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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cooler">Debian Med / python-cooler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/6ab656780301d58624c79ac3b056032baa763793">6ab65678</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-29T10:17:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/13ff5817956e84a449584a79ce73d3cdeb7facaf">13ff5817</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-29T10:17:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.10</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/d315c2366f6e02616fa5fc8c08720c1970145a49">d315c236</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-29T10:18:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.8.10'
Update to upstream version '0.8.10'
with Debian dir 74c73ef4d1ee5e026830f9c5e1b623c0107ccbb3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cooler/-/commit/3961764f28a3241b31f363ef73f84b742ab66061">3961764f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-29T10:51:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Wait until
https://ftp-master.debian.org/new/python-pairix_0.3.7-1.html
will be accepted
</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
</li>
<li class="file-stats">
<a href="#13a20e2186b0b0ca847afd079fd73ebd9a0a6b0b">
cooler/__init__.py
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<li class="file-stats">
<a href="#d9252d1630264e35e18e708f44178eb887c90877">
cooler/_version.py
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<li class="file-stats">
<a href="#9cc5184a33a85c4fd4a16147f4514d69b317c36e">
cooler/cli/cload.py
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<li class="file-stats">
<a href="#1d9095383846c54cd7065e43ebaa45b9d7b1a27d">
cooler/create/__init__.py
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</li>
<li class="file-stats">
<a href="#1638878f2d870a1914c566165cb929e5fc605028">
cooler/create/_create.py
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<li class="file-stats">
<a href="#3a4d1f1256e0dbb60e09ee48c7d7daa042e6cd2e">
cooler/fileops.py
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<li class="file-stats">
<a href="#666281ec0036892d1efe43a2eb0eacf61a8f5ad6">
cooler/reduce.py
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#e91aac6c6631a5ed6134a791868d42a297bafbc0">
docs/api.rst
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<li class="file-stats">
<a href="#e093c51fbebfff6c39e41d2b38d628df2de325a2">
docs/concepts.rst
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<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
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<li class="file-stats">
<a href="#f34e53c7c5195ebd7026b508f17382e09de4d2e7">
docs/schema_v3.rst
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<li class="file-stats">
<a href="#f4fb69164b97e1b6f17984369c9c382573a3f919">
requirements-dev.txt
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#1b0c5863423edca6f8335bfcfddd08c62e72cb0c">
<span class="new-file">
+
tests/data/scool_test_file.scool
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<li class="file-stats">
<a href="#82377f7a510f970e40e70c8be19741d1a5515607">
<span class="new-file">
+
tests/data/toy_hash.pairs.gz
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<li class="file-stats">
<a href="#a4964d06f099a34f5bce6902969f327b805f3676">
tests/test_create.py
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<li class="file-stats">
<a href="#1a2cd0b041cec9088c0e4ed03ab86524f36b6fbe">
tests/test_create_ingest.py
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<li class="file-stats">
<a href="#54ecd4202f00a30f9544f03cd0738f9ed6038a56">
tests/test_fileops.py
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</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Release notes #</span></span>
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Upcoming release...</span></span>
</pre>
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<td class="diff-line-num new old_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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.10](https://github.com/mirnylab/cooler/compare/v0.8.9...v0.8.10)</span></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">Date : 2020-09-25</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="markdown"></span>
</pre>
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<td class="diff-line-num new old_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="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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Bug fixes</span></span>
</pre>
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<td class="diff-line-num new old_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="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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">*</span> Fixed the new header parsing in <span class="sb" style="color: #d14;">`cooler cload pairs`</span> to handle esoteric file stream implementations. Specifically <span class="sb" style="color: #d14;">`GzipFile`</span> had stopped working. By @golobor</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="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.9](https://github.com/mirnylab/cooler/compare/v0.8.8...v0.8.9)</span></span>
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<td class="diff-line-num new new_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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Date : 2020-07-17</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Enhancements</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">*</span> Added single-cell cooler file flavor (.scool) (#201)</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.8.8](https://github.com/mirnylab/cooler/compare/v0.8.7...v0.8.8)</span></span>
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6
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#13a20e2186b0b0ca847afd079fd73ebd9a0a6b0b"><strong>cooler/__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">@@ -12,7 +12,7 @@ A cool place to store your Hi-C.</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="n" style="color: #333;">__format_version__</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.api</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Cooler</span><span class="p">,</span> <span class="n" style="color: #333;">annotate</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create_cooler</span><span class="p">,</span> <span class="n" style="color: #333;">rename_chroms</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create_cooler</span><span class="p">,</span> <span class="n" style="color: #333;">rename_chroms</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">create_scool</span></span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.reduce</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">merge_coolers</span><span class="p">,</span> <span class="n" style="color: #333;">coarsen_cooler</span><span class="p">,</span> <span class="n" style="color: #333;">zoomify_cooler</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.balance</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">balance_cooler</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">binnify</span><span class="p">,</span> <span class="n" style="color: #333;">read_chromsizes</span><span class="p">,</span> <span class="n" style="color: #333;">fetch_chromsizes</span></span>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#d9252d1630264e35e18e708f44178eb887c90877"><strong>cooler/_version.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="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">8</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">10</span>"</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__format_version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__format_version_mcool__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__format_version_scool__</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span></pre>
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<li id="9cc5184a33a85c4fd4a16147f4514d69b317c36e">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#9cc5184a33a85c4fd4a16147f4514d69b317c36e"><strong>cooler/cli/cload.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">@@ -49,17 +49,28 @@ def get_header(instream, comment_char='#'):</td>
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<pre style="margin: 0;"> <span id="LC49" 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;">'Please, provide a comment char!'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">comment_byte</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">comment_char</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="LC51" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get peekable buffer for the instream</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">inbuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">instream</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">current_peek</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inbuffer</span><span class="p">.</span><span class="n" style="color: #333;">peek</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">read_f</span><span class="p">,</span> <span class="n" style="color: #333;">peek_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">instream</span><span class="p">,</span> <span class="s" style="color: #d14;">'buffer'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">peek_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">instream</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span><span class="p">.</span><span class="n" style="color: #333;">peek</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">readline_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">instream</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span><span class="p">.</span><span class="n" style="color: #333;">readline</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">instream</span><span class="p">,</span> <span class="s" style="color: #d14;">'peek'</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;">peek_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">instream</span><span class="p">.</span><span class="n" style="color: #333;">peek</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">readline_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">instream</span><span class="p">.</span><span class="n" style="color: #333;">readline</span></span>
