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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/d47fa8612ed81ea76b42932635118fddd2dedd49">d47fa861</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-01-26T18:01:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: make local-test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/dda26a49925fc993c62d6cee45f72e25f9adcc45">dda26a49</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-04T12:17:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable toil-wdl-runner now that python3-wdlparse is in Debian.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/2539e2d982b61268e0faf583a797e1b16a0c7d52">2539e2d9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-07T13:25:07+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Runs the tests during the build
and as autopkgtests!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/96eb64c9f838600841ec3f54e2463662e0df7296">96eb64c9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-07T13:26:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
debian/clean
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#0866bdca0ff4b612c822931ed876cd5df0453e0d">
<span class="new-file">
+
debian/patches/proxy
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<li class="file-stats">
<a href="#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
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+
debian/patches/python3
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca">
<span class="new-file">
+
debian/patches/ship_tests
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<li class="file-stats">
<a href="#037df6725949b5d76b6bcc0423f4f7b7f07f1ffa">
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+
debian/patches/soften-pydocker-dep
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<li class="file-stats">
<a href="#a4b8bd6a7a72ff6720185f41df4f162bdc674cb6">
<span class="deleted-file">
−
debian/patches/wdlparse_not_available
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
<span class="new-file">
+
debian/tests/run-unit-tests
</span>
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<li class="file-stats">
<a href="#e2b1208a0e749c8deae704fab4193ed3af3060cd">
debian/tests/smoke-test
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">toil (5.2.0-2) unstable; urgency=high</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Enable toil-wdl-runner now that python3-wdlparse is in Debian.</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Enabled running the the tests during the build!</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Feb 2021 13:26:16 +0100</span>
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<td class="diff-line-num new new_line" 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="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">toil (5.2.0-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
</pre>
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<li id="f5f51601866c86e59a004bd93fa415f5675be8c5">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">toilWorkflowRun</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">version_template.pyc</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.pytest_cache/</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">src/toil/version.pyc</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">src/toil.egg-info/</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">docs/vendor/sphinxcontrib/__pycache__/</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,16 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-docker,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-dill,</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-future,</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> python3-pytest-xdist,</span>
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15
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> cwltool (>= 3.0.20201203173111),</span>
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16
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> python3-distutils,</span>
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17
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3-enlighten,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> python3-wdlparse,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-mock <!nocheck>,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-boto3 <!nocheck>,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-boto <!nocheck>,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python3-stubserver <!nocheck>,</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> rsync <!nocheck>,</span>
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18
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># documentation</span>
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19
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python3-urllib3,</span>
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20
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> python3-sphinx</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="38" 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">@@ -32,6 +38,8 @@ Depends: ${python3:Depends},</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> cwltool</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Recommends: python3-boto,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> python3-boto3,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"># for WDL support</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> python3-wdlparse,</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"># for google cloud support</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> python3-libcloud</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"># for mesos support, but needs python3-mesos first</span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#0866bdca0ff4b612c822931ed876cd5df0453e0d"><strong>debian/patches/proxy</strong></a>
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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>
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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>
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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/3447</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Debian purposely sets an invalid HTTP_PROXY during some build situations</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/jobStores/abstractJobStore.py</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/jobStores/abstractJobStore.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -37,6 +37,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> logger = logging.getLogger(__name__)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from botocore.exceptions import ProxyConnectionError</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;">+except ImportError:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ProxyConnectionError = None</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> class InvalidImportExportUrlException(Exception):</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> def __init__(self, url):</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -243,7 +247,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> from importlib import import_module</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> module = import_module(moduleName)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ImportError:</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;">+ except (ImportError, ProxyConnectionError):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> logger.debug("Unable to import '%s' as is expected if the corresponding extra was "</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> "omitted at installation time.", moduleName)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> else:</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc"><strong>debian/patches/python3</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Ensure that python3 and not python (2) is used</span></span>
