.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

 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

+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@debian.org>  Sat, 18 Jan 2020 22:22:51 +0100
+
 seqmagick (0.7.0-1) unstable; urgency=medium
 
   * Initial release (Closes: #900394)

debian/compat

-11

debian/control

@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@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

+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")