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chore(deps): bump the deploy-python-dependencies group across 1 directory with 20 updates - #343
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…tory with 20 updates Bumps the deploy-python-dependencies group with 20 updates in the /deploy directory: | Package | From | To | | --- | --- | --- | | [alembic](https://github.com/sqlalchemy/alembic) | `1.20.0` | `1.20.1` | | [anyio](https://github.com/agronholm/anyio) | `4.15.1` | `4.16.0` | | [certifi](https://github.com/certifi/python-certifi) | `2026.7.22` | `2026.10.23` | | [fastapi](https://github.com/fastapi/fastapi) | `0.142.4` | `0.162.0` | | [httptools](https://github.com/MagicStack/httptools) | `0.8.0` | `0.9.0` | | [markupsafe](https://github.com/pallets/markupsafe) | `3.0.3` | `3.0.4` | | [numpy](https://github.com/numpy/numpy) | `2.5.3` | `2.5.4` | | [ome-types](https://github.com/imaging-formats/ome-types) | `0.6.3` | `0.7.0` | | [opentelemetry-api](https://github.com/open-telemetry/opentelemetry-python) | `1.45.0` | `1.45.2` | | [pillow](https://github.com/python-pillow/Pillow) | `12.3.0` | `13.0.0` | | [pycparser](https://github.com/eliben/pycparser) | `3.0` | `3.12` | | [pydantic](https://github.com/pydantic/pydantic) | `2.13.5` | `2.14.2` | | [pydantic-core](https://github.com/pydantic/pydantic) | `2.46.5` | `2.50.2` | | [pydantic-settings](https://github.com/pydantic/pydantic-settings) | `2.15.0` | `2.16.2` | | [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) | `2.0.54` | `2.1.6` | | [starlette](https://github.com/Kludex/starlette) | `1.7.0` | `1.10.0` | | [tifffile](https://github.com/cgohlke/tifffile) | `2026.9.20` | `2026.10.15` | | [websockets](https://github.com/python-websockets/websockets) | `17.1` | `17.4` | | [xsdata](https://github.com/tefra/xsdata) | `26.2` | `26.10` | | [oci-cli](https://github.com/oracle/oci-cli) | `3.94.1` | `3.95.1` | Updates `alembic` from 1.20.0 to 1.20.1 - [Release notes](https://github.com/sqlalchemy/alembic/releases) - [Changelog](https://github.com/sqlalchemy/alembic/blob/main/CHANGES) - [Commits](https://github.com/sqlalchemy/alembic/commits) Updates `anyio` from 4.15.1 to 4.16.0 - [Release notes](https://github.com/agronholm/anyio/releases) - [Commits](agronholm/anyio@4.15.1...4.16.0) Updates `certifi` from 2026.7.22 to 2026.10.23 - [Commits](certifi/python-certifi@2026.07.22...2026.10.23) Updates `fastapi` from 0.142.4 to 0.162.0 - [Release notes](https://github.com/fastapi/fastapi/releases) - [Commits](fastapi/fastapi@0.142.4...0.162.0) Updates `httptools` from 0.8.0 to 0.9.0 - [Release notes](https://github.com/MagicStack/httptools/releases) - [Commits](MagicStack/httptools@v0.8.0...v0.9.0) Updates `markupsafe` from 3.0.3 to 3.0.4 - [Release notes](https://github.com/pallets/markupsafe/releases) - [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst) - [Commits](pallets/markupsafe@3.0.3...3.0.4) Updates `numpy` from 2.5.3 to 2.5.4 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.5.3...v2.5.4) Updates `ome-types` from 0.6.3 to 0.7.0 - [Release notes](https://github.com/imaging-formats/ome-types/releases) - [Changelog](https://github.com/imaging-formats/ome-types/blob/main/CHANGELOG.md) - [Commits](imaging-formats/ome-types@v0.6.3...v0.7.0) Updates `opentelemetry-api` from 1.45.0 to 1.45.2 - [Release notes](https://github.com/open-telemetry/opentelemetry-python/releases) - [Changelog](https://github.com/open-telemetry/opentelemetry-python/blob/main/CHANGELOG.md) - [Commits](open-telemetry/opentelemetry-python@v1.45.0...v1.45.2) Updates `pillow` from 12.3.0 to 13.0.0 - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.3.0...13.0.0) Updates `pycparser` from 3.0 to 3.12 - [Release notes](https://github.com/eliben/pycparser/releases) - [Commits](eliben/pycparser@release_v3.00...release_v3.12) Updates `pydantic` from 2.13.5 to 2.14.2 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/v2.14.2/HISTORY.md) - [Commits](pydantic/pydantic@v2.13.5...v2.14.2) Updates `pydantic-core` from 2.46.5 to 2.50.2 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@core-v2.46.5...core-v2.50.2) Updates `pydantic-settings` from 2.15.0 to 2.16.2 - [Release notes](https://github.com/pydantic/pydantic-settings/releases) - [Commits](pydantic/pydantic-settings@v2.15.0...v2.16.2) Updates `sqlalchemy` from 2.0.54 to 2.1.6 - [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases) - [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst) - [Commits](https://github.com/sqlalchemy/sqlalchemy/commits) Updates `starlette` from 1.7.0 to 1.10.0 - [Release notes](https://github.com/Kludex/starlette/releases) - [Changelog](https://github.com/Kludex/starlette/blob/main/docs/release-notes.md) - [Commits](Kludex/starlette@1.7.0...1.10.0) Updates `tifffile` from 2026.9.20 to 2026.10.15 - [Release notes](https://github.com/cgohlke/tifffile/releases) - [Changelog](https://github.com/cgohlke/tifffile/blob/master/CHANGES.rst) - [Commits](cgohlke/tifffile@v2026.9.20...v2026.10.15) Updates `websockets` from 17.1 to 17.4 - [Release notes](https://github.com/python-websockets/websockets/releases) - [Commits](python-websockets/websockets@17.1...17.4) Updates `xsdata` from 26.2 to 26.10 - [Release notes](https://github.com/tefra/xsdata/releases) - [Changelog](https://github.com/tefra/xsdata/blob/main/CHANGES.md) - [Commits](tefra/xsdata@v26.2...v26.10) Updates `oci-cli` from 3.94.1 to 3.95.1 - [Release notes](https://github.com/oracle/oci-cli/releases) - [Changelog](https://github.com/oracle/oci-cli/blob/master/CHANGELOG.rst) - [Commits](oracle/oci-cli@v3.94.1...v3.95.1) --- updated-dependencies: - dependency-name: alembic dependency-version: 1.20.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: deploy-python-dependencies - dependency-name: anyio dependency-version: 4.16.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: certifi dependency-version: 2026.10.23 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: fastapi dependency-version: 0.162.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: httptools dependency-version: 0.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: markupsafe dependency-version: 3.0.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: deploy-python-dependencies - dependency-name: numpy dependency-version: 2.5.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: deploy-python-dependencies - dependency-name: ome-types dependency-version: 0.7.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: opentelemetry-api dependency-version: 1.45.2 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: deploy-python-dependencies - dependency-name: pillow dependency-version: 13.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: deploy-python-dependencies - dependency-name: pycparser dependency-version: '3.12' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: pydantic dependency-version: 2.14.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: pydantic-core dependency-version: 2.50.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: pydantic-settings dependency-version: 2.16.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: sqlalchemy dependency-version: 2.1.6 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: starlette dependency-version: 1.10.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: tifffile dependency-version: 2026.10.15 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: websockets dependency-version: '17.4' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: xsdata dependency-version: '26.10' dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies - dependency-name: oci-cli dependency-version: 3.95.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: deploy-python-dependencies ... 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| --hash=sha256:f5c09090b1a7c4d389d1431f820931e8df318f82caafc53f9a72c872fef467c5 \ | ||
| --hash=sha256:f8cc6532f930c27974e9239e5ce5abebe7600ba9807cea4fcf42f1b6cab18fe7 \ | ||
| --hash=sha256:ffba7eb2d67c7505e82a0902aa854d8824b74c28a183820d6a8bd3cfd0f812c2 | ||
| sqlalchemy==2.1.6 \ |
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Keep SQLAlchemy within the declared project range
The CI install steps in .github/workflows/ci.yml extract this pin and pass sqlalchemy==2.1.6 alongside pip install -e .[dev], but pyproject.toml still requires sqlalchemy>=2.0,<2.1. Pip therefore cannot resolve the environment, so the backend, PostgreSQL, and full-stack CI jobs fail before running tests. Update the project constraint together with this pin, or retain a compatible 2.0.x version.
