Fixed JaCoCo error: Can't add different class with same name

Now duplicate classes are added to the JaCoCo report only once - this behavior copies the behavior from Kover report generator

Resolves #634
Resolves #613

kover-gradle-plugin/src/functionalTest/kotlin/kotlinx/kover/gradle/plugin/test/functional/cases/ClassDupTest.kt

@@ -0,0 +1,25 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+package kotlinx.kover.gradle.plugin.test.functional.cases
+
+import kotlinx.kover.gradle.plugin.test.functional.framework.checker.CheckerContext
+import kotlinx.kover.gradle.plugin.test.functional.framework.starter.TemplateTest
+
+internal class ClassDupTest {
+    /**
+     * Checking that if there are duplicate files in different versions, the JaCoCo report still continues to be generated.
+     * This behavior is identical to the behavior in Kover reporter.
+     */
+    @TemplateTest("android-class-dup", [":app:koverXmlReport"])
+    fun CheckerContext.test() {
+        subproject(":app") {
+            xmlReport {
+                // class present in report
+                classCounter("kotlinx.kover.test.android.DupClass").assertFullyMissed()
+            }
+        }
+    }
+
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/build.gradle.kts

@@ -0,0 +1,57 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+plugins {
+    id ("org.jetbrains.kotlinx.kover")
+    id ("com.android.application")
+    id ("org.jetbrains.kotlin.android")
+}
+
+android {
+    namespace = "kotlinx.kover.test.android"
+    compileSdk = 32
+
+    defaultConfig {
+        applicationId = "kotlinx.kover.test.android"
+        minSdk = 21
+        targetSdk = 31
+        versionCode = 1
+        versionName = "1.0"
+
+        testInstrumentationRunner = "androidx.test.runner.AndroidJUnitRunner"
+    }
+
+    buildTypes {
+        release {
+            isMinifyEnabled = true
+        }
+    }
+    compileOptions {
+        sourceCompatibility = JavaVersion.VERSION_1_8
+        targetCompatibility = JavaVersion.VERSION_1_8
+    }
+    kotlinOptions {
+        jvmTarget = "1.8"
+    }
+    buildFeatures {
+        viewBinding = true
+    }
+}
+
+dependencies {
+    implementation("androidx.core:core-ktx:1.8.0")
+    implementation("androidx.appcompat:appcompat:1.5.0")
+    implementation("com.google.android.material:material:1.6.1")
+    implementation("androidx.constraintlayout:constraintlayout:2.1.4")
+    testImplementation("junit:junit:4.13.2")
+}
+
+
+/*
+ * Kover configs
+ */
+
+kover {
+    useJacoco()
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/debug/kotlin/kotlinx/kover/test/android/DupClass.kt

@@ -0,0 +1,11 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+package kotlinx.kover.test.android
+
+object DupClass {
+    fun log(message: String) {
+        println("DEBUG: $message")
+    }
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/main/AndroidManifest.xml

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--
+  ~ Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+  -->
+
+<manifest xmlns:android="http://schemas.android.com/apk/res/android">
+
+    <application android:label="@string/app_name">
+        <uses-library android:name="com.google.android.things" android:required="false" />
+
+        <activity android:name=".MainActivity"
+                  android:exported="true">
+            <intent-filter>
+                <action android:name="android.intent.action.MAIN" />
+
+                <category android:name="android.intent.category.LAUNCHER" />
+            </intent-filter>
+            <!-- Make this the first activity that is displayed when the device boots. -->
+            <intent-filter>
+                <action android:name="android.intent.action.MAIN" />
+
+                <category android:name="android.intent.category.HOME" />
+                <category android:name="android.intent.category.DEFAULT" />
+            </intent-filter>
+        </activity>
+    </application>
+
+</manifest>

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/main/res/layout/activity_main.xml

