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<h3>
Steffen Möller 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/e5d06b9b525a49573053a94ebcc6e465ef2fbb10">e5d06b9b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-10-19T15:23:19+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More refinements for lintian
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
debian/source/lintian-overrides
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,3 +4,7 @@ Tasks to do for next releases of snakemake</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Prepare https://pypi.org/project/py-tes/ as a Debian pacakge</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> - no need to re-activated cognate test in d/rules since this requires internet</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> - add as recommendation to binary</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"> * Decide to remove obscure tests from source tree and have a +dfsg package</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> P: snakemake source: embedded-script-includes-copyright-statement tests/test_module_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> P: snakemake source: embedded-script-includes-copyright-statement tests/test_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,7 +20,7 @@ snakemake (6.9.1-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * fixing one calling pytest -> pytest-3</span>
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<td class="old_line diff-line-num" data-linenumber="21" 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="LC21" class="line" lang="plaintext"> * d/rules: Allowing consecutive builds with better cleaning</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Added d/TODO to remind about missing "tes" Python module</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Sun, 17 Oct 2021 14:19:21 +0000</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">snakemake (5.24.1-2) unstable; urgency=medium</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10#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">@@ -6,7 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k '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_ancient and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_github_issue1062 and not test_env_modules and not test_modules_meta_wrapper and not test_tes'<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k '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_ancient and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_github_issue1062 and not test_env_modules and not test_modules_meta_wrapper and not test_tes'</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"># Skipped because they download executables (which is forbidden in Debian buildd and debci)</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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="40" 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">@@ -40,9 +40,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> find debian -name '__pycache__' | xargs rm -R</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> find debian -name '*.pyc' | xargs -r rm</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> find debian -name '.gitignore' | xargs -r rm</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> find debian/snakemake -name '.gitignore' | xargs -r rm</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"># the modules.sh is a workaround for #928826; putting it in PYBUILD_BEFORE_TEST_python3 doesn't work</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>
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<li id="85ccdeeb03055211183e48520592d9a93592b330">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</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">@@ -3,3 +3,19 @@ snakemake source: source-is-missing tests/test_report/expected-results/report.ht</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">snakemake source: source-is-missing tests/test_report/expected-results/report.html line length is *</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">snakemake source: source-is-missing tests/test_module_report/expected-results/report.html</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">snakemake source: mismatched-override source-is-missing tests/test_report/expected-results/report.html line length is *</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"># Complaints about hand-written documentation / image</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/executing/cluster.rst line 68 is 809 characters long (>512)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/project_info/faq.rst line 339 is 610 characters long (>512)</span>
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<td class="new_line diff-line-num new" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/snakefiles/deployment.rst line 133 is 1046 characters long (>512)</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/snakefiles/remote_files.rst line 528 is 847 characters long (>512)</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/snakefiles/rules.rst line 976 is 1206 characters long (>512)</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="13" 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="LC13" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file docs/tutorial/advanced.rst line 254 is 666 characters long (>512)</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="14" 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="LC14" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file images/biglogo.svg line 68 is 906 characters long (>512)</span>
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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="15" 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="LC15" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="16" 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="LC16" class="line" lang="plaintext"># We might want to discuss if these files + tests should be removed from the source tree that are deselected anyway</span>
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<td class="new_line diff-line-num new" data-linenumber="17" 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="LC17" class="line" lang="plaintext">snakemake source: embedded-script-includes-copyright-statement tests/test_module_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l</span>
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<td class="new_line diff-line-num new" data-linenumber="18" 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="LC18" class="line" lang="plaintext">snakemake source: embedded-script-includes-copyright-statement tests/test_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l</span>
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<td class="new_line diff-line-num new" data-linenumber="19" 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="LC19" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" 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="LC20" class="line" lang="plaintext"># the long line is the test</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">snakemake source: very-long-line-length-in-source-file tests/tests.py line 1186 is 571 characters long (>512)</span></pre>
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