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chore(deps): bump the python-dependencies group across 1 directory with 8 updates - #201

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Bumps the python-dependencies group with 8 updates in the / directory:

Package From To
fastapi 0.138.1 0.141.1
alembic 1.18.5 1.19.0
gitpython 3.1.54 3.1.58
sentence-transformers 5.6.0 5.6.1
pgvector 0.4.2 0.5.0
ruff 0.15.20 0.16.1
mypy 2.1.0 2.3.0
pre-commit 4.6.0 4.6.1

Updates fastapi from 0.138.1 to 0.141.1

Release notes

Sourced from fastapi's releases.

0.141.1

Fixes

  • 🐛 Fix support for background tasks and headers from dependencies in app.frontend(). PR #16105 by @​tiangolo.

Docs

0.141.0

Features

  • ✨ Add app.frontend(check_dir="auto"), to make local development more convenient with fastapi dev. PR #16102 by @​tiangolo.

0.140.13

Fixes

Docs

0.140.12

Fixes

0.140.11

Fixes

  • 🐛 Fix response_model_* params ignored for non-generator endpoints with Iterable[..] return type. PR #15093 by @​YuriiMotov.

0.140.10

Fixes

Internal

0.140.9

Fixes

  • 🐛 Fix exclude_defaults not propagated to dict keys and values in jsonable_encoder. PR #16043 by @​MBGrao.

... (truncated)

Commits
  • 95f8322 🔖 Release version 0.141.1 (#16106)
  • f137944 📝 Update release notes
  • d623544 🐛 Fix support for background tasks and headers from dependencies in `app.fron...
  • 1d211b9 📝 Update release notes
  • 8a1f876 📝 Document FASTAPI_ENV in FastAPI CLI guide (#16104)
  • c7e7b65 🔖 Release version 0.141.0 (#16103)
  • 6bceb84 📝 Update release notes
  • 5429fed ✨ Add app.frontend(check_dir="auto"), to make local development more conven...
  • 628663f 🔖 Release version 0.140.13 (#16096)
  • 0b54fd0 📝 Update release notes
  • Additional commits viewable in compare view

Updates alembic from 1.18.5 to 1.19.0

Release notes

Sourced from alembic's releases.

1.19.0

Released: August 4, 2026

changed

  • [changed] [installation] Environmental updates:

    -   Trove classifiers now include Python 3.15 which is now part of CI
    integration

      

    • 

      Python 3.14 is also added to trove classifiers which had been previously
omitted
      

      • 

    • 

      Implemented PEP 604 style unions in type annotations

feature

  • [feature] [autogenerate] Autogenerate now detects the addition and removal of named CHECK constraints, as part of the default autogenerate behavior. Detection is name-based only; a constraint whose name is unchanged is presumed equivalent regardless of its expression text, as reliably normalizing SQL expressions across backends for comparison purposes is not generally feasible. This behavior is implemented as a plugin named alembic.autogenerate.checkconstraint_byname, and may be disabled if not desired by excluding it from the EnvironmentContext.configure.autogenerate_plugins list. Pull request courtesy Francois van Kempen.

    References: #508

bug

  • [bug] [commands] Fixed inconsistency where running stamp or downgrade to base in offline (--sql) mode would emit a DROP TABLE alembic_version statement, while the same operations in online mode never drop the version table. Offline mode no longer emits this DROP, matching online behavior. The version table continues to be created when it does not exist; only the spurious offline-only drop has been removed. Pull request courtesy imurodl.

    References: #1822

Commits

Updates gitpython from 3.1.54 to 3.1.58

Release notes

Sourced from gitpython's releases.

