JAL-3840 don’t update the modal residue count for gaps

[jalview.git] / build.gradle

diff --git a/build.gradle b/build.gradle
index f16b882..41a972b 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -40,7 +40,7 @@ plugins {
   id 'eclipse'
   id "com.diffplug.gradle.spotless" version "3.28.0"
   id 'com.github.johnrengelman.shadow' version '4.0.3'
-  id 'com.install4j.gradle' version '8.0.4'
+  id 'com.install4j.gradle' version '8.0.10'
   id 'com.dorongold.task-tree' version '1.5' // only needed to display task dependency tree with  gradle task1 [task2 ...] taskTree
   id 'com.palantir.git-version' version '0.12.3'
 }
@@ -204,7 +204,7 @@ ext {
   install4jDMGDSStore = "${install4j_images_dir}/${install4j_dmg_ds_store}"
   install4jDMGBackgroundImage = "${install4j_images_dir}/${install4j_dmg_background}"
   install4jInstallerName = "${jalview_name} Non-Release Installer"
-  install4jExecutableName = jalview_name.replaceAll("[^\\w]+", "_").toLowerCase()
+  install4jExecutableName = install4j_executable_name
   install4jExtraScheme = "jalviewx"
   install4jMacIconsFile = string("${install4j_images_dir}/${install4j_mac_icons_file}")
   install4jWindowsIconsFile = string("${install4j_images_dir}/${install4j_windows_icons_file}")
@@ -370,6 +370,7 @@ ext {
                                     .replaceAll("_*-_*", "-") // collapse _-_
                                     .toLowerCase()
 
+  getdownWrapperLink = install4jUnixApplicationFolder // e.g. "jalview_local"
   getdownAppDir = string("${getdownWebsiteDir}/${getdownAppDistDir}")
   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
   getdownResourceDir = string("${getdownWebsiteDir}/${getdown_resource_dir}")
@@ -1368,13 +1369,12 @@ task linkCheck(type: JavaExec) {
   args = [ "${helpBuildDir}/${help_dir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
-  def errFOS = outFOS
   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    standardOutput)
+    System.out)
   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
     outFOS,
-    errorOutput)
+    System.err)
 
   inputs.dir(helpBuildDir)
   outputs.file(helpLinksCheckerOutFile)
@@ -1572,6 +1572,18 @@ task getdownWebsite() {
         into getdownResourceDir
       }
     }
+    
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+    getdownWrapperScripts.each{ script ->
+      def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
+      if (s.exists()) {
+        copy {
+          from s
+          into "${getdownWebsiteDir}/${getdown_wrapper_script_dir}"
+        }
+        getdownTextString += "resource = ${getdown_wrapper_script_dir}/${script}\n"
+      }
+    }
 
     def codeFiles = []
     fileTree(file(package_dir)).each{ f ->
@@ -1837,12 +1849,6 @@ task copyInstall4jTemplate {
       }
     }
 
-    // remove the "Uninstall Old Jalview (optional)" symlink from DMG for non-release DS_Stores
-    if (! (CHANNEL == "RELEASE" || CHANNEL == "TEST-RELEASE" ) ) {
-      def symlink = install4jConfigXml.'**'.topLevelFiles.symlink.find { sl -> sl.'@name' == "Uninstall Old Jalview (optional).app" }
-      symlink.parent().remove(symlink)
-    }
-
     // write install4j file
     install4jConfFile.text = XmlUtil.serialize(install4jConfigXml)
   }
@@ -1883,6 +1889,8 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'JALVIEW_APPLICATION_NAME': install4jApplicationName,
     'JALVIEW_DIR': "../..",
     'OSX_KEYSTORE': OSX_KEYSTORE,
+    'OSX_APPLEID': OSX_APPLEID,
+    'OSX_ALTOOLPASS': OSX_ALTOOLPASS,
     'JSIGN_SH': JSIGN_SH,
     'JRE_DIR': getdown_app_dir_java,
     'INSTALLER_TEMPLATE_VERSION': install4jTemplateVersion,
@@ -1904,6 +1912,10 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
     'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
+    'WRAPPER_LINK': getdownWrapperLink,
+    'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
+    'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
+    'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,
@@ -1935,15 +1947,25 @@ task installers(type: com.install4j.gradle.Install4jTask) {
   if (install4j_faster.equals("true") || CHANNEL.startsWith("LOCAL")) {
     faster = true
     disableSigning = true
+    disableNotarization = true
   }
 
   if (OSX_KEYPASS) {
     macKeystorePassword = OSX_KEYPASS
+  } 
+  
+  if (OSX_ALTOOLPASS) {
+    appleIdPassword = OSX_ALTOOLPASS
+    disableNotarization = false
+  } else {
+    disableNotarization = true
   }
 
   doFirst {
     println("Using projectFile "+projectFile)
+    if (!disableNotarization) { println("Will notarize OSX App DMG") }
   }
+  //verbose=true
 
   inputs.dir(getdownWebsiteDir)
   inputs.file(install4jConfFile)
@@ -1964,7 +1986,8 @@ spotless {
 task sourceDist(type: Tar) {
   group "distribution"
   description "Create a source .tar.gz file for distribution"
-  
+
+  dependsOn createBuildProperties
   dependsOn convertMdFiles
 
   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
@@ -2052,6 +2075,15 @@ task sourceDist(type: Tar) {
 //    exclude(EXCLUDE_FILES)
 //    exclude(PROCESS_FILES)
 //  }
+
+  from(file(buildProperties).getParent()) {
+    include(file(buildProperties).getName())
+    rename(file(buildProperties).getName(), "build_properties")
+    filter({ line ->
+      line.replaceAll("^INSTALLATION=.*\$","INSTALLATION=Source Release"+" git-commit\\\\:"+gitHash+" ["+gitBranch+"]")
+    })
+  }
+
 }
 
 
@@ -2515,12 +2547,12 @@ DEBUG: ${eclipseDebug}
         new org.apache.tools.ant.util.TeeOutputStream(
           logOutFOS,
           stdout),
-        standardOutput)
+        System.out)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
-        errorOutput)
+        System.err)
     } else {
       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logOutFOS,