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chore(deps): bump the uv group across 1 directory with 2 updates - #234

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Bumps the uv group with 2 updates in the / directory: torch and msgpack.

Updates torch from 2.7.1 to 2.13.0

Release notes

Sourced from torch's releases.

PyTorch 2.13.0 Release Notes

Highlights

For more details about these highlighted features, you can look at the release blogpost. Below are the full release notes for this release.

Tracked Regressions

ROCm wheels break torch.compile on CPU in environments without a GPU

Running a torch==2.13.0+rocm7.2 wheel in an environment where no GPU is available (torch.cuda.is_available() is False) breaks torch.compile on the CPU path: the first compile raises RuntimeError: Can't detect vectorized ISA for CPU (#189194). This is a regression from torch==2.12.1+rocm7.2, which compiles CPU code fine (detecting e.g. VecAVX2) in the same setup. The 2.13 ROCm wheel appears to rely on something present in the ROCm builder image to detect the CPU vectorized ISA, so it works when run on a ROCm image but fails on a plain CPU-only image.

Workaround: run the +rocm wheel on a ROCm image, or install a standard CPU/CUDA build for GPU-less environments.

Backwards Incompatible Changes

  • Stop building CPython 3.13t (free-threaded) binaries (#182951)

    Upstream pypa/manylinux removed CPython 3.13t (free-threaded) on 2026-05-07, because 3.13t was experimental and has been superseded by the now-non-experimental CPython 3.14t. As a result, PyTorch 2.13 no longer ships cp313t wheels (Linux, Triton, and related artifacts). Users on the free-threaded interpreter should move to Python 3.14t.

    PyTorch 2.12:

    # cp313t (free-threaded 3.13) wheels were available
    python3.13t -m pip install torch

    PyTorch 2.13:

... (truncated)

Commits
  • cf30153 [release/2.13] Strip +PTX from CUDA arch list on release/RC builds (#188914) ...
  • 3e3e24b [release/2.13] Restrict cuda-bindings to Python < 3.15 for CUDA 12.9 builds (...
  • 7986b06 [release/2.13] Bump binary build timeout 280 -> 400 minutes (#188551)
  • 0bdbc26 [release/2.13] Add CUDA 12.9 to TORCH_CUDA_ARCH_LIST tables (#188443)
  • 9cabb45 [release/2.13] Update manywheel docker image pin to 78e737ad (#188409)
  • 78e737a [release/2.13] Revert "Tighten generalized scatter graph target (#184075)" (#...
  • 0bb9b5b [release/2.13] Revert "dynamo: round-trip torch.cuda.stream ctx mgr across gr...
  • aaac2bf [release/2.13] Revert "[Reland] Port D104346887/PR 182675 for index_add fast ...
  • 9330813 Fix build_with_debinfo.py broken by CONFIGURE_DEPENDS globbing (#188192)
  • 4e077a7 Remove setuptools upper bound (#188190)
  • Additional commits viewable in compare view

Updates msgpack from 1.1.2 to 1.2.1

Release notes

Sourced from msgpack's releases.

v1.2.1

What's Changed

Full Changelog: msgpack/msgpack-python@v1.2.0...v1.2.1

v1.2.0

What's Changed

New Contributors

... (truncated)

Changelog

Sourced from msgpack's changelog.

1.2.1

Release Date: 2026-06-19

Fix a segfault when calling Unpacker.unpack() or Unpacker.skip() after an unpacking failure. But note that reusing the same Unpacker instance after an unpacking failure is not supported. Please create a new Unpacker instance instead. GHSA-6v7p-g79w-8964

