DatacubeExtension.apply is unaware of variables

[itcarroll]

The recent addition (#699) of the variable setter did not add an accompanying change to the DatacubeExtension.apply method. As a result, you cannot set dimensions and variables in one swoop with the apply method. The documentation implies that apply should allow you to pass in extension properties.

Additionally, there is no test for the apply method, so adding one seems appropriate now and will help with #324.

[itcarroll]

Why does the DatacubeExtension.variables getter return a new dictionary, rather than the result of self._get_property? This quietly breaks ext_item.variables.pop, which will return a name but not remove the variable from ext_item. Feature or bug?

Trying to understand so I can re-write the test_apply_variables method I've introduced in #782 if necessary (or fix a bug).

[duckontheweb]

The result of self._get_property is always going to be a "native" Python type, but the return type of the getter methods often include PySTAC-specific classes. In this case, self._get_property is essentially returning a type of Dict[str, Dict[str, Any]], but the getter needs to return a type of Dict[str, Variable], so we use dictionary comprehension to convert the Dict[str, Any] to a Variable.