@@ -0,0 +1,40 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--
+  ~ Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+  -->
+
+<androidx.constraintlayout.widget.ConstraintLayout xmlns:android="http://schemas.android.com/apk/res/android"
+    xmlns:app="http://schemas.android.com/apk/res-auto"
+    xmlns:tools="http://schemas.android.com/tools"
+    android:layout_width="match_parent"
+    android:layout_height="match_parent"
+    tools:context=".MainActivity">
+
+    <TextView
+        android:id="@+id/main_label"
+        android:layout_width="wrap_content"
+        android:layout_height="wrap_content"
+        android:layout_marginStart="104dp"
+        android:layout_marginTop="28dp"
+        android:text="SERIALIZATION TEST"
+        android:textSize="20sp"
+        android:textStyle="bold"
+        app:layout_constraintStart_toStartOf="parent"
+        app:layout_constraintTop_toTopOf="parent" />
+
+    <EditText
+        android:id="@+id/encoded_text"
+        android:layout_width="373dp"
+        android:layout_height="411dp"
+        android:layout_marginStart="16dp"
+        android:layout_marginTop="16dp"
+        android:editable="false"
+        android:ems="10"
+        android:gravity="start|top"
+        android:inputType="textMultiLine"
+        android:textAlignment="viewStart"
+        android:textSize="12sp"
+        app:layout_constraintStart_toStartOf="parent"
+        app:layout_constraintTop_toBottomOf="@+id/main_label" />
+
+</androidx.constraintlayout.widget.ConstraintLayout>

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/main/res/values/colors.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!--
+  ~ Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+  -->
+
+<resources>
+    <color name="purple_200">#FFBB86FC</color>
+    <color name="purple_500">#FF6200EE</color>
+    <color name="purple_700">#FF3700B3</color>
+    <color name="teal_200">#FF03DAC5</color>
+    <color name="teal_700">#FF018786</color>
+    <color name="black">#FF000000</color>
+    <color name="white">#FFFFFFFF</color>
+</resources>

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/main/res/values/strings.xml

@@ -0,0 +1,7 @@
+<!--
+  ~ Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+  -->
+
+<resources>
+    <string name="app_name">Android Test</string>
+</resources>

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/main/res/values/themes.xml

@@ -0,0 +1,8 @@
+<!--
+  ~ Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+  -->
+
+<resources>
+
+    <style name="Theme.App" parent="android:Theme.Material.Light.DarkActionBar" />
+</resources>

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/release/kotlin/kotlinx/kover/test/android/DupClass.kt

@@ -0,0 +1,11 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+package kotlinx.kover.test.android
+
+object DupClass {
+    fun log(message: String) {
+        println("DEBUG: $message")
+    }
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/app/src/test/java/kotlinx/kover/test/android/LocalTests.kt

@@ -0,0 +1,17 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+package kotlinx.kover.test.android
+
+import org.junit.Test
+
+import org.junit.Assert.*
+
+
+class LocalTests {
+    @Test
+    fun testDebugUtils() {
+        println("test")
+    }
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/build.gradle.kts

@@ -0,0 +1,10 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+plugins {
+    id("com.android.application") version "7.4.0" apply false
+    id("com.android.library") version "7.4.0" apply false
+    id("org.jetbrains.kotlin.android") version "1.8.20" apply false
+    id("org.jetbrains.kotlinx.kover") version "0.7.1" apply false
+}

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/gradle.properties

@@ -0,0 +1,27 @@
+#
+# Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+#
+
+# Project-wide Gradle settings.
+# IDE (e.g. Android Studio) users:
+# Gradle settings configured through the IDE *will override*
+# any settings specified in this file.
+# For more details on how to configure your build environment visit
+# http://www.gradle.org/docs/current/userguide/build_environment.html
+# Specifies the JVM arguments used for the daemon process.
+# The setting is particularly useful for tweaking memory settings.
+org.gradle.jvmargs=-Xmx2048m -Dfile.encoding=UTF-8
+# When configured, Gradle will run in incubating parallel mode.
+# This option should only be used with decoupled projects. More details, visit
+# http://www.gradle.org/docs/current/userguide/multi_project_builds.html#sec:decoupled_projects
+# org.gradle.parallel=true
+# AndroidX package structure to make it clearer which packages are bundled with the
+# Android operating system, and which are packaged with your app's APK
+# https://developer.android.com/topic/libraries/support-library/androidx-rn
+android.useAndroidX=true
+# Kotlin code style for this project: "official" or "obsolete":
+kotlin.code.style=official
+# Enables namespacing of each library's R class so that its R class includes only the
+# resources declared in the library itself and none from the library's dependencies,
+# thereby reducing the size of the R class for that library
+android.nonTransitiveRClass=true

kover-gradle-plugin/src/functionalTest/templates/builds/android-class-dup/settings.gradle.kts

