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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>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f">93ad57da</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-10-03T13:35:50+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtests: skip collection of s3 tests
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#59ad974686407b525dc696c88437dd59de34a805">
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+
debian/patches/cwl_test_path
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">toil (5.5.0-3) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">toil (5.5.0-3) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * toil binary package depedency on recent cwltool as well.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Autopkgtests: skip collection of s3 tests</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left">Fri</span>, 0<span class="idiff">1</span> Oct 2021 <span class="idiff">0</span>0:18<span class="idiff right">:15</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> <span class="idiff left">Sun</span>, 0<span class="idiff">3</span> Oct 2021 <span class="idiff right">13:2</span>0:18 +0200</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">toil (5.5.0-2) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f#59ad974686407b525dc696c88437dd59de34a805"><strong>debian/patches/cwl_test_path</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: CWL: safer test path generation for post-install testing</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/3818</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/cwl/cwlTest.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/cwl/cwlTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -632,7 +632,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> option_1 = '--strict-memory-limit'</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> option_2 = '--force-docker-pull'</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> option_3 = '--clean=always'</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;">- cwl = os.path.join(self._projectRootPath(), 'src/toil/test/cwl/echo_string.cwl')</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;">+ cwl = os.path.join(os.path.dirname(__file__), 'echo_string.cwl')</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> cmd = [toil, jobstore, option_1, option_2, option_3, cwl]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> log.debug(f'Now running: {" ".join(cmd)}')</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cwl_test_path</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">spelling</span>
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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">setting_version.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">no_galaxy_lib</span>
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<a href="https://salsa.debian.org/med-team/toil/-/commit/93ad57da4d43522ac726aae93ae3322523caa29f#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</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">@@ -10,4 +10,4 @@ export LC_ALL=C.UTF-8</td>
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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;">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;">-W</span> ignore <span class="nt" style="color: #000080;">-k</span> <span class="s2" style="color: #d14;">"not test_bioconda <span class="idiff left">and not</span> AWSJobStoreTest <span class="idiff">and not</span> awsjobstoretest <span class="idiff">and not</span> testCwlexample <span class="idiff">and not</span> CWLv10Test <span class="idiff">and not</span> CWLv1<span class="idiff">1</span>Test <span class="idiff right">and not CWLv12</span>Test"</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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<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;"><span class="idiff left">-rs</span></span><span class="idiff"> </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 <span class="idiff">(</span>test_bioconda <span class="idiff">or</span> AWSJobStoreTest <span class="idiff">or</span> awsjobstoretest <span class="idiff">or</span> testCwlexample <span class="idiff">or</span> CWLv10Test <span class="idiff">or CWLv11Test or</span> CWLv1<span class="idiff">2</span>Test <span class="idiff">or AWSAutoscaleTest or AWSStaticAutoscaleTest or AWSManagedAutoscaleTest or AWSAutoscaleTestMultipleNodeTypes or AWSRestartTest or PreemptableDeficitCompensation</span>Test<span class="idiff">)</span>"</span> <span class="nt" style="color: #000080;">--ignore-glob</span> <span class="s1" style="color: #d14;">'*cwlTest*'</span> <span class="nt" style="color: #000080;"><span class="idiff">--ignore</span></span><span class="idiff right"> /usr/lib/python3/dist-packages/toil/test/lib/aws/test_s3.py </span><span class="nt" style="color: #000080;">--pyargs</span> toil.test</span></pre>
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