First of all, I have tested your code on my own jarfile. Indeed, I was presented with such error:

TypeError: Package clip.frontend.Start.main is not Callable

Then, after reading the docs carefully, I've used another method.

import jpype

# I've used other set of parameters to JVM, and modified a bit your classpath setting.
jpype.startJVM(jpype.getDefaultJVMPath(), "-ea", "-Djava.class.path=clip.jar")

# Second difference, I decided to use JClass because it was more clear for me.
# Parameter array was kept empty.
jpype.JClass("clip.frontend.Start").main([])
jpype.shutdownJVM()

And the output was correct:

% python2 main.py
2 2
+>+[<[>>+>+<<<-]>>[<<+>>-]>[[-]>>>>>>+<<<<<<<<<[-]>[-]>>>>>>>>[<<<<<<<<+>+>>>>>>>-]
<<<<<<<[>>>>>>>+<<<<<<<-]>>>>>>>[-]<<<<<<]<<<[>>+>+<<<-]>>[<<+>>-]>[[-]>>>>>>++
[<<<<<+>>>>>>>>>>>>+<<<<<<<-]<<<<<[>>>>>+<<<<<-]>>>>>>>>>>>>>[>>]+<<[<<]>[>[>>]
<+<[<<]>-]<<<<<<<[-]++[<<<<<+>>>>>>>>>>>>+<<<<<<<-]<<<<<[>>>>>+<<<<<-]>>>>>>>>>>>>>
[>>]+<<[<<]>[>[>>]<+<[<<]>-]<<<<<<<[-]#JVM has been shutdown

Now, I decided to translate my solution to match your problem:

import jpype
jpype.startJVM(jpype.getDefaultJVMPath(), "-ea", "-Djava.class.path=astral.jar")
jpype.JClass("phylonet.coalescent.CommandLine").main([])
jpype.shutdownJVM()

And the code works correctly. More important than the actual solution is the fact, why doesn't your code work. You used wrong set of parameters and specified the classpath in the other way.

Replacing JClass with JPackage, the code still works.

import jpype
jpype.startJVM(jpype.getDefaultJVMPath(), "-ea", "-Djava.class.path=astral.jar")
jpype.JPackage('phylonet').coalescent.CommandLine.main([])
jpype.shutdownJVM()

As the way you extract classes from classpath is correct, the only possible cause is specifying invalid parameter set. After removing -ea the code still works, so mistake you made lies in this fragment of code.

'-Djava.class.path="%s"' % jar

And in fact, I've used this in opposition to my answer, and bam, the code yields this:

TypeError: Package phylonet.coalescent.CommandLine.main is not Callable

This means, the parameter contained following:

-Djava.class.path="astral.jar"

instead of following

-Djava.class.path=astral.jar

The quotes were misplaced and raised the error in result.

The issue appears to be that accessing an attribute of a JPackage class returns a JPackage class when what you really want is a JClass. Changing the testjpype.py to be this worked for me:

from jpype import *
cpopt="-Djava.class.path=%s" % ("/Users/me/jpypeTest")
startJVM(getDefaultJVMPath(),"-ea",cpopt)
java.lang.System.out.println("Hello World!!")
Test = JClass('pkg.Test')
Test.speak("hi")
shutdownJVM()