"scanpy-scripts" is currently having dependency problems. This:

johnnydep --output-format pinned scanpy-scripts

fails in a manner which might not be what you intended. In any case, it did not detect a version conflict, it is more like it crashed because of one. Perhaps you might want to have a look before the scanpy-scripts people finally fix whatever is currently wrong there?

The installation of scanpy-scripts in a venv fails because it tries to install louvain 0.6.1. ( Note: louvain 0.7.0 has installed successfully before on this system.) Before louvain installed igraph 0.8.2 had been installed. Then louvain wanted something from it, could not find it, and tried to build igraph 0.7.1 on its own, which is probably why everything blew up in the scanpy-scripts pip3 install. That seems to be pretty much what happened in the johnnydep command above too.