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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/khmer">Debian Med / khmer</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41">fb141c18</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-12-03T21:59:03+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use python-bz2 instead of bz2file
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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+
debian/patches/bz2.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">khmer (2.1.2+dfsg-10) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Use python-bz2 instead of bz2file (addressing bug #987287)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 03 Dec 2021 21:18:55 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">khmer (2.1.2+dfsg-9) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<li id="b4c09c27b749100d1f1028d1c2760d1677d08e50">
<a href="https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41#b4c09c27b749100d1f1028d1c2760d1677d08e50"><strong>debian/patches/bz2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use python-bz2 instead of bz2file</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/987287</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 03 Dec 2021 18:40:00 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/khmer/kfile.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/khmer/kfile.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -41,7 +41,7 @@</span> import sys</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import errno</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from stat import S_ISBLK, S_ISFIFO, S_ISCHR</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import gzip</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import bz2file</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import bz2</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> def check_input_files(file_path, force):</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -241,7 +241,7 @@</span> def get_file_writer(file_handle, do_gzip</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> if do_gzip:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ofile = gzip.GzipFile(fileobj=file_handle, mode='w')</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> elif do_bzip:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ofile = bz2file.open(file_handle, mode='w')</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ofile = bz2.open(file_handle, mode='w')</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> ofile = file_handle</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -268,7 +268,7 @@</span> SETUP_METADATA = \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> "packages": ['khmer', 'khmer.tests', 'oxli', 'khmer._oxli'],</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> "package_data": {'khmer/_oxli': ['*.pxd']},</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> "package_dir": {'khmer.tests': 'tests'},</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "install_requires": ['screed >= 1.0', 'bz2file', 'Cython>=0.25.2'],</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "install_requires": ['screed >= 1.0', 'Cython>=0.25.2'],</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> "setup_requires": ["pytest-runner>=2.0,<3dev", "setuptools>=18.0"],</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> "extras_require": {':python_version=="2.6"': ['argparse>=1.2.1'],</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> 'docs': ['sphinx', 'sphinxcontrib-autoprogram'],</span></pre>
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<a href="https://salsa.debian.org/med-team/khmer/-/commit/fb141c1820253a4b6a9c375e64026b8ff8598b41#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,3 +12,4 @@ setup.py-py3</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">python3</span>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">fix_liboxli_test</span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">gcc11.patch</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">bz2.patch</span></pre>
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