You can file joint or separate (because you are not required to use the same status as on your federal return.)
Your wife's capital gains would not be taxes in Pennsylvania because she was not a resident, but if you file separate you would not have to report it to Pennsylvania. In TurboTax, you do not have to file an "as if" federal separate return to prepare the separate state return so it will not be difficult to prepare the return separate.
@yz493
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