = None

examples/gym/lunar_lander.py

@@ -8,6 +8,7 @@
 import pickle
 import numpy as np
 import cv2
+from tqdm import tqdm
 
 rng = NEAT.RNG()
 rng.TimeSeed()
@@ -72,7 +73,7 @@
 render_during_training = 0
 
 g = NEAT.Genome(0, 8 +1, 0, 4, False,
-                NEAT.ActivationFunction.TANH, NEAT.ActivationFunction.TANH, 0, params, 0)
+                NEAT.ActivationFunction.TANH, NEAT.ActivationFunction.TANH, 0, params, 0, 1)
 pop = NEAT.Population(g, params, True, 1.0, rnd.randint(0, 1000))
 
 
@@ -129,7 +130,7 @@ def do_trial():
 
     for generation in range(20):
 
-        for i_episode, genome in enumerate(NEAT.GetGenomeList(pop)):
+        for i_episode, genome in tqdm(enumerate(NEAT.GetGenomeList(pop))):
 
             net = NEAT.NeuralNetwork()
             genome.BuildPhenotype(net)