Enhance WebAssembly output configuration in compile_to_js.sh

.github/workflows/main.yml

@@ -35,12 +35,4 @@ jobs:
     if: ${{ needs.build_and_test_linux.result == 'success' }}
     uses: ./.github/workflows/windows-reusable.yml
     with:
-      linux_status: ${{ needs.build_and_test_linux.result }}
-
-  javascript_package:
-    name: JavaScript Package (WebAssembly)
-    needs: build_and_test_linux
-    if: ${{ needs.build_and_test_linux.result == 'success' }}
-    uses: ./.github/workflows/webassembly-reusable.yml
-    with:
-      linux_status: ${{ needs.build_and_test_linux.result }}
+      linux_status: ${{ needs.build_and_test_linux.result }}

distributions/Java/README.md

@@ -0,0 +1,192 @@
+# Java GUI for libamtrack (Unmaintained)
+
+> **Note:** This code is not actively maintained. Contributors are welcome!
+
+## Prerequisites
+
+To compile the Java GUI for libamtrack, you need the following:
+
+1. **Web browser** (preferably Firefox) with Java support installed ([Java Runtime Environment](http://java.sun.com/javase/downloads/index.jsp))
+
+2. **GCC compiler** (preferably v4.0+). Linux users usually have it by default. Windows users can download
+   port of GCC for windows - MinGW compiler (Minimalist GNU for Windows), from the [MinGW webpage](http://www.mingw.org/).
+
+3. **Java JDK**, for example Sun Java SE v1.6 ([download](http://java.sun.com/javase/downloads/widget/jdk6.jsp))
+
+4. **Swig interface compiler**, preferably v1.3. On most Linux platforms it's available in the repositories as `swig` package. 
+   Windows users can download it from the [SWIG project webpage](http://www.swig.org/download.html).
+
+5. **GNU Scientific Library** ([GSL](http://www.gnu.org/software/gsl/)). On most Linux platforms, it's available in the repositories (please install
+   also `-dev` version of packages). Windows users can download it from [GnuWin32](http://gnuwin32.sourceforge.net/packages/gsl.htm)
+
+
+
+
+## Compilation
+
+### Windows systems
+
+Locate file `wrapper\Java\make_jar.bat` and setup following variables:
+
+```bat
+set swigexe="Z:\swig\swig.exe"
+set jarsignerexe="C:\Program Files\Java\jdk1.6.0_18\bin\jarsigner.exe"
+set javacexe="C:\Program Files\Java\jdk1.6.0_18\bin\javac.exe"
+set jarexe="C:\Program Files\Java\jdk1.6.0_18\bin\jar.exe"
+set javaincludeA="C:\Program Files\Java\jdk1.6.0_18\include"
+set javaincludeB="C:\Program Files\Java\jdk1.6.0_18\include\win32"
+set gslinclude="C:\Program Files\GnuWin32\include"
+set gsllib="C:\Program Files\GnuWin32\lib"
+set gsldllA="C:\Program Files\GnuWin32\bin\libgsl.dll"
+set gsldllB="C:\Program Files\GnuWin32\bin\libgslcblas.dll"
+set gccexe="C:\Program Files\MinGW\bin\gcc.exe"
+```
+
+Start Windows command line (`Start → Run → cmd.exe`), go to the directory 
+containing `make_jar.bat` file (using `cd` command) and run it (typing `make_jar.bat`).
+
+### Linux systems
+
+Locate file `distributions\Java\make_jar.sh` and setup following variables:
+
+```sh
+SWIGEXE=swig
+JARSIGNEREXE=jarsigner
+JAVACEXE=javac
+JAREXE=jar
+JAVAINCLUDEA="/usr/lib/jvm/java-6-sun/include/"
+JAVAINCLUDEB="/usr/lib/jvm/java-6-sun/include/linux"
+GSLINCLUDE="/usr/include"
+GSLLIB="/usr/lib"
+GSLDLLA="/usr/lib/libgsl.so"
+GSLDLLB="/usr/lib/libgslcblas.so"
+GCCEXE=gcc
+```
+
+Here if you have everything properly installed you will need only to adjust
+Java include path (you can locate them by trying to find `jni.h` file using
+command `locate jni.h`) and GSL libraries (locate `libgsl.so`).
+
+Start your favorite console, go to the directory
+containing `make_jar.sh` file (using `cd` command) and run it (typing `./make_jar.sh`).
+
+
+
+## Compilation details
+
