First commit - GenIe is born

.gitignore

+.idea/
+logs/
+target/
+

geneticOptimization.conf

+
+### Genetic config
+
+
+# Calculates the fitness as specified by the implementing class, but uses as final fitness the runtime needed to calculate the fitness. Lower score is better in this 
+# case (lower runtime), cache is disabled. This can be used for searching time-consuming parameters
+runtimePerformanceCheck=false
+verbose=true
+# If false, if an exception was thrown during fitness calculation, the optimization process won't be interrupted, just a log message will be shown
+interruptIfException=true
+# After genetic optimization an entropy analysis of the last N generation winners will be shown
+evaluateLastWinnersCount=42
+showMonitorGui=true
+
+
+# Whether to use an in-memory or a persistent cache. In the case of runtimePerformanceCheck=true, the caches are disabled
+weakRefCache=false
+# if set, a persistent cache is used
+persistentCacheDir=
+# if multithreaded, the system uses as many threads as cpu cores
+singleThreaded=true
+
+
+## The optimizer first performs a loop over all given values of this parameter, whereby the default(first given) value of the other parameters stay fixed. if true, the
+# succeeding genetic run will be skipped
+skipGeneticRun=false
+
+
+# The names of the parameters that should be absolutely treated as independent. The optimizer performs first a loop over all attribute values, whereby, during iterating
+# the values for one attribute, the values for all other attributes are fixed to their FIRST value of their values list in paramNames2DiscreteValSpaces.
+# If an attribute is explicitly marked as independent, during the genetic run its value in EACH candidate vector will be set to its best value from the initial loop. Thus,
+# this attribute will never get another value beside the best one from the initial loop.
+# If it is clear that an attribute isn't influenced by another one/is independent, you can reduce the complexity for finding it's optimal value drastically by setting it
+# independent. On the other hand, if you set it independent and it is not, you won't get the optimal parameter value combination.
+independentParamNames=
+
+# If true, the system will produce the same results in suceeding calls. (This is true beside possible side effects e.g. sort order of same vector fitness values)
+constantRandomSeed=true
+
+# RouletteWheelSelection (random, fitness-proportionate), StochasticUniversalSampling (less random, fitness-proportionate), SigmaScaling (fitness-proportionate, helps to
+# avoid early dominance of one/two fit candidates. Amplifies minor fitness differences in more mature populations)
+selectionStrategy=SigmaScaling
+# The size of the first population. After the first population, the evolution goes further with the specified population size. This is to start wide spreaded and to
+# evolve the best candidates more focused afterwards. Can be relevant if you have huge fitness calculation runtimes where every calculation counts.
+firstPopulationSize=70
+
+# The population size for each island. Therefore, if you have 5 islands, setting this parameter to 200 will result in 1000 individuals overall, 200 on each island. In the
+# case the island count is <=1, it's just the population size of the non-islands generations
+populationSize=70
+
+# The number of candidates preserved via elitism on each island. In elitism, a sub-set of the population with the best fitness scores are preserved unchanged in the
+# subsequent generation. Candidate solutions that are preserved unchanged through elitism remain eligible for selection for breeding the remainder of the next generation.
+# This value must be non-negative and less than the population size. A value of zero means that no elitism will be applied.
+eliteCount=0
+islandCount=1
+
+# The number of generations that make up an epoch. Islands evolve independently for this number of generations and then migration occurs at the end of the epoch and the
+# next epoch starts. Ignored if the island count is <=1.
+epochLength=-1
+
+#The number of individuals that will be migrated from each island at the end of each epoch. Ignored if the island count is <=1.
+migrationCount=-1
+
+lowerScoreIsBetter=false
+maxNumImprovementGenerationsBreak=70
+# 8h=28800,12h=43200,1day=86400,2d=172800,3d=259200,10day=864000,18d=1555200
+maxDurationSecondsBreak=1555200
+targetFitnessBreak=1
+
+
+
+paramNames2DiscreteValSpaces=
+{
+
+	## The first value will be used as default for the independent parameters check. The count of keys defines the genetic candidates vector length. It can be wise to add
+	# keys with just one possibility in order to get compatible vectors at succeeding runs, e.g. to have a compatible cache file that offers much more performance than
+	# calculating from scratch (if relevant)
+
+	# Example for key-values pair:
+	#defaultActivation=TANH,LEAKYRELU,RELU
+	#learningRate=0.1,0.5,0.05,0.01,0.001
+
+	summandA=0,1,2,3,4,5,6,7
+	summandB=0,5,10,15,20,25
+	summandC=0,10,20,30
+	summandD=0,15,25,35
+	
+}
+
+
+firstGenerationParentMetadata=
+{
+   ## All candidate vectors from the first generation will get this parent metadata. The metadata will be given to the fitness function. Fitness functions are able to generate
+   # new metadata for the evaluated candidate vector, that will be also given as parent metadata to its offsprings.
+   # Double key entries are not allowed
+
+   initialMetadataAtt_1=initVal_1
+   initialMetadataAtt_2=initVal_2
+}
+
+fitnessFunctionExecPath=/home/reuschling/projectz/genIe/src/test/sum23TestFitnessFunction.sh

