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@dependabot dependabot bot commented on behalf of github Jan 1, 2026

Bumps the python-packages group with 9 updates in the / directory:

Package From To
nmdc-api-utilities 0.4.2 0.6.0
pydantic-settings 2.10.1 2.12.0
pymongo 4.14.1 4.15.5
scalar-fastapi 1.4.1 1.5.0
uvicorn 0.35.0 0.40.0
pre-commit 4.3.0 4.5.1
pyright 1.1.404 1.1.407
pytest 8.4.1 9.0.2
ruff 0.12.11 0.14.10

Updates nmdc-api-utilities from 0.4.2 to 0.6.0

Updates pydantic-settings from 2.10.1 to 2.12.0

Release notes

Sourced from pydantic-settings's releases.

v2.12.0

What's Changed

New Contributors

Full Changelog: pydantic/pydantic-settings@v2.11.0...v2.12.0

v2.11.0

What's Changed

New Contributors

Full Changelog: pydantic/pydantic-settings@2.10.1...v2.11.0

Commits

Updates pymongo from 4.14.1 to 4.15.5

Release notes

Sourced from pymongo's releases.

PyMongo 4.15.5

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-5-released/332185

PyMongo 4.15.4

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-4-released/331292

PyMongo 4.15.3

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-3-released/329778

PyMongo 4.15.2

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-2-released/329543

PyMongo 4.15.1

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-1-released/328837

PyMongo 4.15.0

Community notes: https://www.mongodb.com/community/forums/t/pymongo-4-15-released/328574

Changelog

Sourced from pymongo's changelog.

Changes in Version 4.15.5 (2025/12/02)

Version 4.15.5 is a bug fix release.

  • Fixed a bug that could cause AutoReconnect("connection pool paused") errors when cursors fetched more documents from the database after SDAM heartbeat failures.

Changes in Version 4.15.4 (2025/10/21)

Version 4.15.4 is a bug fix release.

  • Relaxed the callback type of :meth:~pymongo.asynchronous.client_session.AsyncClientSession.with_transaction to allow the broader Awaitable type rather than only Coroutine objects.
  • Added the missing Python 3.14 trove classifier to the package metadata.

Issues Resolved ...............

See the PyMongo 4.15.4 release notes in JIRA_ for the list of resolved issues in this release.

.. _PyMongo 4.15.4 release notes in JIRA: https://jira.mongodb.org/secure/ReleaseNote.jspa?projectId=10004&version=47237

Changes in Version 4.15.3 (2025/10/07)

Version 4.15.3 is a bug fix release.

  • Fixed a memory leak when raising :class:bson.errors.InvalidDocument with C extensions.
  • Fixed the return type of the :meth:~pymongo.asynchronous.collection.AsyncCollection.distinct, :meth:~pymongo.synchronous.collection.Collection.distinct, :meth:pymongo.asynchronous.cursor.AsyncCursor.distinct, and :meth:pymongo.asynchronous.cursor.AsyncCursor.distinct methods.

Issues Resolved ...............

See the PyMongo 4.15.3 release notes in JIRA_ for the list of resolved issues in this release.

.. _PyMongo 4.15.3 release notes in JIRA: https://jira.mongodb.org/secure/ReleaseNote.jspa?projectId=10004&version=47293

Changes in Version 4.15.2 (2025/10/01)

Version 4.15.2 is a bug fix release.

  • Add wheels for Python 3.14 and 3.14t that were missing from 4.15.0 release. Drop the 3.13t wheel.

Issues Resolved ...............

... (truncated)

Commits
  • 7a8420c PYTHON-5642 Prep for 4.15.5 patch release. (#2633)
  • 0480525 [v4.15] PYTHON-5642 - getMore operations should do server selection if the se...
  • dfecbdb BUMP 4.15.5.dev0
  • 07d51b1 PYTHON-5639 Prep for 4.15.4 release (#2614)
  • 477217f [TASK]-[PYTHON-5623]: [v4.15] Change with_transaction callback return type to...
  • f3ea373 PYTHON-5624 - Add Python 3.14 trove classifier (#2593)
  • a5a50a8 BUMP 4.15.4.dev0
  • 6116811 PYTHON-5609 Prepare for 4.15.3 Release (#2584)
  • fef10d2 PYTHON-5596 Fix return type for distinct methods (#2576) [v4.15] (#2583)
  • 039c35b [v4.15] PYTHON-5571 - Fix memory leak when raising InvalidDocument with C ext...
  • Additional commits viewable in compare view

Updates scalar-fastapi from 1.4.1 to 1.5.0

Release notes

Sourced from scalar-fastapi's releases.

