Recover branch 1.4 and tag 1.4.3 #404

LinguaPhylo · Aug 2, 2023 · 843388f · 843388f
1 parent f0f0b32
commit 843388f
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Showing 4 changed files with 73 additions and 20 deletions.
diff --git a/bin/slphy.bat b/bin/slphy.bat
@@ -52,7 +52,7 @@ goto fail
 
 :findJavaFromJavaHome
 set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+set JAVA_EXE=%JAVA_HOME%\bin\java.exe
 
 if exist "%JAVA_EXE%" goto setLPHYLIB
 
@@ -65,24 +65,26 @@ echo location of your Java installation.
 goto fail
 
 :setLPHYLIB
-set LPHY_LIB=%APP_HOME%/../lib/
+set LPHY_LIB=%APP_HOME%..\lib
 echo set the LPHY_LIB to "%LPHY_LIB%"
 
 :execute
 @rem Setup the command line
 @rem Execute 
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p %LPHY_LIB% -m lphystudio/lphystudio.app.simulator.SLPhy %*
+set CMD="%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p "%LPHY_LIB%" -m lphystudio/lphystudio.app.simulator.SLPhy %*
+%CMD%
 
 :end
 @rem End local scope for the variables with windows NT shell
 if "%ERRORLEVEL%"=="0" goto mainEnd
 
 :fail
-echo ERROR: fail to run 
-echo "%JAVA_EXE%" %DEFAULT_JVM_OPTS% -p %LPHY_LIB% -m lphystudio/lphystudio.app.simulator.SLPhy %*
-
+echo.
+echo ERROR: fail to run the command
+echo %CMD%
+echo.
+echo Get help from https://linguaphylo.github.io/setup
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal
 
-:omega
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -41,7 +41,7 @@ tasks.build {enabled = false}
 // Configures the sub-projects of this project.
 subprojects {
     group = "io.github.linguaphylo"
-    version = "1.4.2" //-SNAPSHOT"
+    version = "1.4.3" //-SNAPSHOT"
     val webSteam = "github.com/LinguaPhylo/linguaPhylo"
     val web = "https://${webSteam}"
     val homepage = "https://linguaphylo.github.io/"

