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cytomining / pycytominer

Python package for processing image-based profiling data
https://pycytominer.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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build(deps): bump sqlalchemy from 1.4.52 to 2.0.36; move to sqlalchemy.text for queries #469

Closed dependabot[bot] closed 3 weeks ago

dependabot[bot] commented 4 weeks ago

Bumps sqlalchemy from 1.4.52 to 2.0.36.

Release notes

Sourced from sqlalchemy's releases.

2.0.36

Released: October 15, 2024

orm

  • [orm] [usecase] Added new parameter _orm.mapped_column.hash to ORM constructs such as _orm.mapped_column(), _orm.relationship(), etc., which is interpreted for ORM Native Dataclasses in the same way as other dataclass-specific field parameters.

    References: #11923

  • [orm] [bug] Fixed bug in ORM bulk update/delete where using RETURNING with bulk update/delete in combination with populate_existing would fail to accommodate the populate_existing option.

    References: #11912

  • [orm] [bug] Continuing from #11912, columns marked with mapped_column.onupdate, mapped_column.server_onupdate, or Computed are now refreshed in ORM instances when running an ORM enabled UPDATE with WHERE criteria, even if the statement does not use RETURNING or populate_existing.

    References: #11917

  • [orm] [bug] Fixed regression caused by fixes to joined eager loading in #11449 released in 2.0.31, where a particular joinedload case could not be asserted correctly. We now have an example of that case so the assertion has been repaired to allow for it.

    References: #11965

  • [orm] [bug] Improved the error message emitted when trying to map as dataclass a class while also manually providing the __table__ attribute. This usage is currently not supported.

    References: #11973

  • [orm] [bug] Refined the check which the ORM lazy loader uses to detect "this would be loading by primary key and the primary key is NULL, skip loading" to take into account the current setting for the orm.Mapper.allow_partial_pks parameter. If this parameter is False, then a composite PK value that has partial NULL elements should also be skipped. This can apply to some composite overlapping foreign key configurations.

... (truncated)

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📚 Documentation preview 📚: https://pycytominer--469.org.readthedocs.build/en/469/

codecov-commenter commented 3 weeks ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 94.73%. Comparing base (83956c1) to head (fe5eead).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #469 +/- ## ========================================== - Coverage 94.73% 94.73% -0.01% ========================================== Files 57 57 Lines 3155 3154 -1 ========================================== - Hits 2989 2988 -1 Misses 166 166 ``` | [Flag](https://app.codecov.io/gh/cytomining/pycytominer/pull/469/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/cytomining/pycytominer/pull/469/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining) | `94.73% <100.00%> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=cytomining#carryforward-flags-in-the-pull-request-comment) to find out more.

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d33bs commented 3 weeks ago

Hi @gwaybio and @kenibrewer - I made some additional changes here to help pass tests. When there's a chance could I ask for your review of the work (since I've added to what Dependabot changed)?

kenibrewer commented 3 weeks ago

@d33bs Can we remove this line with this addition? https://github.com/cytomining/pycytominer/blob/3f82cc400bb5ff4df3b754ede41878540707c334/.github/workflows/integration-test.yml#L97

d33bs commented 3 weeks ago

Thanks @kenibrewer ! I removed the line you mentioned as I think you're correct, it would no longer apply.

d33bs commented 3 weeks ago

Thanks @kenibrewer and @gwaybio for the reviews! Merging this in.