`ModuleNotFoundError: No module named 'backports.datetime_fromisoformat'` in Biocontainers civicpy image (v5.0.0)

[emmcauley]

Hi Griffith Lab,

I’m encountering an error when running civicpy inside the quay.io/biocontainers/civicpy:5.0.0--pyhdfd78af_0 Docker container:

Status: Downloaded newer image for quay.io/biocontainers/civicpy:5.0.0--pyhdfd78af_0
Traceback (most recent call last):
  File "/usr/local/bin/civicpy", line 6, in <module>
    from civicpy.cli import cli
  File "/usr/local/lib/python3.12/site-packages/civicpy/cli.py", line 4, in <module>
    from civicpy import LOCAL_CACHE_PATH, civic
  File "/usr/local/lib/python3.12/site-packages/civicpy/civic.py", line 13, in <module>
    from backports.datetime_fromisoformat import MonkeyPatch
ModuleNotFoundError: No module named 'backports.datetime_fromisoformat'

I verified this error by running:

docker run --rm -it quay.io/biocontainers/civicpy:5.0.0--pyhdfd78af_0 bash
pip list | grep backports

This is not an issue in the 4.1.0--pyhdfd78af_0 container:

docker run --rm -it quay.io/biocontainers/civicpy:4.1.0--pyhdfd78af_0 bash
root@c066e5e0a2d6:/# pip list | grep backports
backports-datetime-fromisoformat 2.0.0

Would it be possible to update the container to include this missing dependency? Alternatively, if there’s a recommended workaround or a different image I should be using, please let me know.

Thanks so much for your work on this tool!

[susannasiebert]

This very strange. The Docker hub Docker image doesn't have this problem.

$ docker run -it griffithlab/civicpy:5.0.0 /bin/bash
root@f295583544da:/# pip list | grep backports
backports-datetime-fromisoformat 2.0.3

I'm not sure who generates the quay.io biocontainers because I don't think it's something done on our end. I'll ask around.