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<pre style="margin: 0;">+<span id="LC59" 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="LC60" 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;">'Cannot find the peek() function of the provided stream!'</span><span class="p">)</span></span>
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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="LC62" class="line" lang="python"> <span class="n" style="color: #333;">current_peek</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">peek_f</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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54
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">current_peek</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">comment_byte</span><span class="p">):</span></span>
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55
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># consuming a line from buffer guarantees</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that the remainder of the buffer starts</span></span>
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57
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># with the beginning of the line.</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inbuffer</span><span class="p">.</span><span class="n" style="color: #333;">readline</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;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readline_f</span><span class="p">()</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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;">line</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">):</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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59
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># append line to header, since it does start with header</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">decode</span></span><span class="p"><span class="idiff right">().</span></span><span class="n" style="color: #333;">strip</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;">header</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># peek into the remainder of the instream</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">current_peek</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">inbuffer</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">peek</span></span><span class="p"><span class="idiff right">(</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">current_peek</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">peek_f</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># apparently, next line does not start with the comment</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return header and the instream, advanced to the beginning of the data</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">instream</span></span>
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<li id="1d9095383846c54cd7065e43ebaa45b9d7b1a27d">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#1d9095383846c54cd7065e43ebaa45b9d7b1a27d"><strong>cooler/create/__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">@@ -2,6 +2,9 @@ from __future__ import absolute_import, print_function, division</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">MAGIC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"HDF5::Cooler"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">MAGIC_SCOOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"HDF5::SCOOL"</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">MAGIC_MCOOL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"HDF5::MCOOL"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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5
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"https://github.com/mirnylab/cooler"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">CHROM_DTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">(</span><span class="s" style="color: #d14;">"S"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">CHROMID_DTYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32</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">@@ -28,4 +31,4 @@ from ._ingest import (</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">ContactBinner</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create_cooler</span><span class="p">,</span> <span class="n" style="color: #333;">create</span><span class="p">,</span> <span class="n" style="color: #333;">create_from_unordered</span><span class="p">,</span> <span class="n" style="color: #333;">append</span><span class="p">,</span> <span class="n" style="color: #333;">rename_chroms</span></span></pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">create_cooler</span><span class="p">,</span> <span class="n" style="color: #333;">create</span><span class="p">,</span> <span class="n" style="color: #333;">create_from_unordered</span><span class="p">,</span> <span class="n" style="color: #333;">append</span><span class="p">,</span> <span class="n" style="color: #333;">rename_chroms</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">create_scool</span></span></span></pre>
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<li id="1638878f2d870a1914c566165cb929e5fc605028">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#1638878f2d870a1914c566165cb929e5fc605028"><strong>cooler/create/_create.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">@@ -13,7 +13,7 @@ import h5py</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">json</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="n" style="color: #333;">__format_version__</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="n" style="color: #333;">__format_version__</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">__format_version_scool__</span></span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.._logging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_logger</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">put</span><span class="p">,</span> <span class="n" style="color: #333;">get</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">..util</span> <span class="kn" style="font-weight: 600;">import</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">@@ -27,6 +27,7 @@ from ..util import (</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._ingest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">validate_pixels</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">MAGIC</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">MAGIC_SCOOL</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">URL</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">CHROM_DTYPE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">CHROMID_DTYPE</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">@@ -296,7 +297,7 @@ def write_indexes(grp, chrom_offset, bin1_offset, h5opts):</td>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="p">)</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>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_info</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_info</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">scool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;"> Write the file description and metadata attributes.</span></span>
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302
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303
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<pre style="margin: 0;"> <span id="LC303" 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">@@ -317,13 +318,19 @@ def write_info(grp, info):</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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319
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"nbins"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"nnz"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">+<span id="LC321" 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;">scool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"nnz"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">setdefault</span><span class="p">(</span><span class="s" style="color: #d14;">"genome-assembly"</span><span class="p">,</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">json</span><span class="p">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">,</span> <span class="p">{}))</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"creation-date"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">isoformat</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"generated-by"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">text_type</span><span class="p">(</span><span class="s" style="color: #d14;">"cooler-"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAGIC</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format-version"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">text_type</span><span class="p">(</span><span class="n" style="color: #333;">__format_version__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">scool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAGIC_SCOOL</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format-version"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">text_type</span><span class="p">(</span><span class="n" style="color: #333;">__format_version_scool__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC331" 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="LC332" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAGIC</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format-version"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">text_type</span><span class="p">(</span><span class="n" style="color: #333;">__format_version__</span><span class="p">)</span></span>
