Write files in etc directories as python files

[Naomi Parsons (NParsonsMO)]

Closes #538

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[Naomi Parsons (NParsonsMO)]

This is new but needed for variables that Hannah was wanting to retrieve (those with substreams).

There's a new unit test.

Otherwise trying to make this change separately around these other changes seemed tricky to time.

[Naomi Parsons (NParsonsMO)]

This is the new variable that has a substream (see comment on other file).