Security and Fixes

What's Changed

New Contributors

Full Changelog: gitpython-developers/GitPython@3.1.57...3.1.58

3.1.57 - Security and Fixes

What's Changed

New Contributors

Full Changelog: gitpython-developers/GitPython@3.1.56...3.1.57

3.1.56 - SECURITY

What's Changed

Full Changelog: gitpython-developers/GitPython@3.1.55...3.1.56

3.1.55 - Security

What's Changed

... (truncated)

Commits
  • 30be45d prepare changelog for upcoming release
  • fc2f02c Merge pull request #2197 from Cyrus580529/shared-symlink-guard
  • b10e250 test: use the shared guard instead of local copies
  • e3e5da8 test: skip tests that need symlink privileges
  • 30d05e3 test: add a shared symlink capability guard
  • 9a8f6fe Merge pull request #2204 from gitpython-developers/security-fixes
  • f2550b6 Guard pathspec file inputs in high-level commands
  • d9ddb55 Guard unsafe git init options
  • 9b5dcaf Guard read-tree index output paths
  • 96a888f Check joined short-option values before Git execution
  • Additional commits viewable in compare view

Updates sentence-transformers from 5.6.0 to 5.6.1

Release notes

Sourced from sentence-transformers's releases.

v5.6.1 - Flash Attention Fix for XLM-R and RoBERTa Models

This patch release fixes silently degraded embeddings for RoBERTa-family models when flash attention is requested with transformers v5, notably every XLM-R based multilingual embedding model (BAAI/bge-m3, intfloat/multilingual-e5-large, etc.). The bug affected v5.5.0, v5.5.1, and v5.6.0.

Install this version with

# Training + Inference
pip install sentence-transformers[train]==5.6.1

Inference only, use one of:


pip install sentence-transformers==5.6.1
pip install sentence-transformers[onnx-gpu]==5.6.1
pip install sentence-transformers[onnx]==5.6.1
pip install sentence-transformers[openvino]==5.6.1


Multimodal dependencies (optional):


pip install sentence-transformers[image]==5.6.1
pip install sentence-transformers[audio]==5.6.1
pip install sentence-transformers[video]==5.6.1


Or combine as needed:


pip install sentence-transformers[train,onnx,image]==5.6.1

Fix position_ids offsetting for RoBERTa-family models when flattening inputs (#3879)

Since v5.5.0, the Transformer module flattens text-only batches into one packed sequence when flash attention is requested, skipping all padding overhead for a notable performance improvement. The position_ids of that packed sequence restart at 0 for every text, which is correct for the vast majority of models. RoBERTa-family architectures however compute positions as padding_idx + 1 + n for the n-th token, so every token read a position embedding shifted by padding_idx + 1 (usually 2). Nothing crashes, the embeddings are just silently worse.

from sentence_transformers import SentenceTransformer

An affected configuration: flash attention with an XLM-R based model


model = SentenceTransformer(
"BAAI/bge-m3",
model_kwargs={"attn_implementation": "flash_attention_2"},
)

Measured on BAAI/bge-m3:

Evaluation padded packed, 0-based positions packed, with this fix
stsb test Spearman 0.8485 0.7239 0.8485
NanoBEIR mean nDCG@10 0.6041 0.5414 0.6050

The quality loss recovers exactly once the offset is applied. The fix scans the loaded model's modules once for an int padding_idx stored next to a learned position_embeddings table, and offsets the packed position_ids when that pair is found. An audit of transformers finds 16 architectures with that pair (roberta, xlm_roberta, xlm_roberta_xl, camembert, roberta_prelayernorm, xmod, data2vec_text, longformer, luke, ibert, mpnet, markuplm, lilt, layoutlmv3, esm, and pp_doclayout_v2), all offset by exactly padding_idx + 1, and no 0-based or rotary architecture matches.

You are only affected if you encoded text with flash attention requested on transformers v5 with a RoBERTa-family checkpoint. The default padded path (e.g. sdpa) was never affected, and neither were MPNet models like all-mpnet-base-v2 despite mpnet appearing in the audit: transformers does not support flash attention for MPNet at all. If you did index a corpus with such a configuration, re-encode it after upgrading: pre-fix embeddings score notably worse and do not mix with post-fix embeddings.

