The Shrine

Picked up this manga recently. It's about two years old. The main character, codename Twilight, is the top spy of the nation of Westalia which is in a cold war with the nation of Ostania. He needed to infiltrate and find out secret plans of Donovan Desmond, the leader of the ruling party of Ostania, but Donovan Desmond only appears in a gathering for elite students and their parents in the number 1 school of their nation. So to carry out his mission he found some people to make a fake family, and unbeknownst to him (or any of the members minus Anya) everyone in the family is basically a superhuman. You got Yor, the mother which is the most fearsome assassin. Anya, the daughter, which is a psychic that can read people's minds. Eventually they got Bond, a genetically engineered dog that can see the future. However, the plan quickly runs into a snag when Twilight found out that Anya is too dumb to get into the elite status even with mind reading powers (he doesn't know she has that power) since she manages to read all the wrong minds while taking the test, so he went to plan B where he wanted Anya to befriend Damian Desmond, Donovan's son, and hope that'll gain him access to his father.

This is mostly a comedy but the character relationships are pretty heart-warming, and despite its comedic nature, Donovan Desmond so far lives up to his final boss status. Well, to be fair, you literally have no idea what he is capable of, and in a series where it seems like everyone has a super power, it's quite mysterious when you're looking at a guy you just don't know anything about. I'm guessing Anya will not be present when Donovan shows up on purpose in the foreseeable future as Spy X Family spends a lot of time going through each character's thought process and what they're planning, but Donovan is the sole exception as he never communicates in any kind of thought bubbles and gives keeps most of his dialogue to Internet conversation like 'Sup', 'Good day' and so on while Twilight is desperately trying to find some tell that'll indicate what he's thinking of.

Yep, I've been reading this one for a while, it's wholesome as fuck, looking forward to the anime.

On the subject of wholesomeness, obviously the people in this story are all good people so other than when Yor does her job nobody ever dies, but Twilight says he's prepared to kill people in the worst case scenario. I find that to be a lot more realistic compared to Kenshin or similar stuff where they stress about not killing people but it's pretty much just freak luck that nobody died on either side. It helps that even Twilight is like way overpowered so he can usually just KO someone and obviously when you get really tough scenario Yor can usually KO something with a simple punch because she's way overpowered, and of course there is also Anya and her dog. It's similar to Helck. If your main character(s) insist on never killing anybody they better be really awesome to back that up.