Update dependency gemmi to >=0.5.5, <=0.6.5

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
gemmi	>=0.5.5, <=0.6.4 -> >=0.5.5, <=0.6.5

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Release Notes

project-gemmi/gemmi (gemmi)

v0.6.5: 0.6.5

Compare Source

Library:

• gemmi can now be built with zlib-ng, a faster fork of zlib (good for working with large, compressed files)
• experimental: binary serialization of Structure (contained objects, such as Model, Chain or UnitCell, can also be serialized separately)
• finalized handling of 5-character monomer names; uses the tilde-hetnam extension (ABCDE ↔ ~DE) for PDB files
• when atom names in the coordinate file match previous names (_chem_comp_atom.alt_atom_id) from the monomer library (the names in the CCD and therefore also in the ML change occasionally), print better diagnostic; added function MonLib::update_old_atom_names() to update the names in a Structure
• topology: fixed handling of two bonds between the same two residues
• options for handling mmCIF files with incorrect entities (modified add_entity_ids() when called with overwrite=true)
• added function Intensities::prepare_merged_mtz()
• a few bug fixes (for instance, in handling of negative residue numbers in the selection syntax)

Python bindings:

• generating type stubs - see #​293
• python: cif.Loop.val() has been replaced with __getitem__/__setitem__
• fixed Mtz.Batch.ints and Mtz.Batch.floats

Program

• subcommand diff has been renamed to cifdiff
• subcommand prep has been renamed to crd
• validate: more options for checking monomer files
• gemmi-grep: added option --extended-regexp
• mtz2cif: added column names Iplus/Iminus (used by ccp4i2) to the default conversion spec

Note: this list is meant to show important changes only.

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