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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/d91dd9b3b77b6fb0ff2966ec9739c2e206a1dfe0">d91dd9b3</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-08T10:29:14+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another adjustment of disk/memory defaults for the autopkgtests.

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/154ad342f35f1ea30f80fc0fbac98b1960940a62">154ad342</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-08T10:29:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/exit_code_exception: Fix exception checking for exit_code

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/6a75fb74aa13d5826f8dfb7b1f2869d9784f498b">6a75fb74</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-10-08T10:57:25+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">

debian/README.source

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#32807d9d1af431d92c968d062bb3ab0046c56dd1">

<span class="new-file">

+

debian/patches/exit_code_exception

</span>

</a>

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<li class="file-stats">

<a href="#0866bdca0ff4b612c822931ed876cd5df0453e0d">

<span class="deleted-file">

−

debian/patches/proxy

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">

debian/patches/setting_version.patch

</a>

</li>

<li class="file-stats">

<a href="#8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca">

debian/patches/ship_tests

</a>

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<li class="file-stats">

<a href="#6187ccefe18309cfee9995c8b0d7b481c9971218">

debian/patches/test_with_less_memory

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<li class="file-stats">

<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">

debian/tests/run-unit-tests

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="cf9802e192b48f765b1b5c8268d550d89c933053">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" 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">@@ -7,4 +7,7 @@ compatability of toil is recent.</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">The bulk of the manual testing is currently focused on the toil-cwl-runner</span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">using the docker.io package.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" 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="LC10" class="line" lang="plaintext">Maintainers: please update debian/patch/settings_version.patch following the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">instructions within.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Sun, 13 Jan 2019 23:25:16 -0800</span></pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">toil (5.5.0-5) unstable; urgency=medium</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Another adjustment of disk/memory defaults for the autopkgtests.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debian/patches/exit_code_exception: Fix exception checking for</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    exit_code</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Fri, 08 Oct 2021 10:57:25 +0200</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">toil (5.5.0-4) unstable; urgency=medium</span>

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2

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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3

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Adjust disk/memory defaults further downward for 32-bit systems.</span>

</pre>

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<br>

</li>

<li id="32807d9d1af431d92c968d062bb3ab0046c56dd1">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#32807d9d1af431d92c968d062bb3ab0046c56dd1"><strong>debian/patches/exit_code_exception</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix exception checking for exit_code</span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/DataBiosphere/toil/pull/3830</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Otherwise an AttributeError is raised instead of the correct exception</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- toil.orig/src/toil/cwl/cwltoil.py</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/cwl/cwltoil.py</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -3401,7 +3401,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">             except Exception as err:</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">                 # TODO: We can't import FailedJobsException due to a circular</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">                 # import but that's what we'd expect here.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                if getattr(err, "exit_code") == CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE:</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;">+                if getattr(err, "exit_code", None) == CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE:</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">                     # We figured out that we can't support this workflow.</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff">                     logging.error(err)</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">                     logging.error(</span></pre>

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</li>

<li id="0866bdca0ff4b612c822931ed876cd5df0453e0d">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#0866bdca0ff4b612c822931ed876cd5df0453e0d"><strong>debian/patches/proxy</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: cope with an invalid HTTP_PROXY</span></span>

</pre>

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3

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<td class="new_line diff-line-num old" data-linenumber="0" 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="diff"><span class="p">Forwarded: https://github.com/DataBiosphere/toil/pull/3447</span></span>

</pre>

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4

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC4" class="line" lang="diff"></span>

</pre>

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<td class="old_line diff-line-num old" 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">

5

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<td class="new_line diff-line-num old" data-linenumber="0" 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="diff">Debian purposely sets an invalid HTTP_PROXY during some build situations</span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: toil/src/toil/jobStores/abstractJobStore.py</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/jobStores/abstractJobStore.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/jobStores/abstractJobStore.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -54,6 +54,10 @@</span> class InvalidImportExportUrlException(Ex</span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">         """</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC12" class="line" lang="diff">         super().__init__("The URL '%s' is invalid." % url.geturl())</span>

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    from botocore.exceptions import ProxyConnectionError</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except ImportError:</span></span>

</pre>

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<td class="old_line diff-line-num old" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    ProxyConnectionError = None</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="18" 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="LC18" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> class NoSuchJobException(Exception):</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" 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="new_line diff-line-num old" data-linenumber="0" 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="LC20" class="line" lang="diff">     """Indicates that the specified job does not exist."""</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">exit_code_exception</span>

