setuptools and use_2to3

[jeramiahsmith]

Wanted to bring up a minor issues with completing an install of the precompiled binary. It looks like an upgrade of setuptools lost compatibility with some code involving " use_2to3 " using the default version that's installed by pip. changing to setuptools==57 seems to fix the issue though.

[glennhickey]

Yeah, thanks. I guess we should probably document this better -- we've had to make a similar change in our CI scripts here
https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/.gitlab-ci.yml#L28-L32

I think this is on the Toil side (@adamnovak ?) but, if I'm not mistaken, only seems to affect some buggy Python versions?

[jeramiahsmith]

Cool, I was sort of blindly following the instructions here https://github.com/ComparativeGenomicsToolkit/cactus/blob/v2.0.3/BIN-INSTALL.md Don't know if it might be useful to adjust those. but regardless it seems to be working and I'm looking to get the GPU version running on our bigger cluster.

…

On Fri, Nov 12, 2021 at 1:21 PM Glenn Hickey ***@***.***> wrote: Yeah, thanks. I guess we should probably document this better -- we've had to make a similar change in our CI scripts here https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/.gitlab-ci.yml#L28-L32 I think this is on the Toil side ***@***.*** <https://github.com/adamnovak> ?) but, if I'm not mistaken, only seems to affect some buggy Python versions? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#599 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALTZ545BCGVSDCKIJMVHF2LULVLKVANCNFSM5H5MGAUA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

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[adamnovak]

I'm not sure what the issue is on the Toil side here. On Ubuntu 20.04, using the system Python 3.8, doing virtualenv --python python3 venv, . venv/bin/activate, and pip install toil produces an apparently-working Toil for me (although it does complain that some of the dependencies' dependencies conflict, which is tracked in DataBiosphere/toil#3889).

It looks like use_2to3 is dead on purpose and will never work again; is there a package in the Toil dependency tree that needs it that Cactus wants us to rip out?

[glennhickey]

This should be fixed in the latest release, which uses a newer python/toil. Please open again if it isn't.