What's Changed

... (truncated)

Commits
  • 7d3eb16 Release v5.6.1
  • 286dcf3 [tests] Skip bf16 + Windows + CPU forwards, as they can WindowsError on tor...
  • 30bad93 [ci] Exclude librosa/numba/llvmlite on Python 3.13 (#3835)
  • 9ca6bbc 🚨 Fix position_ids offsetting for RoBERTa-family models when flattening input...
  • See full diff in compare view

Updates pgvector from 0.4.2 to 0.5.0

Changelog

Sourced from pgvector's changelog.

0.5.0 (2026-07-06)

  • Added experimental support for type hints
  • Changed vector and halfvec types to return list for Django, SQLAlchemy, SQLModel, and Peewee
  • Changed vector type to return Vector object for Psycopg 3, Psycopg 2, asyncpg, and pg8000
  • Removed utils package (use top-level pgvector package instead)
  • Removed re-exported classes (use top-level pgvector package instead)
  • Removed dependency on NumPy
  • Dropped support for Python < 3.10
  • Dropped support for SQLAlchemy < 2
Commits

Updates ruff from 0.15.20 to 0.16.1

Release notes

Sourced from ruff's releases.

0.16.1

Release Notes

Released on 2026-07-30.

Preview features

  • Add an option to opt out of human-readable names (#27160)
  • [flake8-pytest-style] Make fixes safe by default and unsafe only when comments are present (PT018) (#27201)
  • [pyupgrade] Skip fix when a defaulted TypeVar precedes a non-defaulted one (UP040, UP046, UP047) (#27133)
  • [ruff] Fix false positive with unpacked arguments (RUF065) (#26959)

Bug fixes

  • Bump gen-lsp-types to gracefully handle unknown enumeration values in LSP messages (#27230)
  • [flake8-bugbear] Mark range as immutable (B008) (#27247)
  • [flake8-comprehensions] NFKC-normalize keyword names in C408 fix (#26813)
  • [flake8-return] Fix false positive when variable is read in finally clause (RET504) (#25441)
  • [pydocstyle] Skip section detection inside RST directive bodies (D214, D405, D413) (#23635)
  • [refurb] Parenthesize yield arguments in the FURB192 fix (#27192)

Rule changes

  • [flake8-pytest-style] Mark PT022 fixes as unsafe (#26440)
  • [refurb] Mark fixes that remove unknown separators as unsafe (FURB105) (#27200)

Server

  • Fix indexing of excluded nested Ruff workspaces (#27303)
  • Lint TOML files in the LSP (#26862)

Documentation

  • Cover pycon Markdown formatting (#27153)
  • [flake8-bandit] Document TYPE_CHECKING exception (S101) (#27004)
  • [flake8-import-conventions] Document that extend-aliases can override default aliases (#27191)
  • [pylint] Add missing fix safety gotchas for non-augmented-assignment (PLR6104) (#27250)

Other changes

  • Reduce syntax error noise by swallowing dedents like indents (#27170)
  • Vendor latest annotate-snippets (#27033)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.1

Released on 2026-07-30.

Preview features

  • Add an option to opt out of human-readable names (#27160)
  • [flake8-pytest-style] Make fixes safe by default and unsafe only when comments are present (PT018) (#27201)
  • [pyupgrade] Skip fix when a defaulted TypeVar precedes a non-defaulted one (UP040, UP046, UP047) (#27133)
  • [ruff] Fix false positive with unpacked arguments (RUF065) (#26959)

Bug fixes

  • Bump gen-lsp-types to gracefully handle unknown enumeration values in LSP messages (#27230)
  • [flake8-bugbear] Mark range as immutable (B008) (#27247)
  • [flake8-comprehensions] NFKC-normalize keyword names in C408 fix (#26813)
  • [flake8-return] Fix false positive when variable is read in finally clause (RET504) (#25441)
  • [pydocstyle] Skip section detection inside RST directive bodies (D214, D405, D413) (#23635)
  • [refurb] Parenthesize yield arguments in the FURB192 fix (#27192)