@@ -0,0 +1,23 @@
+/*
+ * Copyright 2017-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+pluginManagement {
+    repositories {
+        google()
+        mavenCentral()
+        gradlePluginPortal()
+    }
+}
+
+dependencyResolutionManagement {
+    repositoriesMode.set(RepositoriesMode.FAIL_ON_PROJECT_REPOS)
+    repositories {
+        google()
+        mavenCentral()
+        gradlePluginPortal()
+    }
+}
+
+rootProject.name = "android_kts"
+include(":app")

kover-gradle-plugin/src/main/kotlin/kotlinx/kover/gradle/plugin/tools/jacoco/JacocoAnt.kt

@@ -6,7 +6,7 @@ package kotlinx.kover.gradle.plugin.tools.jacoco
 
 import groovy.lang.Closure
 import groovy.lang.GroovyObject
-import kotlinx.kover.features.jvm.KoverFeatures
+import kotlinx.kover.features.jvm.KoverFeatures.koverWildcardToRegex
 import kotlinx.kover.gradle.plugin.commons.ReportContext
 import java.io.File
 
@@ -25,24 +25,27 @@ internal fun ReportContext.callAntReport(
         )
     )
 
-
-    val filteredOutput = if (filters.excludesClasses.isNotEmpty() || filters.includesClasses.isNotEmpty()) {
-        val excludeRegexes = filters.excludesClasses.map { Regex(it.wildcardsToClassFileRegex()) }
-        val includeRegexes = filters.includesClasses.map { Regex(it.wildcardsToClassFileRegex()) }
-
-        val outputCollections = files.outputs.map { output ->
-            services.objects.fileCollection().from(output).asFileTree.filter { file ->
-                // the `canonicalPath` is used because a `File.separatorChar` was used to construct the class-file regex
-                val path = file.toRelativeString(output)
-                // if the inclusion rules are declared, then the file must fit at least one of them
-                (includeRegexes.isEmpty() || includeRegexes.any { regex -> path.matches(regex) })
-                        // if the exclusion rules are declared, then the file should not fit any of them
-                        && excludeRegexes.none { regex -> path.matches(regex) }
+    val filesByClassName = mutableMapOf<String, File>()
+    files.outputs.forEach { output ->
+        output.walk().forEach { file ->
+            if (file.isFile && file.name.endsWith(CLASS_FILE_EXTENSION)) {
+                val className = file.toRelativeString(output).filenameToClassname()
+                filesByClassName[className] = file
             }
         }
-        services.objects.fileCollection().from(outputCollections)
+    }
+
+    val classes = if (filters.excludesClasses.isNotEmpty() || filters.includesClasses.isNotEmpty()) {
+        val excludeRegexes = filters.excludesClasses.map { koverWildcardToRegex(it).toRegex() }
+        val includeRegexes = filters.includesClasses.map { koverWildcardToRegex(it).toRegex() }
+
+        filesByClassName.filterKeys { className ->
+            ((includeRegexes.isEmpty() || includeRegexes.any { regex -> className.matches(regex) })
+                    // if the exclusion rules are declared, then the file should not fit any of them
+                    && excludeRegexes.none { regex -> className.matches(regex) })
+        }.values
     } else {
-        services.objects.fileCollection().from(files.outputs)
+        filesByClassName.values
     }
 
 
@@ -55,7 +58,7 @@ internal fun ReportContext.callAntReport(
                 services.objects.fileCollection().from(files.sources).addToAntBuilder(this, "resources")
             }
             invokeWithBody("classfiles") {
-                filteredOutput.addToAntBuilder(this, "resources")
+                services.objects.fileCollection().from(classes).addToAntBuilder(this, "resources")
             }
         }
         block()
@@ -84,10 +87,13 @@ internal inline fun GroovyObject.invokeWithBody(
 }
 
 /**
- * Replaces characters `.` to `|` or `\` and added `.class` as postfix and `.* /` or `.*\` as prefix.
+ * Replaces characters `|` or `\` to `.` and remove postfix `.class`.
  */
-private fun String.wildcardsToClassFileRegex(): String {
-    val filenameWithWildcards = this.replace('.', File.separatorChar) + ".class"
-    return KoverFeatures.koverWildcardToRegex(filenameWithWildcards)
+private fun String.filenameToClassname(): String {
+    return this.replace(File.separatorChar, '.').removeSuffix(CLASS_FILE_EXTENSION)
 }
 
+/**
+ * Extension of class-files.
+ */
+private const val CLASS_FILE_EXTENSION = ".class"