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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/2705e3b8eb3665ba7942d5e7fac5656ac07b4a46">2705e3b8</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-05-04T11:24:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Dockerfile: fix remote root-in-container security hole.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/34852dea3d0fd78ab3dae0a8ee1d077d3db1a72c">34852dea</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-05-04T11:27:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.16.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/2742610624409fb18904fc0a509b1f1ccddf0ed4">27426106</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-05-04T11:28:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.16.0'
Update to upstream version '5.16.0'
with Debian dir ccb919adeba020055e4d3c1e5dc74fc65bc8004e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/snakemake/-/commit/443804191d0ee873fc54e14ad9392386f6c69d13">44380419</a></strong>
<div>
<span>by Rebecca N. Palmer</span>
<i>at 2020-05-04T12:16:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip a new conda-using test.
</pre>
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<h4>22 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
CHANGELOG.rst
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#6315071dfc30fef957f76845b1a74813e8ebadec">
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+
debian/patches/security.patch
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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
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#828e10e8685244cbb6e9a3d9bacdf36fb8984b0a">
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docs/snakefiles/images/snakemake-notebook-demo.gif
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<li class="file-stats">
<a href="#dfeb7b6e739ba66056c1799c63a5a39c7698b59f">
docs/snakefiles/rules.rst
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<li class="file-stats">
<a href="#d366205d7cd679ff6d4a61f70728e92537101763">
snakemake/__init__.py
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<li class="file-stats">
<a href="#5e16cbeea010f59dbef52f8950f4873c94f39c7e">
snakemake/_version.py
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<li class="file-stats">
<a href="#9821437dfb3fff8383b6066a2a3c7aa3f6712a32">
snakemake/dag.py
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<li class="file-stats">
<a href="#1dba76c2cca537b789f8754f5ddbed5dc36c6dee">
snakemake/executors.py
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<li class="file-stats">
<a href="#818384818c4671b8354b6eb98ee2bab61c015a74">
snakemake/jobs.py
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<li class="file-stats">
<a href="#87b26159067ade1d989921cb3240bfabece3aea0">
snakemake/notebook.py
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<li class="file-stats">
<a href="#d70c11793454d64a7b2d77ced116226d2f13378e">
snakemake/parser.py
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<li class="file-stats">
<a href="#55752111e76e9d786fdb84c4e7fd9f6de5c67a24">
snakemake/rules.py
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<li class="file-stats">
<a href="#0ac0ac393192e0b6a8ebf767dd5e206b4afbf3b2">
snakemake/scheduler.py
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<li class="file-stats">
<a href="#66a73d9dd46eb8e71f0039a18d36dbd78aea7977">
snakemake/script.py
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<li class="file-stats">
<a href="#cb9e107597e441fb1c0d61663359d9cf1dbfe04d">
snakemake/workflow.py
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<li class="file-stats">
<a href="#e460778e47b9f9ba01af8e90753151e6a11e3a12">
<span class="new-file">
+
tests/test_jupyter_notebook/expected-results/result_final.txt
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<li class="file-stats">
<a href="#ef87f9232438af307b4ad2b8d1feb87824e1bfdd">
<span class="new-file">
+
tests/test_jupyter_notebook/expected-results/result_intermediate.txt
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<li class="file-stats">
<a href="#002e3bc3eddf51d9e25c30326a4bc060aadbf93b">
tests/tests.py
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<h4>Changes:</h4>
<li id="45267e3a9556cafa9cb7b61dab7a3b6659e73aad">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#45267e3a9556cafa9cb7b61dab7a3b6659e73aad"><strong>CHANGELOG.rst</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">[5.16.0] - 2020-04-29</span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="plaintext">=====================</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Added</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">-----</span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">- Interactive jupyter notebook editing. Notebooks defined by rules can be interactively drafted and updated using snakemake --edit-notebook (see docs).</span>
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<td class="diff-line-num new new_line" 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="LC6" class="line" lang="plaintext">Changed</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext">-------</span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- Fixed group resource usage to occupy one cluster/cloud node.</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">- Minor bug fixes.</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">[5.15.0] - 2020-04-21</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">Changed</span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">snakemake (5.1<span class="idiff left right">5.0-1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">snakemake (5.1<span class="idiff left right">6.0-1) unstable</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. Drop / refresh patches.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Stop using pytest-xdist: it sometimes starts tests from</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> a non-main thread, which breaks snakemake.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Dockerfile: fix remote root-in-container security hole.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Skip a new conda-using test.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Mon, <span class="idiff left right">27 Apr 2020 12:05:59</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Rebecca N. Palmer <rebecca_palmer@zoho.com> Mon, <span class="idiff left right">04 May 2020 12:16:03</span> +0100</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">snakemake (5.14.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<li id="6315071dfc30fef957f76845b1a74813e8ebadec">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#6315071dfc30fef957f76845b1a74813e8ebadec"><strong>debian/patches/security.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix remote root-in-container security hole, and a link</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Repository signatures are only secure if you have the right key</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">to check them with</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Author: Rebecca N. Palmer <rebecca_palmer@zoho.com></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: https://github.com/snakemake/snakemake/pull/371</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff">diff --git a/Dockerfile b/Dockerfile</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index 095b5335..a3afe66b 100644</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Dockerfile</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Dockerfile</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -6,8 +6,8 @@</span> ENV PATH /opt/conda/bin:${PATH}</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ENV LANG C.UTF-8</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ENV SHELL /bin/bash</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> RUN /bin/bash -c "install_packages wget bzip2 ca-certificates gnupg2 squashfs-tools git && \</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wget -O- http://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \</span></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;">- wget -O- http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add - && \</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;">+ wget -O- https://neuro.debian.net/lists/xenial.us-ca.full > /etc/apt/sources.list.d/neurodebian.sources.list && \</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;">+ wget -O- https://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add - && \</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> install_packages singularity-container && \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/examples/c/README.txt b/examples/c/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gh" style="color: #999;">index 995d30fe..d2eaceec 100644</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/examples/c/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/examples/c/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -1 +1 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-http://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+https://www.cs.colby.edu/maxwell/courses/tutorials/maketutor/</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_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="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 @@ local_javascript.patch</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">python3.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">workaround_sphinx_issue.patch</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">remove_ccbysa_snippets.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">security.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#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">@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=snakemake</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export PYBUILD_DESTDIR_python3=debian/snakemake</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}</span>
</pre>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'</span>
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<td class="diff-line-num new old_line" 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">
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container<span class="idiff left right"> and not test_jupyter_notebook</span>'</span>
</pre>
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<td class="diff-line-num old_line" 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"></span>
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<td class="diff-line-num old_line" 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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># test_report</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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">
13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># test_ancient</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not rep</td>
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<td class="diff-line-num old_line" 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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"># test_issue1093 fails due to conda usage; commenting that out and installing bwa produces a different ordering than desired</span>
</pre>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># test_default_resources and test_remote needs moto to be packaged https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777089</span>
</pre>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># test_env_modules relies on "module load" which is not packaged for Debian</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># test_archive<span class="idiff left right"> uses</span> conda</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># test_archive<span class="idiff left right">, test_jupyter_notebook use</span> conda</span>
</pre>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># test_container uses docker://bash</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" 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">
24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="25" 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">
25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HOME</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</span>/tests/test<span class="k" style="font-weight: 600;">*</span>.py <span class="nt" style="color: #000080;">-k</span> <span class="s1" style="color: #d14;">'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container'</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">python3 <span class="nt" style="color: #000080;">-m</span> pytest <span class="nt" style="color: #000080;">-v</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ROOT</span><span class="k" style="font-weight: 600;">}</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 report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container<span class="idiff left right"> and not test_jupyter_notebook</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#828e10e8685244cbb6e9a3d9bacdf36fb8984b0a"><strong>docs/snakefiles/images/snakemake-notebook-demo.gif</strong></a>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#dfeb7b6e739ba66056c1799c63a5a39c7698b59f"><strong>docs/snakefiles/rules.rst</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">@@ -608,18 +608,14 @@ Integration works as follows (note the use of `notebook:` instead of `script:`):</td>
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="plaintext"> rule NAME:</span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="plaintext"> input:</span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="plaintext"> "path/to/inputfile",</span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="plaintext"> "path/to/other/inputfile"</span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> rule hello:</span>
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="plaintext"> output:</span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="plaintext"> "path/to/outputfile",</span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="plaintext"> "path/to/another/outputfile"</span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> "test.txt"</span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="plaintext"> log:</span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="plaintext"> # optional path to the processed notebook</span>
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="plaintext"> notebook<span class="idiff left right"> = </span>"logs/notebooks/processed_notebook.ipynb"</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext"> notebook<span class="idiff left right">=</span>"logs/notebooks/processed_notebook.ipynb"</span>
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="plaintext"> notebook:</span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="plaintext"> "<span class="idiff left right">notebooks/notebook</span>.ipynb"</span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext"> "<span class="idiff left right">hello.py</span>.ipynb"</span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="plaintext">.. note:</span>
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<pre style="margin: 0;"> <span id="LC621" 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">@@ -627,15 +623,41 @@ Integration works as follows (note the use of `notebook:` instead of `script:`):</td>
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627