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1

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cwl_test_path</span>

</pre>

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2

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling</span>

</pre>

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3

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<td class="new_line diff-line-num" 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">setting_version.patch</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">@@ -5,6 +6,5 @@ no_galaxy_lib</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">debianize_docs</span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">soften-mesos-deps</span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">soften-pydocker-dep</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="9" 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">proxy</span>

</pre>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">ship_tests</span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">test_with_less_memory</span></pre>

</td>

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</table>

<br>

</li>

<li id="bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6"><strong>debian/patches/setting_version.patch</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,10 @@ Last-Update: 2020-05-07</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="7" 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="LC7" class="line" lang="diff">Generated by running `python version_template.py` from a git checkout of the</span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">source to the tag corresponding to the release</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="9" 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="LC9" class="line" lang="diff"><span class="p">---</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="10" 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="new_line diff-line-num new" data-linenumber="9" 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="LC9" class="line" lang="diff"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="10" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" 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="LC10" class="line" lang="diff">As of Toil 5.5.0 the `cwltool_version` field is set in setup.py, please</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="10" 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">

</td>

<td class="new_line diff-line-num new" 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="diff"><span class="p">copy/update that field manually, if it doesn't match the value in setup.py or</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="10" 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">

</td>

<td class="new_line diff-line-num new" 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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">is missing</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"></span>

</pre>

</td>

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11

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<td class="new_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">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff">--- /dev/null</span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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">

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;">+++ toil/src/toil/version.py</span></span>

</pre>

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</li>

<li id="8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca"><strong>debian/patches/ship_tests</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: ship the tests</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">not-needed</span></span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/DataBiosphere/toil/issues/3823</span></span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/setup.py</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/setup.py</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -140,12 +140,9 @@</span></span>

</pre>

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<br>

</li>

<li id="6187ccefe18309cfee9995c8b0d7b481c9971218">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#6187ccefe18309cfee9995c8b0d7b481c9971218"><strong>debian/patches/test_with_less_memory</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: reduce default resource usage on 32bit systems</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Remove use of sys.maxsize</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/DataBiosphere/toil/pull/3824</span></span>

</pre>

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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">Python integers can be larger that sys.maxsize</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="diff">And on 32-bit machines the use of sys.maxize made is sot that options.maxMemory</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" 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="LC8" class="line" lang="diff"><span class="p">sets a limit of 1.99GiB memory available unless overridden;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">likewise for options.maxDisk being limited to 1.99GiB disk space available</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">unless overridden.</span></span>

</pre>

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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="LC11" class="line" lang="diff"></span>

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<td class="old_line diff-line-num new" data-linenumber="4" 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="new_line diff-line-num new" 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="diff">The above caused CWLSmallTests.test_workflow_echo_string to fail in Debian on</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">32-bit systems</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"></span>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="diff">--- toil.orig/src/toil/common.py</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/common.py</span></span>

</pre>

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<td class="new_line diff-line-num old" 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="LC6" class="line" lang="diff"><span class="p">@@ -20,<span class="idiff left">6</span> +20,<span class="idiff right">7</span> @@</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" 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="LC17" class="line" lang="diff"><span class="p">@@ -20,<span class="idiff left">10</span> +20,<span class="idiff right">11</span> @@</span></span>

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<td class="new_line diff-line-num" 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="diff"> import tempfile</span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="19" 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="LC19" class="line" lang="diff"> import time</span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="20" 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="LC20" class="line" lang="diff"> import uuid</span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" 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">@@ -11,20 +22,140 @@ Forwarded: not-needed</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> from urllib.parse import urlparse</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, _ArgumentGroup</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="25" 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="LC14" class="line" lang="diff"><span class="p">@@ -99,9 +100,14 @@</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="25" 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="LC15" class="line" lang="diff">         self.statePollingWait: Optional[Union[float, int]] = None  # Number of seconds to wait before querying job state</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="25" 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="LC16" class="line" lang="diff"> </span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="25" 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="diff">         # Resource requirements</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="18" 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="new_line diff-line-num old" data-linenumber="25" 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="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.defaultMemory: int = 2147483648</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" 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="new_line diff-line-num old" data-linenumber="25" 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="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        is_64bits = sys.maxsize > 2**32</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" 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="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if is_64bits:</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;">+            self.defaultMemory = 2147483648</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            self.defaultDisk = 2147483648</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        else:</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            self.defaultMemory = 1073741824</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            self.defaultDisk = 1073741824</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">         self.defaultCores: Union[float, int] = 1</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.defaultDisk: int = 2147483648</span></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;">-from typing import Any, Callable, List, Optional, Tuple, Union</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;">+from typing import Any, Callable, List, Literal, Optional, Tuple, Union</span></span>