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| alembic==1.20.0 \ | ||
| --hash=sha256:77eb101048d95f982c0353e9233404889dcd7a6fc244c107836c0e2fc9cf7d9d \ | ||
| --hash=sha256:db505480647bc60386c5369402f4a57a506b7539c9e9ef5e270d45cbbe4939bf | ||
| alembic==1.20.1 \ |
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Regenerate the dependency and software inventories
Changing the locked package IDs without regenerating docs/supply-chain/dependency-inventory.json leaves 22 new IDs missing and 22 obsolete IDs present. The mandatory validation at .github/workflows/ci.yml:80 compares those sets in scripts/validate_dependency_inventory.py:196-202 and fails, while the later software-inventory validation also rejects the changed requirements input because its committed receipt still describes the old lockfile. Regenerate and commit both inventory artifact sets with these dependency updates.
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| fastapi==0.142.4 \ | ||
| --hash=sha256:7fe2e254a0a948b88f432b02b8f627463285248233bba0998ed9640191e2ff57 \ | ||
| --hash=sha256:8a651aa071a9f92c8217cca1d0b044bf9c326f336578be0a728a1a1f22ec52d2 | ||
| fastapi==0.162.0 \ |
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Update the deployment pin assertions
The deployment regression test still asserts fastapi==0.142.4 at tests/backend/test_deploy_config.py:585, and the same test module asserts oci-cli==3.94.1 at line 642. With this commit's new 0.162.0 and 3.95.1 pins, test_runtime_container_inputs_are_pinned_by_digest and test_production_deploy_uses_temporary_oci_bastion_session deterministically fail once pytest runs; update those expected production versions together with the lockfiles.
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Bumps the deploy-python-dependencies group with 20 updates in the /deploy directory:
1.20.01.20.14.15.14.16.02026.7.222026.10.230.142.40.162.00.8.00.9.03.0.33.0.42.5.32.5.40.6.30.7.01.45.01.45.212.3.013.0.03.03.122.13.52.14.22.46.52.50.22.15.02.16.22.0.542.1.61.7.01.10.02026.9.202026.10.1517.117.426.226.103.94.13.95.1Updates
alembicfrom 1.20.0 to 1.20.1Release notes
Sourced from alembic's releases.
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Commits
Updates
anyiofrom 4.15.1 to 4.16.0Release notes
Sourced from anyio's releases.
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Commits
0ddd02dReleased version 4.16.0576892eFixed certain pending tasks not woken up by the closing of memory object stre...02ff4f8AddedBlockingPortal.call_async()(#1343)1af29a4Moved documentation code snippets into separate, checked files (#1445)f01c041[pre-commit.ci] pre-commit autoupdate (#1448)95a0143Test with blockbuster and uvloop on Python 3.15 too4d51154Modernized the memory object stream tests1e4b448Fixed the as_connectable() example in the networking docs (#1442)cd21b36FixedTypedAttributeSetnot collecting annotations from superclasses (#1358)b7f8c68[pre-commit.ci] pre-commit autoupdate (#1431)Updates
certififrom 2026.7.22 to 2026.10.23Commits
b60466c2026.10.23 (#445)662df63Restore unaffected emSign roots (#439) (#440)5cb238cRemove emsign (#437)69494a7Bump actions/download-artifact from 8.0.1 to 8.0.2 (#436)029c7b0Bump actions/upload-artifact from 7.0.1 to 7.0.2 (#435)9d0a8f1Add support for Python 3.15 (#432)db472abBump pypa/gh-action-pypi-publish from 1.14.1 to 1.14.2 (#431)Updates
fastapifrom 0.142.4 to 0.162.0Release notes
Sourced from fastapi's releases.
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Commits
7a0a3f0🔖 Release version 0.162.0 (#16606)b56f7c6📝 Update release notesf02ef49🐛 Restore default handling for omitted boolean form fields (#16605)69ddc2b🔖 Release version 0.161.1 (#16599)0cafa07📝 Update release notesf90d036🐛 Fix OpenAPI schemas for standalone nullable form unions (#16598)80c8742🔖 Release version 0.161.0 (#16597)b105209📝 Update release notese42ac0a✨ Add support for combining unions of form models (#16596)addd077🔖 Release version 0.160.0 (#16595)Updates
httptoolsfrom 0.8.0 to 0.9.0Release notes
Sourced from httptools's releases.
