- update to 1.80:
* This release of Biopython supports Python 3.7, 3.8, 3.9, 3.10, 3.11. It
has also been tested on PyPy3.7 v7.3.5.
* Functions ``read``, ``parse``, and ``write`` were added to ``Bio.Align``
to read and write ``Alignment`` objects.
* Because dict retains the item order by default since Python3.6, all
instances of ``collections.OrderedDict`` have been replaced by either standard
``dict`` or where appropriate by ``collections.defaultsdict``.
* The ``Bio.motifs.jaspar.db`` now returns ``tf_family`` and ``tf_class``
as a string array since the JASPAR 2018 release.
* The Local Composition Complexity functions from ``Bio.SeqUtils`` now
uses base 4 log instead of 2 as stated in the original reference Konopka
(2005), * Sequence Complexity and Composition. https://doi.org/10.1038/npg.els.0005260
* Append mode is now supported in ``Bio.bgzf`` (and a bug parsing blocked
GZIP files with an internal empty block fixed).
* The experimental warning was dropped from ``Bio.phenotype`` (which was
new in Biopython 1.67).
* Sequences now have a ``defined`` attribute that returns a boolean
indicating if the underlying data is defined or not.
* The ``Bio.PDB`` module now includes a structural alignment module, using
the combinatorial extension algorithm of Shindyalov and Bourne, commonly
known as CEAlign. The module allows for two structures to be aligned based solely
on their 3D conformation, ie. in a sequence-independent manner. The method
is particularly powerful when the structures shared a very low degree of
sequence similarity. The new module is available in ``Bio.PDB.CEAligner`` with an
interface similar to other 3D superimposition modules.
* A new module ``Bio.PDB.qcprot`` implements the QCP superposition
algorithm in pure Python, deprecating the existing C implementation. This leads to a
slight performance improvement and to much better maintainability. The
refactored ``qcprot.QCPSuperimposer`` class has small changes to its API, to better