[med-svn] [Git][med-team/khmer][master] Adapt to a change in Python3

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / khmer


Commits:
de92d8c3 by Andreas Tille at 2022-04-03T08:35:17+02:00
Adapt to a change in Python3

- - - - -


3 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/stringio-buffer.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+khmer (2.1.2+dfsg-11) UNRELEASED; urgency=medium
+
+  * Team upload.
+
+  [ Stefano Rivera ]
+  * Adapt to a change in Python3
+    Closes: #1008402
+
+ -- Andreas Tille <tille at debian.org>  Sun, 03 Apr 2022 08:34:16 +0200
+
 khmer (2.1.2+dfsg-10) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ python3
 fix_liboxli_test
 gcc11.patch
 bz2.patch
+stringio-buffer.patch


=====================================
debian/patches/stringio-buffer.patch
=====================================
@@ -0,0 +1,109 @@
+Author: Stefano Rivera <stefanor at debian.org>
+Date: Sat, 2 Apr 2022 19:03:04 -0400
+Bug-Debian: https://bugs.debian.org/1008402
+Description: The issue seems to be caused by a change in Python where
+  https://bugs.python.org/issue14156 being fixed
+
+--- a/tests/khmer_tst_utils.py
++++ b/tests/khmer_tst_utils.py
+@@ -44,18 +44,13 @@
+ import sys
+ import traceback
+ import subprocess
+-from io import open  # pylint: disable=redefined-builtin
++from io import BufferedWriter, BytesIO, StringIO, TextIOWrapper
+ from hashlib import md5
+ 
+ from khmer import reverse_complement as revcomp
+ 
+ import pytest
+ 
+-try:
+-    from StringIO import StringIO
+-except ImportError:
+-    from io import StringIO
+-
+ 
+ def _equals_rc(query, match):
+     return (query == match) or (revcomp(query) == match)
+@@ -151,6 +146,25 @@
+     return -1
+ 
+ 
++class StdIOBuffer(TextIOWrapper):
++    '''Replacement for writable io.StringIO that behaves more like real file
++    Unlike StringIO, provides a buffer attribute that holds the underlying
++    binary data, allowing it to replace sys.stdout/sys.stderr in more
++    contexts.
++    '''
++
++    name = 'StdIOBuffer'
++
++    def __init__(self, initial_value='', newline='\n'):
++        initial_value = initial_value.encode('utf-8')
++        super().__init__(BufferedWriter(BytesIO(initial_value)),
++                         'utf-8', newline=newline)
++
++    def getvalue(self):
++        self.flush()
++        return self.buffer.raw.getvalue().decode('utf-8')
++
++
+ def runscript(scriptname, args, in_directory=None,
+               fail_ok=False, sandbox=False):
+     """Run a Python script using exec().
+@@ -172,9 +186,8 @@
+         sys.argv = sysargs
+ 
+         oldout, olderr = sys.stdout, sys.stderr
+-        sys.stdout = StringIO()
+-        sys.stdout.name = "StringIO"
+-        sys.stderr = StringIO()
++        sys.stdout = StdIOBuffer()
++        sys.stderr = StdIOBuffer()
+ 
+         if in_directory:
+             os.chdir(in_directory)
+--- a/khmer/khmer_args.py
++++ b/khmer/khmer_args.py
+@@ -158,14 +158,16 @@
+ 
+ # Temporary fix to argparse FileType which ignores the
+ # binary mode flag. Upstream bug tracked in https://bugs.python.org/issue14156
++# Fixed in 3.9.12 and 3.10.3.
+ # pylint: disable=too-few-public-methods,missing-docstring
+ class FileType(argparse.FileType):
+     def __call__(self, fname):
+         # detect if stdout is being faked (StringIO during unit tests) in
+         # which case we do not have to do anything
+         if (fname == '-' and
+-                sys.version_info.major == 3 and
+-                not isinstance(sys.stdout, StringIO)):
++                not isinstance(sys.stdout, StringIO) and
++                (sys.version_info < (3, 9, 12) or
++                 (3, 10) < sys.version_info < (3, 10, 3))):
+             if 'r' in self._mode:
+                 fname = sys.stdin.fileno()
+             elif 'w' in self._mode:
+--- a/khmer/kfile.py
++++ b/khmer/kfile.py
+@@ -209,6 +209,8 @@
+     """Take in a file object and checks to see if it's a block or fifo."""
+     if fthing is sys.stdout or fthing is sys.stdin:
+         return True
++    elif not hasattr(fthing, 'name'):
++        return True
+     else:
+         mode = os.stat(fthing.name).st_mode
+         return S_ISBLK(mode) or S_ISCHR(mode)
+--- a/scripts/trim-low-abund.py
++++ b/scripts/trim-low-abund.py
+@@ -512,7 +512,7 @@
+ 
+     if args.output is None:
+         log_info('output in *.abundtrim')
+-    elif args.output.name == 1:
++    elif not hasattr(args.output, 'name') or args.output.name == 1:
+         log_info('output streamed to stdout')
+     elif args.output.name:
+         log_info('output in {}'.format(args.output.name))



View it on GitLab: https://salsa.debian.org/med-team/khmer/-/commit/de92d8c3f7727b729a02c931131bfbe94682d5a2

-- 
View it on GitLab: https://salsa.debian.org/med-team/khmer/-/commit/de92d8c3f7727b729a02c931131bfbe94682d5a2
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