Accepting request 750002 from home:TheBlackCat:branches:devel:languages:python:numeric

Update to version 1.75

OBS-URL: https://build.opensuse.org/request/show/750002
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=7

python-biopython.changes

@@ -1,3 +1,55 @@
+-------------------------------------------------------------------
+Wed Nov 20 20:17:31 UTC 2019 - Todd R <toddrme2178@gmail.com>
+
+- Update to version 1.75
+  * The restriction enzyme list in Bio.Restriction has been updated to the August
+    2019 release of REBASE.
+  * ``Bio.SeqIO`` now supports reading and writing files in the native format of
+    Christian Marck's DNA Strider program ("xdna" format, also used by Serial
+    Cloner), as well as reading files in the native formats of GSL Biotech's
+    SnapGene ("snapgene") and Textco Biosoftware's Gene Construction Kit ("gck").
+  * ``Bio.AlignIO`` now supports GCG MSF multiple sequence alignments as the "msf"
+    format (work funded by the National Marrow Donor Program).
+  * The main ``Seq`` object now has string-like ``.index()`` and ``.rindex()``
+    methods, matching the existing ``.find()`` and ``.rfind()`` implementations.
+    The ``MutableSeq`` object retains its more list-like ``.index()`` behaviour.
+  * The ``MMTFIO`` class has been added that allows writing of MMTF file format
+    files from a Biopython structure object. ``MMTFIO`` has a similar interface to
+    ``PDBIO`` and ``MMCIFIO``, including the use of a ``Select`` class to write
+    out a specified selection. This final addition to read/write support for
+    PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
+  * Values from mmCIF files are now read in as a list even when they consist of a
+    single value. This change improves consistency and reduces the likelihood of
+    making an error, but will require user code to be updated accordingly.
+  * ``Bio.PDB`` has been updated to support parsing REMARK 99 header entries from
+    PDB-style Astral files.
+  * A new keyword parameter ``full_sequences`` was added to ``Bio.pairwise2``'s
+    pretty print method ``format_alignment`` to restore the output of local
+    alignments to the 'old' format (showing the whole sequences including the
+    un-aligned parts instead of only showing the aligned parts).
+  * A new function ``charge_at_pH(pH)`` has been added to ``ProtParam`` and
+    ``IsoelectricPoint`` in ``Bio.SeqUtils``.
+  * The ``PairwiseAligner`` in ``Bio.Align`` was extended to allow generalized
+    pairwise alignments, i.e. alignments of any Python object, for example
+    three-letter amino acid sequences, three-nucleotide codons, and arrays of
+    integers.
+  * A new module ``substitution_matrices`` was added to ``Bio.Align``, which
+    includes an ``Array`` class that can be used as a substitution matrix. As
+    the ``Array`` class is a subclass of a numpy array, mathematical operations
+    can be applied to it directly, and C code that makes use of substitution
+    matrices can directly access the numerical values stored in the substitution
+    matrices. This module is intended as a replacement of ``Bio.SubsMat``,
+    which is currently unmaintained.
+  * 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 further
+    additions to the test suite, and there has been further work to follow the
+    Python PEP8, PEP257 and best practice standard coding style. We have also
+    started to use the ``black`` Python code formatting tool.
+
+
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 Tue Jul 23 01:23:01 UTC 2019 - Todd R <toddrme2178@gmail.com>