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chore(deps): bump the all-dependencies group across 1 directory with 6 updates#232

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chore(deps): bump the all-dependencies group across 1 directory with 6 updates#232
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@dependabot dependabot Bot commented on behalf of github May 13, 2026

Bumps the all-dependencies group with 6 updates in the / directory:

Package From To
torch 2.11.0 2.12.0
pybind11 3.0.3 3.0.4
pyscf 2.12.1 2.13.0
mypy 1.20.1 2.1.0
ruff 0.15.10 0.15.12
types-pyyaml 6.0.12.20260408 6.0.12.20260510

Updates torch from 2.11.0 to 2.12.0

Commits

Updates pybind11 from 3.0.3 to 3.0.4

Release notes

Sourced from pybind11's releases.

Version 3.0.4

Bug fixes:

  • Fixed test builds with installed Eigen 5 by improving Eigen3 CMake package detection. #6036

  • Fixed move semantics of scoped_ostream_redirect to preserve buffered output and avoid crashes when moved redirects restore stream buffers. #6033

  • Fixed py::dynamic_attr() traversal on Python 3.13+ to correctly propagate PyObject_VisitManagedDict() results. #6032

  • Fixed std::shared_ptr<T> fallback casting to avoid unnecessary copy-constructor instantiation in reference_internal paths. #6028

CI:

  • Updated setup-uv to the maintained GitHub Action tag scheme. #6035

  • Updated pre-commit hooks. #6029

  • Updated GitHub Actions dependencies, including actions-setup-cmake and cibuildwheel. #6027

Changelog

Sourced from pybind11's changelog.

Version 3.0.4 (April 18, 2026)

Bug fixes:

  • Fixed test builds with installed Eigen 5 by improving Eigen3 CMake package detection. #6036

  • Fixed move semantics of scoped_ostream_redirect to preserve buffered output and avoid crashes when moved redirects restore stream buffers. #6033

  • Fixed py::dynamic_attr() traversal on Python 3.13+ to correctly propagate PyObject_VisitManagedDict() results. #6032

  • Fixed std::shared_ptr<T> fallback casting to avoid unnecessary copy-constructor instantiation in reference_internal paths. #6028

CI:

  • Updated setup-uv to the maintained GitHub Action tag scheme. #6035

  • Updated pre-commit hooks. #6029

  • Updated GitHub Actions dependencies, including actions-setup-cmake and cibuildwheel. #6027

Commits

Updates pyscf from 2.12.1 to 2.13.0

Release notes

Sourced from pyscf's releases.

PySCF v2.13.0 release

  • Added
    • ASE band structure interface
    • SOC-ECP for PBC DFT methods
    • get_rho_with_derivatives() function
    • PCM ISWIG surface discretization method
    • grid_response support for the Stratmann grid partition scheme
    • Cartesian basis support in the PCM solvent module
    • gw_ac and ugw_ac methods
    • meta-GGA support in multigrid methods (currently computed in a slower mode)
    • SGX gradients
  • Improvements
    • Warnings for basis-element mismatch
    • Updated GTH basis set and pseudopotential databases
    • Enforced real orbitals for time-reversal symmetric KSCF
    • Added sanity checks to prevent bugs in the Newton solver for PBC mean-field methods
    • Updated ccECP from pseudopotentiallibrary.org
    • Improved PBC 2c2e integral accuracy for better numerical stability in PBC-GDF methods
    • SGX implementation for improved numerical accuracy and performance
    • Canonical orthogonalization by default in the SCF eigenvalue solver
    • Support specifying "autoaux" as a key for auxiliary basis set
  • Fixes
    • RSJK initialization
    • Skipped printing of velocity and magnetic dipole moments when ECP is detected
    • mo_coeff reshape size in PBC SCF HF DF-JK
    • XYZ file parser
    • A bug where PCM assigned incorrect radii to ECP atoms
    • Inconsistent symmetry axis assignment for D₂h molecules (#2773)
    • Load default cell and k-points in KGHF.get_hcore
    • POSCAR parser bug
    • Handle ghost atoms in the QM/MM interface
    • Errors in AO values caused by an incorrect diffuseness estimator
    • Edge case involving empty arrays in DF-JK construction for PBC DF
    • Incorrect DF-MP2 energy when using jkfit in HF and rifit in MP2
    • Edge case for the frozen attribute (frozen=0)
    • PBC nuclear gradients in fft_jk.get_k_e1 with exxdiv=ewald
  • API Updates
    • Set multigrid2 as the default multigrid integrator
    • Smearing functions are moved to a separate module
    • Set default auxbasis_response level to 2 (full response) in density-fitting Hessian methods
    • Dump nelecas in mcscf chkfile
    • Allow to skip .run() for intermediate instances in method chains
    • In method pipelines, .run() of intermediate steps is now executed automatically
    • Linear dependency for orbital bases are removed by default in SCF
Changelog

Sourced from pyscf's changelog.