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="plaintext"> A modular, readable workflow definition with Snakemake, and the ability to quickly explore and plot data with Jupyter.</span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="plaintext"> The benefit will be maximal when integrating many small notebooks that each do a particular job, hence allowing to get away from large monolithic, and therefore unreadable notebooks.</span>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext">It is recommended to prefix the ``.ipynb`` suffix with either ``.py`` or ``.r`` to indicate the notebook language.</span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="plaintext">In the notebook, a snakemake object is available, which can be accessed in the same way as the with :ref:`script integration <snakefiles_external-scripts>`.</span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="plaintext">In other words, you have access to input files via ``snakemake.input`` (in the Python case) and ``snakemake@input`` (in the R case) etc..</span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="plaintext">Hence, integrating a new notebook works by first writing it from scratch in the usual interactive way.</span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="plaintext">Then, you replace all hardcoded variables with references to properties of the rule where it shall be integrated, e.g. replacing the path to an input file with ``snakemake.input[0]``.</span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="plaintext">Once having moved the notebook to the right place in the pipeline (ideally a subfolder ``notebooks``) and referring to it from the rule, Snakemake will be able to re-execute it while inserting the desired variable values from the rule properties.</span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="plaintext">Optionally it is possible to automatically store the processed notebook.</span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="plaintext">This can be achieved by adding a named logfile ``notebook=...`` to the ``log`` directive.</span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext">In order to simplify the coding of notebooks given the automatically inserted ``snakemake`` object, Snakemake provides an interactive edit mode for notebook rules.</span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext">Let us assume you have written above rule, but the notebook does not yet exist.</span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext">By running</span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext">.. code-block:: console</span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext"> snakemake --cores 1 --edit-notebook test.txt</span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext">you instruct Snakemake to allow interactive editing of the notebook needed to create the file ``test.txt``.</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">Snakemake will run all dependencies of the notebook rule, such that all input files are present.</span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">Then, it will start a jupyter notebook server with an empty draft of the notebook, in which you can interactively program everything needed for this particular step.</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext">Once done, you should save the notebook from the jupyter web interface, go to the jupyter dashboard and hit the ``Quit`` button on the top right in order to shut down the jupyter server.</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">Snakemake will detect that the server is closed and automatically store the drafted notebook into the path given in the rule (here ``hello.py.ipynb``).</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext">If the notebook already exists, above procedure can be used to easily modify it.</span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">Note that Snakemake requires local execution for the notebook edit mode.</span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">On a cluster or the cloud, you can generate all dependencies of the notebook rule via</span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">.. code-block:: console</span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext"> snakemake --cluster ... --jobs 100 --until test.txt</span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext">Then, the notebook rule can easily be executed locally.</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext">An demo of the entire interactive editing process can be found by clicking below:</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext">.. image:: images/snakemake-notebook-demo.gif</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext"> :scale: 20%</span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"> :alt: Notebook integration demo</span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext"> :align: center</span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="plaintext">Protected and Temporary Files</span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="plaintext">-----------------------------</span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#d366205d7cd679ff6d4a61f70728e92537101763"><strong>snakemake/__init__.py</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">@@ -153,6 +153,7 @@ def snakemake(</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">show_failed_logs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">keep_incomplete</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">messaging</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run snakemake on a given snakefile.</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></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">@@ -262,7 +263,8 @@ def snakemake(</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;"> cluster_status (str): status command for cluster execution. If None, Snakemake will rely on flag files. Otherwise, it expects the command to return "success", "failure" or "running" when executing with a cluster jobid as single argument.</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"><span class="s" style="color: #d14;"> export_cwl (str): Compile workflow to CWL and save to given file</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"><span class="s" style="color: #d14;"> log_handler (function): redirect snakemake output to this custom log handler, a function that takes a log message dictionary (see below) as its only argument (default None). The log message dictionary for the log handler has to following entries:</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"><span class="s" style="color: #d14;"> keep_incomplete (bool): keep incomplete output files of failed jobs</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="s" style="color: #d14;"> keep_incomplete (bool): keep incomplete output files of failed jobs</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="s" style="color: #d14;"> edit_notebook (object): "notebook.Listen" object to configuring notebook server for interactive editing of a rule notebook. If None, do not edit.</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"><span class="s" style="color: #d14;"> log_handler (list): redirect snakemake output to this list of custom log handler, each a function that takes a log message dictionary (see below) as its only argument (default []). The log message dictionary for the log handler has to following entries:</span></span>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"><span class="s" style="color: #d14;"> :level:</span></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">@@ -334,10 +336,10 @@ def snakemake(</td>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">updated_files</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">updated_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cluster</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">cluster_sync</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">drmaa</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">tibanna</span><span class="p">:</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">maxsiz</span>e</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cluster</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">cluster_sync</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">drmaa</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">tibanna</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kubernetes</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">Non</span>e</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">maxsiz</span>e</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">Non</span>e</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cluster_config</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Loading configuration from one file is still supported for</span></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">@@ -355,9 +357,15 @@ def snakemake(</td>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">cluster_config_content</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">run_local</span> <span class="o" style="font-weight: 600;">=</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">cluster</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">cluster_sync</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">drmaa</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">kubernetes</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">tibanna</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run_local</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dryrun</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clean up all previously recorded jobids.</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">.</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run_local</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dryrun</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clean up all previously recorded jobids.</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">shell</span><span class="p">.</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edit_notebook</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="s" style="color: #d14;">"Notebook edit mode is only allowed with local execution."</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># force thread use for any kind of cluster</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">use_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></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">@@ -491,6 +499,7 @@ def snakemake(</td>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">nodes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nodes</span><span class="p">,</span></span>
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">resources</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">resources</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="p">)</span></span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">include</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1102" 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">@@ -1093,9 +1102,9 @@ def get_argument_parser(profile=None):</td>
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1093
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1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="python"><span class="s" style="color: #d14;"> ),</span></span>
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1094
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1103
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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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1095
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1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="python"></span>
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1096
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<pre style="margin: 0;">-<span id="LC1096" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">utils = parser.add_argument_group("UTILITIE</span>S")</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">report = parser.add_argument_group("REPORT</span>S")</span></span>
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1097
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="python"></span>
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1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">utils</span>.add_argument(</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">report</span>.add_argument(</span></span>
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="python"><span class="s" style="color: #d14;"> "--report",</span></span>
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1100
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="python"><span class="s" style="color: #d14;"> nargs="?",</span></span>
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1101
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="python"><span class="s" style="color: #d14;"> const="report.html",</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1115" 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">@@ -1106,12 +1115,33 @@ def get_argument_parser(profile=None):</td>
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1106
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="python"><span class="s" style="color: #d14;"> "In the latter case, results are stored along with a file report.html in the zip archive. "</span></span>
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1107
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="python"><span class="s" style="color: #d14;"> "If no filename is given, an embedded report.html is the default.",</span></span>
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1108
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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1109
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<pre style="margin: 0;">-<span id="LC1109" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">utils</span>.add_argument(</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="python"><span class="s" style="color: #d14;"> group_<span class="idiff left right">report</span>.add_argument(</span></span>
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1110
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="python"><span class="s" style="color: #d14;"> "--report-stylesheet",</span></span>
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1111
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<td class="diff-line-num new_line" data-linenumber="1120" 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">
1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="python"><span class="s" style="color: #d14;"> metavar="CSSFILE",</span></span>
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<td class="diff-line-num old_line" data-linenumber="1112" 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">
1112
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<td class="diff-line-num new_line" data-linenumber="1121" 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">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="python"><span class="s" style="color: #d14;"> help="Custom stylesheet to use for report. In particular, this can be used for "</span></span>
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<td class="diff-line-num old_line" data-linenumber="1113" 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">
1113
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<td class="diff-line-num new_line" data-linenumber="1122" 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">
1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="python"><span class="s" style="color: #d14;"> "branding the report with e.g. a custom logo, see docs.",</span></span>
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<td class="diff-line-num old_line" data-linenumber="1114" 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">
1114
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<td class="diff-line-num new_line" data-linenumber="1123" 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">
