- update to 1.83:
  * This release reverts the removal of the .strand, .ref, and
    .ref_db attributes of the SeqFeature which was done without a
    deprecation period. They are again aliases for
    .location.strand etc, but trigger deprecation warnings.

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- update to 1.82:
  * The ``inplace`` argument of ``complement`` and
    ``reverse_complement`` in ``Bio.Seq`` now always default to
    ``False`` both for ``Seq`` and ``MutableSeq`` objects.
    To modify a ``MutableSeq`` in-place, use ``inplace=True``.
  * A new class ``CodonAligner`` was added to ``Bio.Align``. A
    ``CodonAligner`` object can align a nucleotide sequence to the
    amino acid sequence it encodes, using a dynamic programming
    algorithm modeled on ``PairwiseAligner`` to take frame shifts
    into account. The ``CodonAligner`` returns ``Alignment``
    objects.
  * By calling the new ``mapall`` method on an ``Alignment``
    object storing a multiple sequence alignment of amino acid
    sequences, with nucleotide-to-amino acid alignments generated
    by ``CodonAligner`` as the argument, a codon-by-codon
    multiple sequence alignment of nucleotide sequences can be
    obtained. The new submodule ``Bio.Align.analysis`` provides
    functions to estimate synonymous and nonsynonymous mutations
    and to perform the McDonald-Kreitman test on the codon
    multiple sequence alignments. Together, this provides the
    same functionality as the ``Bio.codonalign`` module, but uses
    the standard ``Alignment`` class, and does not rely on regular
    expression searching to align a nucleotide sequence to
    an amino acid sequence.
  * The ``hmmer3-text`` SearchIO format now also extracts the
    similarity string of the parsed alignments.
  * HMMER results with the full path to the hmmer executable in
    the banner are now parsed correctly.
  * We now have basic type hint annotations in various modules
    including ``Seq``, ``SeqRecord``, and ``SeqIO``.

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- update to 1.81:
  * The API documentation and the `Biopython Tutorial and
    Cookbook` have been updated to better annotate use and
    application of the ``Bio.PDB.internal_coords`` module.
  * ``Bio.Phylo`` now supports ``Alignment`` and
    ``MultipleSeqAlignment`` objects as input.
  * Several improvements and bug fixes to the snapgene parser

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- 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

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Automatic submission by obs-autosubmit

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- Remove ridiculously wide find commands in %prep, which break a lot
  (binary) files.

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computational molecular biology for python

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