how2build.txt

+build the distributable zip:
+   mvn -Dmaven.test.skip=true clean package appassembler:assemble assembly:single
+

license-gplv2.txt

+The GNU General Public License (GPL) Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite
+330, Boston, MA 02111-1307 USA
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+document, but changing it is not allowed.
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+The licenses for most software are designed to take away your freedom to share
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\ No newline at end of file

pom.xml

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>de.dfki.sds</groupId>
+    <artifactId>genIe</artifactId>
+    <version>1.0-SNAPSHOT</version>
+    <packaging>jar</packaging>
+    <name>genIe</name>
+    <url>http://leechcrawler.github.com/leech/</url>
+
+    <developers>
+        <developer>
+            <name>Christian Reuschling</name>
+            <email>reuschling@dfki.uni-kl.de</email>
+            <organization>DFKI, SDS department</organization>
+            <organizationUrl>https://www.dfki.de/en/web/research/research-departments/smart-data-knowledge-services/</organizationUrl>
+        </developer>
+    </developers>
+
+    <properties>
+        <maven.compiler.source>16</maven.compiler.source>
+        <maven.compiler.target>16</maven.compiler.target>
+
+        <maven.compiler.encoding>UTF-8</maven.compiler.encoding>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+
+        <additionalparam>-Xdoclint:none</additionalparam>
+    </properties>
+
+
+    <distributionManagement>
+        <repository>
+            <id>artifactory-libs-releases-local</id>
+            <url>http://www.dfki.uni-kl.de/artifactory/libs-releases-local</url>
+        </repository>
+        <snapshotRepository>
+            <id>artifactory-libs-snapshots-local</id>
+            <url>http://www.dfki.uni-kl.de/artifactory/libs-snapshots-local</url>
+        </snapshotRepository>
+    </distributionManagement>
+
+
+    <repositories>
+        <repository>
+            <id>artifactory-libs-releases</id>
+            <url>http://www.dfki.uni-kl.de/artifactory/libs-releases</url>
+        </repository>
+        <repository>
+            <id>artifactory-libs-snapshots</id>
+            <url>http://www.dfki.uni-kl.de/artifactory/libs-snapshots</url>
+        </repository>
+    </repositories>
+
+
+    <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.2</version>
+            <scope>test</scope>
+        </dependency>
+
+
+        <dependency>
+            <groupId>de.dfki.sds</groupId>
+            <artifactId>inquisitor</artifactId>
+            <version>23_1-SNAPSHOT</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.uncommons.watchmaker</groupId>
+            <artifactId>watchmaker-framework</artifactId>
+            <version>0.7.1</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.uncommons.watchmaker</groupId>
+            <artifactId>watchmaker-swing</artifactId>
+            <version>0.7.1</version>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math3</artifactId>
+            <version>3.6.1</version>
+        </dependency>
+
+
+        <!-- logback -->
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <version>1.2.5</version>
+
+        </dependency>
+        <dependency>
+            <groupId>org.codehaus.groovy</groupId>
+            <artifactId>groovy-all</artifactId>
+            <version>2.4.13</version>
+        </dependency>
+        <!-- logback -->
+
+        <dependency>
+            <groupId>info.picocli</groupId>
+            <artifactId>picocli</artifactId>
+            <version>4.6.1</version>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.20</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.cedarsoftware</groupId>
+            <artifactId>json-io</artifactId>