1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1125" 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">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="python"><span class="s" style="color: #d14;"> group_notebooks = parser.add_argument_group("NOTEBOOKS")</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="python"></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="python"><span class="s" style="color: #d14;"> group_notebooks.add_argument(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1128" 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">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="python"><span class="s" style="color: #d14;"> "--edit-notebook",</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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="diff-line-num new new_line" data-linenumber="1129" 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">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="python"><span class="s" style="color: #d14;"> metavar="TARGET",</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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="diff-line-num new new_line" data-linenumber="1130" 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">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="python"><span class="s" style="color: #d14;"> help="Interactively edit the notebook associated with the rule used to generate the given target file. "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1131" 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">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="python"><span class="s" style="color: #d14;"> "This will start a local jupyter notebook server. "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1132" 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">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="python"><span class="s" style="color: #d14;"> "Any changes to the notebook should be saved, and the server has to be stopped by "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1133" 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">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="python"><span class="s" style="color: #d14;"> "closing the notebook and hitting the '</span><span class="n" style="color: #333;">Quit</span><span class="s" style="color: #d14;">' button on the jupyter dashboard. "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1134" 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">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="python"><span class="s" style="color: #d14;"> "Afterwards, the updated notebook will be automatically stored in the path defined in the rule. "</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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="diff-line-num new new_line" data-linenumber="1135" 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">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="python"><span class="s" style="color: #d14;"> "If the notebook is not yet present, this will create an empty draft. ",</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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="diff-line-num new new_line" data-linenumber="1136" 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">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" 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">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="python"><span class="s" style="color: #d14;"> group_notebooks.add_argument(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" 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">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="python"><span class="s" style="color: #d14;"> "--notebook-listen",</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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="diff-line-num new new_line" data-linenumber="1139" 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">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="python"><span class="s" style="color: #d14;"> metavar="IP:PORT",</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1115" 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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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="python"><span class="s" style="color: #d14;"> default="localhost:8888",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1141" 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">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="python"><span class="s" style="color: #d14;"> help="The IP address and PORT the notebook server used for editing the notebook (--edit-notebook) will listen on.",</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1142" 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">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="python"></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="python"><span class="s" style="color: #d14;"> group_utils = parser.add_argument_group("UTILITIES")</span></span>
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1115
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<td class="diff-line-num new_line" data-linenumber="1145" 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">
1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="python"><span class="s" style="color: #d14;"> group_utils.add_argument(</span></span>
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1116
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1146
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="python"><span class="s" style="color: #d14;"> "--lint",</span></span>
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<td class="diff-line-num old_line" data-linenumber="1117" 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">
1117
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<td class="diff-line-num new_line" data-linenumber="1147" 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">
1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="python"><span class="s" style="color: #d14;"> nargs="?",</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1121" 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="1151" 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">@@ -1121,6 +1151,7 @@ def get_argument_parser(profile=None):</td>
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1121
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<td class="diff-line-num new_line" data-linenumber="1151" 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">
1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="python"><span class="s" style="color: #d14;"> "specific suggestions to improve code quality (work in progress, more lints "</span></span>
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<td class="diff-line-num old_line" data-linenumber="1122" 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">
1122
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<td class="diff-line-num new_line" data-linenumber="1152" 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">
1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="python"><span class="s" style="color: #d14;"> "to be added in the future). If no argument is provided, plain text output is used.",</span></span>
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1123
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<td class="diff-line-num new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1124" 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="diff-line-num new new_line" data-linenumber="1154" 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">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="python"></span>
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1124
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<td class="diff-line-num new_line" data-linenumber="1155" 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">
1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="python"><span class="s" style="color: #d14;"> group_utils.add_argument(</span></span>
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<td class="diff-line-num old_line" data-linenumber="1125" 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">
1125
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<td class="diff-line-num new_line" data-linenumber="1156" 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">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="python"><span class="s" style="color: #d14;"> "--export-cwl",</span></span>
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<td class="diff-line-num old_line" data-linenumber="1126" 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">
1126
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<td class="diff-line-num new_line" data-linenumber="1157" 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">
1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="python"><span class="s" style="color: #d14;"> action="store",</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2102" 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="2133" 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">@@ -2102,6 +2133,13 @@ def main(argv=None):</td>
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<td class="diff-line-num old_line" data-linenumber="2102" 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">
2102
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2133
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<pre style="margin: 0;"> <span id="LC2133" class="line" lang="python"><span class="s" style="color: #d14;"> slack_logger = logging.SlackLogger()</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2103" 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">
2103
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<td class="diff-line-num new_line" data-linenumber="2134" 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">
2134
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<pre style="margin: 0;"> <span id="LC2134" class="line" lang="python"><span class="s" style="color: #d14;"> log_handler.append(slack_logger.log_handler)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2104" 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">
2104
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<td class="diff-line-num new_line" data-linenumber="2135" 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">
2135
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<pre style="margin: 0;"> <span id="LC2135" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2105" 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="diff-line-num new new_line" data-linenumber="2136" 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">
2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="python"><span class="s" style="color: #d14;"> if args.edit_notebook:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2137" 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">
2137
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<pre style="margin: 0;">+<span id="LC2137" class="line" lang="python"><span class="s" style="color: #d14;"> from snakemake import notebook</span></span>
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2138
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<pre style="margin: 0;">+<span id="LC2138" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="2139" 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">
2139
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<pre style="margin: 0;">+<span id="LC2139" class="line" lang="python"><span class="s" style="color: #d14;"> args.target = [args.edit_notebook]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2140" 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">
2140
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<pre style="margin: 0;">+<span id="LC2140" class="line" lang="python"><span class="s" style="color: #d14;"> args.force = True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2141" 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">
2141
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<pre style="margin: 0;">+<span id="LC2141" class="line" lang="python"><span class="s" style="color: #d14;"> args.edit_notebook = notebook.Listen(args.notebook_listen)</span></span>
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2142
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<pre style="margin: 0;">+<span id="LC2142" class="line" lang="python"></span>
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2105
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<td class="diff-line-num new_line" data-linenumber="2143" 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">
2143
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<pre style="margin: 0;"> <span id="LC2143" class="line" lang="python"><span class="s" style="color: #d14;"> success = snakemake(</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2106" 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">
2106
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<td class="diff-line-num new_line" data-linenumber="2144" 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">
2144
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<pre style="margin: 0;"> <span id="LC2144" class="line" lang="python"><span class="s" style="color: #d14;"> args.snakefile,</span></span>
</pre>
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2107
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2145
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<pre style="margin: 0;"> <span id="LC2145" class="line" lang="python"><span class="s" style="color: #d14;"> batch=batch,</span></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">@@ -2211,6 +2249,7 @@ def main(argv=None):</td>
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2249
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<pre style="margin: 0;"> <span id="LC2249" class="line" lang="python"><span class="s" style="color: #d14;"> export_cwl=args.export_cwl,</span></span>
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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="python"><span class="s" style="color: #d14;"> show_failed_logs=args.show_failed_logs,</span></span>
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2251
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<pre style="margin: 0;"> <span id="LC2251" class="line" lang="python"><span class="s" style="color: #d14;"> keep_incomplete=args.keep_incomplete,</span></span>
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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="python"><span class="s" style="color: #d14;"> edit_notebook=args.edit_notebook,</span></span>
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<pre style="margin: 0;"> <span id="LC2253" class="line" lang="python"><span class="s" style="color: #d14;"> log_handler=log_handler,</span></span>
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<pre style="margin: 0;"> <span id="LC2254" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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2255
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<pre style="margin: 0;"> <span id="LC2255" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#5e16cbeea010f59dbef52f8950f4873c94f39c7e"><strong>snakemake/_version.py</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">@@ -22,9 +22,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: v5.15</span>.0)"</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">6d3aa424cfffaf33f36ca4b6da870ce786ddcb30</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-04-2<span class="idiff left right">1 10:55:47</span> +0200"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: v5.16</span>.0)"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">7ec74f79067b3392607479c6f3bec4a2e90cbc05</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2020-04-2<span class="idiff left right">9 16:01:58</span> +0200"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#9821437dfb3fff8383b6066a2a3c7aa3f6712a32"><strong>snakemake/dag.py</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">@@ -319,6 +319,9 @@ class DAG:</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">update_dynamic</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">postprocess</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_edit_notebook_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">edit_notebook</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">targetfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">targetfiles</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dynamic_output_jobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterate over all jobs with dynamic output files."""</span></span>
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<li id="1dba76c2cca537b789f8754f5ddbed5dc36c6dee">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#1dba76c2cca537b789f8754f5ddbed5dc36c6dee"><strong>snakemake/executors.py</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">@@ -203,15 +203,16 @@ class RealExecutor(AbstractExecutor):</td>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">handle_touch</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">ignore_missing_output</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">postprocess</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">upload_remote</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">upload_remote</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">handle_log</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handle_log</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">handle_touch</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handle_touch</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">ignore_missing_output</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ignore_missing_output</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">latency_wait</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latency_wait</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">assume_shared_fs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assume_shared_fs</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">report_job_end</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dag</span><span class="p">.</span><span class="n" style="color: #333;">is_edit_notebook_job</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">postprocess</span><span class="p">(</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">upload_remote</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">upload_remote</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">handle_log</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handle_log</span><span class="p">,</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">handle_touch</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handle_touch</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">ignore_missing_output</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ignore_missing_output</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">latency_wait</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">latency_wait</span><span class="p">,</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">assume_shared_fs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assume_shared_fs</span><span class="p">,</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="p">)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">report_job_end</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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215