Commits
1041984Merge pull request #154 from MagicStack/release-0.9.0aa5fbf9httptools v0.9.0eab7f64Upgrade llhttp to 9.4.3 (#153)d80e26fModernize test and release workflows (#152)b03516dBuild CPython 3.15 wheels (#148)ff08b99Build PPC64LE wheels (#143)5a2bb07Add Windows ARM64 support in CI (#141)1c6946dci: add riscv64 to wheel build matrix (#137)Updates
markupsafefrom 3.0.3 to 3.0.4Release notes
Sourced from markupsafe's releases.
Changelog
Sourced from markupsafe's changelog.
Commits
ece2607release version 3.0.4620bc80split archs73c3be1fix wheel builds (#536)d8ae19efix wheel buildsff1eaffBuild Android and iOS wheels (#516)87e64f9build Android and iOS wheelsbc33c55Build ppc64le wheels (#518)0ddd6eabuild ppc64le wheels3e07758Build armv7l wheels (#514)39b9aaebuild armv7l wheelsUpdates
numpyfrom 2.5.3 to 2.5.4Release notes
Sourced from numpy's releases.
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Commits
a3d0ef1Merge pull request #32969 from charris/prepare-2.5.4087b536MAINT: Make OpenBLAS version check use 2.5.x branch.91acd87REL: Prepare for the NumPy 2.5.4 release.9cc555bMerge pull request #32956 from charris/backport-typing-1e04b972TYP:dtype[void].names: allow setting with list (#32943)d929969TYP:timedelta64:datetime.timedeltaconstruction isn't deprecated (#...839467fTYP:ma.getmaskarray: accept array-likes (#32934)64b721bTYP:polynomial: accept scalarcoefin the poly constructors (#32931)06b7ad2TYP:void: accept anydtype: strin constructor calls (#32928)c7bcd2cTYP:place: widenmask(#32926)Updates
ome-typesfrom 0.6.3 to 0.7.0Release notes
Sourced from ome-types's releases.
Commits
b220a87Ci/modernize tooling (#313)40c4b67ci: fix readthedocs build and pre-commit mypy (#312)ef0b395fix: handle 2013-06s namespace typo from python-bioformats (#308)690b8c9ci: fix PySide6 widget test crash (#311)2fa7656chore: repo refresh (2026-10) (#310)6a2f40bci: fix tests for pytest-mypy-plugins 4.0 (#309)c9c5438chore: move org (#303)2185f54ci: dependabot quarterly interval and group actionsc6c20d6chore: update schema (#301)Updates
opentelemetry-apifrom 1.45.0 to 1.45.2Release notes
Sourced from opentelemetry-api's releases.
Changelog
Sourced from opentelemetry-api's changelog.
Commits
ad75594[release/v1.45.x-0.66bx] Prepare release 1.45.2/0.66b2 (#5862)78123a2[release/v1.45.x-0.66bx] Backport metric cardinality limits and traceparent p...14971cePrepare release 1.45.1/0.66b1 (#5752)44ac26eopentelemetry-sdk: fix thread leak bug in resource initialization logic (#570...a2ec3f9[release/v1.45.x-0.66bx] opentelemetry-exporter-otlp-proto-http: restore requ...d5224bfopentelemetry-api: improve performance of tracestate parsing (#5746) (#5749)db61173Declare AnyValue and AttributeValue as explicit type aliases (#5703) (#5750)Updates
pillowfrom 12.3.0 to 13.0.0Release notes
Sourced from pillow's releases.
... (truncated)
Commits
293218a13.0.0 version bump262e8e4Update release notes for Pillow 13.0.0 (#10223)af56aceValidate TIFF tag values against libtiff's own field definition before TIFFSe...570df03Validate TIFF tag values against libtiff's own field definition before TIFFSe...53318b5Take libtiff scanline geometry tags from the image, not tiffinfo/exif (#10226)0a87417Bound retained TIFF tag data by stream size (#10225)11582e5Fix heap buffer overflow in _tiffWriteProc when saving TIFF to BytesIO (#10224)8501adcFix testec5f1cbTake libtiff scanline geometry tags from the image, not tiffinfo/exif4b63dffShare TIFF tag data budget across framesUpdates
pycparserfrom 3.0 to 3.12Release notes
Sourced from pycparser's releases.