chore(deps): update dependency gemmi to >=0.5.5, <=0.7.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
gemmi	>=0.5.5, <=0.6.7 -> >=0.5.5, <=0.7.0

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Release Notes

project-gemmi/gemmi (gemmi)

v0.7.0: 0.7.0

Compare Source

C++14 (or later) is required to build the library, C++17 (or later) to build Python bindings.
Expect breaking changes, especially in Python bindings.
The lists below are not complete, but should cover most of the changes.

Library

• Added unified logging of warnings/errors from various gemmi functions (class Logger)
• replaced string Model::name with int Model::num
• mmcif: better handling of null auth_comp_id
• fixes for mmJSON
• Removed deprecated functions:
  • UnitCell.fractionalization_matrix and orthogonalization_matrix – use frac.mat and orth.mat
  • count_hydrogen_sites() – use has_hydrogen() or count_atom_sites(gemmi.Selection('[H,D]')
  • Grid::resample_to() – use interpolate_grid()
• unified API of Grid interpolation functions. They now have parameter order that can be 0 (nearest value), 1 (linear interpolation), or 3 (cubic). In C++ there are also functions such as trilinear_interpolation() to ensure no overhead.
• to_pdb: write HET records
• Extended selection syntax with: [metals] and [nonmetals].
• Added function set_is_metal() intended for debatable metalloids
• improved interoperability with MMDB (a CCP4 library)
• MonLib: removed read_cif args
• mtz: fixed writing BATCH records
• hydrogen placement: fixes needed for new files with metals in CCP4 Monomer Library
• pdb: fixed reading TLS S tensor
• Structure metadata: expanded RefinementInfo

Python

• Python bindings migrated from pybind11 to nanobind.
  • Much lower runtime overhead, faster build times, better error diagnostics.
  • Built-in typing stubs.
  • Only Python 3.8+.
  • Sadly, no support for Buffer Protocol. It was replaced with NumPy __array__ methods.
    For NumPy, you can also use .array properties that were available also in the previous releases.
  • No implicit conversions from list to ndarray, and from bytes to string (let me know where it causes problems)
  • gemmi.ValueSigmaAsuData.value_array has now shape (N,2)
• Added pickling support for Structure, Model, Chain, Residue, Atom, cif.Document, cif.Block.
• Added function interpolate_position_array (#​323).
• Python extension module is now installed into site-packages/gemmi/ (this change should be invisible to the user)

Program

• gemmi convert --sifts-num is now more customizable
• gemmi sf2map: added option --check (see docs)
• gemmi cif2mtz: add a rule to spec to convert pdbx_F_calc_with_solvent to F-model (+phase)
• gemmi xds2mtz: handles merged files from XSCALE
• gemmi mtz2cif and merge: recognize extension .ahkl as XDS file

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