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"></span>
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216
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_job_error</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">upload_remote</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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217
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">postprocess</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="422" 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="423" 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">@@ -422,6 +423,7 @@ class CPUExecutor(RealExecutor):</td>
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422
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
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423
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">shadow_dir</span><span class="p">,</span></span>
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424
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">jobid</span><span class="p">,</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
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425
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="p">)</span></span>
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426
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"></span>
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427
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_single_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2025" 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="2027" 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">@@ -2025,6 +2027,7 @@ def run_wrapper(</td>
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2025
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2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
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2026
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<td class="diff-line-num new_line" data-linenumber="2028" 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">
2028
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<pre style="margin: 0;"> <span id="LC2028" class="line" lang="python"> <span class="n" style="color: #333;">shadow_dir</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="2027" 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">
2027
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<td class="diff-line-num new_line" data-linenumber="2029" 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">
2029
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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="python"> <span class="n" style="color: #333;">jobid</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2028" 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="diff-line-num new new_line" data-linenumber="2030" 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">
2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
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2028
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2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="python"><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="2029" 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">
2029
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<td class="diff-line-num new_line" data-linenumber="2032" 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">
2032
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2032" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="diff-line-num old_line" data-linenumber="2030" 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">
2030
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<td class="diff-line-num new_line" data-linenumber="2033" 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">
2033
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2033" class="line" lang="python"><span class="s" style="color: #d14;"> Wrapper around the run method that handles exceptions and benchmarking.</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2102" 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="2105" 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">@@ -2102,6 +2105,7 @@ def run_wrapper(</td>
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<td class="diff-line-num old_line" data-linenumber="2102" 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">
2102
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<td class="diff-line-num new_line" data-linenumber="2105" 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">
2105
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2105" class="line" lang="python"> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2103" 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">
2103
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<td class="diff-line-num new_line" data-linenumber="2106" 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">
2106
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2106" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2104" 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">
2104
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<td class="diff-line-num new_line" data-linenumber="2107" 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">
2107
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<pre style="margin: 0;"> <span id="LC2107" class="line" lang="python"> <span class="n" style="color: #333;">passed_shadow_dir</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2108" 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">
2108
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<pre style="margin: 0;">+<span id="LC2108" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
</pre>
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2105
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<td class="diff-line-num new_line" data-linenumber="2109" 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">
2109
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2109" class="line" lang="python"> <span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2106" 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">
2106
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<td class="diff-line-num new_line" data-linenumber="2110" 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">
2110
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<pre style="margin: 0;"> <span id="LC2110" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2107" 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">
2107
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<td class="diff-line-num new_line" data-linenumber="2111" 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">
2111
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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The benchmarking is started here as we have a run section</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2129" 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="2133" 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">@@ -2129,6 +2133,7 @@ def run_wrapper(</td>
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<td class="diff-line-num old_line" data-linenumber="2129" 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">
2129
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<td class="diff-line-num new_line" data-linenumber="2133" 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">
2133
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2133" class="line" lang="python"> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2130" 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">
2130
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<td class="diff-line-num new_line" data-linenumber="2134" 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">
2134
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2134" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2131" 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">
2131
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<td class="diff-line-num new_line" data-linenumber="2135" 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">
2135
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<pre style="margin: 0;"> <span id="LC2135" class="line" lang="python"> <span class="n" style="color: #333;">passed_shadow_dir</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2136" 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">
2136
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<pre style="margin: 0;">+<span id="LC2136" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
</pre>
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2132
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2137
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<pre style="margin: 0;"> <span id="LC2137" class="line" lang="python"> <span class="p">)</span></span>
</pre>
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2133
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<td class="diff-line-num new_line" data-linenumber="2138" 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">
2138
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<pre style="margin: 0;"> <span id="LC2138" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Store benchmark record for this iteration</span></span>
</pre>
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2134
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<td class="diff-line-num new_line" data-linenumber="2139" 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">
2139
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<pre style="margin: 0;"> <span id="LC2139" class="line" lang="python"> <span class="n" style="color: #333;">bench_records</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">bench_record</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2154" 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="2159" 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">@@ -2154,6 +2159,7 @@ def run_wrapper(</td>
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2154
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<td class="diff-line-num new_line" data-linenumber="2159" 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">
2159
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<pre style="margin: 0;"> <span id="LC2159" class="line" lang="python"> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2155" 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">
2155
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<td class="diff-line-num new_line" data-linenumber="2160" 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">
2160
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2160" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2156" 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">
2156
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2161
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<pre style="margin: 0;"> <span id="LC2161" class="line" lang="python"> <span class="n" style="color: #333;">passed_shadow_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC2162" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="p">,</span></span>
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2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="python"> <span class="p">)</span></span>
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2164
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<pre style="margin: 0;"> <span id="LC2164" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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2159
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2165
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<pre style="margin: 0;"> <span id="LC2165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Re-raise the keyboard interrupt in order to record an error in the</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#818384818c4671b8354b6eb98ee2bab61c015a74"><strong>snakemake/jobs.py</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">@@ -1173,6 +1173,7 @@ class GroupJob(AbstractJob):</td>
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1173
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1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">resources</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1174
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_resources</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1175
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_resources</span><span class="p">[</span><span class="s" style="color: #d14;">"_nodes"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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1176
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1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="python"> <span class="n" style="color: #333;">pipe_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span><span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">is_pipe</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs</span><span class="p">])</span></span>
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1177
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># iterate over siblings that can be executed in parallel</span></span>
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1178
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">siblings</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">toposorted</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#87b26159067ade1d989921cb3240bfabece3aea0"><strong>snakemake/notebook.py</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">urllib.error</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">URLError</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">urllib.parse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">urlparse</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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2
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.exceptions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">WorkflowError</span></span>
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4
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.shell</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">shell</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.script</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_source</span><span class="p">,</span> <span class="n" style="color: #333;">ScriptBase</span><span class="p">,</span> <span class="n" style="color: #333;">PythonScript</span><span class="p">,</span> <span class="n" style="color: #333;">RScript</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">snakemake.logging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">KERNEL_STARTED_RE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">"Kernel started: (?P<kernel_id></span><span class="si" style="color: #d14;">\</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">S+)</span><span class="se" style="color: #d14;">"</span><span class="s" style="color: #d14;">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">KERNEL_SHUTDOWN_RE = re.compile("</span><span class="n" style="color: #333;">Kernel</span> <span class="n" style="color: #333;">shutdown</span><span class="p">:</span> <span class="p">(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">?</span><span class="n" style="color: #333;">P</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">kernel_id</span><span class="o" style="font-weight: 600;">></span>\<span class="n" style="color: #333;">S</span><span class="o" style="font-weight: 600;">+</span><span class="p">)</span><span class="s" style="color: #d14;">")</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">class Listen:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> def __init__(self, arg):</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> self.ip, self.port = arg.split("</span><span class="p">:</span><span class="s" style="color: #d14;">")</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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8
