[med-svn] [Git][med-team/seqmagick][upstream] New upstream version 0.8.0

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / seqmagick


Commits:
dc635cd2 by Steffen Moeller at 2020-01-18T22:22:07+01:00
New upstream version 0.8.0
- - - - -


7 changed files:

- .travis.yml
- CHANGELOG.rst
- README.rst
- + 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
 ========


=====================================
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/commit/dc635cd249270d865e630837a6c75fd7f5625411

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View it on GitLab: https://salsa.debian.org/med-team/seqmagick/commit/dc635cd249270d865e630837a6c75fd7f5625411
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