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 <[email protected]> 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 <[email protected]> +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 -- View it on GitLab: https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41 You're receiving this email because of your account on salsa.debian.org.
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