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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/56367974d7d277e4617e0d25d63ab3fe6ca25c51">56367974</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T17:15:09+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">move python3 fixes to a single patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/e9fcd301371aee7d9ab1b80af62ad1889f941cc1">e9fcd301</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T17:18:45+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable buggy test (upstream 322) and tests needing conda or docker.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/925c7493de6f1de83645d2ec78c08d6e476ff1e8">925c7493</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T17:20:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Delete unused patches.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/1cf3a516468339a8a3489b681efa689a876cab46">1cf3a516</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-04-09T17:21:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use boto3 (like upstream) not boto.
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#b87ce94d515588473e67ff1a34537b78804288bc">
<span class="deleted-file">
−
debian/patches/0004-drop_test_symlink_time_handling.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#dea10079bcc0218b49bfe0681e0f5b81e03ec4c1">
<span class="deleted-file">
−
debian/patches/0005-drop_test_symlink_temp.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#08eb996a41f3f103ec509664d5b87f2e4f567545">
<span class="deleted-file">
−
debian/patches/0007-noop-rate-limiter.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#34ee3daa9d4be4ccd97667f1571fb614d66e3371">
<span class="deleted-file">
−
debian/patches/0010-skip-test-without-rmarkdown.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#3099d3b193ee5d195e9fef4d6fc3253cd1a1d175">
<span class="deleted-file">
−
debian/patches/boto3_is_just_boto
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ecf7ea490402d32f7bc0944e993eb5782c8b4a5">
<span class="deleted-file">
−
debian/patches/py3_subprocess.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3
→
debian/patches/python3.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,9 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
</pre>
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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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Rebecca N. Palmer ]</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line" data-linenumber="12" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Use Python 3 in subprocess calls.</span>
</pre>
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<td class="diff-line-num new old_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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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Disable buggy test (upstream 322) and tests needing conda or docker.</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Delete unused patches.</span>
</pre>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Use boto3 (like upstream) not boto.</span>
</pre>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Thu, 09 Apr 2020 14:57:00 +0100</span>
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15
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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext"></span>
</pre>
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<br>
</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ Build-Depends: ca-certificates,</td>
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<td class="diff-line-num old_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">
10
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> imagemagick,</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="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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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="12" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-biopython,</span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> python3-boto,</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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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<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"> python3-boto<span class="idiff left right">3</span>,</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-botocore,</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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-configargparse,</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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3-datrie,</span>
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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">@@ -71,7 +71,7 @@ Depends: ca-certificates,</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Recommends: cwltool,</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> imagemagick,</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> python3-boto,</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> python3-boto<span class="idiff left right">3</span>,</span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> python3-botocore,</span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> python3-dropbox,</span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> python3-flask,</span>
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<li id="b87ce94d515588473e67ff1a34537b78804288bc">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#b87ce94d515588473e67ff1a34537b78804288bc"><strong>debian/patches/0004-drop_test_symlink_time_handling.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 13 Dec 2016 16:05:05 +0100</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/845737</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: Ignore failures of test that might happpen in pbuilder</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/tests/tests.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/tests/tests.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -371,7 +371,11 @@</span> def test_input_generator():</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> def test_symlink_time_handling():</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> #See Snakefile for notes on why this fails on some systems</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> if os.utime in os.supports_follow_symlinks:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(dpath("test_symlink_time_handling"))</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ run(dpath("test_symlink_time_handling"))</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;">+ except:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # skip this test that might fail when building in a pbuilder chroot</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> def test_issue328():</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#dea10079bcc0218b49bfe0681e0f5b81e03ec4c1"><strong>debian/patches/0005-drop_test_symlink_temp.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 13 Dec 2016 16:05:05 +0100</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/848820</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Description: Ignore failures of test that might happpen in pbuilder</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> .</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> According to upstream this is fixed in commit d697f23</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> so the patch is deactivated</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">--- a/tests/tests.py</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/tests.py</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -308,10 +308,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> cluster_sync="./qsub")</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>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def test_symlink_temp():</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- run(dpath("test_symlink_temp"), shouldfail=True)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> def test_empty_include():</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> run(dpath("test_empty_include"))</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#08eb996a41f3f103ec509664d5b87f2e4f567545"><strong>debian/patches/0007-noop-rate-limiter.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Christian Amsüss <chrysn@fsfe.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 14 Nov 2017 09:28:21 CET +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Temporary workaround for missing ratelimiter package (#880661).</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> This removes functionality and should not be left in for the package for a</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> released version, but eases fixing the build failures.</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- a/snakemake/executors.py</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/executors.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -405,7 +405,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> exec_job=None,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> assume_shared_fs=True,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> max_status_checks_per_second=1):</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from ratelimiter import RateLimiter</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</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;">+ import contextlib</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @contextlib.contextmanager</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def _cm(): yield</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RateLimiter = lambda *args, **wkargs: _cm()</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> local_input = local_input or []</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> super().__init__(workflow, dag,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snakemake/scheduler.py</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snakemake/scheduler.py</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -61,7 +61,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> force_use_threads=False,</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> assume_shared_fs=True):</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> """ Create a new instance of KnapsackJobScheduler. """</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from ratelimiter import RateLimiter</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import contextlib</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @contextlib.contextmanager</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def _cm(): yield</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RateLimiter = lambda *args, **wkargs: _cm()</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> self.cluster = cluster</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> self.cluster_config = cluster_config</span></pre>
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<li id="34ee3daa9d4be4ccd97667f1571fb614d66e3371">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#34ee3daa9d4be4ccd97667f1571fb614d66e3371"><strong>debian/patches/0010-skip-test-without-rmarkdown.patch</strong>
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The diff for this file was not included because it is too large.
