Gemmi

* 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

* determining lattice symmetry and (psuedo-)merohedral twinning laws
* added GroupOps::derive_symmorphic() and GroupOps::add_inversion()
* getting change-of-basis in the Niggli reduction
* added transform_to_assembly() – it does a bit more than make_assembly()
* removed Op::negated()
* python: add bindings to UnitCell.orth and UnitCell.frac
* additional options in gemmi-mtz2cif and gemmi-cif2mtz
* bug fixes (in Ccp4::set_extent(), merge_atoms_in_expanded_model(), status column in mtz2cif)

- new sub-program under development: gemmi-prep
- parse pdb AUTHOR record and corresponding mmCIF category
- new function flood_fill_above()
- mtz2cif: rhombohedral groups in hexagonal settings start with H now
- renamed MonLib::find_link() to get_link(), modified MonLib::match_link()
- CIF files can be written with left-aligned columns
- bug fixes and minor changes (in particular in class Topo)

* API change: changed arguments for Ccp4.setup()
* added Binner class for analyzing reflections in resolution bins
* added support for neutron scattering in gemmi-sfcalc and the library
* new functions: seitz_to_op, normalize_grid, Grid.get_subarray, Grid.set_subarray
* minor improvements in programs mtz2cif, cif2mtz, map
* fix: CIF tags are now case insensitive
* changes in preparing topology accounting for changes in Refmac and CCP4 monomer library