Dependencies in `yml` and `setup.py`

[samwaseda]

It looks to me that currently a lot of bumps are failing because there’s inconsistency with dependencies, which I think are caused by the fact that there are yml files and setup.py which contain packages independently. I looked into the setup.py in pyiron_atomistics, which does not contain anything. Shouldn’t it be like this here as well? @jan-janssen @mbruns91