If you are a student in the US on a Visa, don't count the days you are here in that capacity for the Physical Presence Test.
You are correct that you would need to file a 1040-NR in that instance.
Here's more Tax Tips for Resident and Non-Resident Aliens.
You should be able to file a Form W-7 for your spouse with your 1040-NR tax return, prepared through Sprintax.
@Sam Hopi
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