Residency

I live in PA in rented apartment. Have lived here for 5 years. My wife was on H-4 upto June and then changed to F-1 to start school in Boston, MA in late july. She rented an apartment in Boston for rest of the year. She had a small income from on campus jobs and both federal and MA state tax was held for her in W-2. I have income in PA and PA income tax was held for me. I am wondering how should I file the state returns in terms of residency and filing status. I am filing the federal as married filing jointly. Also, smart check keeps giving an error when trying to finalize state return and keeps asking me to fill non-MA deduction which is 0 but keeps bringing up the same error?

Thanks

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