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">class JupyterNotebook(ScriptBase):</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> editable = True</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> def draft(self, listen):</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> import nbformat</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> preamble = self.get_preamble()</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> nb = nbformat.v4.new_notebook()</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> self.insert_preamble_cell(preamble, nb)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> nb["</span><span class="n" style="color: #333;">cells</span><span class="s" style="color: #d14;">"].append(nbformat.v4.new_code_cell("</span><span class="c1" style="color: #998; font-style: italic;"># start coding here"))</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">writes</span><span class="p">(</span><span class="n" style="color: #333;">nb</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_path</span><span class="p">).</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="n" style="color: #333;">edit</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">listen</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_script</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">preamble</span><span class="p">,</span> <span class="n" style="color: #333;">fd</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">nbformat</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">as_version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># nbformat.NO_CONVERT</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">preamble_cell</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nbformat</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">v4</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">new_code_cell</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">preamble</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">nb</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"cells"</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">insert</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">preamble_cell</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">remove_preamble_cell</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">nb</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">insert_preamble_cell</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">preamble</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">nb</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">fd</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">writes</span><span class="p">(</span><span class="n" style="color: #333;">nb</span><span class="p">).</span><span class="n" style="color: #333;">encode</span><span class="p">())</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute_script</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">execute_script</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">edit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">nbformat</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">fname_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"notebook"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname_out</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname_out</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">edit</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">output_parameter</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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23
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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24
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">fname_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">(),</span> <span class="n" style="color: #333;">fname_out</span><span class="p">)</span></span>
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25
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">output_parameter</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--output {fname_out:q}"</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">cmd_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"jupyter-nbconvert --execute {output_parameter} --to notebook --ExecutePreprocessor.timeout=-1 {{fname:q}}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">output_parameter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_parameter</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Opening notebook for editing."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter notebook --log-level ERROR --ip {edit.ip} --port {edit.port} "</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">"--no-browser --NotebookApp.quit_button=True {{fname:q}}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">edit</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">edit</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter-nbconvert --log-level ERROR --execute {output_parameter} "</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"--to notebook --ExecutePreprocessor.timeout=-1 {{fname:q}}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">output_parameter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output_parameter</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_execute_cmd</span><span class="p">(</span><span class="n" style="color: #333;">cmd_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">fname_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname_out</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_execute_cmd</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">fname_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname_out</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edit</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Saving modified notebook."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">nb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">as_version</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">remove_preamble_cell</span><span class="p">(</span><span class="n" style="color: #333;">nb</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">nb</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">insert_preamble_cell</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">preamble</span><span class="p">,</span> <span class="n" style="color: #333;">notebook</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">nbformat</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">preamble_cell</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbformat</span><span class="p">.</span><span class="n" style="color: #333;">v4</span><span class="p">.</span><span class="n" style="color: #333;">new_code_cell</span><span class="p">(</span><span class="n" style="color: #333;">preamble</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">preamble_cell</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">][</span><span class="s" style="color: #d14;">"tags"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"snakemake-job-properties"</span><span class="p">]</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">notebook</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">preamble_cell</span><span class="p">)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_preamble_cell</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">notebook</span><span class="p">):</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">preambles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">i</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">cell</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">notebook</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">])</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"snakemake-job-properties"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cell</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">].</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"tags"</span><span class="p">,</span> <span class="p">[])</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="p">]</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">preambles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"More than one snakemake preamble cell found in notebook. "</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">"Please clean up the notebook first, by removing all or all but one of them."</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">preambles</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">preamble</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">preambles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># remove old preamble</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">notebook</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">][</span><span class="n" style="color: #333;">preamble</span><span class="p">]</span></span>
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32
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PythonJupyterNotebook</span><span class="p">(</span><span class="n" style="color: #333;">JupyterNotebook</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" 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="168" 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">@@ -91,6 +168,16 @@ class RJupyterNotebook(JupyterNotebook):</td>
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91
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="p">)</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>
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93
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_exec_class</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">):</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">exec_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter_python"</span><span class="p">:</span> <span class="n" style="color: #333;">PythonJupyterNotebook</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter_r"</span><span class="p">:</span> <span class="n" style="color: #333;">RJupyterNotebook</span><span class="p">,</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="p">}.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">exec_class</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unsupported notebook: Expecting Jupyter Notebook (.ipynb)."</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">exec_class</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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94
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">notebook</span><span class="p">(</span></span>
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95
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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96
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">basedir</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" 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>
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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">@@ -112,20 +199,42 @@ def notebook(</td>
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112
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">bench_iteration</span><span class="p">,</span></span>
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113
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
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114
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">shadow_dir</span><span class="p">,</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">edit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"><span class="p">):</span></span>
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116
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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117
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> Load a script from the given basedir + path and execute it.</span></span>
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118
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_source</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">draft</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">urlparse</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">).</span><span class="n" style="color: #333;">scheme</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># draft the notebook, it does not exist yet</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">draft</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"file://{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".py.ipynb"</span><span class="p">):</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"jupyter_python"</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".r.ipynb"</span><span class="p">):</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"jupyter_r"</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">"Notebook to edit has to end on .py.ipynb or .r.ipynb in order "</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="s" style="color: #d14;">"to decide which programming language shall be used."</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">WorkflowError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">"Notebook {} is not local, but edit mode is only allowed for "</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">"local notebooks."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="p">)</span></span>
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">ExecClass</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter_python"</span><span class="p">:</span> <span class="n" style="color: #333;">PythonJupyterNotebook</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"jupyter_r"</span><span class="p">:</span> <span class="n" style="color: #333;">RJupyterNotebook</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="p">}.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ExecClass</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unsupported notebook: Expecting Jupyter Notebook (.ipynb)."</span><span class="p">)</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">draft</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">language</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_source</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">basedir</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">executor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ExecClass</span><span class="p">(</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">exec_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_exec_class</span><span class="p">(</span><span class="n" style="color: #333;">language</span><span class="p">)</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">executor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exec_class</span><span class="p">(</span></span>
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129
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span></span>
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130
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">source</span><span class="p">,</span></span>
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131
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">basedir</span><span class="p">,</span></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">@@ -148,4 +257,8 @@ def notebook(</td>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">cleanup_scripts</span><span class="p">,</span></span>
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">shadow_dir</span><span class="p">,</span></span>
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150
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">()</span></span></pre>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">draft</span><span class="p">:</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="n" style="color: #333;">draft</span><span class="p">(</span><span class="n" style="color: #333;">listen</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">edit</span><span class="p">)</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="n" style="color: #333;">evaluate</span><span class="p">(</span><span class="n" style="color: #333;">edit</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">edit</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#d70c11793454d64a7b2d77ced116226d2f13378e"><strong>snakemake/parser.py</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">@@ -470,7 +470,7 @@ class Run(RuleKeywordState):</td>
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="s" style="color: #d14;">"def __rule_{rulename}(input, output, params, wildcards, threads, "</span></span>
