From 6dcb8028ff88bbad2b032435b8e49ae1caeca3b6 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 12 Apr 2019 17:35:32 +0100
Subject: [PATCH] =?utf8?q?JAL-3130=20instrument=20main=20and=20compile=20sep?=
 =?utf8?q?arately=20to=20test=20classes=20so=20Clover=20doesn=E2=80=99t=20mi?=
 =?utf8?q?sclassify=20them?=
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---
 build.gradle |   53 +++++++++++++++++++++++++++++------------------------
 1 file changed, 29 insertions(+), 24 deletions(-)

diff --git a/build.gradle b/build.gradle
index c6f86d6..ed8a9ab 100644
--- a/build.gradle
+++ b/build.gradle
@@ -61,7 +61,7 @@ sourceSets {
   clover {
     java {
         srcDirs = [ cloverInstrDir ]
-        outputDir = file("$jalviewDir/$testOutputDir")
+        outputDir = file("${buildDir}/clover-classes")
     }
     
     resources {
@@ -80,7 +80,7 @@ sourceSets {
   
   test {
     java {
-      srcDirs = [ cloverInstrDir ]
+      srcDirs "$jalviewDir/$testSourceDir"
       outputDir = file("$jalviewDir/$testOutputDir")
     }
 
@@ -89,7 +89,10 @@ sourceSets {
     }
 
 
-    compileClasspath += configurations.cloverRuntime + files( sourceSets.test.java.outputDir )
+    compileClasspath = configurations.cloverRuntime 
+    compileClasspath += files( sourceSets.test.java.outputDir ) 
+    compileClasspath += files( sourceSets.clover.java.outputDir )
+    compileClasspath += files( sourceSets.main.resources.srcDirs)
     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
     if (JAVA_VERSION.equals("1.8")) {
@@ -113,7 +116,8 @@ configurations {
 }
  
 task cloverInstr() {
-    inputs.files files (sourceSets.main.allJava, fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+  // only instrument source, we build test classes as normal
+    inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
     outputs.dir cloverInstrDir
 
     doFirst {
@@ -130,6 +134,7 @@ task cloverInstr() {
 }
 
 test.dependsOn cloverInstr
+
  
 task cloverReport {
     inputs.dir "${buildDir}/clover"
@@ -169,7 +174,7 @@ compileJava {
 }
 
 compileTestJava {
-
+  dependsOn compileCloverJava
   doFirst {
     if (JAVA_VERSION.equals("1.8")) {
       sourceCompatibility = 1.8
@@ -189,25 +194,25 @@ compileTestJava {
 }
 
 
-//compileCloverJava {
-//
-//  doFirst {
-//    if (JAVA_VERSION.equals("1.8")) {
-//      sourceCompatibility = 1.8
-//      targetCompatibility = 1.8
-//    } else if (JAVA_VERSION.equals("11")) {
-//      sourceCompatibility = 11
-//      targetCompatibility = 11
-//
-//      options.compilerArgs += [
-//        '--module-path', sourceSets.modules.compileClasspath.asPath,
-//        '--add-modules', j11modules
-//      ]
-//    }
-//    print ("Setting target compatibility to "+targetCompatibility+"\n")
-//  }
-//  classpath += configurations.cloverRuntime
-//}
+compileCloverJava {
+
+  doFirst {
+    if (JAVA_VERSION.equals("1.8")) {
+      sourceCompatibility = 1.8
+      targetCompatibility = 1.8
+    } else if (JAVA_VERSION.equals("11")) {
+      sourceCompatibility = 11
+      targetCompatibility = 11
+
+      options.compilerArgs += [
+        '--module-path', sourceSets.modules.compileClasspath.asPath,
+        '--add-modules', j11modules
+      ]
+    }
+    print ("Setting target compatibility to "+targetCompatibility+"\n")
+  }
+  classpath += configurations.cloverRuntime
+}
 
 clean {
   delete sourceSets.main.java.outputDir
-- 
1.7.10.2