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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/3446</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/src/toil/test/utils/toilDebugTest.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/src/toil/test/utils/toilDebugTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> from toil.test import ToilTest, slow, travis_test</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> from toil.utils.toilDebugFile import recursiveGlob</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from toil.version import python</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> logger = logging.getLogger(__name__)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> class ToilDebugFileTest(ToilTest):</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> def setUp(self):</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> """Initial set up of variables for the test."""</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subprocess.check_call(['python', os.path.abspath('src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py')])</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call([python, os.path.abspath('src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py')])</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> self.jobStoreDir = os.path.abspath('toilWorkflowRun')</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> self.tempDir = self._createTempDir(purpose='tempDir')</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> self.outputDir = os.path.abspath('testoutput')</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -54,7 +54,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> contents = ['A.txt', 'B.txt', 'C.txt', 'ABC.txt', 'mkFile.py']</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subprocess.check_call(['python', os.path.abspath('src/toil/utils/toilDebugFile.py'), self.jobStoreDir, '--listFilesInJobStore=True'])</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ subprocess.check_call([python, os.path.abspath('src/toil/utils/toilDebugFile.py'), self.jobStoreDir, '--listFilesInJobStore=True'])</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> jobstoreFileContents = os.path.abspath('jobstore_files.txt')</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> files = []</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> match = 0</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -95,7 +95,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> then delete them.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> contents = ['A.txt', 'B.txt', 'C.txt', 'ABC.txt', 'mkFile.py']</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = ['python', os.path.abspath('src/toil/utils/toilDebugFile.py'),</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = [python, os.path.abspath('src/toil/utils/toilDebugFile.py'),</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> self.jobStoreDir,</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> '--fetch', '*A.txt', '*B.txt', '*C.txt', '*ABC.txt', '*mkFile.py',</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> '--localFilePath=' + self.outputDir,</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,4 +3,7 @@ setting_version.patch</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no_galaxy_lib</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">debianize_docs</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">soften-mesos-deps</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">wdlparse_not_available</span></pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">soften-pydocker-dep</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">python3</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">proxy</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ship_tests</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#8f10e7fbf208d7b374153f7fd9e71e1bb75ca9ca"><strong>debian/patches/ship_tests</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: ship the tests</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</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>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -132,12 +132,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 'wdl': wdl_reqs,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 'all': all_reqs},</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> package_dir={'': 'src'},</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- packages=find_packages(where='src',</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Note that we intentionally include the top-level `test` package for</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # functionality like the @experimental and @integrative decorators:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exclude=['*.test.*']),</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;">+ packages=find_packages(where='src'),</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> package_data={</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '': ['*.yml', 'cloud-config'],</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '': ['*.yml', 'cloud-config', '*.cwl'],</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> },</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # Unfortunately, the names of the entry points are hard-coded elsewhere in the code base so</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> # you can't just change them here. Luckily, most of them are pretty unique strings, and thus</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#037df6725949b5d76b6bcc0423f4f7b7f07f1ffa"><strong>debian/patches/soften-pydocker-dep</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Allow for use of python3-docker package</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</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>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> pytz = 'pytz>=2012'</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> dill = 'dill>=0.3.2, <0.4'</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> requests = 'requests>=2, <3'</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- docker = 'docker==4.3.1'</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ docker = 'docker'</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> dateutil = 'python-dateutil'</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> enlighten = 'enlighten>=1.5.2, <2'</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> wdlparse = 'wdlparse==0.1.0'</span></pre>
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<li id="a4b8bd6a7a72ff6720185f41df4f162bdc674cb6">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#a4b8bd6a7a72ff6720185f41df4f162bdc674cb6"><strong>debian/patches/wdlparse_not_available</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: wdlparse is not yet packaged for Debian</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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4
