Changing python's upper limit version to python<3.12

[axiomcura]

Description

Thank you for your contribution to CytoTable!
Please succinctly summarize your proposed change.
What motivated you to make this change?

This PR addresses the current compatibility issues between duckdb and Python 3.12. As duckdb does not yet support Python 3.12, it is best to downgrade the upper limit of the Python version in the environment poetry.lock file.

Below is the current issue

Issue mentioned: duckdb/duckdb#9301 (comment)
Current PR (however closed) : duckdb/duckdb#9222

Changes:

• Downgrade the upper limit Python version to Python <3.12 to maintain compatibility with duckdb.

Additionally, I have written an issue explaining why Python >3.12 does not work with DuckDB, which directly impacts the installation of CytoTable. #157

Please also link to any relevant issues that your code is associated with.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

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• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
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[d33bs]

Thanks @axiomcura ! Looks great. Before an approval, could you make sure there are no changes to the poetry.lock file as a result of this change (adding those changes here if there are any updates)?

[axiomcura]

Hello @d33bs Just check my editor and no changes that being shown in the poetry.lock file.

[d33bs]

Hi @axiomcura , thanks for checking. When updates are made to the project.toml dependencies (including the Python version) there typically are lockfile updates to be made. These manifest when running poetry install among other places. I recommend running poetry lock --no-update to help observe any possible changes.

[kenibrewer]

@d33bs we experimented with some of the poetry precommit checks right? I can't remember which ones we used and why we removed them. I've been using the poetry lock hook in other repos more recently and it works well and would catch this pretty common miss.

…

On Tue, Feb 13, 2024 at 14:45 Dave Bunten ***@***.***> wrote: Hi @axiomcura <https://github.com/axiomcura> , thanks for checking. When updates are made to the project.toml dependencies (including the Python version) there typically are lockfile updates to be made. These manifest when running poetry install among other places. I recommend running poetry lock --no-update to help observe any possible changes. — Reply to this email directly, view it on GitHub <#158 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEFHAFKGAIZ2CXB64K25SDTYTNVANAVCNFSM6AAAAABDC6ODRCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBRGU2TGNZXGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[d33bs]

Thanks @kenibrewer ! I think it's a good idea to include Poetry pre-commit checks for the lockfile! I have a vague recollection there may have been slight inconsistency between Poetry lockfiles from OS to OS (for example, MacOS vs Ubuntu Linux), incurring an "endless loop" of pre-commit check fix-failures. Either way, it'd be great to have this functionality if we can get it working! I'll add an issue to this effect.

[d33bs]

Hi @axiomcura - I wanted to double check whether you were able to adjust the lockfile with the updates related to your changes. Please don't hesitate to let me know if I may assist.

[axiomcura]

Hey @d33bs sorry for the late response, Just ran poetry lock no-update there are some changes. Would you like me to push those changes into this PR?

[d33bs]

Hi @axiomcura, no worries at all - I suggest updating your forked branch at axiomcura:python3.11-upperlimit from cytomining:main, re-running poetry lock --no-update, and checking that pre-commit run -a passes.

[axiomcura]

@d33bs poetry-lock file update added!

[d33bs]

Hi @axiomcura, thanks! It looks like your forked branch has a conflict that we need to address before merging. Could you update your forked branch from cytomining:main and re-run poetry lock --no-update (checking that all pre-commit run -a also passes)?

[axiomcura]

@d33bs I have updated my branch and reran poetry lock --no-update should work now!

[d33bs]

Thanks @axiomcura - LGTM! Appreciate your help with this! Please feel free to squash + merge when ready.

[axiomcura]

Merging! Thank you!