Release 2025-12-23

Releases

@​scalar/aspnetcore@​2.11.10

Patch Changes

  • #7609: fix: escape request path

Release 2025-12-21

Releases

@​scalar/nuxt@​0.5.35

Patch Changes

Updated Dependencies

  • @​scalar/api-client@​2.17.1

    • #7562: feat(components): remove headless ui from dropdown component
  • @​scalar/api-reference@​1.40.9

@​scalar/api-client@​2.17.1

Patch Changes

  • #7562: feat(components): remove headless ui from dropdown component

Updated Dependencies

  • @​scalar/components@​0.16.12

    • #7562: feat(components): remove headless ui from dropdown component
  • @​scalar/sidebar@​0.7.2

    • #7562: feat(components): remove headless ui from dropdown component
  • @​scalar/use-codemirror@​0.13.6

@​scalar/api-client-react@​1.3.59

Patch Changes

Updated Dependencies

  • @​scalar/api-client@​2.17.1
    • #7562: feat(components): remove headless ui from dropdown component

@​scalar/api-reference@​1.40.9

Patch Changes

... (truncated)

Commits

Updates uvicorn from 0.35.0 to 0.40.0

Release notes

Sourced from uvicorn's releases.

Version 0.40.0

What's Changed

Full Changelog: Kludex/uvicorn@0.39.0...0.40.0

Version 0.39.0

What's Changed

New Contributors

Full Changelog: Kludex/uvicorn@0.38.0...0.39.0

Version 0.38.0

What's Changed


New Contributors

Full Changelog: Kludex/uvicorn@0.37.0...0.38.0

Version 0.37.0

What's Changed

New Contributors

Full Changelog: Kludex/uvicorn@0.36.1...0.37.0

Version 0.36.1

What's Changed

Full Changelog: Kludex/uvicorn@0.36.0...0.36.1

Version 0.36.0

Added

... (truncated)

Changelog

Sourced from uvicorn's changelog.

0.40.0 (December 21, 2025)

Remove

  • Drop support for Python 3.9 (#2772)

0.39.0 (December 21, 2025)

Fixed

  • Send close frame on ASGI return for WebSockets (#2769)
  • Explicitly start ASGI run with empty context (#2742)

0.38.0 (October 18, 2025)

Added

  • Support Python 3.14 (#2723)

0.37.0 (September 23, 2025)

Added

  • Add --timeout-worker-healthcheck option (#2711)
  • Add os.PathLike[str] type to ssl_ca_certs (#2676)

0.36.1 (September 23, 2025)

Fixed

  • Raise an exception when calling removed Config.setup_event_loop() (#2709)

0.36.0 (September 20, 2025)

Added

  • Support custom IOLOOPs (#2435)
  • Allow to provide importable string in --http, --ws and --loop (#2658)
Commits

Updates pre-commit from 4.3.0 to 4.5.1

Release notes

Sourced from pre-commit's releases.

pre-commit v4.5.1

Fixes

  • Fix language: python with repo: local without additional_dependencies.

pre-commit v4.5.0

Features

pre-commit v4.4.0

Features

Fixes

Changelog

Sourced from pre-commit's changelog.

4.5.1 - 2025-12-16

Fixes

  • Fix language: python with repo: local without additional_dependencies.

4.5.0 - 2025-11-22

Features

4.4.0 - 2025-11-08

Features

Fixes

Commits
  • 8a0630c v4.5.1
  • fcbc745 Merge pull request #3597 from pre-commit/empty-setup-py
  • 51592ee fix python local template when artifact dirs are present
  • 67e8faf Merge pull request #3596 from pre-commit/pre-commit-ci-update-config
  • c251e6b [pre-commit.ci] pre-commit autoupdate
  • 98ccafa Merge pull request #3593 from pre-commit/pre-commit-ci-update-config
  • 4895355 [pre-commit.ci] pre-commit autoupdate
  • 2cedd58 Merge pull request #3588 from pre-commit/pre-commit-ci-update-config
  • 465192d [pre-commit.ci] pre-commit autoupdate
  • fd42f96 Merge pull request #3586 from pre-commit/zipapp-sha256-file-not-needed
  • Additional commits viewable in compare view

Updates pyright from 1.1.404 to 1.1.407

Commits

Updates pytest from 8.4.1 to 9.0.2

Release notes

Sourced from pytest's releases.

9.0.2

pytest 9.0.2 (2025-12-06)

Bug fixes

  • #13896: The terminal progress feature added in pytest 9.0.0 has been disabled by default, except on Windows, due to compatibility issues with some terminal emulators.

