1. When she  travels with you. If she is nearby when you level up you get +35 points.
2. When you take her to a location in Tour of The Commonwealth you get +35 points.
3. When you meet her she can hack novice level objects (she has a 100% success rate when hacking objects she's trained to handle). She will get better at this with practice. If you tell her to hack something and she is successful then her skills increase. When she unlocks or hacks five terminals she'll increase in level. With enough activity she will progress to hacking Master terminals.

A successful hack awards +15 points. There is a cooldown period of one hour to earn affinity points. She can continue to hack objects during that time, but you cannot get more points until an hour has passed.
4. She uses the chemistry station to make products for her store. She awards +15 points per use. She will use the station by herself or you can send her to it. Either way awards points and affects her store inventory. There is a 1 hour cooldown period for points being awarded.
5. Using one of her Alternative Medicine products awards +10 points per use. There is a cooldown period of one hour to earn these affinity points.
6. Completing Sweet Revenge awards +100 points.
7. There are two optional objectives included in Tour of the Commonwealth that yield +20 Affinity Points each.
8. She awards Affinity Points once for the following events:
-The first time you put her into a set of PA +20
-When you give her Buzzbites for the first time +20
-When you go to the bunker for the first time +20
-When you fulfill the quest objective to give her Mutated Fern flowers + 50; talk to her in her
"Chat With Heather" dialogue topic to get that quest objective. There will be several comments available in that topic when you first pick her up.

You do not need Charisma to successfully progress through her affinity quest. As time goes on she likes you more and conversations reflect that.