</pre>

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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"> import requests</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -92,7 +93,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">         self.metrics: bool = False</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">         # Parameters to limit service jobs, so preventing deadlock scheduling scenarios</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.maxPreemptableServiceJobs: int = sys.maxsize</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        self.maxPreemptableServiceJobs: int = 9223372036854775807 </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" 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="LC36" class="line" lang="diff">         self.maxServiceJobs: int = sys.maxsize</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">         self.deadlockWait: Union[float, int] = 60  # Number of seconds we must be stuck with all services before declaring a deadlock</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">         self.deadlockCheckInterval: Union[float, int] = 30  # Minimum polling delay for deadlocks</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" 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="LC39" class="line" lang="diff"><span class="p">@@ -104,9 +105,9 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">         self.defaultDisk: int = 2147483648</span>

</pre>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff">         self.readGlobalFileMutableByDefault: bool = False</span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff">         self.defaultPreemptable: bool = False</span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">         self.maxCores: int = sys.maxsize</span></pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.maxCores: int = sys.maxsize</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.maxMemory: int = sys.maxsize</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.maxDisk: int = sys.maxsize</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        self.maxCores: int = 9223372036854775807</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        self.maxMemory: int = 9223372036854775807</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        self.maxDisk: int = 9223372036854775807</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="LC49" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff">         # Retrying/rescuing jobs</span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">         self.retryCount: int = 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -1393,7 +1394,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff">     return d</span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-def iC(minValue, maxValue=sys.maxsize):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def iC(minValue, maxValue=9223372036854775807):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff">     # Returns function that checks if a given int is in the given half-open interval</span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff">     assert isinstance(minValue, int) and isinstance(maxValue, int)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff">     return lambda x: minValue <= x < maxValue</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/cwl/cwltoil.py</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/cwl/cwltoil.py</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -1618,7 +1618,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff">     def __init__(self, cwljob: dict):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff">         """Store the dictionary of promises for later resolution."""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(ResolveIndirect, self).__init__(cores=1, memory=1024 ^ 2, disk=0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(ResolveIndirect, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">         self.cwljob = cwljob</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">     def run(self, file_store: AbstractFileStore) -> dict:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -1770,7 +1770,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">         conditional: Union[Conditional, None] = None,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff">     ):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">         """Store our context for later evaluation."""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(CWLJobWrapper, self).__init__(cores=1, memory=1024 * 1024, disk=8 * 1024)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(CWLJobWrapper, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff">         self.cwltool = remove_pickle_problems(tool)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">         self.cwljob = cwljob</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff">         self.runtime_context = runtime_context</span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -2125,7 +2125,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff">         conditional: Union[Conditional, None],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff">     ):</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="84" 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="LC84" class="line" lang="diff">         """Store our context for later execution."""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(CWLScatter, self).__init__(cores=1, memory=100 * 1024 ^ 2, disk=0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(CWLScatter, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="87" 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="LC87" class="line" lang="diff">         self.step = step</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="88" 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="LC88" class="line" lang="diff">         self.cwljob = cwljob</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="89" 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="LC89" class="line" lang="diff">         self.runtime_context = runtime_context</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="90" 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="LC90" class="line" lang="diff"><span class="p">@@ -2268,7 +2268,7 @@</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="91" 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="LC91" class="line" lang="diff">         outputs: Union[Mapping, MutableSequence],</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff">     ):</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="93" 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="LC93" class="line" lang="diff">         """Collect our context for later gathering."""</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(CWLGather, self).__init__(cores=1, memory=10 * 1024 ^ 2, disk=0)</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="95" 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="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(CWLGather, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" 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="LC96" class="line" lang="diff">         self.step = step</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" 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="LC97" class="line" lang="diff">         self.outputs = outputs</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" 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="LC98" class="line" lang="diff"> </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -2310,7 +2310,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff">     def __init__(self, j: "CWLWorkflow", v: dict):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">         """Record the workflow and dictionary."""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(SelfJob, self).__init__(cores=1, memory=1024 ^ 2, disk=0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(SelfJob, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff">         self.j = j</span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff">         self.v = v</span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="p">@@ -2364,7 +2364,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff">         conditional: Union[Conditional, None] = None,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff">     ):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">         """Gather our context for later execution."""</span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        super(CWLWorkflow, self).__init__(cores=1, memory=100 * 1024 ^ 2, disk=0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        super(CWLWorkflow, self).__init__(cores=1, memory="1GiB", disk="1MiB")</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff">         self.cwlwf = cwlwf</span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff">         self.cwljob = cwljob</span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff">         self.runtime_context = runtime_context</span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/batchSystems/parasol.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/batchSystems/parasol.py</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -48,7 +48,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="121" 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="LC121" class="line" lang="diff">     def __init__(self, config, maxCores, maxMemory, maxDisk):</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="122" 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="LC122" class="line" lang="diff">         super(ParasolBatchSystem, self).__init__(config, maxCores, maxMemory, maxDisk)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="123" 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">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if maxMemory != sys.maxsize:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="124" 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">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if maxMemory != 9223372036854775807:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="125" 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">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff">             logger.warning('The Parasol batch system does not support maxMemory.')</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="126" 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">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff">         # Keep the name of the results file for the pstat2 command..</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="127" 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="LC127" class="line" lang="diff">         command = config.parasolCommand</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="128" 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="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/batchSystems/singleMachine.py</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="129" 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">

