Replace call to deprecated set_ methods with set_option

[sphuber]

Fixes #2360

The Node._set_internal method was still calling deprecated set_
methods for options of the CalcJobNode sub class. These should now
be set through the explicit set_option method. The JobProcess
was likewise violating this rule, when setting the options of the
underlying CalcJobNode it is using as a storage record.

[coveralls]

Coverage increased (+1.2%) to 68.871% when pulling dccc05b on sphuber:fix_2360_remove_call_deprecated_set_methods into 097fa6a on aiidateam:provenance_redesign.

[giovannipizzi]

Funny, though, that we need to do special treatment for set_computer...

[sphuber]

Yes, I wasn't quite sure about this solution, so let's not merge this quite yet and discuss. The problem is if I remember correctly that set_computer is a method of Node and not one of the deprecated explicit option setters defined on the CalcJobNode like all of the other options. I also put in a check for None in the set_option because that was being passed in and tripping up validation, but I'm not sure that is he right thing to do

[sphuber]

@giovannipizzi I have looked again in more depth into why we need an exception for computer. The reason is that all options are stored as attributes on the Node except for the computer, which needs to set a foreign key. I looked into whether we could remove computer from the list of available options, but this is not possible I think. For local codes, a user needs to be able to specify what computer to use, and since this is not an actual input node, defined through the use_methods, it has to go in the options. In the old AiiDA, one could call directly call set_computer on the Node, but now that the user no longer directly gets access to the node, setting it through the options is the only way. We could try to rework it some other way, but I think that will end up in code that is uglier than just this single exception in the set_option method.

If you agree as well, I think this is ready to merge