search

PoonLab / sierra-local

Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
GNU General Public License v3.0
6 stars 3 forks source link

AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren' #104

Closed marcbennedbaek closed 2 weeks ago

marcbennedbaek commented 3 weeks ago

Hi! I am trying to run sierra-local, but I get an error when I try to run with the example given I get an error message: sierra_error message

The installation completed with no errors and I am able to see options for running the program.

I am running this with Python 3.10.9 on Ubuntu 20.04.06 LTS. I looked at a closed issue with a similar error, but there are differences, so it seems the error I encount is different from the one that is closed.

Not sure if it is just me doing something wrong or have misunderstood some directions.

Thanks! Best regards, Marc

ArtPoon commented 3 weeks ago

Looks like we left a deprecated function in there https://docs.python.org/3.8/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren Most of our testing was back in the pre-3.9 era. I'll have a look.

ArtPoon commented 3 weeks ago

Looks like I patched this problem a couple of years ago: https://github.com/PoonLab/sierra-local/commit/0310f13e2216c2539df863c11ad1eb9ef5a21407

Can you update sierralocal to the current version?

marcbennedbaek commented 2 weeks ago

Thank you for the response!

I tried to reinstall again, but got the older version again. When I cloned from my browser instead of a terminal and installed from that repository I got the most recent version.

And now it works!

ArtPoon commented 2 weeks ago

Glad you were able to resolve the problem. Strange that pulling from the repository in your terminal did not retrieve the latest version.