129

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/batchSystems/singleMachine.py</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="130" 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="LC130" class="line" lang="diff"><span class="p">@@ -16,7 +16,6 @@</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="131" 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="LC131" class="line" lang="diff"> import os</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="132" 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">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> import signal</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="133" 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="LC133" class="line" lang="diff"> import subprocess</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="134" 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">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import sys</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="135" 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">

135

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> import time</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="136" 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">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> import traceback</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="137" 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">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> from contextlib import contextmanager</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="138" 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">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -80,12 +79,12 @@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="139" 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="LC139" class="line" lang="diff">         # If we don't have up to the limit of the resource (and the resource</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="140" 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="LC140" class="line" lang="diff">         # isn't the inlimited sentinel), warn.</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="141" 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="LC141" class="line" lang="diff">         if maxCores > self.numCores:</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="142" 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="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if maxCores != sys.maxsize:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if maxCores != 9223372036854775807:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="144" 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="LC144" class="line" lang="diff">                 # We have an actually specified limit and not the default</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="145" 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="LC145" class="line" lang="diff">                 log.warning('Not enough cores! User limited to %i but we only have %i.', maxCores, self.numCores)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="146" 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="LC146" class="line" lang="diff">             maxCores = self.numCores</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="147" 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="LC147" class="line" lang="diff">         if maxMemory > self.physicalMemory:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if maxMemory != sys.maxsize:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if maxMemory != 9223372036854775807:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="150" 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="LC150" class="line" lang="diff">                 # We have an actually specified limit and not the default</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" 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="LC151" class="line" lang="diff">                 log.warning('Not enough memory! User limited to %i bytes but we only have %i bytes.', maxMemory, self.physicalMemory)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="152" 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="LC152" class="line" lang="diff">             maxMemory = self.physicalMemory</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="153" 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="LC153" class="line" lang="diff"><span class="p">@@ -93,7 +92,7 @@</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="154" 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="LC154" class="line" lang="diff">         workdir = Toil.getLocalWorkflowDir(config.workflowID, config.workDir)  # config.workDir may be None; this sets a real directory</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="155" 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="LC155" class="line" lang="diff">         self.physicalDisk = toil.physicalDisk(workdir)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="156" 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="LC156" class="line" lang="diff">         if maxDisk > self.physicalDisk:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if maxDisk != sys.maxsize:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if maxDisk != 9223372036854775807:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="31" 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="new_line diff-line-num new" data-linenumber="159" 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="LC159" class="line" lang="diff">                 # We have an actually specified limit and not the default</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="160" 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="LC160" class="line" lang="diff">                 log.warning('Not enough disk space! User limited to %i bytes but we only have %i bytes.', maxDisk, self.physicalDisk)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff">             maxDisk = self.physicalDisk</span></pre>

