Code Signing Issues

I have an Executable which is a binary created using a tool called Nuitka, which is similiar to PyInstaller. I creates a self-contain package of all items needs to run the python contained inside. When I build the package and then codesign it, I need to add the --no-strict parameter. But no matter how I sign it, when it tries to execute after signing it tells me it is no longer in the proper format. I tried only signing the .PKG which does work but with the standard security warning since it is not notorized. Eskimo if you out there I really need some help here... this is a simple terminal app, nothing special.