Merge branch 'develop'

README.md

@@ -1,10 +1,49 @@
+# Iconic Project
+
 ## Build Status
 
+## What's New
+
+### Release Notes - 0.1.0 - May 28th, 2018
+
+#### Improvements
+
+* Gene Expression Programming is now in, if a few decades late.
+* A new and improved user interface! Still no isomorphism.
+* A much better build process, we're done with Batch scripts.
+
+#### Fixes
+
+* The back end has changed so much practically everything's been
+fixed in some way. Or at least broken more nicely.
+
 ### Compiling
 
-From the root folder:
+All commands are assumed to be made from the root project folder
+
+#### Application Programming Interface
+
+```bash
+gradlew :api:build
+```
+
+#### Command Line Interface
+
+```bash
+gradlew :cli:run
+gradlew :cli:run -PappArgs="['-i', 'dataChronicKidneyDisease2.txt', '-p', '100', '-g', '500', '-mP', '1.0', '-cP', '1.0']"
+```
+
+#### Workbench
+
+To run the client:
+
+```bash
+gradlew :client:jfxRun
+```
+
+To package a native executable:
 
 ```bash
-gradle build
-java -jar ./api/build/libs/gene-expression-core-0.0.5.jar %1
+gradlew :client:jfxNative
 ```

api/build.gradle

@@ -1,18 +1,43 @@
-apply plugin: 'application'
+plugins {
+    id 'java-library'
+}
 
-mainClassName = 'org.aiconic.Main'
+// Jupiter requires Java 8
+compileTestJava {
+    sourceCompatibility = 1.8
+    targetCompatibility = 1.8
+    options.compilerArgs << "-Xlint:all" << "-Xlint:-processing"
+}
+
+test {
+    useJUnitPlatform()
+}
+
+dependencies {
+    testCompileOnly group: 'org.apiguardian', name: 'apiguardian-api', version: '1.0.0'
+    testCompile group: 'org.junit.jupiter', name: 'junit-jupiter-params', version: '5.1.0'
+    testCompile group: 'org.mockito', name: 'mockito-core', version: '2.11.0'
+    testImplementation group: 'org.junit.jupiter', name: 'junit-jupiter-api', version: '5.1.0'
+    testRuntimeOnly group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.1.0'
+}
+
+version = '0.1.0'
 
 jar {
-  baseName = 'gene-expression-core'
-  version = '0.0.5'
+    baseName = 'iconic-api'
+
+    // The Java plugin doesn't specify any of the
+    // manifest attributes, so we need at least
+    // these two attributes for the JAR to work
+    manifest {
+        attributes(
+                'Implementation-Title': project.name,
+                'Implementation-Version': project.version,
+                'Class-Path': configurations.compile.collect { it.getName() }.join(' '),
+        )
+    }
 
-  // The Java plugin doesn't specify any of the 
-  // manifest attributes, so we need at least
-  // these two attributes for the JAR to work
-  manifest {
-    attributes(
-      'Class-Path': configurations.compile.collect { it.getName() }.join(' '),
-      'Main-Class': 'org.aiconic.Main'
-    )
-  }
+    from {
+        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
+    }
 }