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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>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -43,7 +43,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> docker = 'docker==4.3.1'</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> dateutil = 'python-dateutil'</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> enlighten = 'enlighten>=1.5.2, <2'</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wdlparse = 'wdlparse==0.1.0'</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> core_reqs = [</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> dill,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -74,9 +73,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> mesos_reqs = [</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> pymesos,</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> psutil]</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wdl_reqs = [</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wdlparse</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ]</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> # htcondor is not supported by apple</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> # this is tricky to conditionally support in 'all' due</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -88,8 +84,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> encryption_reqs + \</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> google_reqs + \</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> kubernetes_reqs + \</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mesos_reqs + \</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wdl_reqs</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mesos_reqs</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> setup(</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> name='toil',</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -129,7 +124,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> 'htcondor:sys_platform!="darwin"': htcondor_reqs,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> 'kubernetes': kubernetes_reqs,</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> 'mesos': mesos_reqs,</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'wdl': wdl_reqs,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> 'all': all_reqs},</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> package_dir={'': 'src'},</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> packages=find_packages(where='src',</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="p">@@ -148,7 +142,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> '_toil_worker = toil.worker:main',</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> 'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]',</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> 'toil-cwl-runner = toil.cwl.cwltoil:main [cwl]',</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'toil-wdl-runner = toil.wdl.toilwdl:main',</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> '_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]',</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> '_toil_kubernetes_executor = toil.batchSystems.kubernetes:executor [kubernetes]']})</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> </span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,9 +5,8 @@ export PYBUILD_NAME=toil</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/toil/</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">export PYBUILD_DISABLE=test</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"><span class="idiff left right">#</span>export PYBUILD_DISABLE=test</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_DISABLE_python2=1</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">#CURDIR ?= $(realpath $(dir $(firstword $(MAKEFILE_LIST)))/..)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,15 +20,14 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> # remove the below once mesos is packaged and tested</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> find $(CURDIR)/debian -name _toil_mesos_executor -delete</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"># more py3 test fixes need to be cherry-picked from upstream</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># PYBUILD_SYSTEM=custom \</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"># PYBUILD_TEST_ARGS='TOIL_SKIP_DOCKER=True {interpreter} -m pytest -vv \</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"># -W ignore \</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"># -k "not test_bioconda and not test_run_conformance and not testImportFtpFile" -n auto\</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> {dir}/src/toil/test' dh_auto_test --buildsystem pybuild</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> PYBUILD_SYSTEM=custom \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> PYBUILD_TEST_ARGS='HOME={home_dir} {interpreter} setup.py develop --user && PYTHONPATH={dir}/src:$$PYTHONPATH PATH={home_dir}/.local/bin/:$$PATH TOIL_TEST_QUICK=True TOIL_SKIP_DOCKER=True {interpreter} -m pytest -vv -W ignore --ignore src/toil/test/provisioners/aws/awsProvisionerTest.py --ignore src/toil/test/wdl/toilwdlTest.py --ignore src/toil/test/cwl/cwlTest.py -k "not test_bioconda and not test_run_conformance and not testImportFtpFile and not ToilWdlIntegrationTest and not SortTest" {dir}/src/toil/test' \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"><span class="idiff left right"> </span># If you need to rebuild the Sphinx documentation</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"># If you need to rebuild the Sphinx documentation</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"># Add spinxdoc to the dh --with line</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">#override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"># dh_auto_build</span>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: smoke-test</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: toil</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: toil<span class="idiff left right">, python3-wdlparse</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: superficial</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Tests: run-unit-tests</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Depends: toil, python3-wdlparse, python3-pytest, python3-mock, python3-boto3, rsync, python3-boto</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</strong></a>
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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>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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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>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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>
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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 [ "${AUTOPKGTEST_TMP}" = "" ] ; then</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)</span></span>
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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 ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># </span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cd "${AUTOPKGTEST_TMP}"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><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;">-W</span> ignore <span class="nt" style="color: #000080;">-k</span> <span class="s2" style="color: #d14;">"not test_bioconda and not testCwlexample and not CWLv10Test and not CWLv11Test and not CWLv12Test"</span> <span class="nt" style="color: #000080;">--ignore-glob</span> <span class="s1" style="color: #d14;">'*cwlTest*'</span> <span class="nt" style="color: #000080;">--pyargs</span> toil.test</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/compare/f63eb972952f6be44b41d31fdad93363a28baa8b...96eb64c9f838600841ec3f54e2463662e0df7296#e2b1208a0e749c8deae704fab4193ed3af3060cd"><strong>debian/tests/smoke-test</strong></a>
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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 -e</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell">toil <span class="nt" style="color: #000080;">--help</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell">toil-cwl-runner <span class="nt" style="color: #000080;">--help</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell">toil-wdl-runner <span class="nt" style="color: #000080;">--help</span></span></pre>
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