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471
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="s" style="color: #d14;">"resources, log, version, rule, conda_env, container_img, "</span></span>
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="s" style="color: #d14;">"singularity_args, use_singularity, env_modules, bench_record, jobid, "</span></span>
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473
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="s" style="color: #d14;">"is_shell, bench_iteration, cleanup_scripts, shadow_dir):"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="s" style="color: #d14;">"is_shell, bench_iteration, cleanup_scripts, shadow_dir<span class="idiff left right">, edit_notebook</span>):"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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474
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">rulename</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rulename</span></span>
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475
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rulename</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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476
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">snakefile</span><span class="p">.</span><span class="n" style="color: #333;">rulecount</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="582" 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">@@ -582,6 +582,17 @@ class Notebook(Script):</td>
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582
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"> <span class="n" style="color: #333;">start_func</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@workflow.notebook"</span></span>
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583
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">end_func</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"notebook"</span></span>
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584
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># basedir</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="s" style="color: #d14;">", {!r}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">snakefile</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># other args</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"> <span class="s" style="color: #d14;">", input, output, params, wildcards, threads, resources, log, "</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="s" style="color: #d14;">"config, rule, conda_env, container_img, singularity_args, env_modules, "</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"bench_record, jobid, bench_iteration, cleanup_scripts, shadow_dir, "</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="s" style="color: #d14;">"edit_notebook"</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Wrapper</span><span class="p">(</span><span class="n" style="color: #333;">Script</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">start_func</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@workflow.wrapper"</span></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">@@ -679,7 +690,9 @@ class Rule(GlobalKeywordState):</td>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">token</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected name or colon after rule keyword."</span><span class="p">,</span> <span class="n" style="color: #333;">token</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"> <span class="s" style="color: #d14;">"Expected name or colon after "</span> <span class="s" style="color: #d14;">"rule or checkpoint keyword."</span><span class="p">,</span> <span class="n" style="color: #333;">token</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">block_content</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">token</span><span class="p">):</span></span>
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_name</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#55752111e76e9d786fdb84c4e7fd9f6de5c67a24"><strong>snakemake/rules.py</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">@@ -964,7 +964,9 @@ class Rule:</td>
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="python"> <span class="s" style="color: #d14;">"Resources function did not return int or str."</span><span class="p">,</span> <span class="n" style="color: #333;">rule</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span></span>
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965
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="python"> <span class="p">)</span></span>
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966
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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967
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">),</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="python"> <span class="n" style="color: #333;">global_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">global_res</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">global_res</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span></span>
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="python"></span>
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970
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="python"> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="s" style="color: #d14;">"_cores"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">[</span><span class="s" style="color: #d14;">"_cores"</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#0ac0ac393192e0b6a8ebf767dd5e206b4afbf3b2"><strong>snakemake/scheduler.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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>
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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">@@ -98,7 +98,11 @@ class JobScheduler:</td>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">max_jobs_per_second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_jobs_per_second</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">keepincomplete</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">keepincomplete</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">maxsize</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">)</span></span>
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102
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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103
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">use_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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104
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">force_use_threads</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="511" 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">@@ -507,7 +511,7 @@ Problem", Akcay, Li, Xu, Annals of Operations Research, 2012</td>
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">c_j</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">y_j</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c_j</span><span class="p">,</span> <span class="n" style="color: #333;">y_j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">)]</span></span>
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508
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"></span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">workflow</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">global_resources</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span></span>
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># resource capacities</span></span>
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"></span>
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></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">@@ -548,12 +552,12 @@ Problem", Akcay, Li, Xu, Annals of Operations Research, 2012</td>
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548
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"></span>
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">solution</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">job</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">job</span><span class="p">,</span> <span class="n" style="color: #333;">sel</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">jobs</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sel</span><span class="p">]</span></span>
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># update resources</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">b_i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">workflow</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">global_resources</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">b_i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b_i</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">solution</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calc_resource</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">gres</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">workflow</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">global_resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">gres</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gres</span><span class="p">:</span></span>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"_cores"</span><span class="p">:</span></span>
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"threads"</span></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">@@ -569,15 +573,13 @@ Problem", Akcay, Li, Xu, Annals of Operations Research, 2012</td>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rule_weight</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">rule</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">resources</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">calc_resource</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span></span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">calc_resource</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">job_weight</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">resources</span></span>
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">calc_resource</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">workflow</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">calc_resource</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python"> <span class="p">]</span></span>
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">job_reward</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#66a73d9dd46eb8e71f0039a18d36dbd78aea7977"><strong>snakemake/script.py</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">@@ -244,6 +244,8 @@ class JuliaEncoder:</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;">class ScriptBase(ABC):</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"> editable = False</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"><span class="s" style="color: #d14;"> def __init__(</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;"> self,</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;"> path,</span></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">@@ -291,7 +293,9 @@ class ScriptBase(ABC):</td>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;"> self.cleanup_scripts = cleanup_scripts</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> self.shadow_dir = shadow_dir</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> def evaluate(self):</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> def evaluate(self, edit=False):</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> assert not edit or self.editable</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> fd = None</span></span>
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296
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"><span class="s" style="color: #d14;"> try:</span></span>
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297
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"><span class="s" style="color: #d14;"> # generate preamble</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" 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="311" 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">@@ -307,7 +311,7 @@ class ScriptBase(ABC):</td>
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307
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;"> self.write_script(preamble, fd)</span></span>
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308
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></span>
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309
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> # execute script</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;"> self.execute_script(fd.name)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;"> self.execute_script(fd.name<span class="idiff left right">, edit=edit</span>)</span></span>
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311
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;"> except URLError as e:</span></span>
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312
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;"> raise WorkflowError(e)</span></span>
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313
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;"> finally:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" 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="324" 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">@@ -320,6 +324,10 @@ class ScriptBase(ABC):</td>
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320
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"><span class="s" style="color: #d14;"> # nothing to clean up (TODO: ??)</span></span>
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321
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;"> pass</span></span>
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322
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"><span class="s" style="color: #d14;"> @property</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="s" style="color: #d14;"> def local_path(self):</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"><span class="s" style="color: #d14;"> return self.path[7:]</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"></span>
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323
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;"> @abstractmethod</span></span>
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324
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;"> def get_preamble(self):</span></span>
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325
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;"> ...</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" 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="337" 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">@@ -329,7 +337,7 @@ class ScriptBase(ABC):</td>
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329
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;"> ...</span></span>
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330
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"></span>
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331
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"><span class="s" style="color: #d14;"> @abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname):</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname<span class="idiff left right">, edit=False</span>):</span></span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"><span class="s" style="color: #d14;"> ...</span></span>
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"></span>
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335
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"><span class="s" style="color: #d14;"> def _execute_cmd(self, cmd, **kwargs):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" 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="406" 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">@@ -398,9 +406,9 @@ class PythonScript(ScriptBase):</td>
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398
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"></span>
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399
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"><span class="s" style="color: #d14;"> return textwrap.dedent(</span></span>
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400
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Snakemake header</span> ########</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble start (automatically inserted, do not edit)</span> ########</span></span>
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402
