From 6fa882584a8e33a1c9975391dfe34520940ba8c6 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 20 Sep 2021 14:25:48 +0100
Subject: [PATCH] JAL-3521 working minimal build.gradle for debian and 2.11.2.
 Flexmark plugin might be a problem

---
 utils/debian/debian_build.gradle |   37 +++++++++++++++++++++++++++++++------
 1 file changed, 31 insertions(+), 6 deletions(-)

diff --git a/utils/debian/debian_build.gradle b/utils/debian/debian_build.gradle
index b609ec6..998645a 100644
--- a/utils/debian/debian_build.gradle
+++ b/utils/debian/debian_build.gradle
@@ -65,7 +65,7 @@ def overrideProperties(String propsFileName, boolean output = false) {
   }
 }
 
-project.ext {
+ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
   jalviewDirRelativePath = jalviewDir
 
@@ -103,6 +103,8 @@ project.ext {
 
   classesDir = string("${jalviewDir}/${classes_dir}")
 
+  useClover = false
+
   resourceClassesDir = classesDir
 
   testSourceDir = testDir
@@ -163,16 +165,18 @@ sourceSets {
     }
 
     resources {
-      srcDirs resourceDir
-      srcDirs += helpParentDir
+      srcDirs = [ resourcesBuildDir, docBuildDir, helpBuildDir ]
     }
 
-    jar.destinationDir = file("${jalviewDir}/${package_dir}")
+    compileClasspath = files(sourceSets.main.java.outputDir)
+    compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
+
 
     compileClasspath = files(sourceSets.main.java.outputDir)
     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.main.resources.srcDirs)
   }
 
   test {
@@ -182,16 +186,33 @@ sourceSets {
     }
 
     resources {
-      srcDirs = sourceSets.main.resources.srcDirs
+      srcDirs = useClover ? sourceSets.clover.resources.srcDirs : sourceSets.main.resources.srcDirs
     }
 
     compileClasspath = files( sourceSets.test.java.outputDir )
-    compileClasspath += sourceSets.main.compileClasspath
+    compileClasspath += useClover ? sourceSets.clover.compileClasspath : sourceSets.main.compileClasspath
     compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**/*.jar"])
 
     runtimeClasspath = compileClasspath
+    runtimeClasspath += files(sourceSets.test.resources.srcDirs)
   }
+ /*  test {
+    java {
+      srcDirs testSourceDir
+      outputDir = file(testClassesDir)
+    }
 
+    resources {
+      srcDirs = sourceSets.main.resources.srcDirs
+    }
+
+    compileClasspath = files( sourceSets.test.java.outputDir )
+    compileClasspath += sourceSets.main.compileClasspath
+    compileClasspath += fileTree(dir: "${jalviewDir}/${utils_dir}/testnglibs", include: ["**   REMOVE_THIS_GAP  /*.jar"])
+
+    runtimeClasspath = compileClasspath
+  }
+*/
 }
 
 
@@ -615,6 +636,10 @@ jar {
   exclude "**/*.jar.*"
 
   inputs.dir(sourceSets.main.java.outputDir)
+  sourceSets.main.resources.srcDirs.each{ dir ->
+    inputs.dir(dir)
+  }
+
   outputs.file("${outputDir}/${archiveFileName}")
 }
 
-- 
1.7.10.2