chore(deps): bump the all-dependencies group with 4 updates

[dependabot]

Bumps the all-dependencies group with 4 updates: pybind11, pyscf, mypy and ruff.

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

• d03662f build: support Eigen 5 (#6036)
• 3d8aabc Bump version from v3.0.3 → v3.0.4
• 2c1b391 [skip ci] docs: add v3.0.4 changelog updates. (#6041)
• 804e2c1 fix: segfault when moving scoped_ostream_redirect (#6033)
• a15579c ci: bump setup-uv to maintained tag scheme (#6035)
• e2fdf43 Handle result from PyObject_VisitManagedDict (#6032)
• 98003e2 chore(deps): update pre-commit hooks (#6029)
• ab392bd fix: avoid copy constructor instantiation in shared_ptr fallback cast (#6028)
• ad5bc9e chore(deps): bump the actions group with 2 updates (#6027)
• See full diff in compare view

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 1.20.2

Changelog

Sourced from mypy's changelog.

Mypy 1.20.1

• Always disable sync in SQLite cache (Ivan Levkivskyi, PR 21184)
• Temporarily skip few base64 tests (Ivan Levkivskyi, PR 21193)
• Revert dict.__or__ typeshed change (Ivan Levkivskyi, PR 21186)
• Fix narrowing for match case with variadic tuples (Shantanu, PR 21192)
• Avoid narrowing type[T] in type calls (Shantanu, PR 21174)
• Fix regression for catching empty tuple in except (Shantanu, PR 21153)
• Fix reachability for frozenset and dict view narrowing (Shantanu, PR 21151)
• Fix narrowing with chained comparison (Shantanu, PR 21150)
• Avoid narrowing to unreachable at module level (Shantanu, PR 21144)
• Allow dangerous identity comparisons to Any typed variables (Shantanu, PR 21142)
• --warn-unused-config should not be a strict flag (Ivan Levkivskyi, PR 21139)

Mypy 1.20.2

• Use WAL with SQLite cache and fix close (Shantanu, PR 21154)
• Adjust SQLite journal mode (Ivan Levkivskyi, PR 21217)
• Correctly aggregate narrowing information on parent expressions (Shantanu, PR 21206)
• Fix regression related to generic callables (Shantanu, PR 21208)
• Fix regression by avoiding widening types in some contexts (Shantanu, PR 21242)
• Fix slicing in non-strict optional mode (Shantanu, PR 21282)
• mypyc: Fix match statement semantics for "or" pattern (Shantanu, PR 21156)
• mypyc: Fix issue with module dunder attributes (Piotr Sawicki, PR 21275)
• Initial support for Python 3.15.0a8 (Marc Mueller, PR 21255)

Acknowledgements

Thanks to all mypy contributors who contributed to this release:

• A5rocks
• Aaron Wieczorek
• Adam Turner
• Ali Hamdan
• asce
• BobTheBuidler
• Brent Westbrook
• Brian Schubert
• bzoracler
• Chris Burroughs
• Christoph Tyralla
• Colin Watson
• Donghoon Nam
• E. M. Bray
• Emma Smith
• Ethan Sarp
• George Ogden
• getzze
• grayjk
• Gregor Riepl
• Ivan Levkivskyi

... (truncated)

Commits

• 145a062 Bump version to 1.20.2
• 81cd492 Fix slicing with nonstrict optional (#21282)
• 908d344 [mypyc] Set dunder attrs when adding module to sys.modules (#21275)
• ba28610 Initial support for Python 3.15.0a8 (#21255)
• 7b0e09f Fix match statement semantics for "or" pattern (#21156)
• 92b74f2 Avoid widening types in conditional_types (#21242)
• 0dcbfaa Fix is_overlapping_types for generic callables (#21208)
• 210f518 Correctly aggregate narrowing information on parent expressions (#21206)
• c34530e Only set journal mode in coordinator (#21217)
• 79a3ec6 Use WAL with SQLite cache, fix close (#21154)
• Additional commits viewable in compare view

Updates ruff from 0.15.10 to 0.15.11

Release notes

Sourced from ruff's releases.

0.15.11

Release Notes

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)

Bug fixes

• [flake8-async] Omit overridden methods for ASYNC109 (#24648)

Documentation

• [flake8-async] Add override mention to ASYNC109 docs (#24666)
• Update Neovim config examples to use vim.lsp.config (#24577)

Contributors

• @​augustelalande
• @​anishgirianish
• @​benberryallwood
• @​charliermarsh
• @​Dev-iL

Install ruff 0.15.11

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.15.11/ruff-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.15.11/ruff-installer.ps1 | iex"

Download ruff 0.15.11

File	Platform	Checksum
ruff-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum
ruff-x86_64-apple-darwin.tar.gz	Intel macOS	checksum
ruff-aarch64-pc-windows-msvc.zip	ARM64 Windows	checksum
ruff-i686-pc-windows-msvc.zip	x86 Windows	checksum

... (truncated)

Changelog

Sourced from ruff's changelog.

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)

Bug fixes

• [flake8-async] Omit overridden methods for ASYNC109 (#24648)

Documentation

• [flake8-async] Add override mention to ASYNC109 docs (#24666)
• Update Neovim config examples to use vim.lsp.config (#24577)

Contributors

• @​augustelalande
• @​anishgirianish
• @​benberryallwood
• @​charliermarsh
• @​Dev-iL

Commits

• 53554b1 Bump 0.15.11 (#24678)
• 08c56c8 Factor out the mdtest crate (#24616)
• 725fbb7 [ty] Use partially qualified names when reporting diagnostics regarding bad c...
• ddd6a30 [ty] Do not suggest argument completion when at value of keyword argument (#2...
• 9282e61 Disallow @​disjoint_base on TypedDicts and Protocols (#24671)
• e9986d8 [ty] Reject using properties with Never setters or deleters (#24510)
• 9cf212f [ty] Normalize property setter and deleter wrappers (#24509)
• 12a1589 Add override mention to ASYNC109 docs (#24666)
• dccb03d [ty] Avoid panicking on overloaded Callable type context (#24661)
• 61f9a0a [ty] Sync vendored typeshed stubs (#24646)
• Additional commits viewable in compare view

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