If you really want to recreate what setup.py did, you can try
pip install --target /home/weewx/bin weewx
python3 /home/weewx/bin/weectl.py station create /home/weewx
Normally, pip installs into the site-packages subdirectory of whatever instance of python you are using. The first line tells pip to install into /home/weewx/bin instead.
The second line says to create a new station under the directory /home/weewx. So the configuration file, skins, archive database, etc, will all be put in /home/weewx
The results will approximate an old setup.py install with a couple of differences:
1. Everything will be put in /home/weewx. That is, not just the weewx code, but also its dependencies.
2. The files weewxd.py and weectl.py are not executable. You have to give them as an argument to python3. For example,
python3 /home/weewx/bin/weewxd.py /home/weewx/weewx.conf