Enh: allow apps to be referenced by scope to avoid namespace collisions

[khiron]

_get_app_matching_name (and get_app) will take a full scope but only use the app name when requesting app attributes to construct the app instance so get_app will return the first app that matches the name without reference to scope.

Modify get_app(name) and available_apps(name) and app_help(name) to support scoped names, and get the following test to pass

# add a new to_json app that should collide with the internal to_json app
@define_app
class to_json:
    def main(self, data: c3types.SerialisableType) -> str:
        """Convert primitive python types to json string."""
        return json.dumps(data)
    @classmethod
    def _requires_imports(cls):
        return ["from cogent3.app import typing as c3types"]   

from stevedore.extension import ExtensionManager

@pytest.mark.parametrize("install_temp_app", [to_json], indirect=True)
def test_app_namespace_collision(install_temp_app):
    em = ExtensionManager(namespace="cogent3.app", invoke_on_load=False)
    to_json_extensions = [ext for ext in em.extensions if ext.name == "to_json"]
    assert len(to_json_extensions) == 2

    with pytest.raises(NameError):  # should raise an error if name is not scoped
        to_json = get_app("to_json")

    assert available_apps("to_json").shape[0] == 2

    # get apps by scope 
    internal_to_json = get_app("cogent3.app.io.to_json")
    added_to_json = get_app("temp_app_to_json.to_json")

    # test the new app and internal app are equivalent
    data = {"a": 1, "b": 2}
    assert internal_to_json(data) == added_to_json(data) == json.dumps(data)

[khiron]

Create a new test_plugin.py for testing plugin apps, that includes the

def install_temp_app(request: pytest.FixtureRequest):

fixture for dynamically loading and unloading test apps. Move tests into this file from test_composable.py that specifically test registration of apps and remove the xfail decoration from these tests.

Test help documentation using a test app and _make_apphelp_docstring(app)