PySCF 2.13.0 (2026-04-20)

  • Added
    • ASE band structure interface
    • SOC-ECP for PBC DFT methods
    • get_rho_with_derivatives() function
    • PCM ISWIG surface discretization method
    • grid_response support for the Stratmann grid partition scheme
    • Cartesian basis support in the PCM solvent module
    • gw_ac and ugw_ac methods
    • meta-GGA support in multigrid methods (currently computed in a slower mode)
    • SGX gradients
  • Improvements
    • Warnings for basis-element mismatch
    • Updated GTH basis set and pseudopotential databases
    • Enforced real orbitals for time-reversal symmetric KSCF
    • Added sanity checks to prevent bugs in the Newton solver for PBC mean-field methods
    • Updated ccECP from pseudopotentiallibrary.org
    • Improved PBC 2c2e integral accuracy for better numerical stability in PBC-GDF methods
    • SGX implementation for improved numerical accuracy and performance
    • Canonical orthogonalization by default in the SCF eigenvalue solver
    • Support specifying "autoaux" as a key for auxiliary basis set
  • Fixes
    • RSJK initialization
    • Skipped printing of velocity and magnetic dipole moments when ECP is detected
    • mo_coeff reshape size in PBC SCF HF DF-JK
    • XYZ file parser
    • A bug where PCM assigned incorrect radii to ECP atoms
    • Inconsistent symmetry axis assignment for D₂h molecules (#2773)
    • Load default cell and k-points in KGHF.get_hcore
    • POSCAR parser bug
    • Handle ghost atoms in the QM/MM interface
    • Errors in AO values caused by an incorrect diffuseness estimator
    • Edge case involving empty arrays in DF-JK construction for PBC DF
    • Incorrect DF-MP2 energy when using jkfit in HF and rifit in MP2
    • Edge case for the frozen attribute (frozen=0)
    • PBC nuclear gradients in fft_jk.get_k_e1 with exxdiv=ewald
  • API Updates
    • Set multigrid2 as the default multigrid integrator
    • Smearing functions are moved to a separate module
    • Set default auxbasis_response level to 2 (full response) in density-fitting Hessian methods
    • Dump nelecas in mcscf chkfile
    • Allow to skip .run() for intermediate instances in method chains
    • In method pipelines, .run() of intermediate steps is now executed automatically
    • Linear dependency for orbital bases are removed by default in SCF
Commits
  • e620426 Release 2.13.0 (#3190)
  • 8ede098 Support specifying "autoaux" as a key for basis set
  • dbc0ad3 Improve PBC 2c2e integral accuracy (#3186)
  • 1b0caae Disable density-based grid pruning by default (#3192)
  • 54c2aa3 Faster SGX and SGX Gradients (#3076)
  • 9fe5b82 Canonical orthogonalization for eigenvalue solver in SCF (#3191)
  • 18a99eb basis parser does not load bse due to commit 2fe92bcf
  • 06f05dc Mole.to_gpu only works for gpu4pyscf 1.5 or newer
  • c8a4215 add MGGA support to multigrid.py (#3188)
  • 8ae29f6 Fix PBC nuclear gradients fft_jk.get_k_e1 with exxdiv=ewald (#3158)
  • Additional commits viewable in compare view

Updates mypy from 1.20.1 to 2.1.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Mypy 2.1

We’ve just uploaded mypy 2.1.0 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.

librt.vecs: Fast Growable Array Type for Mypyc

The new librt.vecs module provides an efficient growable array type vec that is optimized for mypyc use. It provides fast, packed arrays with integer and floating point value types, which can be several times faster than list, and tens of times faster than array.array in code compiled using mypyc. It also supports nested vec objects and non-value-type items, such as vec[vec[str]].

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo.

librt.random: Fast Pseudo-Random Number Generation

The new librt.random module provides fast pseudo-random number generation that is optimized for code compiled using mypyc. It can be 3x to 10x faster than the stdlib random module in compiled code.

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo (PR 21433).

Mypyc Improvements

  • Make compilation order with multiple files consistent (Piotr Sawicki, PR 21419)
  • Fix crash on accessing StopAsyncIteration (Piotr Sawicki, PR 21406)
  • Fix incremental compilation with separate flag (Vaggelis Danias, PR 21299)

Fixes to Crashes

  • Fix crash on partial type with --allow-redefinition and global declaration (Jukka Lehtosalo, PR 21428)
  • Fix broken awaitable generator patching (Ivan Levkivskyi, PR 21435)

Changes to Messages

... (truncated)

Commits

Updates ruff from 0.15.10 to 0.15.12

Release notes

Sourced from ruff's releases.

