Deprecation is a big issue in python. I’m in need of Molecular Dynamic (MD) simulations tools. The error above comes from one tool I already posted about, called LipIDens, more specifically, it’s a complain thrown away by vermouth. Vermouth (for VERsatile, MOdular, and Universal Tranformation Helper) is also a drink and the python library that powers Martinize2. The vermouth source comes here. It is supposed to be used to apply transformation on molecular structures. Which means I don’t really know what it does! Anyway, my error reads
Installed
/usr/local/lib/python3.9/site-packages/lipidens-1.0.0-py3.9.egg
Processing dependencies for lipidens==1.0.0
error: networkx 3.0 is installed but
networkx~=2.0 is required by {'vermouth'}
What to do here? I found the solution and the explanation once more on StackOverflow. It’s very interesting to know that the the grammar for a mathematical library changed after Python 3.5. So then, why on the LipIDens documentation it is recommended to use a python above 3.9? I’m going to leave the answer to this question open (old developer environments with remnants or insufficient tests) and show you my solution. We install a specific python package. I choose pip to install it instead of conda because it goes to my python site-packages, which I personally consider a more elegant solution. Here you have my output:
bash-5.1# pip install networkx==2.5
Collecting networkx==2.5
Downloading networkx-2.5-py3-none-any.whl (1.6 MB)
|XXXXXXX| 1.6 MB 4.3 MB/s
Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.9/site-packages (from networkx==2.5) (5.1.1)
Installing collected packages: networkx
Attempting uninstall: networkx
Found existing installation: networkx 2.0
Uninstalling networkx-2.0:
Successfully uninstalled networkx-2.0
Successfully installed networkx-2.5
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
bash-5.1# python setup.py install
After the pip install over my local python I run again the LipIDens installer and it works. Another issue is to get meaningful results from the program! BTW, I decided to keep writing my bits thanks to some good feedback that I was missing before… thank you guys. I appreciate it.
Bits and Dragons 