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<h3>
Rebecca N. Palmer pushed to branch master
at <a href="https://salsa.debian.org/med-team/snakemake">Debian Med / snakemake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/50113c1d69e107d2a6bc1d77870776b6be2154b2">50113c1d</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2022-02-01T20:25:46+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests: skip an FTP-using test.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/4e527e8b5abd7b9a0528fc469562d2f11f231f2d">4e527e8b</a></strong>
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<span>by Rebecca N. Palmer</span>
<i>at 2022-02-01T20:27:39+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">salsa-ci: run additional reproducibility tests.
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
debian/salsa-ci.yml
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1f4fb628f59ccd70805ff2be59ff504b23b67a13...4e527e8b5abd7b9a0528fc469562d2f11f231f2d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">snakemake (6.14.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snakemake (6.14.0-1) <span class="idiff left right">UNRELEASED</span>; 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"> * New upstream release. Refresh patches, d/copyright.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Split up the binary package (main, -doc) to save space.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Tests: skip a<span class="idiff left"> new conda</span>-using test<span class="idiff">, mark</span> a<span class="idiff">s</span> ne<span class="idiff right">eds-interne</span>t,</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> copy the test tree to avoid writing to it.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Tests: skip a<span class="idiff left">n FTP</span>-using test<span class="idiff"> and</span> a ne<span class="idiff right">w conda-using tes</span>t,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right">mark as needs-internet, </span>copy the test tree to avoid writing to it.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Don't ship the test suite, as some of it doesn't work from a</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> non-writable directory.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Reproducibility: fix sphinx locale,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> skip a test that fails under faketime.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> * salsa-ci: ignore expected Lintian error.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * salsa-ci: ignore expected Lintian error<span class="idiff left right">, test reproducibility more</span>.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> <span class="idiff left">Mon</span>, <span class="idiff">3</span>1 <span class="idiff">Jan</span> 2022 2<span class="idiff right">1:12:41</span> +0000</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> <span class="idiff left">Tue</span>, <span class="idiff">0</span>1 <span class="idiff">Feb</span> 2022 2<span class="idiff right">0:23:02</span> +0000</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">snakemake (6.12.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" 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">@@ -22,8 +22,10 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># python3-tibanna: test_tibanna (possibly also specific to one cloud provider?)</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># python3-tes: test_tes</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># Skipped in build due to network use, but run in autopkgtest: test_ancient test_github_issue1062</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># Tests marked @connected skip themselves in this case</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># Skipped due to network use</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># skipped in build, but run in autopkgtest: test_ancient</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># skipped in both as it uses FTP and some autopkgtest environments are http-only: test_github_issue1062</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"># Tests marked @connected skip themselves if network access isn't available</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="LC30" class="line" lang="plaintext"># Skipped in build to let reproducibility tests pass (it fails under faketime, with what looks like the outer script but not the rules running under it), but run in autopkgtest: test_symlink_time_handling</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1f4fb628f59ccd70805ff2be59ff504b23b67a13...4e527e8b5abd7b9a0528fc469562d2f11f231f2d#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</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">@@ -6,3 +6,6 @@ variables:</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># real but deliberately left in because the obvious fix is</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># too likely to break things, see README.source</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">SALSA_CI_LINTIAN_SUPPRESS_TAGS</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">privacy-breach-uses-embedded-file"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># one of the sphinx inventories seems to be binary garbage - find out why</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">SALSA_CI_ENABLE_DIFFOSCOPE</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">SALSA_CI_ATOMIC_REPROTEST</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/1f4fb628f59ccd70805ff2be59ff504b23b67a13...4e527e8b5abd7b9a0528fc469562d2f11f231f2d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -22,4 +22,4 @@ export HOME="${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">.</span> /etc/profile.d/modules.sh</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#See debian/rules for why these are excluded</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_env_modules'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_env_modules<span class="idiff left right"> and not test_github_issue1062</span>'</span></span></pre>
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