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<h3>
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/13a15261cc8ba2b641dcfaf1410a298f60d5f496">13a15261</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-09T11:17:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/ddcda055132d11c2aa238342983065fcd0fd74fe">ddcda055</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T14:27:49+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Python 3 in subprocess calls.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/c828485311e9ad238e27c94d3a76e366b458564d">c8284853</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T14:58:47+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into debian_for_upstream_5.14.0_which_requires_conda
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8ecf7ea490402d32f7bc0944e993eb5782c8b4a5">
<span class="new-file">
+
debian/patches/py3_subprocess.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/f671d67b08614c65e4da995dc1d3cba2a7ee2ba4...c828485311e9ad238e27c94d3a76e366b458564d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">snakemake (5.14.0-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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"></span>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> [ Rebecca N. Palmer ]</span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * Exclude lazy_property to make Sphinx succeed.</span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Closes: #955056</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new_line" data-linenumber="4" 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">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
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<td class="diff-line-num new_line" data-linenumber="5" 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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog (routine-update)</span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +8,18 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> Repository-Browse.</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 09 Apr 2020 10:39:25 +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> [ Rebecca N. Palmer ]</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Use Python 3 in subprocess calls.</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Thu, 09 Apr 2020 14:57:00 +0100</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">snakemake (5.10.0-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> [ Rebecca N. Palmer ]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * Exclude lazy_property to make Sphinx succeed.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Closes: #955056</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 09 Apr 2020 11:09:24 +0200</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">snakemake (5.10.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<li id="8ecf7ea490402d32f7bc0944e993eb5782c8b4a5">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/f671d67b08614c65e4da995dc1d3cba2a7ee2ba4...c828485311e9ad238e27c94d3a76e366b458564d#8ecf7ea490402d32f7bc0944e993eb5782c8b4a5"><strong>debian/patches/py3_subprocess.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use Python 3 in subprocess calls</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">TODO - are any of the ones in snakemake/script.py:execute_script a problem?</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- snakemake-5.14.0.orig/tests/test_linting.py</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake-5.14.0/tests/test_linting.py</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span> def test_lint(lint, case):</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> out = (</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> sp.check_output(</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> [</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "python",</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "python3",</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> "-m",</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> "snakemake",</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> "--lint",</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake-5.14.0.orig/tests/test_tibanna.py</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake-5.14.0/tests/test_tibanna.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> from common import *</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> # run tibanna test before any moto-related tests because they apparently render AWS environment variables invalid or uneffective.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> def test_tibanna():</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> workdir = dpath("test_tibanna")</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subprocess.check_call(["python", "cleanup.py"], cwd=workdir)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call(["python3", "cleanup.py"], cwd=workdir)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> os.environ["TEST_ENVVAR1"] = "test"</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> os.environ["TEST_ENVVAR2"] = "test"</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/f671d67b08614c65e4da995dc1d3cba2a7ee2ba4...c828485311e9ad238e27c94d3a76e366b458564d#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 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">boto3_is_just_boto</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">python3</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">workaround_sphinx_issue.patch</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">py3_subprocess.patch</span></pre>
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