Bump calorine from 3.4 to 3.5

[dependabot]

Bumps calorine from 3.4 to 3.5.

Release notes

Sourced from calorine's releases.

3.5

• Added mode='fixed' to setup_training for pre-defined train/test splits !258
• Added Model.reorder to align species order across models sharing a GPUMD run.in !250
• Added batch_predict_properties for fast batch prediction via the nep executable's prediction mode !249
• Changed read_nepfile to parse n_max, l_max, basis_size, and charge_mode as lists of ints, supporting the optional flip_charge value on nep.in's charge_mode line !248
• Added the CALORINE_GPUMD_COMMAND environment variable for GPUNEP !246
• Changed setup_fine_tuning_nep89 to validate parameters against a blacklist instead of a whitelist !253
• Fixed handling of type-wise cutoff factors: removed the non-functional radial_typewise_cutoff_factor/angular_typewise_cutoff_factor fields and fixed zbl_typewise_cutoff_factor round-tripping through Model.write !260
• Fixed the norm calculation for per-atom rank-2 tensors (e.g. polarizability) in get_parity_data !255
• Fixed negative volume for triclinic cells in read_thermodynamic_data !254
• Fixed read_structures/get_parity_data returning virial/stress/polarizability values in nep's native component order instead of ASE's Voigt order, and unified Voigt-conversion handling via the new calorine.nep.tensor_conventions module !251
• Fixed Model read/write to correctly round-trip the qNEP charge_mode (1 vs 2) !247
• Fixed CPUNEP forces for qNEP (charge_mode 1/2) models disagreeing with finite differences due to a missing charge-response correction !244
• read_model now raises a clear ValueError for truncated/malformed nep.txt parameter counts !245
• Replaced bare assert statements in read_model with descriptive ValueError/IOError exceptions, and added version/model_type to its required-field check for malformed nep.txt files !243
• Routed dipole-gradient nep invocations through CALORINE_NEP_COMMAND !257
• Restructured the tutorial suite to remove reliance on repository files !259
• Closed remaining test coverage gaps !261
• Fixed flaky GPUNEP MD tests !256
• Fixed missing entries in the documentation reference section !252
• Updated links to the ASE documentation !242
• Reviewed and expanded documentation: updated the compiler requirement to C++17, documented rebuilding the C++ extension in place, added get_born_effective_charges to the calculator reference, and added a "Modifying NEP models" reference section !262

Commits

• b1229db Merge branch 'release-3.5' into 'master'
• b4a8726 Release 3.5
• a1b4cd1 Merge branch 'maint/review-documentation' into 'master'
• 9d6400b Review documentation
• f998591 Merge branch 'maint/removed-reliance-on-repo-files-in-tutorials' into 'master'
• 1629972 Restructured tutorial suite
• e67d44e Merge branch 'tests/extended-test-coverage' into 'master'
• 118959c Close remaining coverage gaps
• 348b8b9 Merge branch '138-fixed-typewise-cutoff-factors' into 'master'
• 857bbdc Fixed the handling of type-wise cutoff factors
• Additional commits viewable in compare view

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