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Bump the pip group across 2 directories with 2 updates#1621

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Bump the pip group across 2 directories with 2 updates#1621
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dependabot/pip/applications/ehr_query_llm/lmm/pip-12da87992b

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Bumps the pip group with 1 update in the /applications/ehr_query_llm/lmm directory: pypdf.
Bumps the pip group with 1 update in the /applications/nvidia_nim/nvidia_nim_nvclip directory: torch.

Updates pypdf from 6.10.2 to 6.13.3

Release notes

Sourced from pypdf's releases.

Version 6.13.3, 2026-06-17

What's new

Security (SEC)

Performance Improvements (PI)

Robustness (ROB)

Maintenance (MAINT)

Full Changelog

Version 6.13.2, 2026-06-10

What's new

Security (SEC)

Robustness (ROB)

Full Changelog

Version 6.13.1, 2026-06-08

What's new

Security (SEC)

Full Changelog

Version 6.13.0, 2026-06-05

What's new

Security (SEC)

New Features (ENH)

Robustness (ROB)

... (truncated)

Changelog

Sourced from pypdf's changelog.

Version 6.13.3, 2026-06-17

Security (SEC)

  • Apply MAX_DECLARED_STREAM_LENGTH to streams without length as well (#3871)

Performance Improvements (PI)

  • Avoid per-pixel getpixel loop for 1-bit indexed images (#3854)

Robustness (ROB)

  • Several fixes

Maintenance (MAINT)

  • Make mypy assert messages consistent (#3849)

Full Changelog

Version 6.13.2, 2026-06-10

Security (SEC)

  • Detect multi-hop cyclic /Pages trees in _flatten to prevent SIGSEGV (#3847)

Robustness (ROB)

  • Fix UnboundLocalError in _read_standard_xref_table on a malformed entry (#3841)
  • Raise PdfStreamError on non-hexadecimal bytes in hex readers (#3832)

Full Changelog

Version 6.13.1, 2026-06-08

Security (SEC)

  • Prevent infinite loops when processing threads/articles (#3839)

Full Changelog

Version 6.13.0, 2026-06-05

Security (SEC)

  • Avoid infinite loops for outlines and text extraction (#3830)

New Features (ENH)

  • Add Japanese predefined CMaps (#3800)
  • Font: Collect all character widths, not only those that can be unicode mapped (#3798)

Robustness (ROB)

  • Recover a corrupt trailing startxref pointer (closes #3238) (#3826)
  • Handle /Pages node without /Kids during flattening (#3825)
  • Accept inline image EI marker at the end of a content stream (#3827)

Maintenance (MAINT)

  • Type the always-raising deprecation helpers as NoReturn (#3819)

... (truncated)

Commits
  • 9aa05e7 REL: 6.13.3
  • bbd083d SEC: Apply MAX_DECLARED_STREAM_LENGTH to streams without length as well (#3871)
  • d5cd266 ROB: Guard text operators against missing operands in extract_text (#3861)
  • 82f1f90 ROB: Tolerate malformed /Limits in index2label (#3858)
  • 0276a6f PI: Avoid per-pixel getpixel loop for 1-bit indexed images (#3854)
  • 41a9c3c MAINT: Make mypy assert messages consistent (#3849)
  • d1bba60 MAINT: Increase readability of PdfDocCommon (#3834)
  • 53b6fbc DEV: Bump codecov/codecov-action from 6.0.1 to 7.0.0 (#3859)
  • e07c223 MAINT: Enforce G004 (no f-strings in logging) (#3845)
  • 5270f76 ROB: Guard zero unitsPerEm in from_truetype_font_file (#3846)
  • Additional commits viewable in compare view

Updates torch from 2.8.0 to 2.12.1

Release notes

Sourced from torch's releases.

PyTorch 2.12.1 Release, bug fix release

This release is meant to fix the following regressions and silent correctness issues:

Regression fixes

  • Fix nondeterministic outputs in test_batch_invariance with FLASH_ATTN on NVIDIA B200 GPUs (#181248), fixed by updating Triton to 3.7.1 (#186814)
  • Fix illegal memory access in the Triton convolution2d_bwd_weight kernel on B100/B200 (sm100) GPUs (#187081), fixed by updating Triton to 3.7.1 (#186814)
  • Fix fill_ on byte-dtype views with misaligned storage offset (#186821)

Releng / Build

  • Drop CPython 3.13t from the binary build matrix (#182951)

PyTorch 2.12.0 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.

Backwards Incompatible Changes

Build Frontend

  • Strengthened SVE compile checks in FindARM.cmake, which may reject previously accepted but incorrect SVE configurations (#176646)

    Source builds that enable SVE now validate the compiler configuration more strictly. If a build previously passed with an incomplete or mismatched SVE setup, it may now fail during CMake configuration instead of later in compilation. Update the compiler/toolchain flags so they accurately describe the target SVE support, or disable SVE for that build.

  • Updated the minimum CUDA version required to build PyTorch from source to CUDA 12.6 (#178925)

    Building PyTorch from source with CUDA versions older than 12.6 is no longer supported. Users building custom binaries should install CUDA 12.6 or newer and make sure CUDA_HOME points to that installation.

    Version 2.11:

    CUDA_HOME=/usr/local/cuda-12.4 python setup.py develop

... (truncated)

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Bumps the pip group with 1 update in the /applications/ehr_query_llm/lmm directory: [pypdf](https://github.com/py-pdf/pypdf).
Bumps the pip group with 1 update in the /applications/nvidia_nim/nvidia_nim_nvclip directory: [torch](https://github.com/pytorch/pytorch).


Updates `pypdf` from 6.10.2 to 6.13.3
- [Release notes](https://github.com/py-pdf/pypdf/releases)
- [Changelog](https://github.com/py-pdf/pypdf/blob/main/CHANGELOG.md)
- [Commits](py-pdf/pypdf@6.10.2...6.13.3)

Updates `torch` from 2.8.0 to 2.12.1
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](pytorch/pytorch@v2.8.0...v2.12.1)

---
updated-dependencies:
- dependency-name: pypdf
  dependency-version: 6.13.3
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: torch
  dependency-version: 2.12.1
  dependency-type: direct:production
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Jun 20, 2026
@dependabot @github

dependabot Bot commented on behalf of github Jun 20, 2026

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Superseded by #1622.

@dependabot dependabot Bot closed this Jun 20, 2026
@dependabot dependabot Bot deleted the dependabot/pip/applications/ehr_query_llm/lmm/pip-12da87992b branch June 20, 2026 05:10
@github-project-automation github-project-automation Bot moved this to Done in Holohub Jun 20, 2026
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