Accepting request 717711 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/717711
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-biopython?expand=0&rev=3

biopython-1.73.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0
-size 15715102

biopython-1.74.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0
+size 16129257

python-biopython.changes

@@ -1,3 +1,53 @@
+-------------------------------------------------------------------
+Tue Jul 23 01:23:01 UTC 2019 - Todd R <toddrme2178@gmail.com>
+
+- Update to version 1.74
+  * Our core sequence objects (``Seq``, ``UnknownSeq``, and ``MutableSeq``) now
+    have a string-like ``.join()`` method.
+  * The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning
+    the fields may not always follow the historical column based positions. We
+    no longer give a warning when parsing these. We now allow writing such files
+    (although with a warning as support for reading them is not yet widespread).
+  * Support for the ``mysqlclient`` package, a fork of MySQLdb, has been added.
+  * We now capture the IDcode field from PDB Header records.
+  * ``Bio.pairwise2``'s pretty-print output from ``format_alignment`` has been
+    optimized for local alignments: If they do not consist of the whole sequences,
+    only the aligned section of the sequences are shown, together with the start
+    positions of the sequences (in 1-based notation). Alignments of lists will now
+    also be prettily printed.
+  * ``Bio.SearchIO`` now supports parsing the text output of the HHsuite protein
+    sequence search tool. The format name is ``hhsuite2-text`` and
+    ``hhsuite3-text``, for versions 2 and 3 of HHsuite, respectively.
+  * ``Bio.SearchIO`` HSP objects has a new attribute called ``output_index``. This
+    attribute is meant for capturing the order by which the HSP were output in the
+    parsed file and is set with a default value of -1 for all HSP objects. It is
+    also used for sorting the output of ``QueryResult.hsps``.
+  * ``Bio.SeqIO.AbiIO`` has been updated to preserve bytes value when parsing. The
+    goal of this change is make the parser more robust by being able to extract
+    string-values that are not utf-8-encoded. This affects all tag values, except
+    for ID and description values, where they need to be extracted as strings
+    to conform to the ``SeqRecord`` interface. In this case, the parser will
+    attempt to decode using ``utf-8`` and fall back to the system encoding if that
+    fails. This change affects Python 3 only.
+  * ``Bio.motifs.mast`` has been updated to parse XML output files from MAST over
+    the plain-text output file. The goal of this change is to parse a more
+    structured data source with minimal loss of functionality upon future MAST
+    releases. Class structure remains the same plus an additional attribute
+    ``Record.strand_handling`` required for diagram parsing.
+  * ``Bio.Entrez`` now automatically retries HTTP requests on failure. The
+    maximum number of tries and the sleep between them can be configured by
+    changing ``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.
+    (The defaults are 3 tries and 15 seconds, respectively.)
+  * All tests using the older print-and-compare approach have been replaced by
+    unittests following Python's standard testing framework.
+  * On the documentation side, all the public modules, classes, methods and
+    functions now have docstrings (built in help strings). Furthermore, the PDF
+    version of the *Biopython Tutorial and Cookbook* now uses syntax coloring
+    for code snippets.
+  * 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.
+
 -------------------------------------------------------------------
 Fri Jan  4 17:31:38 UTC 2019 - Todd R <toddrme2178@gmail.com>
 

python-biopython.spec

@@ -21,10 +21,10 @@
 
 %{?!python_module:%define python_module() python-%{**} python3-%{**}}
 Name:           python-biopython
-Version:        1.73
+Version:        1.74
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
-License:        MIT
+License:        MIT AND BSD-3-Clause
 Group:          Development/Libraries/Python
 Url:            http://www.biopython.org
 Source0:        https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
@@ -47,7 +47,6 @@ Recommends:     python-pydot
 Recommends:     python-pygraphviz
 Recommends:     python-rdflib
 Recommends:     python-reportlab
-BuildRoot:      %{_tmppath}/%{name}-%{version}-build
 %python_subpackages
 
 %description