RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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Need to Upgrade from Python 3.7 #379

Open ecwood opened 4 months ago

ecwood commented 4 months ago

While working on #378, I found this error: (see run https://github.com/RTXteam/RTX-KG2/actions/runs/9669257959/job/26675319107)

NEEDRESTART-KEXP: 6.5.0-1022-azure
NEEDRESTART-KSTA: 1
++ curl -s -k https://bootstrap.pypa.io/get-pip.py -o /tmp/get-pip.py
++ apt-get download python3-distutils
Get:1 file:/etc/apt/apt-mirrors.txt Mirrorlist [142 B]
Get:2 http://azure.archive.ubuntu.com/ubuntu jammy-updates/main amd64 python3-distutils all 3.10.8-1~22.04 [139 kB]
Fetched 139 kB in 0s (1126 kB/s)
++ '[' -f python3-distutils_3.6.9-1~18.04_all.deb ']'
++ '[' -f python3-distutils_3.8.10-0ubuntu1~20.04_all.deb ']'
++ '[' -f python3-distutils_3.10.6-1~22.04_all.deb ']'
++ '[' -f python3-distutils_3.10.8-1~22.04_all.deb ']'
++ python3_distutils_filename=python3-distutils_3.10.8-1~22.04_all.deb
++ mv python3-distutils_3.10.8-1~22.04_all.deb /tmp
++ sudo dpkg-deb -x /tmp/python3-distutils_3.10.8-1~22.04_all.deb /
++ sudo -H python3.7 /tmp/get-pip.py
++ grep -v 'WARNING: Running pip as the '\''root'\'' user'
ERROR: This script does not work on Python 3.7 The minimum supported Python version is 3.8. Please use https://bootstrap.pypa.io/pip/3.7/get-pip.py instead.

It looks like we need to update to at least Python 3.8. Should we upgrade more than that, @saramsey? (The latest version of Python is 3.12).

ecwood commented 4 months ago

I was able to fix this by downloading https://bootstrap.pypa.io/pip/3.7/get-pip.py instead. However, this seems like a temporary fix.

ecwood commented 4 months ago

This is also causing issues with Dependabot:

https://github.com/RTXteam/RTX-KG2/security/dependabot/19 https://github.com/RTXteam/RTX-KG2/security/dependabot/9

(See commits f2fb19b and 80266d9)

ecwood commented 4 months ago

Also, see: https://github.com/RTXteam/RTX/issues/2290

saramsey commented 4 weeks ago

I think we really should look into upgrading the build system so that it can be run on a modern version of cpython. Marking high priority.