You are still considered as common-law partners for tax filing if you were not separated or moved because of a breakdown in your relationship or you are living away from your common-law-partner due to work, school, or health reasons. 

This situation applies when you are living in a conjugal relationship for at least continuous 12 months (including the period of separation less than 90 days due to down situation your relationship) and,

They are parents of your child or have custody or control over your child. 

Make sure you claim your status accurately. CRA (Canada Revenue Agency) considered you officially separated if you were part for at least 90 days from your common-law partner.

For more information, please visit the links below:

CRA - Marital Status

TurboTax - Facts Every Canadian Needs to Know About Filing Coupled Tax Returns