Gemmi

* various bug fixes and small improvements, many of them for the MTZ -> mmCIF conversion
* new and documented functions: cif.Table.move_row(), ResidueInfo.fasta_code(), GroupOps.add_missing_elements(), NeighborSearch.add_chain()
* added customizable form factors for unknown element (X) 167
* improved reading of unusual PDB files 169
* calculate_superposition(): added option to use backbone only
* calculating RMSD without superposition is a separate function now: calculate_current_rmsd()
* simplified MaskedGrid, Grid.asu() renamed to masked_asu()
* renamed Intensities.Type to DataType
* a few experimental functions (not documented and not sufficiently tested yet):
* read_first_block_gz() – read only first block of CIF without reading the whole file
* Mtz.ensure_asu() – changes Miller indices together with phase shifts and anomalous data swapping
* interpolate_grid_of_aligned_model() – for grid interpolation based on model alignment (currently global alignment only, local alignment such as in PanDDA is not implemented yet)
* check_data_type_under_symmetry() – for checking if mmCIF refln category contains mean, anomalous or unmerged data

* various bug fixes
* support for huge MTZ files (>2GB) using the format extension added in CCP4 8.0 – implemented by Claus
* better handling of NaNs in maps
* option to detect the format of a coordinate file (format=CoorFormat.Detect)
* major changes in class Topo (which is undocumented yet)
* store _atom_site.label_entity_id from mmCIF as Residue::entity_id
* two more tabulated space group settings: C 4 2 2 and C 4 2 21
* new functions Mtz.copy_column() and Mtz.replace_column(), SmallStructure.make_cif_block()
* and a number of minor additions including: Grid.clone(), Grid.change_values(), Model.remove_*(), transform_pos_and_adp(), MonLib.mon_lib_list, SmallStructure.wavelength, UnitCell.approx(), SMat33.multiply(), Structure.input_format
* new options in the command-line program: gemmi mtz --histogram, gemmi cif2mtz --add

* bug fixes
* Selling-Delaunay reduction
* gemmi program: enhancements in `mtz2cif`, `cif2mtz` and `merge`
* SymImage renamed to NearestImage, its properties has also changed
* calculate_superposition(): optional outlier rejection (inspired by PyMOL)

* centred to primitive lattce transformation
* Niggli reduction and Buerger reduction for lattice basis
* added ``UnitCell::is_compatible_with_spacegroup()``
* Topology-related improvements (Keitaro)
* functions ``SMat33::elements()`` and ``change_basis()`` were replaced – each was replaced with two new functions
* more options in gemmi-merge
* more Python bindings
* various fixes, in particular in validation in ``gemmi mtz2cif --depo``.

* reindexing MTZ files,
* tricubic map interpolation,
* extended selection syntax,
* merge_atoms_in_expanded_model() – sort out atoms on special positions after expanding NCS or making bioassembly,
* IT92::normalize() – makes exactly the same scattering coefficients that Refmac uses,
* Mtz::remove_column(),
* understanding triplets with x/N ("h/2+k/2, -h/2+k/2, l"),
* better inference of elements in a PDB file with missing element field,
* Topo::Force was renamed to Topo::Rule,
* various other additions and, most importantly, bug fixes.

Python porting note: CIF parsing may raise `ValueError`; opening a file may rise `IOError`. Previously it was `RuntimeError`.