CODEX-CELIDA / execution-engine

Execution engine for mapping clinical guideline recommendations on OMOP CDM patient data
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chore(deps): bump the dependencies group with 5 updates #226

Closed dependabot[bot] closed 4 weeks ago

dependabot[bot] commented 4 weeks ago

Bumps the dependencies group with 5 updates:

Package From To
sqlalchemy 2.0.35 2.0.36
pydantic-settings 2.5.2 2.6.0
uvicorn[standard] 0.31.1 0.32.0
networkx 3.4.1 3.4.2
setuptools 75.1.0 75.2.0

Updates sqlalchemy from 2.0.35 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)

Commits


Updates pydantic-settings from 2.5.2 to 2.6.0

Release notes

Sourced from pydantic-settings's releases.

v2.6.0

What's Changed

New Contributors

Full Changelog: https://github.com/pydantic/pydantic-settings/compare/v2.5.2...v2.6.0

Commits
  • eeea989 Prepare release 2.6.0 (#444)
  • a72fa73 Fix bug in dotenv source when there is env with and without prefix (#440)
  • d2e498a Add support for suppressing fields from CLI help. (#436)
  • 0d605d0 Update nested model partial update docs example. (#433)
  • 8f7653c Put tests for non-default sources in separate files (#429)
  • f3a25f2 Fix a regression in dotenv optional nested field (#423)
  • 76ba2c6 Fix context not passed to field validators bug (#417)
  • 84cab2b Add CLI App Support (#389)
  • fdd666b Fix nested model AliasChoices in validation alias (#411)
  • 9b73e92 Add cli_flag_prefix_char config option. (#418)
  • Additional commits viewable in compare view


Updates uvicorn[standard] from 0.31.1 to 0.32.0

Release notes

Sourced from uvicorn[standard]'s releases.

Version 0.32.0

Added

  • Officially support Python 3.13 (#2482)
  • Warn when max_request_limit is exceeded (#2430)

Full Changelog: https://github.com/encode/uvicorn/compare/0.31.1...0.32.0

Changelog

Sourced from uvicorn[standard]'s changelog.

0.32.0 (2024-10-15)

Added

  • Officially support Python 3.13 (#2482)
  • Warn when max_request_limit is exceeded (#2430)
Commits


Updates networkx from 3.4.1 to 3.4.2

Release notes

Sourced from networkx's releases.

NetworkX 3.4.2

We're happy to announce the release of networkx 3.4.2!

Bug Fixes

  • Fix docstrings of dispatchable functions (#7679).
  • Fix draw_networkx_nodes return type (#7685).

Documentation

  • Add disclaimer about LLM driven PRs (#7683).

Maintenance

  • Fix doc warnings from recently added docs (#7682).

Contributors

6 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

These lists are automatically generated, and may not be complete or may contain duplicates.

Commits


Updates setuptools from 75.1.0 to 75.2.0

Changelog

Sourced from setuptools's changelog.

v75.2.0

Features

  • Made errors when parsing Distribution data more explicit about the expected type (tuple[str, ...] | list[str]) -- by :user:Avasam (#4578)

Bugfixes

  • Fix a TypeError when a Distribution's old included attribute was a tuple -- by :user:Avasam (#4578)
  • Add workaround for bdist_wheel --dist-info-dir errors when customisation does not inherit from setuptools. (#4684)

v75.1.1

Bugfixes

  • Re-use pre-existing .dist-info dir when creating wheels via the build backend APIs (PEP 517) and the metadata_directory argument is passed -- by :user:pelson. (#1825)
  • Changed egg_info command to avoid adding an empty .egg-info directory while iterating over entry-points. This avoids triggering integration problems with importlib.metadata/importlib_metadata (reference: pypa/pyproject-hooks#206). (#4680)
Commits
  • 61a5a03 Bump version: 75.1.1 → 75.2.0
  • 8ad3ea7 Workaround for bdist_wheel.dist_info_dir problems (#4684)
  • 9af0877 Type sequence checks in setuptools/dist.py (#4578)
  • 0534fde Add news fragment
  • 50b732a Check for more specific error message
  • a663287 Add pragma for edge-case code path
  • 96be735 Workaround for bdist_wheel.dist_info_dir problems
  • 000a413 Deprecate public access to setuptools.dist.sequence
  • 00995c1 Use variable msg instead of tmpl in setuptools/dist
  • d457d0e Type sequence checks in setuptools/dist.py
  • Additional commits viewable in compare view


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