This should work just fine on master

class PhakeTest_MockedClass
{

    public function callInnerFunc()
    {
        return $this->innerFunc();
    }

    protected function innerFunc()
    {
        return 'test';
    }
}

class Test extends PHPUnit_Framework_TestCase
{
    public function testPartialMockCallsInnerMethods()
    {
        $pmock = Phake::partialMock('PhakeTest_MockedClass');
        $this->assertEquals('test', $pmock->callInnerFunc());

        Phake::verify($pmock)->innerFunc();
    }
}

This is on master branch of phake.

You are calling a public method though. I'm looking to be able to call a protected method.

I see, I misread your example. I am sorry about that. I can look at providing functionality similar to etsy's extension. The problem with using etsy's extension is my generated files don't have the annotation, so you are probably getting a reflection exception. A short term solution while I sort out a work around can be to create an extension of the class in question and override the methods you want to test to be public. Extending classes can make methods more visible.

I won't go into a big diatribe about testing protected methods since I don't know your exact situation. However, I would feel bad if I didn't at least say I think you'd realize some benefit from moving these methods out into their own classes if they provide services outside of a typical abstract class setup (concrete public method calling a protected abstract method.) Either way, I know this isn't always a practical solution so I'll see about a decent work-around.

We like to break down our code into small pieces. So if there is a complicated method, rather than have it do everything, we split it out into smaller methods doing a specific task. So while yes, those smaller methods can be encapsulated via a different object, in most cases, it doesn't make much sense for us to split it out when it isn't going to be use elsewhere.

I have already written a utility class much like Etsy's that will make this work so this isn't a high priority. As mentioned though, I think it would be nice if this was built into the base framework itself since I don't see a particular reason why in the realm of unit testing, we need to follow the strict guidelines of the visibility of the methods (this wouldn't be much of an issue if PHP have the package visibility support like Java but I digress). So, my suggestion is to update the __call magic method (I'm assuming this is used somewhere) so that when a method that can't be invoke, the code simply change its visibility before calling it.

+1 - I'd also like to see this as native Phake functionality. Right now we're using an extra layer to accomplish this, e.g. $this->createDummy(Phake::mock(SomeClass::class))->callProtectedMethod(). It ain't pretty.

This is now doable in the 2.1 branch. It's not really that much different from what mollierobbert posted, but it is at least code you don't have too write now. Documentation can be found here: http://phake.readthedocs.org/en/2.1/mocks.html#calling-private-and-protected-methods-on-mocks

Great work Mike! Cheers.