Accepting request 662924 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/662924
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=2

python-biopython.changes

@@ -1,3 +1,55 @@
+-------------------------------------------------------------------
+Fri Jan  4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>
+
+- Update to version 1.73
+  * 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.
+  * The dictionary-like indexing in SeqIO and SearchIO will now explicitly preserve
+    record order to match a behaviour change in the Python standard dict object.
+    This means looping over the index will load the records in the on-disk order,
+    which will be much faster (previously it would be effectively at random, based
+    on the key hash sorting).
+  * The "grant" matrix in Bio.SubsMat.MatrixInfo has been replaced as our original
+    values taken from Gerhard Vogt's old webpages at EMBL Heidelberg were
+    discovered to be in error. The new values have been transformed following
+    Vogt's approach, taking the global maximum 215 minus the similarity scores
+    from the original paper Grantham (1974), to give a distance measure.
+  * 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.
+  * Double-quote characters in GenBank feature qualifier values in ``Bio.SeqIO``
+    are now escaped as per the NCBI standard. Improperly escaped values trigger a
+    warning on parsing.
+  * There is a new command line wrapper for the BWA-MEM sequence mapper.
+  * The string-based FASTA parsers in ``Bio.SeqIO.FastaIO`` have been optimised,
+    which also speeds up parsing FASTA files using ``Bio.SeqIO.parse()``.
+- Update to version 1.72
+  * Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and
+    SeqIO.write (especially when used in a for loop).
+  * The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use
+    inclusive end co-ordinates to better handle searches at end points. This
+    will require you to rebuild any existing MAF index files.
+  * In this release 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.
+  * The Entrez module now supports the NCBI API key. Also you can now set a custom
+    directory for DTD and XSD files. This allows Entrez to be used in environments
+    like AWS Lambda, which restricts write access to specific directories.
+    Improved support for parsing NCBI Entrez XML files that use XSD schemas.
+  * Internal changes to our C code mean that NumPy is no longer required at
+    compile time - only at run time (and only for those modules which use NumPy).
+  * Seq, UnknownSeq, MutableSeq and derived classes now support integer
+    multiplication methods, matching native Python string methods.
+  * A translate method has been added to Bio.SeqFeature that will extract a
+    feature and translate it using the codon_start and transl_table qualifiers
+    of the feature if they are present.
+  * Bio.SearchIO is no longer considered experimental, and so it does not raise
+    warnings anymore when imported.
+  * A new pairwise sequence aligner is available in Bio.Align, as an alternative
+    to the existing pairwise sequence aligner in Bio.pairwise2.
+
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 Wed May  9 03:23:14 UTC 2018 - toddrme2178@gmail.com