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"format-url"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">URL</span></span>
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC336" 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">@@ -439,6 +446,8 @@ def create(</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">ensure_sorted</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="LC447" class="line" lang="python"> <span class="n" style="color: #333;">lock</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="LC448" class="line" lang="python"> <span class="n" style="color: #333;">append</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="LC449" class="line" lang="python"> <span class="n" style="color: #333;">append_scool</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="LC450" class="line" lang="python"> <span class="n" style="color: #333;">scool_root_uri</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="LC451" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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">@@ -470,7 +479,10 @@ def create(</td>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="s" style="color: #d14;">"Note that the `chromsizes` argument is now deprecated: "</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="s" style="color: #d14;">"see documentation for `create`."</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">append_scool</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">scool_root_uri</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="LC483" 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>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">"If the parameter `append_scool` is set, the parameter `scool_root_uri` must be defined."</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_dtypes_arg</span><span class="p">(</span><span class="n" style="color: #333;">dtypes</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</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">@@ -572,23 +584,52 @@ def create(</td>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="n" style="color: #333;">group_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python"></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;"># Write chroms, bins and pixels</span></span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">h5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">append_scool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">src_path</span><span class="p">,</span> <span class="n" style="color: #333;">src_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">(</span><span class="n" style="color: #333;">scool_root_uri</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">dst_path</span><span class="p">,</span> <span class="n" style="color: #333;">dst_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">(</span><span class="n" style="color: #333;">cool_uri</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">src_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">dst_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dst</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">dst_group</span><span class="p">][</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># hard link to root bins table, but only the three main datasets</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">dst_group</span><span class="p">][</span><span class="s" style="color: #d14;">"bins/chrom"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="s" style="color: #d14;">"bins/chrom"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">dst_group</span><span class="p">][</span><span class="s" style="color: #d14;">"bins/start"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="s" style="color: #d14;">"bins/start"</span><span class="p">]</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">dst_group</span><span class="p">][</span><span class="s" style="color: #d14;">"bins/end"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="s" style="color: #d14;">"bins/end"</span><span class="p">]</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># create per cell the additional columns e.g. 'weight'</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># these columns are individual for each cell</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">]:</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">columns</span><span class="p">:</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">put</span><span class="p">(</span><span class="n" style="color: #333;">dst</span><span class="p">[</span><span class="n" style="color: #333;">dst_group</span><span class="p">][</span><span class="s" style="color: #d14;">'bins'</span><span class="p">],</span> <span class="n" style="color: #333;">bins</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">])</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">h5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"pixels"</span><span class="p">)</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">symmetric_upper</span><span class="p">:</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_bins</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_bins</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">prepare_pixels</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">n_bins</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">,</span> <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">dtypes</span><span class="p">),</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">h5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC578" 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;">"Writing chroms"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"chroms"</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;">write_chroms</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="idiff left right"> </span><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;">"Writing chroms"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">write_chroms</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC582" 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;">"Writing bins"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"bins"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="python"> <span class="n" style="color: #333;">write_bins</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">],</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="idiff left right"> </span><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;">"Writing bins"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"bins"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">write_bins</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">],</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"pixels"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">symmetric_upper</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_bins</span></span>
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<pre style="margin: 0;">-<span id="LC589" 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="LC590" class="line" lang="python"> <span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_bins</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">prepare_pixels</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">n_bins</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">,</span> <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">dtypes</span><span class="p">),</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"pixels"</span><span class="p">)</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">symmetric_upper</span><span class="p">:</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_bins</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">max_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_bins</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">prepare_pixels</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">n_bins</span><span class="p">,</span> <span class="n" style="color: #333;">max_size</span><span class="p">,</span> <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">dtypes</span><span class="p">),</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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592
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Multiprocess HDF5 reading is supported only if the same HDF5 file is not</span></span>
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># open in write mode anywhere. To read and write to the same file, pass a</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">@@ -629,8 +670,6 @@ def create(</td>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span></span>
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671
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">write_info</span><span class="p">(</span><span class="n" style="color: #333;">h5</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">)</span></span>
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC632" 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;">"Done"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_from_unordered</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">cool_uri</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">@@ -822,55 +861,7 @@ def append(cool_uri, table, data, chunked=False, force=False, h5opts=None, lock=</td>
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">lock</span><span class="p">.</span><span class="n" style="color: #333;">release</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>