+            <version>4.12.0</version>
+        </dependency>
+
+    </dependencies>
+
+
+    <build>
+
+        <plugins>
+
+
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>appassembler-maven-plugin</artifactId>
+                <version>2.1.0</version>
+                <configuration>
+                    <assembleDirectory>${project.build.directory}/assembleDir</assembleDirectory>
+                    <extraJvmArguments>-Xmx5G --add-opens java.base/java.lang=ALL-UNNAMED</extraJvmArguments>
+                    <binFolder>/bin</binFolder>
+                    <repositoryName>lib</repositoryName>
+                    <repositoryLayout>flat</repositoryLayout>
+                    <useWildcardClassPath>true</useWildcardClassPath>
+                    <projectArtifactFirstInClassPath>true</projectArtifactFirstInClassPath>
+
+
+                    <binFileExtensions>
+                        <unix>.sh</unix>
+                    </binFileExtensions>
+                    <programs>
+
+                        <program>
+                            <mainClass>de.dfki.sds.genie.genIe</mainClass>
+                            <name>genIe</name>
+                        </program>
+
+                    </programs>
+                </configuration>
+            </plugin>
+
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>3.2.1</version>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+        </plugins>
+
+
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-compiler-plugin</artifactId>
+                    <version>3.8.1</version>
+                    <configuration>
+                        <source>${maven.compiler.source}</source>
+                        <target>${maven.compiler.target}</target>
+                        <encoding>${maven.compiler.encoding}</encoding>
+
+                        <compilerArgs>
+                            <arg>-parameters</arg>
+                        </compilerArgs>
+
+                        <annotationProcessorPaths>
+                            <path>
+                                <groupId>org.projectlombok</groupId>
+                                <artifactId>lombok</artifactId>
+                                <version>1.18.20</version>
+                            </path>
+                        </annotationProcessorPaths>
+                    </configuration>
+                </plugin>
+
+                <plugin>
+                    <artifactId>maven-assembly-plugin</artifactId>
+                    <version>2.3</version>
+                    <configuration>
+                        <descriptors>
+                            <descriptor>src/main/assembly/distributable.xml</descriptor>
+                        </descriptors>
+                    </configuration>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+    </build>
+
+
+    <profiles>
+
+        <profile>
+            <id>disable-java8-doclint</id>
+            <activation>
+                <jdk>[1.8,)</jdk>
+            </activation>
+            <properties>
+                <additionalparam>-Xdoclint:none</additionalparam>
+            </properties>
+        </profile>
+
+    </profiles>
+
+
+</project>

src/main/assembly/distributable.xml

+<assembly
+	xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+	<id>dist</id>
+	<formats>
+		<format>zip</format>
+		<format>tar.gz</format>
+	</formats>
+
+	<includeBaseDirectory />
+
+	<fileSets>
+		<fileSet>
+			<directory>${project.build.directory}/assembleDir/</directory>
+			<outputDirectory>/</outputDirectory>
+			<excludes>
+				<exclude>**/*.sh</exclude>
+			</excludes>
+		</fileSet>
+
+		<fileSet>
+			<directory>${project.build.directory}/assembleDir/</directory>
+			<outputDirectory>/</outputDirectory>
+			<includes>
+				<include>**/*.sh</include>
+			</includes>
+			<fileMode>700</fileMode>
+		</fileSet>
+	</fileSets>
+
+	<files>
+		<file>