create basic gradle build files and rename :model:core to :model:mode…

…l-core

The renaming was necessary because it clashed with the :core module

.gitignore

@@ -13,3 +13,12 @@ benchmark/experiments/*/*result.xml
 *.csv
 benchmark/results
 benchamer/results-processed
+
+# Gradle cache and build directories
+.gradle
+build
+*.ipr
+*.iws
+
+# Idea project files
+.idea

application/build.gradle

@@ -0,0 +1,18 @@
+group = 'org.sybila.parasim.application'
+
+dependencies {
+	compile 'org.mod4j.org.apache.commons:cli:1.0.0'
+	compile project(':model:ode')
+	compile project(':model:space')
+	compile project(':model:trajectory')
+	compile project(':model:verification')
+	compile project(':extensions:computation-simulation-impl')
+	compile project(':extensions:computation-density-impl')
+	compile project(':extensions:computation-verification-impl')
+	compile project(':extensions:computation-lifecycle-impl')
+	compile project(':extensions:computation-cycledetection-impl')
+	compile project(':extensions:visualisation-plot-impl')
+	compile project(':extensions:result-export-impl')
+	compile project(':extensions:project-manager-simple')
+	compile project(':extensions:progress-logger')
+}

build.gradle

@@ -0,0 +1,44 @@
+buildscript {
+    repositories {
+        jcenter()
+    }
+    dependencies {
+        //place for global plugins
+    }
+}
+
+allprojects {
+    apply plugin: 'java'
+
+    version = '2.1.0-SNAPSHOT'
+    group = 'org.sybila.parasim'
+
+    repositories {
+        jcenter()
+        mavenCentral()        
+        // jsbml
+        maven { url "http://jsbml.sourceforge.net/m2repo" }
+        // mangosdk
+        maven { url 'http://www.ebi.ac.uk/~maven/m2repo' }
+        // javaoctave
+        maven { url 'https://kenai.com/svn/javaoctave~maven-repository/maven2/' }
+    }
+
+    //global configuration
+    ext {
+        javaoctave = '0.6.4'
+        commonsLogging = '1.1.1'
+        jsbml = '1.2-beta1'
+    }
+
+    //common dependencies for everyone
+    dependencies {
+        testCompile group: 'junit', name: 'junit', version: '4.11'  
+        testCompile 'org.testng:testng:6.9.12'
+        compile 'net.jcip:jcip-annotations:1.0'
+        compile 'javassist:javassist:3.12.1.GA'
+        compile 'org.slf4j:slf4j-log4j12:1.7.21'
+        compile 'org.apache.commons:commons-lang3:3.5'
+    }
+
+}

core/build.gradle

@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.model.core'
+
+dependencies {
+	compile 'org.testng:testng:6.9.12'
+}

extensions/computation-cycledetection-api/build.gradle

@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.computation.cycledetection.api'
+
+dependencies {
+	compile project(':model:trajectory')
+}

extensions/computation-cycledetection-impl/build.gradle

@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.cycledetection.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':extensions:computation-cycledetection-api')
+}

extensions/computation-density-api/build.gradle

@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.density.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:space')
+	compile project(':model:trajectory')
+}

extensions/computation-density-impl/build.gradle

@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.computation.density.impl'
+
+dependencies {
+	testCompile project(':extensions:computation-lifecycle-impl')
+	compile project(':core')
+	compile project(':extensions:computation-density-api')
+	compile project(':extensions:computation-lifecycle-api')
+}

extensions/computation-lifecycle-api/build.gradle

@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.computation.lifecycle.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:model-core')	
+}

extensions/computation-lifecycle-impl/build.gradle

@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.computation.lifecycle.impl'
+
+dependencies {
+	compile project(':extensions:computation-lifecycle-api')
+}

extensions/computation-simulation-api/build.gradle

@@ -0,0 +1,10 @@
+group = 'org.sybila.parasim.computation.simulation.api'
+
+dependencies {
+	compile project(':model:ode')
+	compile project(':model:trajectory')
+	compile project(':model:space')
+	compile project(':core')
+	compile "dk.ange:javaoctave:$javaoctave"
+	compile "commons-logging:commons-logging:$commonsLogging"
+}

extensions/computation-simulation-impl/build.gradle

@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.simulation.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':extensions:computation-simulation-api')
+	compile project(':extensions:computation-lifecycle-api')
+}

extensions/computation-verification-api/build.gradle

@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.computation.verification.api'
+
+dependencies {
+	compile project(':model:verification')
+	compile project(':model:trajectory')
+	compile project(':extensions:computation-density-api')
+	compile project(':extensions:computation-cycledetection-api')
+}

extensions/computation-verification-impl/build.gradle

@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.verification.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':extensions:computation-verification-api')
+}

extensions/progress-logger/build.gradle

@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.extension.progresslogger'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':resources')
+	compile project(':model:verification')	
+}

extensions/project-manager-api/build.gradle

@@ -0,0 +1,11 @@
+group = 'org.sybila.parasim.extension.projectmanager.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':resources')
+	compile project(':util')
+	compile project(':model:ode')
+	compile project(':model:space')
+	compile project(':model:verification')
+	compile project(':extensions:computation-simulation-api')
+}

extensions/project-manager-simple/build.gradle

@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.extension.projectmanager.impl'
+
+dependencies {
+	compile project(':extensions:project-manager-api')
+}

extensions/result-export-api/build.gradle

@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.extension.exporter.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:verification')
+}

extensions/result-export-impl/build.gradle

@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.extension.exporter.impl'
+
+dependencies {
+	compile project(':extensions:result-export-api')
+}

extensions/visualisation-plot-api/build.gradle

@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.visualisation.plot.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:verification')
+}

extensions/visualisation-plot-impl/build.gradle

@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.visualisation.plot.impl'
+
+dependencies {
+	compile project(':extensions:visualisation-plot-api')
+	compile project(':core')
+	compile project(':util')
+}

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Thu Nov 24 14:07:31 CET 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.1-all.zip