From a3ab8b587ee3a4bc9e334deb14c492d3e3a307d0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 16 Apr 2019 17:36:45 +0100
Subject: [PATCH] =?utf8?q?JAL-3130=20refactored=20=E2=80=98clover=E2=80=99=20?=
 =?utf8?q?to=20=E2=80=98use=5Fclover=E2=80=99=20since=20clover=20is=20an=20a?=
 =?utf8?q?mbiguous=20property=20-=20still=20offer=20-Pclover=3Dtrue=20as=20c?=
 =?utf8?q?ommand=20line=20switch=20to=20enable=20clover=20coverage?=
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---
 build.gradle      |   19 ++++++++++++-------
 gradle.properties |    1 +
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/build.gradle b/build.gradle
index 291d718..c34128e 100644
--- a/build.gradle
+++ b/build.gradle
@@ -28,10 +28,10 @@ mainClassName = launcherClass
 def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
 def classes = "$jalviewDir/$classesDir"
 if (clover.equals("true")) {
-  clover = true
+  use_clover = true
   classes = "$buildDir/$cloverClassesDir"
 } else {
-  clover = false
+  use_clover = false
   classes = "$jalviewDir/$classesDir"
 }
 
@@ -97,10 +97,11 @@ sourceSets {
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir ) 
-    if (clover) {
+    if (use_clover) {
       compileClasspath += sourceSets.clover.compileClasspath
     } else {
       compileClasspath += sourceSets.main.compileClasspath
+      compileClasspath += files(sourceSets.main.java.outputDir)
     }
     compileClasspath += files( sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
@@ -116,7 +117,7 @@ sourceSets {
 
 // clover bits
 dependencies {
-  if (clover) {
+  if (use_clover) {
     cloverCompile 'org.openclover:clover:4.3.1'
     testCompile 'org.openclover:clover:4.3.1'
   }
@@ -189,9 +190,12 @@ compileJava {
 }
 
 compileTestJava {
-  if (clover) {
+
+  if (use_clover) {
     dependsOn compileCloverJava
     classpath += configurations.cloverRuntime
+  } else {
+    classpath += sourceSets.main.runtimeClasspath
   }
   doFirst {
     if (JAVA_VERSION.equals("1.8")) {
@@ -334,10 +338,11 @@ task prepare {
 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 test {
   dependsOn prepare
-  if (clover) {
+  dependsOn compileJava
+  if (use_clover) {
     dependsOn cloverInstr
   }
-  print("Running tests " + (clover?"WITH":"WITHOUT") + " clover [clover="+clover+"]\n") 
+  print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n") 
   
   useTestNG() {
     includeGroups testngGroups
diff --git a/gradle.properties b/gradle.properties
index 15d1e1d..6c5c1f1 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -26,6 +26,7 @@ sourceDir = src
 schemaDir = schemas
 classesDir = classes
 clover = false
+use_clover = false
 cloverClassesDir = clover-classes
 cloverSourcesInstrDir = sources-instr
 packageDir = dist
-- 
1.7.10.2