chemfiles / chemfiles

New features

• Add a public Residue class to C++ and C API to represent residue data.
  Residues are groups of atoms bonded together, which may or may not correspond
  to molecules; and are often used for bio-molecules.
• Add the resname and resid selector, to select atoms based on their
  residue.
• Account for the difference between the atom name ("H1") and atom type ("H")
  in some formats (PDB, TNG, ...). This introduces the Atom::type member
  function and the chfl_atom_type C API function.
• Add the type selector, to select atoms based on their type.
• Add "Frame::add_atom" function to add an atom and the corresponding position
  (and velocity) data to a frame, and the C API chfl_frame_add_atom function.
• Rename UnitCell::type to UnitCell::shape. This also affect
  chfl_cell_shape_t, chfl_cell_shape, and chfl_cell_set_shape.
• All the floating point data uses doubles instead of floats. This concerns
  atomic data, positions and velocities.
• Add "Selection::string" function and the corresponding chfl_selection_string
  to get the string used to build a selection.
• Selection variables uses the #3 syntax instead of the $3 syntax to allow
  passing selection string as shell arguments.
• Add Frame::remove and chfl_frame_remove to remove an atom in a frame.
• Allow to use chemfiles with Cmake find_package.

Changes in supported formats

• Add read support for TNG files, an new portable and compressed binary format
  used by GROMACS.

C API changes

• All the integers at C boundary have a fixed size, most of the time using
  uint64_t.
• Add missing chfl_topology_resize function to C API.
• C API functions taking three lengths/angles now take a double[3] parameter
  instead.
• Rename chfl_topology_are_linked to chfl_topology_residues_linked.
• Rename chfl_topology_append to chfl_topology_add_atom.
• Remove chfl_strerror, as it is redundant with chfl_last_error.
• Merge chfl_trajectory_set_topology_file and chfl_trajectory_set_topology_with_format
  into chfl_trajectory_topology_file.
• The chfl_frame function no longer take the frame size as argument. It always
  creates an empty frame, that you can resize using chfl_frame_resize.
• chfl_selection_evalutate was a typo, it is renamed to chfl_selection_evaluate.

Deprecation and removals

• Remove the Atom::type enum from C and C++ API.
• Remove the Trajectory::sync and the chfl_trajectory_sync functions.
  To ensure that all content of a file is written to the disk, the user need to
  close it.
• Remove the Logger and all the chfl_log* functions. Instead, the users can
  use chemfiles::set_warning_callback or chfl_set_warning_callback to set a
  global callback to call on warnings events.