You can file Married Filing Jointly for your federal tax return.
California allowed married taxpayers with mixed residencies to file jointly. You would need to file a part-year resident return and allocate only your wife's income to California.
For Pennsylvania, you can file Married Filing Jointly for convenience, but this may subject your wife's income to Pennsylvania tax. Filing separately in Pennsylvania may be the best option, but you can try it both ways to see what's best.
