You're on the right track, but making a slight mistake: instead of running cjio on the command line, you start python on the command line and run cjio with python. Instead, just run cjio --help
on the command line. This will only work if you have cjio installed in your global python packages.
When working with python, it is always good to have a virtual environment. This is a separate python environment, where you have your local python packages stored (the reason is that many packages depend on specific versions of other packages and if you have two of them installed that demand a different version, one of them will not work). Generally for each new project, you can make a new venv. What I suggest to you is:
(1) create a python3 venv using venv
(this is in the standard python packages) on the command line, in the same directory as the CityJSON file:
python3 -m venv venv
(2) now a virtual environment called venv
is created. You first need to activate it:
venv\bin\activate
(windows) or . venv/bin/activate
(linux)
(3) Now your virtual env is created and activated, you can install cjio:
pip install cjio
(4) Run cjio on the command line:
cjio --help
or cjio 3dbag_v210908_fd2cee53_2932.json upgrade save 3dbag_new.json
I hope this helps