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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/5f7a3d5be84d259e365a6e6da34b2abeedc3833f">5f7a3d5b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-10-19T01:51:22+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Testing.
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#28b0709ae4054bc48d823b79dcfc13f75eccbb7e">
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+
debian/patches/fix_test_pytest.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" 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">@@ -14,8 +14,11 @@ snakemake (6.9.1-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * d/control:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> + Add versioned Dep on pulp (>= 2.0)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> + Add B-D on python3-smart-open</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">TODO: pulp new version is needed, which has a dep on amply. Mail sent to -openstack mailing list</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">to update this one.</span>
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<td class="old_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="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * Unselected tests needing internet access</span>
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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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<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"></span>
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<pre style="margin: 0;"> <span id="LC23" 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="LC24" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,35 +10,35 @@ Build-Depends: ca-certificates,</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> environment-modules,</span>
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<td class="old_line diff-line-num" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> imagemagick,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python3-appdirs,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> python3-boto3,</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> python3-botocore,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-appdirs<span class="idiff left right"> <!nocheck></span>,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> python3-biopython<span class="idiff left right"> <!nocheck></span>,</span>
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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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> python3-boto3<span class="idiff left right"> <!nocheck></span>,</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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-botocore<span class="idiff left right"> <!nocheck></span>,</span>
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17
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<td class="new_line diff-line-num" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-configargparse,</span>
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18
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<td class="new_line diff-line-num" data-linenumber="18" 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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-datrie,</span>
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<td class="old_line diff-line-num" data-linenumber="19" 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">
19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> python3-docutils,</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> python3-dropbox,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-dropbox<span class="idiff left right"> <!nocheck></span>,</span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> python3-filelock,</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> python3-flask,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python3-flask<span class="idiff left right"> <!nocheck></span>,</span>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> python3-git,</span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> python3-jinja2,</span>
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25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> python3-jsonschema,</span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> python3-nbformat,</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> python3-networkx,</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> python3-pandas,</span>
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<td class="old_line diff-line-num new" data-linenumber="29" 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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> python3-networkx<span class="idiff left right"> <!nocheck></span>,</span>
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<td class="new_line diff-line-num new" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> python3-pandas<span class="idiff left right"> <!nocheck></span>,</span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> python3-pkg-resources,</span>
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<td class="old_line diff-line-num" data-linenumber="30" 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">
30
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> python3-psutil,</span>
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<td class="old_line diff-line-num" data-linenumber="31" 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">
31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> python3-pulp (>= 2.0),</span>
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<td class="old_line diff-line-num old" data-linenumber="32" 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">
32
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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC32" class="line" lang="plaintext"> python3-pygments,</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="33" 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">
33
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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC33" class="line" lang="plaintext"> python3-pygraphviz,</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="34" 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">
34
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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC34" class="line" lang="plaintext"> python3-pytest,</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="35" 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="32" 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">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> python3-pygments<span class="idiff left right"> <!nocheck></span>,</span>
</pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> python3-pygraphviz<span class="idiff left right"> <!nocheck></span>,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> python3-pytest<span class="idiff left right"> <!nocheck></span>,</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"># sometimes fails tests https://github.com/pytest-dev/pytest-xdist/issues/469 python3-pytest-xdist,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> python3-pytools,</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> python3-pytools<span class="idiff left right"> <!nocheck></span>,</span>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> python3-ratelimiter,</span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> python3-recommonmark <!nodoc>,</span>
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39
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> python3-requests,</span>
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40
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> python3-requests-mock <!nocheck>,</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> python3-rpy2,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> python3-rpy2<span class="idiff left right"> <!nocheck></span>,</span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> python3-setuptools,</span>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> python3-smart-open (>= 3.0),</span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> python3-sphinx <!nodoc>,</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">@@ -47,11 +47,11 @@ Build-Depends: ca-certificates,</td>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> python3-sphinx-rtd-theme <!nodoc>,</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> python3-stopit,</span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> python3-tabulate,</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> python3-toposort,</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> python3-toposort<span class="idiff left right"> <!nocheck></span>,</span>
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51
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> python3-wrapt,</span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> python3-yaml,</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> r-cran-rmarkdown,</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> stress</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> stress<span class="idiff left right"> <!nocheck></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/snakemake</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/snakemake.git</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f#28b0709ae4054bc48d823b79dcfc13f75eccbb7e"><strong>debian/patches/fix_test_pytest.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: pytest has the -3 suffix on Debian</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: Not required since Debian-specific</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Index: snakemake/tests/tests.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- snakemake.orig/tests/tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ snakemake/tests/tests.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1173,7 +1173,7 @@</span> def test_generate_unit_tests():</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> check_md5=False,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> cleanup=False,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sp.check_call(["pytest", ".tests", "-vs"], cwd=tmpdir)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sp.check_call(["pytest-3", ".tests", "-vs"], cwd=tmpdir)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </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"> @skip_on_windows</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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 +6,4 @@ local_javascript.patch</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">workaround_sphinx_issue.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">remove_ccbysa_snippets.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">fix_test_pytest.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">@@ -6,7 +6,7 @@</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
</pre>
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<td class="old_line diff-line-num" 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">
7
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<td class="new_line diff-line-num" 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">
7
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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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<td class="old_line diff-line-num" data-linenumber="8" 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">
8
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<td class="new_line diff-line-num" data-linenumber="8" 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">
8
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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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<td class="old_line diff-line-num old" data-linenumber="9" 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">
9
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<td class="new_line diff-line-num old" data-linenumber="9" 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="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<span class="idiff left right">'</span></span>
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<td class="old_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">
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<td class="new_line diff-line-num new" data-linenumber="9" 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">
9
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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<span class="idiff left right"> 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' </span></span>
</pre>
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<td class="old_line diff-line-num" 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">
10
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<td class="new_line diff-line-num" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11" 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">
11
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11
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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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="12" 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">
12
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12
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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>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="49" 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">@@ -49,3 +49,14 @@ override_dh_auto_test:</td>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="50" 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">
50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> . /etc/profile.d/modules.sh && PYBUILD_SYSTEM=custom dh_auto_test</span>
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<td class="old_line diff-line-num" data-linenumber="51" 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">
51
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<td class="new_line diff-line-num" data-linenumber="51" 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">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">endif</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="52" 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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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="52" 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="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<td class="old_line diff-line-num new" data-linenumber="52" 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="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> dh_auto_clean</span>
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<td class="old_line diff-line-num new" data-linenumber="52" 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="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> rm -f tests/test_filegraph/fg.pdf</span>
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<td class="old_line diff-line-num new" data-linenumber="52" 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="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> rm -f tests/test_filegraph/fg.dot</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> rm -rf tests/test_github_issue413/.snakemake</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> rm -f tests/test_github_issue413/stats.txt</span>
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<td class="new_line diff-line-num new" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> find tests/test_metadata_migration -name "path.txt" -delete</span>
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<td class="new_line diff-line-num new" data-linenumber="60" 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">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> find tests -name "*.log" | grep -v expected-results | xargs -r rm -f</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> rm -rf .snakemake</span>
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<td class="new_line diff-line-num new" data-linenumber="62" 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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> rm -rf tests/test_metadata_migration/.snakemake</span></pre>
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