Bump phonopy from 3.5.1 to 4.0.1

[dependabot]

Bumps phonopy from 3.5.1 to 4.0.1.

Changelog

Sourced from phonopy's changelog.

May-18-2026: Version 4.0.1

• Bug fix: AttributeError in phonopy-init when plotting with certain graph attributes.

May-16-2026: Version 4.0.0

Major breaking changes. See {ref}migration_v4 for the upgrade guide.

• CLI split into phonopy-init (setup: displacements, FORCE_SETS / FORCE_CONSTANTS conversion, --symmetry) and phonopy (phonon calculation). phonopy-load is kept as a deprecated alias of phonopy. The phonopy argument parser now rejects setup flags (-d, --rd, -f, --fz, --fc, --symmetry) and points the user to phonopy-init.
• primitive_matrix default changed to "auto" across Phonopy, phonopy.load, and the CLI (--pa). Pass "P" (or --pa P) for the identity transformation. A value stored in a phonopy.yaml file still takes priority over the default.
• --nac was removed. NAC is now enabled automatically when a BORN file is present or nac_params is stored in phonopy.yaml. Pass --nonac to disable NAC explicitly.
• Auto-fall back to full force constants when the input "primitive" cell is not actually primitive (e.g. an I-centered conventional cell) and symfc detects a smaller true primitive cell. The previous behaviour produced shape-mismatched compact force constants and crashed during drift evaluation or post-symmetrisation.
• Rust backend (phonors crate) is now the default and a required runtime dependency. Phonopy(), phonopy.load(), and the CLI run on Rust out of the box. The C extension is retained as a legacy backend selectable via lang="C" or the new --legacy-backend flag (conf-file equivalent: LEGACY_BACKEND = .true.). The previous --rust flag becomes a deprecated no-op. A no-C-extension build is available via PHONOPY_NO_C_EXT=1 at install time. See {ref}rust_backend.
• The behaviour when a sampling mesh breaks the primitive-cell point-group symmetry has changed. As a result, mesh-based calculations (DOS, thermal properties, etc.) on such meshes may give different numerical results from previous versions. When the mesh was specified by a length (float input), the grid is now rebuilt as a generalized regular grid that keeps full point-group symmetry; the resulting mesh_numbers may differ from the regular-grid value.
• VCA / mixed-species site support: PhonopyAtoms gains a species table, apply_vca() helper, and --site-mixture CLI flag (was initially --vca). VASP POSCAR writes expand mixed sites; force I/O and FC-time computation handle site-mixture cells.
• Bug fix: copy-by-reference issue in qpoints.py.

Commits

• 0f1825b Merge branch 'develop'
• 58bf4e3 Merge pull request #827 from phonopy/release
• 71c7547 Set version 4.0.1
• dea7672 Merge pull request #826 from phonopy/fix/phonopy-init-graph-attrs
• 5b420d2 Fix AttributeError in phonopy-init and add plot-saved messages
• 37aa5fb Merge branch 'develop'
• 8b0b618 Merge pull request #824 from phonopy/run-ci-with-phonors-build
• 58b100b Run CI with phonors build
• 00c6076 Run CI with phonors build
• 3aacf1d Run CI with phonors build
• Additional commits viewable in compare view

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.06%. Comparing base (93f0cc6) to head (b656231).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #500   +/-   ##
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  Coverage   97.06%   97.06%           
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  Files          29       29           
  Lines        1978     1978           
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  Hits         1920     1920           
  Misses         58       58           

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