</td>

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<br>

</li>

<li id="b8880ead45e8d099a1552defb95ea70479f1572e">

<a href="https://salsa.debian.org/med-team/toil/-/compare/a45778cc1e3a12ddee2003324b94a1238aa18b4d...6a75fb74aa13d5826f8dfb7b1f2869d9784f498b#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -ex</span></span>

</pre>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>

</pre>

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3

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<td class="new_line diff-line-num 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="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>toil</span>

</pre>

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4

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<td class="new_line diff-line-num 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="LC4" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num" 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">

5

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>

</pre>

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<td class="old_line diff-line-num old" 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">

6

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<td class="new_line diff-line-num old" data-linenumber="4" 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="shell"><span class="c" style="color: #998; font-style: italic;"># if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</span></span>

</pre>

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<td class="old_line diff-line-num old" 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">

7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)</span></span>

</pre>

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8

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<td class="new_line diff-line-num old" data-linenumber="4" 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="shell"><span class="c" style="color: #998; font-style: italic;">#   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" 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">

9

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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="10" 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">

10

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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </span></span>

</pre>

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11

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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cd "${AUTOPKGTEST_TMP}"</span></span>

</pre>

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12

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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC12" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num old" 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">

13

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<td class="new_line diff-line-num old" data-linenumber="4" 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="shell"><span class="nv" style="color: #008080;">TMP</span><span class="o" style="font-weight: 600;">=</span>AUTOPKGTEST_TMP <span class="nv" style="color: #008080;">TOIL_TEST_QUICK</span><span class="o" style="font-weight: 600;">=</span>True <span class="nv" style="color: #008080;">TOIL_SKIP_DOCKER</span><span class="o" style="font-weight: 600;">=</span>True python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-vv</span> <span class="nt" style="color: #000080;">-rs</span> <span class="nt" style="color: #000080;">-W</span> ignore <span class="nt" style="color: #000080;">-k</span> <span class="s2" style="color: #d14;">"not (test_bioconda or AWSJobStoreTest or awsjobstoretest or testCwlexample or CWLv10Test or CWLv11Test or CWLv12Test or AWSAutoscaleTest or AWSStaticAutoscaleTest or AWSManagedAutoscaleTest or AWSAutoscaleTestMultipleNodeTypes or AWSRestartTest or PreemptableDeficitCompensationTest)"</span> <span class="nt" style="color: #000080;">--ignore-glob</span> <span class="s1" style="color: #d14;">'*cwlTest*'</span> <span class="nt" style="color: #000080;">--ignore</span> /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py <span class="nt" style="color: #000080;">--pyargs</span> toil.test</span></pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="4" 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">

4

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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="LC4" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" 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">

5

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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="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span>/tmp</span>

</pre>

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<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="7" 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">

7

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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="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">TMPDIR</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">HOME</span><span class="k" style="font-weight: 600;">}</span>/tmp <span class="nv" style="color: #008080;">TOIL_TEST_QUICK</span><span class="o" style="font-weight: 600;">=</span>True <span class="nv" style="color: #008080;">TOIL_SKIP_DOCKER</span><span class="o" style="font-weight: 600;">=</span>True python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="8" 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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">  <span class="nt" style="color: #000080;">--junit-xml</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_ARTIFACTS</span>/toil-tests-junit.xml <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" 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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">  <span class="nt" style="color: #000080;">-vv</span> <span class="nt" style="color: #000080;">-rs</span> <span class="nt" style="color: #000080;">-W</span> ignore <span class="nt" style="color: #000080;">-k</span> <span class="s2" style="color: #d14;">"not (test_bioconda or AWSJobStoreTest or </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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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="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;"> awsjobstoretest or testCwlexample or CWLv10Test or CWLv11Test or </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

11

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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="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;"> CWLv12Test or AWSAutoscaleTest or AWSStaticAutoscaleTest or </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;"> AWSManagedAutoscaleTest or AWSAutoscaleTestMultipleNodeTypes or </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

13

</td>

<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="shell"><span class="s2" style="color: #d14;"> AWSRestartTest or PreemptableDeficitCompensationTest)"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

14

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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="LC14" class="line" lang="shell"> <span class="nt" style="color: #000080;">--ignore-glob</span> <span class="s1" style="color: #d14;">'*cwlTest*'</span> <span class="nt" style="color: #000080;">--ignore</span> /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" 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">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"> <span class="nt" style="color: #000080;">--pyargs</span> toil.test</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" 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">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span></pre>

</td>

</tr>

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