0.15.12

Release Notes

Released on 2026-04-24.

Preview features

  • Implement #ruff:file-ignore file-level suppressions (#23599)
  • Implement #ruff:ignore logical-line suppressions (#23404)
  • Revert preview changes to displayed diagnostic severity in LSP (#24789)
  • [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
  • [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
  • [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

  • [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

  • Respect default Unix permissions for cache files (#24794)

Documentation

  • [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
  • [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
  • Improve rules table accessibility (#24711)

Contributors

Install ruff 0.15.12

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.15.12/ruff-installer.sh | sh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.12

Released on 2026-04-24.

Preview features

  • Implement #ruff:file-ignore file-level suppressions (#23599)
  • Implement #ruff:ignore logical-line suppressions (#23404)
  • Revert preview changes to displayed diagnostic severity in LSP (#24789)
  • [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
  • [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
  • [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

  • [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

  • Respect default Unix permissions for cache files (#24794)

Documentation

  • [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
  • [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
  • Improve rules table accessibility (#24711)

Contributors

0.15.11

Released on 2026-04-16.

Preview features

  • [ruff] Ignore RUF029 when function is decorated with asynccontextmanager (#24642)
  • [airflow] Implement airflow-xcom-pull-in-template-string (AIR201) (#23583)
  • [flake8-bandit] Fix S103 false positives and negatives in mask analysis (#24424)

... (truncated)

Commits
  • 66f93cf Bump 0.15.12 (#24815)
  • 476a4d0 [ty] Complete support for more detailed diagnostics on possibly unbound error...
  • ed669ea Implement #ruff:file-ignore file-level suppressions (#23599)
  • e73d952 [ty] Include inferred type in invalid-key concise diagnostic for union/inte...
  • 80feb29 [ty] report only dead annotation-only locals as unused (#24811)
  • 0fbf2bc Drop deprecated license classifier (#24808)
  • 43b174c [ty] Infer lambda parameter types with Callable type context (#24317)
  • 4f449ae [ty] Add error context for intersection types (#24772)
  • 5b4e753 [ty] Add support for goto in literal enum member inlay hint (#24792)
  • e7cc762 [ty] Add error context for TypedDict assignments (#24790)
  • Additional commits viewable in compare view

Updates types-pyyaml from 6.0.12.20260408 to 6.0.12.20260510

Commits

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@dependabot
chore(deps): bump the all-dependencies group across 1 directory with …
bbbf46b 
…6 updates

Bumps the all-dependencies group with 6 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [torch](https://github.com/pytorch/pytorch) | `2.11.0` | `2.12.0` |
| [pybind11](https://github.com/pybind/pybind11) | `3.0.3` | `3.0.4` |
| [pyscf](https://github.com/pyscf/pyscf) | `2.12.1` | `2.13.0` |
| [mypy](https://github.com/python/mypy) | `1.20.1` | `2.1.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.10` | `0.15.12` |
| [types-pyyaml](https://github.com/python/typeshed) | `6.0.12.20260408` | `6.0.12.20260510` |



Updates `torch` from 2.11.0 to 2.12.0
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](https://github.com/pytorch/pytorch/commits)

Updates `pybind11` from 3.0.3 to 3.0.4
- [Release notes](https://github.com/pybind/pybind11/releases)
- [Changelog](https://github.com/pybind/pybind11/blob/master/docs/changelog.md)
- [Commits](pybind/pybind11@v3.0.3...v3.0.4)

Updates `pyscf` from 2.12.1 to 2.13.0
- [Release notes](https://github.com/pyscf/pyscf/releases)
- [Changelog](https://github.com/pyscf/pyscf/blob/master/CHANGELOG)
- [Commits](pyscf/pyscf@v2.12.1...v2.13.0)

Updates `mypy` from 1.20.1 to 2.1.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.20.1...v2.1.0)

Updates `ruff` from 0.15.10 to 0.15.12
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.10...0.15.12)

Updates `types-pyyaml` from 6.0.12.20260408 to 6.0.12.20260510
- [Commits](https://github.com/python/typeshed/commits)

---
updated-dependencies:
- dependency-name: torch
  dependency-version: 2.12.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: pybind11
  dependency-version: 3.0.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: pyscf
  dependency-version: 2.13.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: mypy
  dependency-version: 2.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: all-dependencies
- dependency-name: ruff
  dependency-version: 0.15.12
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: types-pyyaml
  dependency-version: 6.0.12.20260510
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
...

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 May 13, 2026
@hzhangxyz hzhangxyz merged commit 080003e into main May 14, 2026
7 checks passed
@dependabot dependabot Bot deleted the dependabot/uv/all-dependencies-bf7850ac73 branch May 14, 2026 05:29
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