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Container using system packages

See original GitHub issue

When running a sorter using run_sorter_container some system volumens are mounted. On ubuntu and using singularity this can lead to the system installation of spikeinterface (e.g. in ~.local/pythonX.X/site-packages) to shadow the spikeinterface version installed in the container. This can lead to confusing version conflicts, but can also be used to provide the container with a specific spikeinterface version. Is this an intended feature or a bug? In the first case it might be good to add a warning if the container internal spikeinterface version is shadowed by the system version.

Issue Analytics

State:
Created a year ago
Comments:6 (6 by maintainers)

Top GitHub Comments

1reaction

chyumincommented, Sep 13, 2022

I believe we don’t have spikeinterface installed in any docker image, so it should always try to install, no?

What happens is that one of the system volumes that is binded in singularity mode is the host’s $HOME folder, so one of the paths that Python searches for (and installs) packages is /home/<user>/.local/pythonX.X/site-packages, so when running in singularity mode it turns out that Python inside container also shares this folder with the host. Which I believe is not desired and also doesn’t happen in docker mode

1reaction

samuelgarciacommented, Sep 13, 2022

Hi Yu Min, I am OK with the patch you did. What I do not understand in that case of Julia is why we try to install spikeinterface package in the container when it is already installed. This should not happen. Am I missing something ?

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