Gemmi

* a number of fixes, mostly in topology preparation
* support for extended (longer) CCD and PDB codes that are about to be introduced by the PDB
* gemmi-convert: added option to rename a monomer
* a few changes and additions in cif2mtz, including:
* anomalous data written as separate rows for F+ and F- is now converted as expected
* _refln.F_squared_meas is now a synonym for F_squared_meas
* gemmi-grep: new option --only-tags
* gemmi-validate: a couple of new checks and options
* pdb and mmCIF: convert MODRES <-> _pdbx_struct_mod_residue
* cif.Block: blocks with no name (just ``data_``) used to have the name set to "", now it's " "

* changed how CISPEP is stored: previously, it was assumed that a link between two residues is either TRANS or CIS; if the residues have atoms with alternative conformations, both link types can be present at the same time
* riding hydrogens: previously, hydrogens had the same altlocs as the parent atom; now if the parent atom has a single conformation, but it has neighbors in multiple conformations, the hydrogens will be also added in multiple conformations
* major changes in NearestNeighbor: now it's possible to search atoms not only in the first nearest [cells][1], but in any number of nearest cells; find_nearest_atom() was changed to find, by default, a nearest atom within any distance
* changes in Mtz.reindex(), primarily to fix determination of the new space group
* gemmi-convert: added option --all-auth to write `_atom_site.auth_atom_id` and `auth_comp_id`, which are skipped by default (because they are always the same as label_…_id)
* added more options to gemmi-rmsz, gemmi-xds2mtz, gemmi-cif2mtz
* fix a recent regression in check_polymer_type(): RNA was returned instead of DNA
* improved heuristic of detecting where the polymer ends (if TER record is missing)
* selection syntax: fix parsing a single sequence id such as "A/208" (it was parsed as A/208-/)
* removed SMat33::calculate_eigenvector() – use eigen_decomposition() instead; SoftwareItem::pdbx_ordinal; NeighborSearch::Mark::x,y,z (use ::pos)
* more code was moved from headers to src/*.cpp

[1]: https://en.wikipedia.org/wiki/Cell_lists

* C++ library is no longer header-only, several function were moved from headers to src/ to make compilation faster
* major changes in cmake build, requiring now cmake 3.15+
* improvements in calculating riding hydrogen positions
* changed again the scheme of automatically assigned subchain names (A-p -> Axp, because PDB software can't handle non-alphanumeric characters there)
* a function for calculating polarization correction for XDS INTEGRATE.HKL
* improvements in xds2mtz, converting more data and filling more records in MTZ batch headers
* added SpaceGroup::change_of_hand_op()
* various bug fixes and small improvements

* gemmi program has new subcommand xds2mtz that converts from XDS_ASCII to multirecord MTZ
* subcommand gemmi-residues has new option -s (--short) for shorter overview of model chains (can be used twice)
* cif2mtz: more flexible spec for converting symbols to numbers
* preparation of Refmac intermediate files – it can be used to substitute a part of Refmac
* MonLib and Topo: a number of changes related to reading a monomer library and in prepare_topology()
* changed the scheme of automatically assigned subchain names (Apoly -> A-p)
* read_structure(): added optional arg `save_doc` that stores cif.Document if the read file is mmCIF or mmJSON
* reading PDB files: more metadata is read by default
* writing mmCIF files: _atom_site.group_PDB is written by default
* support for mmCIF extension _atom_site.ccp4_deuterium_fraction
* added function copy_from_mmdb(mmdb::Manager* manager) -> Structure
* improved check_polymer_type()
* Grid::set_size_from_spacing() with different rounding modes
* rename src/ to prog/; in the next version the library won't be fully header-only, cpp files will go into src/

* new functions for working with Structure: assign_serial_numbers(), assign_cis_flags(), has_hydrogen()
* enhanced transform_to_assembly()
* functions count_atom_sites() and count_occupancies() now take Selection as an optional arg
* deprecated count_hydrogen_sites(): can be replaced with has_hydrogen() or count_atom_sites(Selection("[H,D]"))
* selection syntax extended with ";polymer" and ";solvent" (it can also be "!polymer,solvent")
* improved preparation of the intermediate file (crd) for Refmac
* gemmi program: several options were added to subprograms
* Ccp4.setup() now returns void (previously – number)
* python: cif.Block.find_pair() and Item.pair were changed to return tuple (previously – list)

* calculating ASU brick for given space group settings
* add reciprocal ASU definitions used by [TNT](http://www.uoxray.uoregon.edu/tnt/)
* add option `style` to Op.triplet()
* add cif.Block.set_pairs() – it adds name-value pairs to a given category
* various bug fixes, as usual
* Python 2.7 is no longer listed as supported