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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/cwltool">Debian Med / cwltool</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/26ea60b705052a1179823e40e73feffa174b500f">26ea60b7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-12-24T19:09:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">speed up autopkgtesting
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cwltool/commit/7f42ec5b24a6371afa78229d4dd9578edf534a5d">7f42ec5b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-12-24T19:51:18Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix the packing test
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ad60c772d52fffa2f34e88e1072db2c0ec19e12c">
debian/patches/add-exec-line
</a>
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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="#aab2726ed6daf419caf178b1480b6d7da8a85af6">
debian/tests/run-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/cwltool/compare/2cb6089753229f26aaf3abc4d8e21150bd6a58ee...7f42ec5b24a6371afa78229d4dd9578edf534a5d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cwltool (1.0.20181217162649+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix our patches to the tests, run them in parallel</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 24 Dec 2018 11:51:11 -0800</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">cwltool (1.0.20181217162649+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * debian/tests/control: fix typo in name of py.test-3</span>
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<li id="ad60c772d52fffa2f34e88e1072db2c0ec19e12c">
<a href="https://salsa.debian.org/med-team/cwltool/compare/2cb6089753229f26aaf3abc4d8e21150bd6a58ee...7f42ec5b24a6371afa78229d4dd9578edf534a5d#ad60c772d52fffa2f34e88e1072db2c0ec19e12c"><strong>debian/patches/add-exec-line</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" 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="218" 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">@@ -218,3 +218,27 @@ Forwarded: https://github.com/common-workflow-language/cwltool/pull/1023</td>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(time.time())</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="diff">\ No newline at end of file</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(time.time())</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- cwltool.orig/tests/test_pack.py</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ cwltool/tests/test_pack.py</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,10 +1,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import json</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> from functools import partial</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> from six import StringIO</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> import pytest</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import json</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from ruamel import yaml</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> import cwltool.pack</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> import cwltool.workflow</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +26,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> document_loader, workflowobj, uri, [], {})</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> with open(get_data("tests/wf/expect_packed.cwl")) as packed_file:</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expect_packed = json.load(packed_file)</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ expect_packed = yaml.load(packed_file)</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> packed = cwltool.pack.pack(document_loader, processobj, uri, metadata)</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> adjustFileObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/cwltool/compare/2cb6089753229f26aaf3abc4d8e21150bd6a58ee...7f42ec5b24a6371afa78229d4dd9578edf534a5d#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">@@ -30,6 +30,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/bin:$$PATH ; \</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> cd {build_dir}; export PYTHONPATH=$$(pwd); python3 -m pytest \</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> -k 'not test_http_path_mapping and not test_pack and not test_get_subgraph and not TestUdocker' \</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> -n auto --ignore cwltool/schemas/ --pyarg cwltool" dh_auto_test</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> -n auto --<span class="idiff left right">dist=loadfile --</span>ignore cwltool/schemas/ --pyarg cwltool" dh_auto_test</span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">endif</span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/cwltool/compare/2cb6089753229f26aaf3abc4d8e21150bd6a58ee...7f42ec5b24a6371afa78229d4dd9578edf534a5d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, python3-pytest, python3-mock, python3-pytest-runner, nodejs, singularity-container, docker.io</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3-pytest<span class="idiff left right">-xdist</span>, python3-mock, python3-pytest-runner, nodejs, singularity-container, docker.io</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/cwltool/compare/2cb6089753229f26aaf3abc4d8e21150bd6a58ee...7f42ec5b24a6371afa78229d4dd9578edf534a5d#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-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">@@ -5,4 +5,5 @@ if [ "$ADTTMP" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">ADTTMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell">py.test-3 <span class="nt" style="color: navy;">--ignore</span> cwltool/schemas <span class="nt" style="color: navy;">--pyarg</span> cwltool</span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">py.test-3 <span class="nt" style="color: navy;">--numprocesses</span><span class="o" style="font-weight: 600;">=</span>auto <span class="nt" style="color: navy;">--dist</span><span class="o" style="font-weight: 600;">=</span>loadfile <span class="nt" style="color: navy;">--ignore</span> cwltool/schemas <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nt" style="color: navy;">--pyarg</span> cwltool</span></pre>
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