1.2.0

Release Date: 2026-06-11

  • Support free threaded Python. #654, #686
  • Dropped support for Python 3.9. #656
  • Fix missing error checks in C code. #665, #666, #667, #672
  • Fix strict_map_key option didn't work for object_pairs_hook. #673
  • Increase DEFAULT_RECURSE_LIMIT of Unpacker to 1024. #676
  • Fix memory leak when Unpacker returns error for invalid input. #671
  • Fix Packer.pack_ext_type() ignored autoreset option. #663
  • Fix Timestamp.from_datetime() returning wrong value for pre-epoch datetimes. #662
  • Fix use-after-free in unpackb() and Unpacker.unpack() for non-contiguous input. #677
  • Fix possible memory leak when calling Unpacker.__init__() several times. #687
Commits
  • 448d43f release v1.2.1 (#698)
  • 2c56ddb Merge commit from fork
  • 0f4f350 Bump pypa/cibuildwheel from 4.0.0 to 4.1.0 in the all-dependencies group (#694)
  • 11ed0a5 release v1.2.0 (#692)
  • c410a38 Bump pypa/cibuildwheel from 3.4.1 to 4.0.0 (#691)
  • 97ba6ca skip ci: remove unneeded CIBW_SKIP option
  • cdde1b0 Wheels CI hangs for MacOS Intel (#689)
  • 5eb57e1 release v1.2.0rc1 (#681)
  • 77395c1 Harden Unpacker.__init__ re-entry cleanup to prevent buffer/context leaks (...
  • 7df7136 Guard Packer buffer protocol hooks with Cython critical sections (#686)
  • Additional commits viewable in compare view

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Bumps the uv group with 2 updates in the / directory: [torch](https://github.com/pytorch/pytorch) and [msgpack](https://github.com/msgpack/msgpack-python).


Updates `torch` from 2.7.1 to 2.13.0
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](pytorch/pytorch@v2.7.1...v2.13.0)

Updates `msgpack` from 1.1.2 to 1.2.1
- [Release notes](https://github.com/msgpack/msgpack-python/releases)
- [Changelog](https://github.com/msgpack/msgpack-python/blob/main/CHANGELOG.md)
- [Commits](msgpack/msgpack-python@v1.1.2...v1.2.1)

---
updated-dependencies:
- dependency-name: torch
  dependency-version: 2.13.0
  dependency-type: direct:production
  dependency-group: uv
- dependency-name: msgpack
  dependency-version: 1.2.1
  dependency-type: indirect
  dependency-group: uv
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jul 29, 2026
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Coverage

Coverage Report
FileStmtsMissCoverMissing
__init__.py00100% 
data_types.py40100% 
calibration
   __init__.py00100% 
   calibration_features.py90100% 
   calibrator.py4963293%61, 64, 79, 84–85, 203, 302–303, 305, 308, 353–354, 495–496, 552, 616–617, 621, 626, 692–695, 1069–1070, 1221, 1225, 1251, 1255, 1264, 1281, 1286
   diagnostics.py1384468%71, 156–171, 214–215, 219, 260, 262–277, 288–294
calibration/features
   __init__.py100100% 
   base.py26196%84
   beam.py900100% 
   chimeric.py82198%213
   constants.py90100% 
   fragment_match.py78198%203
   mass_error.py68494%17, 21, 37–38
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   sequence.py190100% 
   token_score.py37197%82
   utils.py261398%96, 368, 594
compat
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   instanovo.py10640%12, 14–15, 17, 24–25
datasets
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   feature_dataset.py84495%21, 88, 183–184
   interfaces.py30100% 
   psm_dataset.py250100% 
datasets/data_loaders
   __init__.py60100% 
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   mztab.py1793083%103, 106, 157, 161, 210–211, 223, 268, 271, 283–284, 317–318, 320–321, 323, 325, 331, 334–335, 342–344, 351, 353–356, 360, 501
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   utils.py186398%25, 170, 441
   winnow.py41587%55–56, 86, 100–101
fdr
   __init__.py00100% 
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   database_grounded.py37197%100
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scripts
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utils
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   config_path.py76593%24–26, 117–118
   hydra_overrides.py12283%12, 15
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   koina_intensity_config.py903363%42, 68, 76, 78, 108, 111, 131, 160–172, 177–178, 182–183, 189–192, 201–202, 204–205, 209
   paths.py210100% 
   peptide.py69395%37–38, 94
   proteome.py1151289%41, 48, 68, 79, 84, 88, 119, 144–146, 174, 180
   rich_console.py70100% 
TOTAL357171080% 

Tests Skipped Failures Errors Time
671 0 💤 0 ❌ 0 🔥 57.286s ⏱️

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