[med-svn] [Git][med-team/seqmagick][master] 7 commits: New upstream version 0.8.0
Steffen Möller
gitlab at salsa.debian.org
Sat Jan 18 21:33:07 GMT 2020
Steffen Möller pushed to branch master at Debian Med / seqmagick
Commits:
dc635cd2 by Steffen Moeller at 2020-01-18T22:22:07+01:00
New upstream version 0.8.0
- - - - -
75b1bb9c by Steffen Moeller at 2020-01-18T22:22:07+01:00
routine-update: New upstream version
- - - - -
0da30484 by Steffen Moeller at 2020-01-18T22:22:09+01:00
Update upstream source from tag 'upstream/0.8.0'
Update to upstream version '0.8.0'
with Debian dir a4cf568c590f8829cc908e3a30faf8cfb1380ab4
- - - - -
bdbed89d by Steffen Moeller at 2020-01-18T22:22:09+01:00
routine-update: debhelper-compat 12
- - - - -
bcd033cb by Steffen Moeller at 2020-01-18T22:22:12+01:00
routine-update: Standards-Version: 4.4.1
- - - - -
c95d759d by Steffen Moeller at 2020-01-18T22:26:09+01:00
Preparing for 0.8
- - - - -
9179005c by Steffen Moeller at 2020-01-18T22:32:32+01:00
Remove autogenerated version string and egg-info
- - - - -
12 changed files:
- .travis.yml
- CHANGELOG.rst
- README.rst
- debian/changelog
- − debian/compat
- debian/control
- debian/patches/biopython_1.71_dual_coding_support.patch
- debian/rules
- + requirements-rtd.txt
- seqmagick/scripts/cli.py
- seqmagick/transform.py
- setup.py
Changes:
=====================================
.travis.yml
=====================================
@@ -2,9 +2,11 @@ language: python
python:
# - "2.7"
# - "pypy"
- - "3.4"
+ # - "3.4"
- "3.5"
- "3.6"
+ - "3.7"
+ - "3.8"
# Install numpy, then BioPython
# BioPython doesn't always play well with pip install.
=====================================
CHANGELOG.rst
=====================================
@@ -1,6 +1,15 @@
Changes for seqmagick
=====================
+0.8.0
+-----
+
+* Supports Python 3.5+
+* Drops support for Python 3.4
+* Fix issue: "seqmagick with no params gives KeyError:None" [GH-77]
+* Fix for Biopython 1.71 dual coding support [GH-76]; also fixes issue: "Translation error with new BioPython" [GH-79]
+* Send logging to stderr, not stdout [GH-75]
+
0.7.0
-----
=====================================
README.rst
=====================================
@@ -32,7 +32,7 @@ Use pip::
Note that as of version 0.7.0, this package requires Python 3.4+. If
you want to use the most recent version compatible with Python 2.7::
- pip install seqmagick==1.6.2
+ pip install seqmagick==0.6.2
Features
========
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+seqmagick (0.8.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * debhelper-compat 12 (routine-update)
+ * Standards-Version: 4.4.1 (routine-update)
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 18 Jan 2020 22:22:51 +0100
+
seqmagick (0.7.0-1) unstable; urgency=medium
* Initial release (Closes: #900394)
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
python3-all,
python3-setuptools,
python3-nose,
python3-biopython
-Standards-Version: 4.1.4
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/seqmagick
Vcs-Git: https://salsa.debian.org/med-team/seqmagick.git
Homepage: https://github.com/fhcrc/seqmagick/
=====================================
debian/patches/biopython_1.71_dual_coding_support.patch
=====================================
@@ -17,11 +17,13 @@ forwarding this to the wrapped forward table.
seqmagick/transform.py | 4 ++++
1 file changed, 4 insertions(+)
---- a/seqmagick/transform.py
-+++ b/seqmagick/transform.py
-@@ -668,6 +668,10 @@ class CodonWarningTable(object):
- else:
- return self.wrapped.__getitem__(codon)
+Index: seqmagick/seqmagick/transform.py
+===================================================================
+--- seqmagick.orig/seqmagick/transform.py
++++ seqmagick/seqmagick/transform.py
+@@ -673,6 +673,10 @@ class CodonWarningTable(object):
+ return value in self.wrapped
+
+ def __contains__(self, value):
+ return value in self.wrapped
=====================================
debian/rules
=====================================
@@ -5,3 +5,8 @@ export LC_ALL=C.UTF-8
%:
dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf seqmagick/data
+ rm -rf seqmagick.egg-info
=====================================
requirements-rtd.txt
=====================================
@@ -0,0 +1,2 @@
+biopython
+sphinx
=====================================
seqmagick/scripts/cli.py
=====================================
@@ -24,7 +24,7 @@ def main(argv=sys.argv[1:]):
logformat = '%(message)s'
# set up logging
- logging.basicConfig(stream=sys.stdout, format=logformat, level=loglevel)
+ logging.basicConfig(stream=sys.stderr, format=logformat, level=loglevel)
return action(arguments)
@@ -65,6 +65,8 @@ def parse_arguments(argv):
arguments.argv = argv
action = arguments.subparser_name
+ if action is None:
+ parse_arguments(['-h'])
if action == 'help':
return parse_arguments([str(arguments.action), '-h'])
=====================================
seqmagick/transform.py
=====================================
@@ -43,7 +43,8 @@ def _record_buffer(records, buffer_size=DEFAULT_BUFFER_SIZE):
def record_iter():
tf.seek(0)
- unpickler = pickle.Unpickler(tf)
+ # _file is used below because it implements the necessary methods for pickle.Unpickler(), namely 'readinto' which is newly required in 3.8. See https://docs.python.org/3/library/tempfile.html#tempfile.SpooledTemporaryFile for details on the _file attribute of tempfile.SpooledTemporaryFile.
+ unpickler = pickle.Unpickler(tf._file)
while True:
try:
yield unpickler.load()
@@ -668,6 +669,10 @@ class CodonWarningTable(object):
else:
return self.wrapped.__getitem__(codon)
+ def __contains__(self, value):
+ return value in self.wrapped
+
+
def translate(records, translate):
"""
Perform translation from generic DNA/RNA to proteins. Bio.Seq
=====================================
setup.py
=====================================
@@ -33,15 +33,16 @@ setup(name='seqmagick',
'seqmagick.test.integration': ['data/*']
},
setup_requires=['nose>=1.0'],
- python_requires='>=3.4',
+ python_requires='>=3.5',
test_suite='nose.collector',
install_requires=['biopython>=1.70'],
classifiers=[
'License :: OSI Approved :: GNU General Public License (GPL)',
'Development Status :: 4 - Beta',
- 'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
+ 'Programming Language :: Python :: 3.7',
+ 'Programming Language :: Python :: 3.8',
'Topic :: Scientific/Engineering :: Bio-Informatics',
],
license="GPL V3")
View it on GitLab: https://salsa.debian.org/med-team/seqmagick/compare/f8203ad8e6456a4d2705c4a32fc246e44f1bb5e3...9179005c3920850ee3759fcac0cbbe4e57098829
--
View it on GitLab: https://salsa.debian.org/med-team/seqmagick/compare/f8203ad8e6456a4d2705c4a32fc246e44f1bb5e3...9179005c3920850ee3759fcac0cbbe4e57098829
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