+Both `make_jar` scripts do the same job, just with slightly different parameters of compiler.
+
+### Step 1. Generate interface elements using SWIG
+
+First - please read [SWIG tutorial](http://www.swig.org/tutorial.html), then please 
+inspect file `example.i`. This file includes header files from libamtrack C library and contains list
+of functions that we will use in GUI.
+
+Command:
+```sh
+swig -java -o c-swig-src/$SWIGWRAPPER.c -outdir java-swig-src example.i
+```
+
+will create interface files which consist of two sets:
+
+A) **C interface** (`*.c`) which will be saved into `c-swig-src` directory and will be later compiled
+together with the C libamtrack library
+
+B) **Java interface files** (`*.java`) which will be saved into `java-swig-src` directory and will be
+later compiled with Java libamtrack GUI
+
+> **Note:** Please do not commit generated files into the repository.
+
+
+### Step 2. Compile libamtrack C library + SWIG C wrapper
+
+In this step all the `*.c` files will be compiled to the `*.o` files (these
+will go to `obj` directory). SWIG C wrappers need to be compiled
+with Java JDK include directory as they contain JNI stubs.
+
+Finally all `*.o` files and necessary libraries (GSL) will be linked together
+to create C library file (`example.dll` or `libamtrack.so` respectively).
+
+Please note that there is difference in compilation flags:
+- Windows: `-fno-strict-aliasing` 
+- Linux: `-fPIC` 
+
+and in linking flags:
+- Windows: `-mno-cygwin -Wl,--add-stdcall-alias` 
+- Linux: *(none specified)*
+
+
+### Step 3. Compile Java GUI
+
+All Java source files (`*.java`) will be compiled in this
+step to the Java bytecode (`*.class`):
+
+```sh
+$JAVACEXE java-swig-src/*.java src/*.java -d bin/
+```
+
+Compilation is done on SWIG generated stubs and on JAVA GUI source files.
+Generated `*.class` files will be saved in the `bin` directory.
+
+
+### Step 4. Create JAR file
+
+Java bytecode files (`*.class`), manifest file together with libamtrack C library
+and with GSL libraries will be packed into a JAR file:
+
+```sh
+$JAREXE cvfm example.jar MANIFEST.MF *.class libexample.so libgsl.so libgslcblas.so
+```
+
+or
+
+```bat
+%jarexe% cvfm example.jar MANIFEST.MF *.class example.dll libgsl.dll libgslcblas.dll
+```
+
+Previously generated `*.class` files are deleted in this step.
+
+Generated `example.jar` file can be now used as local GUI.
+Can be started by typing command:
+```sh
+java -jar example.jar
+```
+
+
+### Step 5. Sign JAR file
+
+All JAR files that need to be used in Java Web Start technology
+need to be signed. I've prepared self-signed certificate, stored
+in `myk` file. During signing process it will ask for password, which
+is "libamtrack". If you want to generate your own certificate,
+please use command:
+```sh
+keytool -genkey -keystore myk -alias jdc
+```
+
+Signed JAR file will be saved as `webstart/examplesigned-Linux.jar` or
+`webstart/examplesigned-Windows.jar`.
+
+
+### Step 6. Deploying Web Start Application
+
+In order to run generated JAR archive from within web browser
+you will need to adjust `*.jnlp` file. Please inspect
+`webstart/libamtrack-linux.jnlp` or `webstart/libamtrack-windows.jnlp`
+respectively.
+
+In the second line of that file you will find:
+```xml
+<jnlp spec="1.0+" codebase="XXX">
+```
+
+Instead of XXX you need to put URL. If you test how the applet works
+locally, please put there local URL, like:
+`file:///home/libamtrack/workspace/AmTrack_reorgan/wrapper/Java/webstart`
+if you test it on the webserver, put there usual URL:
+`http://libamtrack.dkfz.org/libamtrack`
+
+This URL should point to location where JAR file is stored.
+
+There is also `webstart/HelloWorld.html` file with links to jnlp files.
+