Accepting request 874100 from home:andythe_great:branches:devel:languages:python:numeric

- 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.

OBS-URL: https://build.opensuse.org/request/show/874100
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=13

biopython-1.77.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:fb1936e9ca9e7af8de1050e84375f23328e04b801063edf0ad73733494d8ec42
-size 16837021

biopython-1.78.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564
+size 16895184

python-biopython.changes

@@ -1,3 +1,25 @@
+-------------------------------------------------------------------
+Sat Feb 20 19:29:23 UTC 2021 - andy great <andythe_great@pm.me>
+
+- 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.
+
 -------------------------------------------------------------------
 Tue Nov  3 15:58:16 UTC 2020 - Matej Cepl <mcepl@suse.com>
 

python-biopython.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-biopython
 #
-# Copyright (c) 2020 SUSE LLC
+# Copyright (c) 2021 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -20,8 +20,9 @@
 # Tests require a network connection
 %bcond_with test
 %define skip_python2 1
+%define skip_python36 1
 Name:           python-biopython
-Version:        1.77
+Version:        1.78
 Release:        0
 Summary:        Python Tools for Computational Molecular Biology
 License:        MIT AND BSD-3-Clause
@@ -54,7 +55,6 @@ available Python tools for computational molecular biology.
 %prep
 %setup -q -n biopython-%{version}
 find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
-sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' Scripts/Structure/hsexpo
 # Example scripts cannot be in a subdirectory
 mv -v Doc/examples examples