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_cooler</span><span class="p">(</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="python"> <span class="n" style="color: #333;">cool_uri</span><span class="p">,</span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">pixels</span><span class="p">,</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="n" style="color: #333;">columns</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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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</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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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">assembly</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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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">ordered</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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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="python"> <span class="n" style="color: #333;">symmetric_upper</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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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">mode</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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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="python"> <span class="n" style="color: #333;">mergebuf</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="mf" style="color: #099;">20e6</span><span class="p">),</span></span>
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837
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">delete_temp</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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838
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<pre style="margin: 0;">-<span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</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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839
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">max_merge</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</span><span class="p">,</span></span>
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840
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">boundscheck</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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841
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">dupcheck</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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842
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python"> <span class="n" style="color: #333;">triucheck</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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843
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<pre style="margin: 0;">-<span id="LC843" class="line" lang="python"> <span class="n" style="color: #333;">ensure_sorted</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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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">h5opts</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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845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">lock</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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846
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="python"><span class="p">):</span></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="python"><span class="s" style="color: #d14;"> Create a cooler from bins and pixels at the specified URI.</span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python"></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python"><span class="s" style="color: #d14;"> Because the number of pixels is often very large, the input pixels are</span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python"><span class="s" style="color: #d14;"> normally provided as an iterable (e.g., an iterator or generator) of</span></span>
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852
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="python"><span class="s" style="color: #d14;"> DataFrame **chunks** that fit in memory.</span></span>
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853
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="python"></span>
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854
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"><span class="s" style="color: #d14;"> .. versionadded:: 0.8.0</span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="python"></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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858
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"><span class="s" style="color: #d14;"> cool_uri : str</span></span>
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859
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python"><span class="s" style="color: #d14;"> Path to cooler file or URI string. If the file does not exist,</span></span>
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860
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="python"><span class="s" style="color: #d14;"> it will be created.</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;"> bins : pandas.DataFrame</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;"> Segmentation of the chromosomes into genomic bins as a BED-like</span></span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"><span class="s" style="color: #d14;"> DataFrame with columns ``chrom``, ``start`` and ``end``. May contain</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"><span class="s" style="color: #d14;"> additional columns.</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="python"><span class="s" style="color: #d14;"> pixels : DataFrame, dictionary, or iterable of either</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;"> A table, given as a dataframe or a column-oriented dict, containing</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;"> columns labeled ``bin1_id``, ``bin2_id`` and ``count``, sorted by</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python"><span class="s" style="color: #d14;"> (``bin1_id``, ``bin2_id``). If additional columns are included in the</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;"> pixel table, their names and dtypes must be specified using the</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="python"><span class="s" style="color: #d14;"> ``columns`` and ``dtypes`` arguments. For larger input data, an</span></span>
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871
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="python"><span class="s" style="color: #d14;"> **iterable** can be provided that yields the pixel data as a sequence</span></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;"> of chunks. If the input is a dask DataFrame, it will also be processed</span></span>
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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;"> one chunk at a time.</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"><span class="n" style="color: #333;">_DOC_OTHER_PARAMS</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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874
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"><span class="s" style="color: #d14;"> columns : sequence of str, optional</span></span>
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875
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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;"> Customize which value columns from the input pixels to store in the</span></span>
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876
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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;"> cooler. Non-standard value columns will be given dtype ``float64``</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="930" 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="921" 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">@@ -930,12 +921,9 @@ def create_cooler(</td>
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930
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="python"><span class="s" style="color: #d14;"> triucheck : bool, optional</span></span>
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<td class="diff-line-num old_line" data-linenumber="931" 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">
931
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<td class="diff-line-num new_line" data-linenumber="922" 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">
922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="python"><span class="s" style="color: #d14;"> Input validation: Check that ``bin1_id`` <= ``bin2_id`` when creating</span></span>
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<td class="diff-line-num old_line" data-linenumber="932" 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">
932
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<td class="diff-line-num new_line" data-linenumber="923" 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">
923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"><span class="s" style="color: #d14;"> coolers in symmetric-upper mode.</span></span>
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<td class="diff-line-num new old_line" data-linenumber="933" 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="924" 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">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="python"><span class="s" style="color: #d14;">"""</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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933
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<td class="diff-line-num new_line" data-linenumber="925" 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">
925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="934" 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">
934
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<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="python"><span class="s" style="color: #d14;"> See also</span></span>