    You may enable it again by passing -p terminalprogress. We may enable it by default again once compatibility improves in the future.

    Additionally, when the environment variable TERM is dumb, the escape codes are no longer emitted, even if the plugin is enabled.

  • #13904: Fixed the TOML type of the tmp_path_retention_count settings in the API reference from number to string.

  • #13946: The private config.inicfg attribute was changed in a breaking manner in pytest 9.0.0. Due to its usage in the ecosystem, it is now restored to working order using a compatibility shim. It will be deprecated in pytest 9.1 and removed in pytest 10.

  • #13965: Fixed quadratic-time behavior when handling unittest subtests in Python 3.10.

Improved documentation

  • #4492: The API Reference now contains cross-reference-able documentation of pytest's command-line flags <command-line-flags>.

9.0.1

pytest 9.0.1 (2025-11-12)

Bug fixes

  • #13895: Restore support for skipping tests via raise unittest.SkipTest.
  • #13896: The terminal progress plugin added in pytest 9.0 is now automatically disabled when iTerm2 is detected, it generated desktop notifications instead of the desired functionality.
  • #13904: Fixed the TOML type of the verbosity settings in the API reference from number to string.
  • #13910: Fixed UserWarning: Do not expect file_or_dir on some earlier Python 3.12 and 3.13 point versions.

Packaging updates and notes for downstreams

  • #13933: The tox configuration has been adjusted to make sure the desired version string can be passed into its package_env through the SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYTEST environment variable as a part of the release process -- by webknjaz.

Contributor-facing changes

  • #13891, #13942: The CI/CD part of the release automation is now capable of creating GitHub Releases without having a Git checkout on disk -- by bluetech and webknjaz.
  • #13933: The tox configuration has been adjusted to make sure the desired version string can be passed into its package_env through the SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYTEST environment variable as a part of the release process -- by webknjaz.

... (truncated)

Commits
  • 3d10b51 Prepare release version 9.0.2
  • 188750b Merge pull request #14030 from pytest-dev/patchback/backports/9.0.x/1e4b01d1f...
  • b7d7bef Merge pull request #14014 from bluetech/compat-note
  • bd08e85 Merge pull request #14013 from pytest-dev/patchback/backports/9.0.x/922b60377...
  • bc78386 Add CLI options reference documentation (#13930)
  • 5a4e398 Fix docs typo (#14005) (#14008)
  • d7ae6df Merge pull request #14006 from pytest-dev/maintenance/update-plugin-list-tmpl...
  • 556f6a2 pre-commit: fix rst-lint after new release (#13999) (#14001)
  • c60fbe6 Fix quadratic-time behavior when handling unittest subtests in Python 3.10 ...
  • 73d9b01 Merge pull request #13995 from nicoddemus/patchback/backports/9.0.x/1b5200c0f...
  • Additional commits viewable in compare view

Updates ruff from 0.12.11 to 0.14.10

Release notes

Sourced from ruff's releases.

0.14.10

Release Notes

Released on 2025-12-18.

Preview features

  • [formatter] Fluent formatting of method chains (#21369)
  • [formatter] Keep lambda parameters on one line and parenthesize the body if it expands (#21385)
  • [flake8-implicit-str-concat] New rule to prevent implicit string concatenation in collections (ISC004) (#21972)
  • [flake8-use-pathlib] Make fixes unsafe when types change in compound statements (PTH104, PTH105, PTH109, PTH115) (#22009)
  • [refurb] Extend support for Path.open (FURB101, FURB103) (#21080)

Bug fixes

  • [pyupgrade] Fix parsing named Unicode escape sequences (UP032) (#21901)

Rule changes

  • [eradicate] Ignore ruff:disable and ruff:enable comments in ERA001 (#22038)
  • [flake8-pytest-style] Allow match and check keyword arguments without an expected exception type (PT010) (#21964)
  • [syntax-errors] Annotated name cannot be global (#20868)

Documentation

  • Add uv and ty to the Ruff README (#21996)
  • Document known lambda formatting deviations from Black (#21954)
  • Update setup.md (#22024)
  • [flake8-bandit] Fix broken link (S704) (#22039)

Other changes

  • Fix playground Share button showing "Copied!" before clipboard copy completes (#21942)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.14.10

Released on 2025-12-18.

