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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/d25e0f367a8400830377dedebe4ae4fa28e1f75b">d25e0f36</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-02-10T11:36:53+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/test_with_less_memory: reduce default resource reqs for 32bit systems
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#6187ccefe18309cfee9995c8b0d7b481c9971218">
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+
debian/patches/test_with_less_memory
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
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/d25e0f367a8400830377dedebe4ae4fa28e1f75b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">toil (5.2.0-5) unstable; urgency=high</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debian/patches/test_with_less_memory: reduce default resource reqs</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> for 32bit systems</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="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Wed, 10 Feb 2021 11:24:49 +0100</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 (5.2.0-4) unstable; urgency=high</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"> * autopkgtests: skip some s3 related tests.</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/toil/-/commit/d25e0f367a8400830377dedebe4ae4fa28e1f75b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -7,3 +7,4 @@ soften-pydocker-dep</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">python3</span>
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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>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">test_with_less_memory</span></pre>
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<li id="6187ccefe18309cfee9995c8b0d7b481c9971218">
<a href="https://salsa.debian.org/med-team/toil/-/commit/d25e0f367a8400830377dedebe4ae4fa28e1f75b#6187ccefe18309cfee9995c8b0d7b481c9971218"><strong>debian/patches/test_with_less_memory</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: reduce default resource usage on 32bit systems</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/src/toil/common.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/common.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -21,6 +21,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> import tempfile</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import time</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import uuid</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import platform</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"> from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> from typing import Optional, Callable, Any, List</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -96,9 +97,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> self.statePollingWait = 1 # Number of seconds to wait before querying job state</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"> # Resource requirements</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;">- self.defaultMemory = 2147483648</span></span>
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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>
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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>
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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>
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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 = 1610612736</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 = 1610612736</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> self.defaultCores = 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 = 2147483648</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> self.readGlobalFileMutableByDefault = False</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> self.defaultPreemptable = False</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> self.maxCores = sys.maxsize</span></pre>
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<a href="https://salsa.debian.org/med-team/toil/-/commit/d25e0f367a8400830377dedebe4ae4fa28e1f75b#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">@@ -23,7 +23,7 @@ override_dh_auto_install:</td>
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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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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> PYBUILD_SYSTEM=custom \</span>
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<td class="diff-line-num old old_line" data-linenumber="26" 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="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="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<span class="idiff left right"> and not testCwlexample</span>" {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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<td class="diff-line-num old_line" data-linenumber="28" 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="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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<a href="https://salsa.debian.org/med-team/toil/-/commit/d25e0f367a8400830377dedebe4ae4fa28e1f75b#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;">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 AWSJobStoreTest and not awsjobstoretest 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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">T<span class="idiff left">MP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff">AUTOPKGTEST_TMP </span><span class="nv" style="color: #008080;"><span class="idiff right">T</span>OIL_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 AWSJobStoreTest and not awsjobstoretest 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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