Update to Python 3.11 (3.7 end of life)

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

https://balsamic.readthedocs.io/

MIT License

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Update to Python 3.11 (3.7 end of life) #1169

Closed ivadym closed 1 year ago

ivadym commented 1 year ago

Need

Balsamic is currently built using Python version 3.7, which is reaching its end of life (27 Jun 2023).

Considered alternatives

The alternative involves maintaining the current Python 3.7 version. However, this approach is risky in terms of compatibility with future developments, lack of security updates, and limited access to the latest Python features.

Can be closed when

[ ] Perform compatibility evaluation and decide on the new Python version.
[ ] Analyse the current Balsamic's codebase to identify any potential issues that might arise during the migration process and update dependencies (also Balsamic container).
[ ] Update documentation.

pbiology commented 1 year ago

I agree that maintaining a deprecated python version seems quite tricky.
To what version should we upgrade?

ivadym commented 1 year ago

I would say the latest which doesn't break the workflow and rendering of the documentation

@khurrammaqbool mentioned some time ago that he run successfully Balsamic with python 3.10. I could do some more testing including the docs generation.

Python 3.11 is also interesting since it includes Support for parsing TOML in the Standard Library

pbiology commented 1 year ago

Would there be any issues on the hasta side of things to use a higher version?

ivadym commented 1 year ago

I don't think so. Having a specific Balsamic environment (P_balsamic/S_balsamic) isolates it from the rest of the tools we have. But we would need to bump some tools versions according to the python version we choose

ivadym commented 1 year ago

Done. S_balsamic has been updated accordingly FYI @Clinical-Genomics/cancer-bioinfo.