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"><span class="s" style="color: #d14;"> import sys; sys.path.extend([{searchpath}]); import pickle; snakemake = pickle.loads({snakemake}); from snakemake.logging import logger; logger.printshellcmds = {printshellcmds}; {preamble_addendum}</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Original script</span> #########</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble end</span> #########</span></span>
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404
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"><span class="s" style="color: #d14;"> ).format(</span></span>
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406
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"><span class="s" style="color: #d14;"> searchpath=searchpath,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" 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>
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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">@@ -444,7 +452,7 @@ class PythonScript(ScriptBase):</td>
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444
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(preamble.encode())</span></span>
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445
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(self.source)</span></span>
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446
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname):</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname<span class="idiff left right">, edit=False</span>):</span></span>
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448
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"><span class="s" style="color: #d14;"> py_exec = sys.executable</span></span>
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449
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"><span class="s" style="color: #d14;"> if self.conda_env is not None:</span></span>
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450
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"><span class="s" style="color: #d14;"> py = os.path.join(self.conda_env, "</span><span class="nb" style="color: #0086b3;">bin</span><span class="s" style="color: #d14;">", "</span><span class="n" style="color: #333;">python</span><span class="s" style="color: #d14;">")</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="513" 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">@@ -505,7 +513,7 @@ class RScript(ScriptBase):</td>
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505
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"><span class="s" style="color: #d14;"> ):</span></span>
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506
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"><span class="s" style="color: #d14;"> return textwrap.dedent(</span></span>
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507
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Snakemake header</span> ########</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble start (automatically inserted, do not edit)</span> ########</span></span>
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509
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"><span class="s" style="color: #d14;"> library(methods)</span></span>
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510
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"><span class="s" style="color: #d14;"> Snakemake <- setClass(</span></span>
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511
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">Snakemake</span><span class="s" style="color: #d14;">",</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="545" 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="553" 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">@@ -545,7 +553,7 @@ class RScript(ScriptBase):</td>
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545
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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546
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"><span class="s" style="color: #d14;"> {preamble_addendum}</span></span>
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547
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Original script</span> #########</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble end</span> #########</span></span>
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549
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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550
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"><span class="s" style="color: #d14;"> ).format(</span></span>
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551
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"><span class="s" style="color: #d14;"> REncoder.encode_namedlist(input_),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="609" 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">@@ -601,7 +609,7 @@ class RScript(ScriptBase):</td>
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601
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(preamble.encode())</span></span>
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602
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(self.source)</span></span>
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603
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname):</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname<span class="idiff left right">, edit=False</span>):</span></span>
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605
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"><span class="s" style="color: #d14;"> if self.conda_env is not None and "</span><span class="n" style="color: #333;">R_LIBS</span><span class="s" style="color: #d14;">" in os.environ:</span></span>
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606
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"><span class="s" style="color: #d14;"> logger.warning(</span></span>
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607
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">R</span> <span class="n" style="color: #333;">script</span> <span class="n" style="color: #333;">job</span> <span class="n" style="color: #333;">uses</span> <span class="n" style="color: #333;">conda</span> <span class="n" style="color: #333;">environment</span> <span class="n" style="color: #333;">but</span> <span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="619" 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="627" 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">@@ -619,7 +627,7 @@ class RMarkdown(ScriptBase):</td>
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619
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"><span class="s" style="color: #d14;"> def get_preamble(self):</span></span>
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620
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"><span class="s" style="color: #d14;"> return textwrap.dedent(</span></span>
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621
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Snakemake header</span> ########</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble start (automatically inserted, do not edit)</span> ########</span></span>
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623
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631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"><span class="s" style="color: #d14;"> library(methods)</span></span>
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624
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;"> Snakemake <- setClass(</span></span>
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625
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">Snakemake</span><span class="s" style="color: #d14;">",</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="658" 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="666" 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">@@ -658,7 +666,7 @@ class RMarkdown(ScriptBase):</td>
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658
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"><span class="s" style="color: #d14;"> }}</span></span>
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659
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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660
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668
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python"></span>
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661
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Original script</span> #########</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble end</span> #########</span></span>
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662
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670
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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663
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671
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"><span class="s" style="color: #d14;"> ).format(</span></span>
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664
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python"><span class="s" style="color: #d14;"> REncoder.encode_namedlist(self.input),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="708" 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">@@ -700,7 +708,7 @@ class RMarkdown(ScriptBase):</td>
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700
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(preamble.encode())</span></span>
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701
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(str.encode(code[pos:]))</span></span>
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702
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname):</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname<span class="idiff left right">, edit=False</span>):</span></span>
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704
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"><span class="s" style="color: #d14;"> if len(self.output) != 1:</span></span>
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705
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"><span class="s" style="color: #d14;"> raise WorkflowError(</span></span>
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706
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">RMarkdown</span> <span class="n" style="color: #333;">scripts</span> <span class="p">(.</span><span class="n" style="color: #333;">Rmd</span><span class="p">)</span> <span class="n" style="color: #333;">may</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">single</span> <span class="n" style="color: #333;">output</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="718" 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="726" 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">@@ -718,7 +726,7 @@ class JuliaScript(ScriptBase):</td>
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718
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"><span class="s" style="color: #d14;"> def get_preamble(self):</span></span>
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719
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;"> return textwrap.dedent(</span></span>
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720
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728
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Snakemake header</span> ########</span></span>
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<td class="diff-line-num new old_line" data-linenumber="722" 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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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble start (automatically inserted, do not edit)</span> ########</span></span>
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722
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="python"><span class="s" style="color: #d14;"> struct Snakemake</span></span>
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723
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"><span class="s" style="color: #d14;"> input::Dict</span></span>
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724
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="python"><span class="s" style="color: #d14;"> output::Dict</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="747" 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="755" 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">@@ -747,7 +755,7 @@ class JuliaScript(ScriptBase):</td>
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747
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"><span class="s" style="color: #d14;"> {}, #scriptdir::String</span></span>
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748
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="python"><span class="s" style="color: #d14;"> #, #source::Any</span></span>
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749
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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750
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">Original script</span> #########</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"><span class="s" style="color: #d14;"> ######## <span class="idiff left right">snakemake preamble end</span> #########</span></span>
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751
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python"><span class="s" style="color: #d14;"> """.format(</span></span>
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752
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="python"><span class="s" style="color: #d14;"> JuliaEncoder.encode_namedlist(self.input),</span></span>
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753
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="python"><span class="s" style="color: #d14;"> JuliaEncoder.encode_namedlist(self.output),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="779" 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="787" 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">@@ -779,13 +787,11 @@ class JuliaScript(ScriptBase):</td>
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779
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(preamble.encode())</span></span>
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780
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"><span class="s" style="color: #d14;"> fd.write(self.source)</span></span>
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781
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname):</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="python"><span class="s" style="color: #d14;"> def execute_script(self, fname<span class="idiff left right">, edit=False</span>):</span></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"><span class="s" style="color: #d14;"> self._execute_cmd("</span><span class="n" style="color: #333;">julia</span> <span class="p">{</span><span class="n" style="color: #333;">fname</span><span class="p">:</span><span class="n" style="color: #333;">q</span><span class="p">}</span><span class="s" style="color: #d14;">", fname=fname)</span></span>
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784
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"></span>
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785
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"></span>
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"><span class="s" style="color: #d14;">def get_source(path, basedir="</span><span class="p">.</span><span class="s" style="color: #d14;">"):</span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"><span class="s" style="color: #d14;"> import nbformat</span></span>
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788
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"></span>
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789
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"><span class="s" style="color: #d14;"> source = None</span></span>
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790
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"><span class="s" style="color: #d14;"> if not path.startswith("</span><span class="n" style="color: #333;">http</span><span class="s" style="color: #d14;">") and not path.startswith("</span><span class="n" style="color: #333;">git</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">file</span><span class="s" style="color: #d14;">"):</span></span>
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791
