[med-svn] [Git][med-team/khmer][master] Use python-bz2 instead of bz2file

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / khmer


Commits:
fb141c18 by Andreas Tille at 2021-12-03T21:59:03+01:00
Use python-bz2 instead of bz2file

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/bz2.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+khmer (2.1.2+dfsg-10) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Use python-bz2 instead of bz2file (addressing bug #987287)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 03 Dec 2021 21:18:55 +0100
+
 khmer (2.1.2+dfsg-9) unstable; urgency=medium
 
   [ Nilesh Patra ]


=====================================
debian/patches/bz2.patch
=====================================
@@ -0,0 +1,36 @@
+Description: Use python-bz2 instead of bz2file
+Bug-Debian: https://bugs.debian.org/987287
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 03 Dec 2021 18:40:00 +0100
+
+--- a/khmer/kfile.py
++++ b/khmer/kfile.py
+@@ -41,7 +41,7 @@ import sys
+ import errno
+ from stat import S_ISBLK, S_ISFIFO, S_ISCHR
+ import gzip
+-import bz2file
++import bz2
+ 
+ 
+ def check_input_files(file_path, force):
+@@ -241,7 +241,7 @@ def get_file_writer(file_handle, do_gzip
+     if do_gzip:
+         ofile = gzip.GzipFile(fileobj=file_handle, mode='w')
+     elif do_bzip:
+-        ofile = bz2file.open(file_handle, mode='w')
++        ofile = bz2.open(file_handle, mode='w')
+     else:
+         ofile = file_handle
+ 
+--- a/setup.py
++++ b/setup.py
+@@ -268,7 +268,7 @@ SETUP_METADATA = \
+         "packages": ['khmer', 'khmer.tests', 'oxli', 'khmer._oxli'],
+         "package_data": {'khmer/_oxli': ['*.pxd']},
+         "package_dir": {'khmer.tests': 'tests'},
+-        "install_requires": ['screed >= 1.0', 'bz2file', 'Cython>=0.25.2'],
++        "install_requires": ['screed >= 1.0', 'Cython>=0.25.2'],
+         "setup_requires": ["pytest-runner>=2.0,<3dev", "setuptools>=18.0"],
+         "extras_require": {':python_version=="2.6"': ['argparse>=1.2.1'],
+                            'docs': ['sphinx', 'sphinxcontrib-autoprogram'],


=====================================
debian/patches/series
=====================================
@@ -12,3 +12,4 @@ setup.py-py3
 python3
 fix_liboxli_test
 gcc11.patch
+bz2.patch



View it on GitLab: https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41

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View it on GitLab: https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41
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