- add py313-support.patch to fix build with python 3.13

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- update to 1.84:
  * The old parser stores information in a
    Bio.Blast.NCBIXML.Blast object, with attribute names based on
    plain-text Blast output. The new parser stores information in
    a Bio.Blast.Record object. This class follows the DTD that
    describes the XML in terms of attribute names and dictionary
    key names, class structure, and object types. This makes it
    easier to find the detailed description of each field in the
    NCBI Blast documentation.
  * The old parser stores alignment information directly as seen
    in the BLAST XML output, i.e. as strings with dashes to
    represent gaps. The new parser stores the alignment
    information as a Bio.Align.Alignment object, which can then
    be used to e.g. print the alignment in a different format.

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- 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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- update to 1.79:
  * This is intended to be our final release supporting Python 3.6. It also
  supports Python 3.7, 3.8 and 3.9, and has also been tested on PyPy3.6.1 v7.1.1.
  * Detailed list of changes see 
  https://github.com/biopython/biopython/blob/biopython-179/NEWS.rst#1-june-2021-biopython-179

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- Update to version 1.7.8.
  * The main change is that Bio.Alphabet is no longer used. In some
    cases you will now have to specify expected letters, molecule 
    type (DNA, RNA, protein), or gap character explicitly.
  * Bio.SeqIO.parse() is faster with "fastq" format due to small 
    improvements in the Bio.SeqIO.QualityIO module.
  * The SeqFeature object's .extract() method can now be used for 
    trans-spliced locations via an optional dictionary of references.
  * As in recent releases, more of our code is now explicitly 
    available under either our original "Biopython License Agreement",
    or the very similar but more commonly used "3-Clause BSD License".
    See the LICENSE.rst file for more details.
  * Additionally, a number of small bugs and typos have been fixed
    with additions to the test suite. There has been further work to
    follow the Python PEP8, PEP257 and best practice standard coding
    style, and all of the tests have been reformatted with the black
    tool to match the main code base.
- Skip python36 because numpy no longer support it.

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

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- Update to version 1.77
  * **We have dropped support for Python 2 now.**
  * ``pairwise2`` now allows the input of parameters with keywords and returns the
    alignments as a list of ``namedtuples``.
  * The codon tables have been updated to NCBI genetic code table version 4.5,
    which adds Cephalodiscidae mitochondrial as table 33.
  * Updated ``Bio.Restriction`` to the January 2020 release of REBASE.
  * A major contribution by Rob Miller to ``Bio.PDB`` provides new methods to
    handle protein structure transformations using dihedral angles (internal
    coordinates). The new framework supports lossless interconversion between
    internal and cartesian coordinates, which, among other uses, simplifies the
    analysis and manipulation of coordinates of proteins structures.
  * ``PDBParser`` and ``PDBIO`` now support PQR format file parsing and input/
    output.
  * In addition to the mainstream ``x86_64`` aka ``AMD64`` CPU architecture, we
    now also test every contribution on the ``ARM64``, ``ppc64le``, and ``s390x``
    CPUs under Linux thanks to Travis CI. Further post-release testing done by
    Debian and other packagers and distributors of Biopython also covers these
    CPUs.
  * ``Bio.motifs.PositionSpecificScoringMatrix.search()`` method has been
    re-written: it now applies ``.calculate()`` to chunks of the sequence
    to maintain a low memory footprint for long sequences.
  * Additionally, a number of small bugs and typos have been fixed with further
    additions to the test suite. There has been further work to follow the Python
    PEP8, PEP257 and best practice standard coding style, and more of the code
    style has been reformatted with the ``black`` tool.

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