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935
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<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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936
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<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create.sanitize_records</span></span>
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937
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<td class="diff-line-num new_line old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create.sanitize_pixels</span></span>
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938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="python"></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="python"><span class="n" style="color: #333;">_DOC_NOTES</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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939
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="python"><span class="s" style="color: #d14;"> Notes</span></span>
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940
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<td class="diff-line-num new_line" data-linenumber="928" 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">
928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="python"><span class="s" style="color: #d14;"> -----</span></span>
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941
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<td class="diff-line-num new_line" data-linenumber="929" 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">
929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="python"><span class="s" style="color: #d14;"> If the pixel chunks are provided in the correct order required for the</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="953" 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="941" 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">@@ -953,6 +941,75 @@ def create_cooler(</td>
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953
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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="python"><span class="s" style="color: #d14;"> Each chunk of pixels will go through a validation pipeline, which can be</span></span>
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954
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<td class="diff-line-num new_line" data-linenumber="942" 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">
942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="python"><span class="s" style="color: #d14;"> customized with the following options: ``boundscheck``, ``triucheck``,</span></span>
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955
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<td class="diff-line-num new_line" data-linenumber="943" 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">
943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="python"><span class="s" style="color: #d14;"> ``dupcheck``, ``ensure_sorted``.</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="python"><span class="s" style="color: #d14;">"""</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_format_docstring</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">decorate</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">):</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="python"> <span class="n" style="color: #333;">func</span><span class="p">.</span><span class="n" style="color: #333;">__doc__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">func</span><span class="p">.</span><span class="n" style="color: #333;">__doc__</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">func</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">decorate</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="python"></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python"></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">_format_docstring</span><span class="p">(</span><span class="n" style="color: #333;">other_parameters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_DOC_OTHER_PARAMS</span><span class="p">,</span> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_DOC_NOTES</span><span class="p">)</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_cooler</span><span class="p">(</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="python"> <span class="n" style="color: #333;">cool_uri</span><span class="p">,</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="python"> <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="python"> <span class="n" style="color: #333;">pixels</span><span class="p">,</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="python"> <span class="n" style="color: #333;">columns</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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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</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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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="python"> <span class="n" style="color: #333;">assembly</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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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="python"> <span class="n" style="color: #333;">ordered</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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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="python"> <span class="n" style="color: #333;">symmetric_upper</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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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">,</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="python"> <span class="n" style="color: #333;">mergebuf</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="mf" style="color: #099;">20e6</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;">delete_temp</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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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</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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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="python"> <span class="n" style="color: #333;">max_merge</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</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="n" style="color: #333;">boundscheck</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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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="python"> <span class="n" style="color: #333;">dupcheck</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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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="python"> <span class="n" style="color: #333;">triucheck</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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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="python"> <span class="n" style="color: #333;">ensure_sorted</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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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="python"> <span class="n" style="color: #333;">h5opts</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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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="python"> <span class="n" style="color: #333;">lock</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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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="python"><span class="p">):</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="python"> <span class="s" style="color: #d14;">r"""</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="python"><span class="s" style="color: #d14;"> Create a cooler from bins and pixels at the specified URI.</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="python"></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="python"><span class="s" style="color: #d14;"> Because the number of pixels is often very large, the input pixels are</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="python"><span class="s" style="color: #d14;"> normally provided as an iterable (e.g., an iterator or generator) of</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="python"><span class="s" style="color: #d14;"> DataFrame **chunks** that fit in memory.</span></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="python"></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="python"><span class="s" style="color: #d14;"> .. versionadded:: 0.8.0</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="python"></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="python"><span class="s" style="color: #d14;"> cool_uri : str</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="python"><span class="s" style="color: #d14;"> Path to cooler file or URI string. If the file does not exist,</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="python"><span class="s" style="color: #d14;"> it will be created.</span></span>
