UPDATE: SQLAlchemy 2.0

[jzluo]

As mentioned in #92, SQLAlchemy is pinned to <1.5. All tests pass with SQLAlchemy 2.0.6 - the only SQLAlchemy warning is:

jupyter_cache/cache/db.py:17
  /home/jon/projects/jupyter-cache/jupyter_cache/cache/db.py:17: MovedIn20Warning: The ``declarative_base()`` 
function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 1.4) (Background on 
SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
    OrmBase = declarative_base()

because of https://docs.sqlalchemy.org/en/20/changelog/migration_14.html#change-5508. sqlalchemy.ext.declarative.declarative_base is still present.

[welcome]

Thanks for submitting your first pull request! You are awesome! 🤗

If you haven't done so already, check out EBP's Code of Conduct and our Contributing Guide, as this will greatly help the review process.

Welcome to the EBP community! 🎉

[jzluo]

@choldgraf apologies for the ping - I saw that you were the reviewer for a similar PR about SQLAlchemy 1.4. Do you have an estimate for when someone can check this PR or create a different solution? Currently projects can't use myst-nb and SQLAlchemy 2.

[jzluo]

@chrisjsewell could we get eyes on this? Thank you

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.02 ⚠️

Comparison is base (47e90f4) 83.32% compared to head (894bb29) 83.30%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #93      +/-   ##
==========================================
- Coverage   83.32%   83.30%   -0.02%     
==========================================
  Files          20       20              
  Lines        1355     1354       -1     
==========================================
- Hits         1129     1128       -1     
  Misses        226      226              

Flag	Coverage Δ
pytests	83.30% <100.00%> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
jupyter_cache/cache/db.py	85.39% <100.00%> (-0.06%)	⬇️

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

[choldgraf]

LGTM as long as the tests are happy 👍 . Does sqalchemy often make breaking changes at minor versions? If not, then why not pin it to <3.0?

[jzluo]

LGTM as long as the tests are happy 👍 . Does sqalchemy often make breaking changes at minor versions? If not, then why not pin it to <3.0?

Thanks! Was just following the PR for supporting 1.4 where you mentioned preference for pinning to minor versions. I'm not sure if sqlalchemy had a history of making breaking changes at minor versions, but I think pinning to <3.0 should be fine. What do you think would be best?

[jzluo]

@choldgraf @chrisjsewell sorry for the ping again - I think it's important to resolve this quickly as it prevents projects that use myst-nb from using sqlalchemy 2.0.

[choldgraf]

I'll try to take a look this weekend if I have a moment. In the meantime it'd be helpful if you made the modifications to the codebase to avoid the new warning that pops up. Not crucial but it'd be helpful since we'll need to do that at some point anyway

[choldgraf]

LGTM thanks! Appreciate the extra fix to get rid of the warning 👍

[welcome]

Congrats on your first merged pull request in this project! 🎉


Thank you for contributing, we are very proud of you! ❤️

[jzluo]

Thank you Chris!

[DimitriPapadopoulos]

Updating jupyter_cache from 0.5.0 to 0.6.0 breaks the “stable (ubuntu-latest, 3.8, pip, doc)” CI test of bids-standard/pybids with:

ImportError: cannot import name 'declarative_base' from 'sqlalchemy.orm' (/home/runner/work/pybids/pybids/virtenv/lib/python3.8/site-packages/sqlalchemy/orm/__init__.py)

See https://github.com/bids-standard/pybids/actions/runs/4767649000/jobs/8476115124

It is unclear from the logs which version of SQLAlchemy we use. Most probably python3-sqlalchemy 1.4.31 which is bundled with Ubuntu 22.04.

[choldgraf]

Ah i bet you're using old version of sqlalchemy. Given that sqlalchemy 2 is still less than a year old we should try to support both for a bit. We should have used a try/except block for the import instead of just changing it. If somebody wants to make a quick PR (@jzluo ?) Im happy to review and cut a quick patch release

[DimitriPapadopoulos]

You're correct, from pybids/pyproject.toml:

  "sqlalchemy <1.4.0.dev0",

Perhaps we should update. I'll look into why we need SQLAlchemy < 1.4.0.

[DimitriPapadopoulos]

In the meantime, see PR #105 for compatibility with SQLAlchemy 1.3.