Preview features

  • [formatter] Fluent formatting of method chains (#21369)
  • [formatter] Keep lambda parameters on one line and parenthesize the body if it expands (#21385)
  • [flake8-implicit-str-concat] New rule to prevent implicit string concatenation in collections (ISC004) (#21972)
  • [flake8-use-pathlib] Make fixes unsafe when types change in compound statements (PTH104, PTH105, PTH109, PTH115) (#22009)
  • [refurb] Extend support for Path.open (FURB101, FURB103) (#21080)

Bug fixes

  • [pyupgrade] Fix parsing named Unicode escape sequences (UP032) (#21901)

Rule changes

  • [eradicate] Ignore ruff:disable and ruff:enable comments in ERA001 (#22038)
  • [flake8-pytest-style] Allow match and check keyword arguments without an expected exception type (PT010) (#21964)
  • [syntax-errors] Annotated name cannot be global (#20868)

Documentation

  • Add uv and ty to the Ruff README (#21996)
  • Document known lambda formatting deviations from Black (#21954)
  • Update setup.md (#22024)
  • [flake8-bandit] Fix broken link (S704) (#22039)

Other changes

  • Fix playground Share button showing "Copied!" before clipboard copy completes (#21942)

Contributors

0.14.9

... (truncated)

Commits
  • 45bbb4c Bump 0.14.10 (#22058)
  • 42b9727 [ty] Use datatest instead of dirtest (#21937)
  • f7ec178 [ty] Gracefully handle client requests that can't be deserialized (#22051)
  • c315164 [ty] Don't suggest keyword statements when only expressions are valid
  • bb1955e [ty] Use cursor context in a few more places...
  • 070e08a [ty] Move completion function to the top
  • bab3924 [ty] Refactor completion generation
  • 10748b2 [flake8-pytest-style] Allow match and check keyword arguments without a...
  • 56539db [ty] Fix some configuration panics in the LSP (#22040)
  • 8d32ad1 [ty] Add support for attribute docstrings (#22036)
  • Additional commits viewable in compare view

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Bumps the python-packages group with 9 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| nmdc-api-utilities | `0.4.2` | `0.6.0` |
| [pydantic-settings](https://github.com/pydantic/pydantic-settings) | `2.10.1` | `2.12.0` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.14.1` | `4.15.5` |
| [scalar-fastapi](https://github.com/scalar/scalar) | `1.4.1` | `1.5.0` |
| [uvicorn](https://github.com/Kludex/uvicorn) | `0.35.0` | `0.40.0` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.3.0` | `4.5.1` |
| [pyright](https://github.com/RobertCraigie/pyright-python) | `1.1.404` | `1.1.407` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.4.1` | `9.0.2` |
| [ruff](https://github.com/astral-sh/ruff) | `0.12.11` | `0.14.10` |



Updates `nmdc-api-utilities` from 0.4.2 to 0.6.0

Updates `pydantic-settings` from 2.10.1 to 2.12.0
- [Release notes](https://github.com/pydantic/pydantic-settings/releases)
- [Commits](pydantic/pydantic-settings@2.10.1...v2.12.0)

Updates `pymongo` from 4.14.1 to 4.15.5
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](mongodb/mongo-python-driver@4.14.1...4.15.5)

Updates `scalar-fastapi` from 1.4.1 to 1.5.0
- [Release notes](https://github.com/scalar/scalar/releases)
- [Changelog](https://github.com/scalar/scalar/blob/main/CHANGELOG.md)
- [Commits](https://github.com/scalar/scalar/commits)

Updates `uvicorn` from 0.35.0 to 0.40.0
- [Release notes](https://github.com/Kludex/uvicorn/releases)
- [Changelog](https://github.com/Kludex/uvicorn/blob/main/docs/release-notes.md)
- [Commits](Kludex/uvicorn@0.35.0...0.40.0)

Updates `pre-commit` from 4.3.0 to 4.5.1
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v4.3.0...v4.5.1)

Updates `pyright` from 1.1.404 to 1.1.407
- [Release notes](https://github.com/RobertCraigie/pyright-python/releases)
- [Commits](RobertCraigie/pyright-python@v1.1.404...v1.1.407)

Updates `pytest` from 8.4.1 to 9.0.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.4.1...9.0.2)

Updates `ruff` from 0.12.11 to 0.14.10
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.11...0.14.10)

---
updated-dependencies:
- dependency-name: nmdc-api-utilities
  dependency-version: 0.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pydantic-settings
  dependency-version: 2.12.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pymongo
  dependency-version: 4.15.5
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: scalar-fastapi
  dependency-version: 1.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: uvicorn
  dependency-version: 0.40.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pre-commit
  dependency-version: 4.5.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pyright
  dependency-version: 1.1.407
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: pytest
  dependency-version: 9.0.2
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: ruff
  dependency-version: 0.14.10
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
...

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