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="python"><span class="s" style="color: #d14;"> bins : pandas.DataFrame</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="python"><span class="s" style="color: #d14;"> Segmentation of the chromosomes into genomic bins as a BED-like</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="python"><span class="s" style="color: #d14;"> DataFrame with columns ``chrom``, ``start`` and ``end``. May contain</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="python"><span class="s" style="color: #d14;"> additional columns.</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="python"><span class="s" style="color: #d14;"> pixels : DataFrame, dictionary, or iterable of either</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="python"><span class="s" style="color: #d14;"> A table, given as a dataframe or a column-oriented dict, containing</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="python"><span class="s" style="color: #d14;"> columns labeled ``bin1_id``, ``bin2_id`` and ``count``, sorted by</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="python"><span class="s" style="color: #d14;"> (``bin1_id``, ``bin2_id``). If additional columns are included in the</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="python"><span class="s" style="color: #d14;"> pixel table, their names and dtypes must be specified using the</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="python"><span class="s" style="color: #d14;"> ``columns`` and ``dtypes`` arguments. For larger input data, an</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="python"><span class="s" style="color: #d14;"> **iterable** can be provided that yields the pixel data as a sequence</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="python"><span class="s" style="color: #d14;"> of chunks. If the input is a dask DataFrame, it will also be processed</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="python"><span class="s" style="color: #d14;"> one chunk at a time.</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="python"><span class="s" style="color: #d14;"> {other_parameters}</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="python"></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="python"><span class="s" style="color: #d14;"> See also</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create_scool</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create.sanitize_records</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create.sanitize_pixels</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="python"></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="python"><span class="s" style="color: #d14;"> {notes}</span></span>
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956
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python"></span>
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957
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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958
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># dispatch to the approprate creation method</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">@@ -1000,3 +1057,200 @@ def create_cooler(</td>
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1000
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span></span>
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1001
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="python"> <span class="n" style="color: #333;">max_merge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_merge</span><span class="p">,</span></span>
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1002
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1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="python"> <span class="p">)</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="python"></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="python"></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">_format_docstring</span><span class="p">(</span><span class="n" style="color: #333;">other_parameters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_DOC_OTHER_PARAMS</span><span class="p">,</span> <span class="n" style="color: #333;">notes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_DOC_NOTES</span><span class="p">)</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_scool</span><span class="p">(</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="python"> <span class="n" style="color: #333;">cool_uri</span><span class="p">,</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">bins</span><span class="p">,</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="python"> <span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">,</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="python"> <span class="n" style="color: #333;">columns</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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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</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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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="python"> <span class="n" style="color: #333;">metadata</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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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="python"> <span class="n" style="color: #333;">assembly</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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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="python"> <span class="n" style="color: #333;">ordered</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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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="python"> <span class="n" style="color: #333;">symmetric_upper</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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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">,</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="python"> <span class="n" style="color: #333;">mergebuf</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="mf" style="color: #099;">20e6</span><span class="p">),</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="python"> <span class="n" style="color: #333;">delete_temp</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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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</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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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="python"> <span class="n" style="color: #333;">max_merge</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">200</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="python"> <span class="n" style="color: #333;">boundscheck</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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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="python"> <span class="n" style="color: #333;">dupcheck</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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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="python"> <span class="n" style="color: #333;">triucheck</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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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="python"> <span class="n" style="color: #333;">ensure_sorted</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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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="python"> <span class="n" style="color: #333;">h5opts</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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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="python"> <span class="n" style="color: #333;">lock</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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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="python"> <span class="s" style="color: #d14;">r"""</span></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="python"><span class="s" style="color: #d14;"> Create a single-cell (scool) file.</span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="python"></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="python"><span class="s" style="color: #d14;"> For each cell store a cooler matrix under **/cells**, where all matrices</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="python"><span class="s" style="color: #d14;"> have the same dimensions.</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="python"></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="python"><span class="s" style="color: #d14;"> Each cell is a regular cooler data collection, so the input must be a</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="python"><span class="s" style="color: #d14;"> bin table and pixel table for each cell. The pixel tables are provided as</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="python"><span class="s" style="color: #d14;"> a dictionary where the key is a unique cell name. The bin tables can be</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="python"><span class="s" style="color: #d14;"> provided as a dict with the same keys or a single common bin table can be</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="python"><span class="s" style="color: #d14;"> given.</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="python"></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="python"><span class="s" style="color: #d14;"> .. versionadded:: 0.8.9</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="python"></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="python"><span class="s" style="color: #d14;"> cool_uri : str</span></span>
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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;"> Path to scool file or URI string. If the file does not exist,</span></span>
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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;"> it will be created.</span></span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="python"><span class="s" style="color: #d14;"> bins : :class:`pandas.DataFrame` or Dict[str, DataFrame]</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;"> A single bin table or dictionary of cell names to bins tables. A bin</span></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="python"><span class="s" style="color: #d14;"> table is a dataframe with columns ``chrom``, ``start`` and ``end``.</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;"> May contain additional columns.</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;"> cell_name_pixels_dict : Dict[str, DataFrame]</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;"> Cell name as key and pixel table DataFrame as value.</span></span>