Rule changes

  • [flake8-pytest-style] Mark PT022 fixes as unsafe (#26440)
  • [refurb] Mark fixes that remove unknown separators as unsafe (FURB105) (#27200)

Server

  • Fix indexing of excluded nested Ruff workspaces (#27303)
  • Lint TOML files in the LSP (#26862)

Documentation

  • Cover pycon Markdown formatting (#27153)
  • [flake8-bandit] Document TYPE_CHECKING exception (S101) (#27004)
  • [flake8-import-conventions] Document that extend-aliases can override default aliases (#27191)
  • [pylint] Add missing fix safety gotchas for non-augmented-assignment (PLR6104) (#27250)

Other changes

  • Reduce syntax error noise by swallowing dedents like indents (#27170)
  • Vendor latest annotate-snippets (#27033)

Contributors

... (truncated)

Commits
  • 80790b3 Bump 0.16.1 (#27330)
  • 63830f3 [ty] Borrow from constraint set storage less often (#27328)
  • f40dca9 [ty] Preserve forwarded expanded-variadic diagnostic sources (#27266)
  • 0d80497 Lint TOML files in the LSP (#26862)
  • d91586b Update prek dependencies (#27293)
  • 7da4b8b [ty] Respect bounds and constraints in generic materializations (#27228)
  • b20daf7 [ty] refactor: add helper function to send partial results (#27249)
  • 4d4c8fa [ty] Emit diagnostic when specializing a non-generic class (#26883)
  • 7c3e2db [ty] Fix enum class container assignability (#27318)
  • d5ef97f [flake8-return] Fix false positive when variable is read in finally claus...
  • Additional commits viewable in compare view

Updates mypy from 2.1.0 to 2.3.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Packaging changes

Mypy 2.3

We've just uploaded mypy 2.3.0 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance improvements and bug fixes. You can install it as follows:

python3 -m pip install -U mypy

You can read the full documentation for this release on Read the Docs.

The Upcoming Switch to the New Native Parser

We are planning to enable the new native parser (--native-parser) by default soon. We recommend that you test the native parser in your projects and report any issues in the mypy issue tracker.

Mypyc Free-threading Memory Safety

Free-threaded Python builds that don't have the GIL require additional synchronization primitives or lock-free algorithms to ensure memory safety when there are race conditions (for example, when a thread reads a list item while another thread writes the same list item concurrently). This release greatly improves memory safety of free threading.

List operations are now memory-safe on free threaded Python builds, even in the presence of race conditions. This has some performance cost. For list-heavy workloads, using librt.vecs.vec instead of list is often significantly faster, but note that vec is not (and likely won't be) fully memory safe, and the user is expected to avoid race conditions. The newly introduced librt.threading.Lock helps with this. Using variable-length tuples can also be more efficient than lists, since tuples are immutable and don't require expensive synchronization to ensure memory safety.

Instance attribute access is also (mostly) memory safe now on free-threaded builds in the presence of race conditions. We are planning to fix the remaining unsafe cases in a future release.

Full list of changes:

  • Make attribute access memory safe on free-threaded builds (Jukka Lehtosalo, PR 21705)
  • Fix unsafe borrowing of instance attributes with free-threading (Jukka Lehtosalo, PR 21688)
  • Make list get/set item more memory safe on free-threaded builds (Jukka Lehtosalo, PR 21683)
  • Don't borrow list items on free-threaded builds (Jukka Lehtosalo, PR 21679)
  • Make multiple assignment from list memory-safe on free-threaded builds (Jukka Lehtosalo, PR 21684)

... (truncated)

Commits
  • 8aabf84 Drop +dev from version
  • 4d8ad2a Update changelog for 2.3 release (#21728)
  • 2c21546 [mypyc] Update documentation of race conditions under free threading (#21726)
  • a9f62a3 [mypyc] Make attribute access memory safe on free-threaded builds (#21705)
  • 0faa413 Use PYODIDE environment variable for Emscripten cross-compilation detection...
  • 3d75cdb [mypyc] Borrow final attributes more aggressively (#21702)
  • 24c237d [mypyc] Improve documentation of Final (#21713)
  • b5be217 [mypyc] Update free threading Python compatibility docs (#21711)
  • cbcb51a Narrow for frozendict membership check (#21709)
  • af2bc0f Sync typeshed (#21707)
  • Additional commits viewable in compare view

Updates pre-commit from 4.6.0 to 4.6.1

Release notes

Sourced from pre-commit's releases.

pre-commit v4.6.1

Fixes

Changelog

Sourced from pre-commit's changelog.