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"><span class="s" style="color: #d14;"> if path.startswith("</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span><span class="o" style="font-weight: 600;">//</span><span class="s" style="color: #d14;">"):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="795" 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="801" 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">@@ -795,6 +801,7 @@ def get_source(path, basedir="."):</td>
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795
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"><span class="s" style="color: #d14;"> if not os.path.isabs(path):</span></span>
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796
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"><span class="s" style="color: #d14;"> path = os.path.abspath(os.path.join(basedir, path))</span></span>
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797
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="python"><span class="s" style="color: #d14;"> path = "</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span><span class="o" style="font-weight: 600;">//</span><span class="s" style="color: #d14;">" + path</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python"><span class="s" style="color: #d14;"> # TODO this should probably be removed again. It does not work for report and hash!</span></span>
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798
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"><span class="s" style="color: #d14;"> path = format(path, stepout=1)</span></span>
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799
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"><span class="s" style="color: #d14;"> if path.startswith("</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span><span class="o" style="font-weight: 600;">//</span><span class="s" style="color: #d14;">"):</span></span>
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800
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"><span class="s" style="color: #d14;"> sourceurl = "</span><span class="nb" style="color: #0086b3;">file</span><span class="p">:</span><span class="s" style="color: #d14;">" + pathname2url(path[7:])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="809" 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="816" 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">@@ -809,6 +816,14 @@ def get_source(path, basedir="."):</td>
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809
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;"> with urlopen(sourceurl) as source:</span></span>
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810
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;"> source = source.read()</span></span>
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811
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="819" 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">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="python"><span class="s" style="color: #d14;"> language = get_language(path, source)</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"><span class="s" style="color: #d14;"> return path, source, language</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"><span class="s" style="color: #d14;">def get_language(path, source):</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"><span class="s" style="color: #d14;"> import nbformat</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="python"></span>
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812
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"><span class="s" style="color: #d14;"> language = None</span></span>
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<td class="diff-line-num old_line" data-linenumber="813" 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">
813
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<td class="diff-line-num new_line" data-linenumber="828" 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">
828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"><span class="s" style="color: #d14;"> if path.endswith("</span><span class="p">.</span><span class="n" style="color: #333;">py</span><span class="s" style="color: #d14;">"):</span></span>
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<td class="diff-line-num old_line" data-linenumber="814" 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">
814
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<td class="diff-line-num new_line" data-linenumber="829" 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">
829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="python"><span class="s" style="color: #d14;"> language = "</span><span class="n" style="color: #333;">python</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="828" 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="843" 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">@@ -828,7 +843,7 @@ def get_source(path, basedir="."):</td>
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<td class="diff-line-num old_line" data-linenumber="828" 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">
828
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"></span>
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829
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<td class="diff-line-num new_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="python"><span class="s" style="color: #d14;"> language += "</span><span class="n" style="color: #333;">_</span><span class="s" style="color: #d14;">" + kernel_language.lower()</span></span>
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830
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="831" 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">
831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"><span class="s" style="color: #d14;"> return <span class="idiff left right">path, source, </span>language</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"><span class="s" style="color: #d14;"> return language</span></span>
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832
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847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="python"></span>
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833
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="python"></span>
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834
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="python"><span class="s" style="color: #d14;">def script(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="858" 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="873" 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">@@ -858,18 +873,18 @@ def script(</td>
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858
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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859
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="python"><span class="s" style="color: #d14;"> path, source, language = get_source(path, basedir)</span></span>
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<td class="diff-line-num old_line" data-linenumber="860" 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">
860
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="python"></span>
</pre>
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861
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">ExecC</span>lass = {</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">exec_c</span>lass = {</span></span>
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">python</span><span class="s" style="color: #d14;">": PythonScript,</span></span>
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="python"><span class="s" style="color: #d14;"> "r": RScript,</span></span>
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">rmarkdown</span><span class="s" style="color: #d14;">": RMarkdown,</span></span>
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">julia</span><span class="s" style="color: #d14;">": JuliaScript,</span></span>
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866
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="python"><span class="s" style="color: #d14;"> }.get(language, None)</span></span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python"><span class="s" style="color: #d14;"> if <span class="idiff left right">ExecC</span>lass is None:</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"><span class="s" style="color: #d14;"> if <span class="idiff left right">exec_c</span>lass is None:</span></span>
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868
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="python"><span class="s" style="color: #d14;"> raise ValueError(</span></span>
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869
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="python"><span class="s" style="color: #d14;"> "</span><span class="n" style="color: #333;">Unsupported</span> <span class="n" style="color: #333;">script</span><span class="p">:</span> <span class="n" style="color: #333;">Expecting</span> <span class="n" style="color: #333;">either</span> <span class="n" style="color: #333;">Python</span> <span class="p">(.</span><span class="n" style="color: #333;">py</span><span class="p">),</span> <span class="n" style="color: #333;">R</span> <span class="p">(.</span><span class="n" style="color: #333;">R</span><span class="p">),</span> <span class="n" style="color: #333;">RMarkdown</span> <span class="p">(.</span><span class="n" style="color: #333;">Rmd</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">Julia</span> <span class="p">(.</span><span class="n" style="color: #333;">jl</span><span class="p">)</span> <span class="n" style="color: #333;">script</span><span class="p">.</span><span class="s" style="color: #d14;">"</span></span>
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870
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python"><span class="s" style="color: #d14;"> )</span></span>
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871
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"></span>
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872
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python"><span class="s" style="color: #d14;"> executor = <span class="idiff left right">ExecC</span>lass(</span></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"><span class="s" style="color: #d14;"> executor = <span class="idiff left right">exec_c</span>lass(</span></span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"><span class="s" style="color: #d14;"> path,</span></span>
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"><span class="s" style="color: #d14;"> source,</span></span>
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890
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="python"><span class="s" style="color: #d14;"> basedir,</span></span>
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<li id="cb9e107597e441fb1c0d61663359d9cf1dbfe04d">
<a href="https://salsa.debian.org/med-team/snakemake/-/compare/9667f24ac33e6204cd6801693ca496db43c21384...443804191d0ee873fc54e14ad9392386f6c69d13#cb9e107597e441fb1c0d61663359d9cf1dbfe04d"><strong>snakemake/workflow.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" 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">@@ -103,6 +103,7 @@ class Workflow:</td>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">resources</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">conda_cleanup_pkgs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">edit_notebook</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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106
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="p">):</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> Create the controller.</span></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">@@ -162,6 +163,7 @@ class Workflow:</td>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_local</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_local</span></span>
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">report_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">conda_cleanup_pkgs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">conda_cleanup_pkgs</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">edit_notebook</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">edit_notebook</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># environment variables to pass to jobs</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># These are defined via the "envvars:" syntax in the Snakefile itself</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">envvars</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></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">@@ -851,16 +853,21 @@ class Workflow:</td>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="s" style="color: #d14;">"Provided cluster nodes: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">)</span></span>
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">kubernetes</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">tibanna</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span><span class="s" style="color: #d14;">"Provided cloud nodes: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nodes</span><span class="p">))</span></span>
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">warning</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python"> <span class="s" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" (use --cores to define parallelism)"</span></span>
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python"> <span class="s" style="color: #d14;">"Provided cores: {}{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">warning</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="s" style="color: #d14;">"Rules claiming more threads "</span> <span class="s" style="color: #d14;">"will be scaled down."</span></span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"> <span class="p">)</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cores</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python"> <span class="n" style="color: #333;">warning</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="s" style="color: #d14;">""</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" (use --cores to define parallelism)"</span></span>
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="p">)</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="python"> <span class="s" style="color: #d14;">"Provided cores: {}{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">warning</span><span class="p">)</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="p">)</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">resources_info</span><span class="p">(</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="s" style="color: #d14;">"Rules claiming more threads "</span> <span class="s" style="color: #d14;">"will be scaled down."</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="python"> <span class="p">)</span></span>
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"> <span class="n" style="color: #333;">provided_resources</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format_resources</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">global_resources</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">provided_resources</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">result of serious computation!!!!!!</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">result of serious computation!!!</span></pre>
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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">@@ -1014,3 +1014,7 @@ def test_string_resources():</td>
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python"> <span class="n" style="color: #333;">default_resources</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">DefaultResources</span><span class="p">([</span><span class="s" style="color: #d14;">"gpu_model='nvidia-tesla-1000'"</span><span class="p">]),</span></span>
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="python"> <span class="n" style="color: #333;">cluster</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"./qsub.py"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_jupyter_notebook</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">dpath</span><span class="p">(</span><span class="s" style="color: #d14;">"test_jupyter_notebook"</span><span class="p">),</span> <span class="n" style="color: #333;">use_conda</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span></pre>
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