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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;"> A table, given as a dataframe or a column-oriented dict, containing</span></span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="python"><span class="s" style="color: #d14;"> columns labeled ``bin1_id``, ``bin2_id`` and ``count``, sorted by</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="python"><span class="s" style="color: #d14;"> (``bin1_id``, ``bin2_id``). If additional columns are included in the</span></span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="python"><span class="s" style="color: #d14;"> pixel table, their names and dtypes must be specified using the</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="python"><span class="s" style="color: #d14;"> ``columns`` and ``dtypes`` arguments. For larger input data, an</span></span>
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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;"> **iterable** can be provided that yields the pixel data as a sequence</span></span>
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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;"> of chunks. If the input is a dask DataFrame, it will also be processed</span></span>
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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;"> one chunk at a time.</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;"> {other_parameters}</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="python"></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="python"><span class="s" style="color: #d14;"> See also</span></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="python"><span class="s" style="color: #d14;"> --------</span></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.create_cooler</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="python"><span class="s" style="color: #d14;"> cooler.zoomify_cooler</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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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="python"><span class="s" style="color: #d14;"> {notes}</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;"> """</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">group_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">(</span><span class="n" style="color: #333;">cool_uri</span><span class="p">)</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="python"> <span class="n" style="color: #333;">h5opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_set_h5opts</span><span class="p">(</span><span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="python"></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="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;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</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="n" style="color: #333;">bins_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">cell_name</span><span class="p">:</span> <span class="n" style="color: #333;">bins</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cell_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">}</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="n" style="color: #333;">cell_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">)</span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Assume bins is a dict of cell name -> dataframe</span></span>
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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="n" style="color: #333;">bins_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</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="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;">bins_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</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="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;">"At least one bin must be given."</span><span class="p">)</span></span>
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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="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="python"> <span class="n" style="color: #333;">bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins_dict</span><span class="p">[</span><span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">bins_dict</span><span class="p">))][[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">]]</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="python"></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Sort bins_dict and cell_name_pixels_dict to guarantee matching keys</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="python"> <span class="n" style="color: #333;">bins_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">bins_dict</span><span class="p">)</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="python"> <span class="n" style="color: #333;">cell_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1145" 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">
1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key_bins</span><span class="p">,</span> <span class="n" style="color: #333;">key_pixels</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;">bins_keys</span><span class="p">,</span> <span class="n" style="color: #333;">cell_names</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1146" 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">
1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key_bins</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">key_pixels</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1147" 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">
1147
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<pre style="margin: 0;">+<span id="LC1147" 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;">'Bins and pixel dicts do not have matching keys'</span><span class="p">)</span></span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="python"></span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_dtypes_arg</span><span class="p">(</span><span class="n" style="color: #333;">dtypes</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="python"></span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">]:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1152" 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">
1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bins</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;">+<span id="LC1153" 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;">"Missing column from bin table: '{}'."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">))</span></span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="python"></span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Populate dtypes for expected pixel columns, and apply user overrides.</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dtypes</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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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">PIXEL_DTYPES</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="python"> <span class="n" style="color: #333;">dtypes_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">dtypes</span><span class="p">)</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">PIXEL_DTYPES</span><span class="p">)</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">dtypes_</span><span class="p">)</span></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="python"></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Determine the appropriate iterable</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1164" 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">
1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1165" 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">
1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dask.dataframe</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DataFrame</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">dask_df</span></span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ImportError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># pragma: no cover</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="python"> <span class="n" style="color: #333;">dask_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">()</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="python"></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Prepare chroms and bins</span></span>
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="python"> <span class="n" style="color: #333;">bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="python"> <span class="n" style="color: #333;">bins</span><span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bins</span><span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">)</span></span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="python"> <span class="n" style="color: #333;">chromsizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_chromsizes</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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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;">try</span><span class="p">:</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="python"> <span class="n" style="color: #333;">chromsizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">(</span><span class="n" style="color: #333;">chromsizes</span><span class="p">)</span></span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</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="k" style="font-weight: 600;">pass</span></span>
