Changelog

Additions

Added shape property to structure.AtomArray() and
structure.AtomArrayStack()
structure.Atom() has default values for annotation arrays
The functions structure.rmsf(), structure.rmsd() and structure.average()
accept directly coordinates
Added use_author_fields parameter to structure.io.pdbx.get_structure(),
that allows to decide between the usage of label_xxx and auth_xxx fields
Added chunk_size parameter to read() method of trajectory files to
resolve memory issues
Added density() function for calculating atom densities.
Added sequence.align.get_pairwise_sequence_identity()
API reference shows source files of Cython modules

The module name (__module__ attribute) of functions/classes are
changed to the name of the respective Biotite subpackage
(e.g. biotite.structure.atoms to biotite.structure)
Changed handling of PDB insertion codes:
- Atoms with insertion codes are not filtered out
- Removed insertion_code parameter in
  biotite.structure.io.xxx.get_structure()
- New mandatory annotation category ins_code
- Changed structure.filter_inscode_and_altloc() to
  structure.filter_altloc()

The step parameter in the read() method of trajectory files does not
increase the stop frame
Negative residue IDs are handled correctly by structure file readers/writers
Fixed issues with indexing behavior in sequence.align.Alignment class
structure.remove_pbc() raises proper error message when box is missing
in the given atom array (stack)
sequence.align.align_multiple() raises proper error message, if
pairwise distance cannot be calculated due to great sequence dissimilarity
In sequence.io.genbank.get_annotation() qualifier keys without values
(e.g. /pseudo) are handled properly
Added pyproject.toml specifying build dependencies for setup.py