diff --git a/lphy-studio/lphystudio.xml b/lphy-studio/lphystudio.xml
@@ -1,7 +1,7 @@
 <project>
     <shortName>lphystudio</shortName>
     <fullName>LPhyStudio</fullName>
-    <version>1.4.2</version>
+    <version>1.4.3</version>
     <readmeFile>${build_project_directory}/../README.md</readmeFile>
     <licenseFile>${build_project_directory}/../LICENSE</licenseFile>
     <componentList>
@@ -145,12 +145,14 @@
         </autodetectJava>
     </preInstallationActionList>
     <postInstallationActionList>
-        <addEnvironmentVariable>
-            <explanation>Adding environmental path</explanation>
-            <name>LPHY_PATH</name>
-            <scope>system</scope>
-            <value>${installdir}</value>
-        </addEnvironmentVariable>
+        <!-- TODO bug 1 to append not replace; bug 2 both ~/.bash_profile and ~/.zshrc are changed  -->
+<!--        <addEnvironmentVariable>-->
+<!--            <explanation>Adding environmental path</explanation>-->
+<!--&lt;!&ndash; Important to launch lphybeast  &ndash;&gt;-->
+<!--            <name>LPHY_LIB</name>-->
+<!--            <scope>system</scope>-->
+<!--            <value>${installdir}</value>-->
+<!--        </addEnvironmentVariable>-->
         <createJavaLaunchers>
             <destination>${installdir}</destination>
             <explanation>Creating launcher</explanation>
@@ -164,15 +166,16 @@
                     <classpath></classpath>
                     <jarFile></jarFile>
                     <mainClass></mainClass>
-                    <osxApplicationBundleIcon>${installdir}/src/lphy.icns</osxApplicationBundleIcon>
                     <preferredJavaBinary></preferredJavaBinary>
                     <runInBackground>0</runInBackground>
                     <runInConsole>0</runInConsole>
+                    <!-- TODO not working -->
                     <useLauncherDirectoryAsWorkingDirectory>1</useLauncherDirectoryAsWorkingDirectory>
                     <usePropertiesFile>0</usePropertiesFile>
                     <vmParameters>-Xms256m -Xmx4g -Dfile.encoding=UTF-8 -p lib -m lphystudio</vmParameters>
-                    <windowsResourceFileVersion>1.0.0.0</windowsResourceFileVersion>
+                    <!-- TODO have to keep this otherwise launcher failed, but cannot mv it to diff dir -->
                     <workingDirectory>${installdir}</workingDirectory>
+
                     <validVersionList>
                         <validVersion>
                             <bitness></bitness>
@@ -186,18 +189,31 @@
             </javaLauncherList>
         </createJavaLaunchers>
     </postInstallationActionList>
+
+    <!--  mac OS Dmg -->
     <createOsxBundleDmg>1</createOsxBundleDmg>
     <enableRollback>0</enableRollback>
     <enableTimestamp>1</enableTimestamp>
-    <osxApplicationBundleIdentifier>io.github.linguaphylo.LPhyStudioLauncher</osxApplicationBundleIdentifier>
     <osxDmgTitle>LPhyStudio DMG</osxDmgTitle>
+    <!-- mac OS Signing -->
     <osxSigningIdentity>Developer ID Application: Walter Xie</osxSigningIdentity>
+
+    <!--  mac OS Bundle -->
+    <osxApplicationBundleIdentifier>io.github.linguaphylo.LPhyStudioLauncher</osxApplicationBundleIdentifier>
+    <!--TODO still invalid ? -->
+<!--    <osxApplicationBundleIcon>${build_project_directory}/build/distributions/lphy-studio-${product_version}/src/lphy512x512.icns</osxApplicationBundleIcon>&ndash;&gt;-->
+
+    <!--  windows  -->
+    <windowsResourceFileVersion>1.0.0.0</windowsResourceFileVersion>
+    <windowsExecutableIcon>${installdir}/src/lphy.ico</windowsExecutableIcon>
+
     <vendor>LPhy Development Team</vendor>
+
     <parameterList>
         <directoryParameter>
             <name>installdir</name>
-            <description>Installer.Parameter.installdir.description</description>
-            <explanation>Installer.Parameter.installdir.explanation</explanation>
+            <description>Installation Directory</description>
+            <explanation>Please specify the directory where ${project.fullName} will be installed. This directory will be the parent directory of the LPhy library path, $LPHY_LIB, required by LPhyBEAST.</explanation>
             <value></value>
             <default>${platform_install_prefix}/${product_shortname}-${product_version}</default>
             <allowEmptyValue>0</allowEmptyValue>
@@ -206,6 +222,41 @@
             <mustBeWritable>yes</mustBeWritable>
             <mustExist>0</mustExist>
             <width>30</width>
+            <postShowPageActionList>
+                <!-- This will skip the readytoinstall page -->
+                <setInstallerVariable name="next_page" value="installation" />
+            </postShowPageActionList>
+<!--  TODO  ${installdir} can be refreshed  -->
+<!--            <validationActionList>-->
+<!--                <throwError>-->
+<!--                    <text>-->
+<!--                        Please replace "x" in the folder to the version numbers : ${installdir} !-->
+<!--                    </text>-->
+<!--                    <ruleList>-->
+<!--                        <compareText>-->
+<!--                            <logic>does_not_contain</logic>-->
+<!--                            <nocase>1</nocase>-->
+<!--                            <text>BEAST 2.x.x</text>-->
+<!--                            <value>${installdir}</value>-->
+<!--                        </compareText>-->
+<!--                    </ruleList>-->
+<!--                </throwError>-->
+<!--                <throwError>-->
+<!--                    <text>-->
+<!--                        To use LPhy with LPhyBEAST, LPhy Studio must be installed inside the BEAST 2.x.x folder (e.g., BEAST 2.7.5).-->
+<!--                        But it is set to be installed in ${installdir} !-->
+<!--                        Please read the User Manual https://linguaphylo.github.io/setup/.-->
+<!--                    </text>-->
+<!--                    <ruleList>-->
+<!--                        <compareText>-->
+<!--                            <logic>contains</logic>-->
+<!--                            <nocase>1</nocase>-->
+<!--                            <text>BEAST</text>-->
+<!--                            <value>${installdir}</value>-->
+<!--                        </compareText>-->
+<!--                    </ruleList>-->
+<!--                </throwError>-->
+<!--            </validationActionList>-->
         </directoryParameter>
     </parameterList>
 </project>

diff --git a/lphy-studio/src/main/resources/lphy512x512.icns b/lphy-studio/src/main/resources/lphy512x512.icns