This is amazingly field dependent. I am from a field where you only cite the most significant tools you use (Machine Learning). E.g. "We implemented this with a neural network build with TensorFlow (cite). We augmented the data using skew tranforms from Augumentor.jl"

But the convention of other fields is to recursively cite all software that is loaded by your experimental code. And is strictly required by their journals.

and I am not one to tell other fields what their conventions should be. Especially not when they give more credit.