ImportError: attempted relative import with no known parent package

[peabreu]

When we try to use the instructions for downloading a stand alone version, namely:
wget -O calculate_rmsd https://raw.githubusercontent.com/charnley/rmsd/master/rmsd/calculate_rmsd.py
chmod +x calculate_rmsd

We get the following error:
./calculate_rmsd
Traceback (most recent call last):
File "calculate_rmsd", line 58, in
from .version import version
ImportError: attempted relative import with no known parent package

OS version: Fedora 41
python --version
Python 3.13.9

[nbehrnd]

@peabreu Bypass: i) set up a virtual environment, ii) activate it, iii) clone the repo, iv) run the computation(s). Example with Linux Debian 14/forky:

python -m venv sup
source ./sup/bin/activate
git clone https://github.com/charnley/rmsd.git
cd rmsd
pip install -e .
calculate_rmsd -h

With two of the water geometries (/tests/resources/)

$ calculate_rmsd water.xyz water_swapped.xyz --reorder
0.4238435495557745

Setup: Debian 14/forky, Python 3.13.12 and

$ pip list
Package Version
------- -------
numpy   2.4.3
pip     26.0.1
rmsd    1.6.5
scipy   1.17.1

[charnley]

hi @peabreu ,
Yeah, the install is outdated now given the "external dependency" of version.py. You can just delete the import line and set __version__ = "1.0.0" and it should work fine. Given that you have the dependencies installed. Does that work for you?

[charnley]

@peabreu Interesting, I didn't know people still preferred wget over pip. Can you explain why you prefer that way?

[peabreu]

I was planning to write a small script for my students to use in "Computational Drug Discovery" course and I wanted to make a self-contained script. That's why I was downloading only the file as to not force anyone to install something that they might not need to use later on. I might try to just 'sed' to fix the version, or maybe ask them to install it via pip. Thanks a lot for the quick answer and solution.

[charnley]

I do recommend getting a Python environment in general. However, I always like the idea of rmsd is a self-contained one-file package. So I merged #132 to capture the import error so wget works again.

they might not need to use later on

Of course your students will need to used rmsd the future ; )

Let me know if this works for your setup.

[nbehrnd]

@peabreu Maybe the descriptor libraries of MolSSI could be of interest for you/your class; but this only is guess.

[peabreu]

@charnley Now it works as I expected. Thanks a lot for the quick response and modification.