ubuntu 18.04 support (GLIBC >= 2.28)

[toloudis]

Describe the Bug

Multiple users have reported crashes due to dependency conflicts related to requiring GLIBC version 2.28 or greater. Ubuntu 18.04 only seems to supports up to glibc 2.27.

Expected Behavior

need to examine our dependencies for bioio and bioio-base, and maybe readers too. Decide if we can possibly support this older version of ubuntu. Make a clear statement in our documentation either way.

[SeanDuHare]

If the crashes occur on a version of GLIBC that is required by Ubuntu 18.04 what would supporting 18.04 look like? That seems like a third-party issue if I'm understanding this

[toloudis]

If the crashes occur on a version of GLIBC that is required by Ubuntu 18.04 what would supporting 18.04 look like? That seems like a third-party issue if I'm understanding this

pinning dependency versions, and/or making a special bioio build.

Or just deciding that we wont support it.. but this the version our slurm cluster is on at the moment.

[pgarrison]

Matheus's stacktrace here suggests to me that scikit-image is the dependency responsible for this issue (or one of them).

When I try to install scikit-image 0.23.0 on our SLURM cluster I can reproduce Matheus's error. Other scikit-image versions install without error.

scikit-image 0.23.0 was yanked from PyPi due to improperly built wheels. But due to a known issue with our internal AICS Artifactory instance, packages yanked from PyPi are not yanked from Artifactory. This issue should therefore only affect internal AICS users.

scikit-image is not a direct dependency of bioio, so I think this is not bioio's responsibility.

Instead, while we wait for a fix to Artifactory, AICS users can either:

• specify scikit-image != 0.23.0 for downstream projects, or
• configure pip to use PyPi instead of Artifactory.

[toloudis]

That's great news. Thanks for starting to examine this. Can we do some kind of test with Matheus or others' use case, to confirm that it's scikit-image? Also I think infra does intend to update ubuntu on the cluster eventually but idk when.

[pgarrison]

I failed to reproduce the original error.

I was able to successfully install the latest bioio on our SLURM cluster (Ubuntu 18.04.4) using the following pyproject.toml.

[project]
name = "bioio-test"
version = "0.0.0"
requires-python = ">=3.9"
dependencies = [
    "bioio>=1.1",
]

For reference, I got scikit-image 0.22.0.