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<li id="3099d3b193ee5d195e9fef4d6fc3253cd1a1d175">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#3099d3b193ee5d195e9fef4d6fc3253cd1a1d175"><strong>debian/patches/boto3_is_just_boto</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: In Debian, boto3 is just boto</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/snakemake/remote/S3.py</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/remote/S3.py</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> # third-party modules</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> import botocore</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> except ImportError as e:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> raise WorkflowError(</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;">--- snakemake.orig/snakemake/remote/S3Mocked.py</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/snakemake/remote/S3Mocked.py</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> # third-party</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> from moto import mock_s3</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> except ImportError as e:</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> raise WorkflowError(</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;">--- snakemake.orig/tests/test_static_remote/S3MockedForStaticTest.py</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;">+++ snakemake/tests/test_static_remote/S3MockedForStaticTest.py</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> # third-party</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import boto3</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import boto as boto3</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> from moto import mock_s3</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> import filechunkio</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> except ImportError as e:</span></pre>
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<li id="8ecf7ea490402d32f7bc0944e993eb5782c8b4a5">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#8ecf7ea490402d32f7bc0944e993eb5782c8b4a5"><strong>debian/patches/py3_subprocess.patch</strong>
deleted
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1
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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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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"></span>
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3
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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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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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5
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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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6
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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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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"></span>
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8
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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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9
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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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10
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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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14
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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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19
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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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20
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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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<strong>debian/patches/python3.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: Use python3 instead of python</span></span>
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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: Michael R. Crusoe <michael.crusoe@gmail.com>, 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">--- a/tests/test_delete_all_output/Snakefile</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;">+++ b/tests/test_delete_all_output/Snakefile</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -8,9 +8,9 @@</span> rule delete_all_output:</span>
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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">@@ -59,3 +64,25 @@ Subject: Use python3 instead of python</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> shell:</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "python -m snakemake --cores 1 --profile . -s Snakefile.internal"</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "python3 -m snakemake --cores 1 --profile . -s Snakefile.internal"</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_linting.py</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_linting.py</span></span>
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<pre style="margin: 0;">+<span id="LC69" 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="LC70" class="line" lang="diff"> out = (</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> sp.check_output(</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> [</span>
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<pre style="margin: 0;">+<span id="LC73" 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="LC74" 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="LC75" class="line" lang="diff"> "-m",</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> "snakemake",</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> "--lint",</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_tibanna.py</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_tibanna.py</span></span>
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<pre style="margin: 0;">+<span id="LC80" 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="LC81" 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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> def test_tibanna():</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> workdir = dpath("test_tibanna")</span>
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84
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<pre style="margin: 0;">+<span id="LC84" 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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85
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<pre style="margin: 0;">+<span id="LC85" 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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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> os.environ["TEST_ENVVAR1"] = "test"</span>
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<pre style="margin: 0;">+<span id="LC88" 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/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">0001-Use-the-inbuild-sphinx.ext.napoleon.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">0003-Use-debian-s-mathjax-package.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">0003-Compat-fix.patch</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># 0004-drop_test_symlink_time_handling.patch</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"># 0005-drop_test_symlink_temp.patch - should be fixed in commit d697f23</span>
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6
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">0006-restore-bin.patch</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># 0007-noop-rate-limiter.patch - broken and obsolete with https://bugs.debian.org/880661</span>
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8
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">0008-remove_sphinx.ext.patch</span>
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9
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">0009-skip-test-without-google-cloud-sdk.patch</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># 0010-skip-test-without-rmarkdown.patch</span>
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11
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">0011-fix-privacy-breach.patch</span>
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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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">workaround_sphinx_issue.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">py3_subprocess.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules'</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules<span class="idiff left right"> and not test_archive and not test_container and not test_cluster_sync</span>'</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># test_report</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># test_ancient</span>
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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">@@ -19,6 +19,9 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'no</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"># test_issue1093 fails due to conda usage; commenting that out and installing bwa produces a different ordering than desired</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># test_default_resources and test_remote needs moto to be packaged https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777089</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># test_env_modules relies on "module load" which is not packaged for Debian</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># test_archive uses conda</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># test_container uses docker://bash</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># test_cluster_sync is broken (https://github.com/snakemake/snakemake/issues/322)</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/c828485311e9ad238e27c94d3a76e366b458564d...1cf3a516468339a8a3489b681efa689a876cab46#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-n</span> auto <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-n</span> auto <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules<span class="idiff left right"> and not test_archive and not test_container and not test_cluster_sync</span>'</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" 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="LC21" class="line" lang="shell"></span></pre>
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