4.6.1 - 2026-07-21

Fixes

Commits
  • 242ce8a v4.6.1
  • 766e550 Merge pull request #3727 from pre-commit/dedupe
  • 1558d06 Merge pull request #3726 from pre-commit/exists-faster
  • 8a1c47a avoid duplicate files in --all-files during conflict
  • 2e01c99 faster check of rev existing locally as a commit
  • 3613bf2 Merge pull request #3701 from pre-commit/autoupdate-repos
  • 1d811d9 Return an error for invalid --repo
  • 374d354 Merge pull request #3711 from damonbayer/dmb_JULIA_DEPOT_PATH
  • 1e7994f set JULIA_DEPOT_PATH
  • b2b9119 Merge pull request #3719 from pre-commit/npm-unknown-options
  • Additional commits viewable in compare view

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@dependabot
chore(deps): bump the python-dependencies group across 1 directory wi…
2ba1a03 
…th 8 updates

Bumps the python-dependencies group with 8 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [fastapi](https://github.com/fastapi/fastapi) | `0.138.1` | `0.141.1` |
| [alembic](https://github.com/sqlalchemy/alembic) | `1.18.5` | `1.19.0` |
| [gitpython](https://github.com/gitpython-developers/GitPython) | `3.1.54` | `3.1.58` |
| [sentence-transformers](https://github.com/huggingface/sentence-transformers) | `5.6.0` | `5.6.1` |
| [pgvector](https://github.com/pgvector/pgvector-python) | `0.4.2` | `0.5.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.20` | `0.16.1` |
| [mypy](https://github.com/python/mypy) | `2.1.0` | `2.3.0` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.6.0` | `4.6.1` |



Updates `fastapi` from 0.138.1 to 0.141.1
- [Release notes](https://github.com/fastapi/fastapi/releases)
- [Commits](fastapi/fastapi@0.138.1...0.141.1)

Updates `alembic` from 1.18.5 to 1.19.0
- [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 `gitpython` from 3.1.54 to 3.1.58
- [Release notes](https://github.com/gitpython-developers/GitPython/releases)
- [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES)
- [Commits](gitpython-developers/GitPython@3.1.54...3.1.58)

Updates `sentence-transformers` from 5.6.0 to 5.6.1
- [Release notes](https://github.com/huggingface/sentence-transformers/releases)
- [Commits](huggingface/sentence-transformers@v5.6.0...v5.6.1)

Updates `pgvector` from 0.4.2 to 0.5.0
- [Changelog](https://github.com/pgvector/pgvector-python/blob/master/CHANGELOG.md)
- [Commits](pgvector/pgvector-python@v0.4.2...v0.5.0)

Updates `ruff` from 0.15.20 to 0.16.1
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.20...0.16.1)

Updates `mypy` from 2.1.0 to 2.3.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v2.1.0...v2.3.0)

Updates `pre-commit` from 4.6.0 to 4.6.1
- [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@v4.6.0...v4.6.1)

---
updated-dependencies:
- dependency-name: fastapi
  dependency-version: 0.141.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: alembic
  dependency-version: 1.19.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: gitpython
  dependency-version: 3.1.58
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: sentence-transformers
  dependency-version: 5.6.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: pgvector
  dependency-version: 0.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: ruff
  dependency-version: 0.16.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: mypy
  dependency-version: 2.3.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: pre-commit
  dependency-version: 4.6.1
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
...

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