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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;">chromnames</span><span class="p">,</span> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">chromsizes</span><span class="p">)</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333;">chroms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>
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1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="python"> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">:</span> <span class="n" style="color: #333;">chromnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"length"</span><span class="p">:</span> <span class="n" style="color: #333;">lengths</span><span class="p">},</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"length"</span><span class="p">]</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="python"> <span class="p">)</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="python"> <span class="n" style="color: #333;">binsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_binsize</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python"> <span class="n" style="color: #333;">n_chroms</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chroms</span><span class="p">)</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="python"></span>
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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create root group</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" 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;">'Creating cooler at "{}::{}"'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">group_path</span><span class="p">))</span></span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group_path</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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1189
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<pre style="margin: 0;">+<span id="LC1189" 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="p">[</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bins"</span><span class="p">]:</span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1192" 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">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1194" 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">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="n" style="color: #333;">group_path</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1195" 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">
1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1196" 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">
1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="n" style="color: #333;">group_path</span><span class="p">)</span></span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1199" 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">
1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python"> <span class="n" style="color: #333;">h5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="python"></span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" 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;">"Writing chroms"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1203" 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">
1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1204" 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">
1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="python"> <span class="n" style="color: #333;">write_chroms</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1205" 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">
1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1206" 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">
1206
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<pre style="margin: 0;">+<span id="LC1206" 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;">"Writing bins"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1207" 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">
1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="python"> <span class="n" style="color: #333;">grp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5</span><span class="p">.</span><span class="n" style="color: #333;">create_group</span><span class="p">(</span><span class="s" style="color: #d14;">"bins"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1208" 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">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="python"> <span class="n" style="color: #333;">write_bins</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">[</span><span class="s" style="color: #d14;">"name"</span><span class="p">],</span> <span class="n" style="color: #333;">h5opts</span><span class="p">)</span></span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="python"></span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="python"> <span class="n" style="color: #333;">h5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="n" style="color: #333;">group_path</span><span class="p">]</span></span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="python"></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" 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;">"Writing info"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1214" 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">
1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1215" 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">
1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"bin-type"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"fixed"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">binsize</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="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">u"variable"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1216" 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">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"bin-size"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">binsize</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">binsize</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="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">u"null"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1217" 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">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"nchroms"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_chroms</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1218" 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">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"ncells"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1219" 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">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"nbins"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_bins</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1220" 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">
1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">assembly</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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<td class="diff-line-num new new_line" data-linenumber="1221" 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">
1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"genome-assembly"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1222" 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">
1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">metadata</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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<td class="diff-line-num new new_line" data-linenumber="1223" 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">
1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="python"> <span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"metadata"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1224" 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">
1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="python"> <span class="n" style="color: #333;">write_info</span><span class="p">(</span><span class="n" style="color: #333;">h5</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1226" 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">
1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Append single cells</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1227" 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">
1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cell_names</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1228" 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">
1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'/'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">key</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1229" 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">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="python"> <span class="n" style="color: #333;">cell_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</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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<td class="diff-line-num new new_line" data-linenumber="1230" 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">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="python"> <span class="n" style="color: #333;">cell_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span></span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1233" 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">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="python"> <span class="n" style="color: #333;">create</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1234" 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">
1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="python"> <span class="n" style="color: #333;">cool_uri</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'::/cells/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cell_name</span><span class="p">,</span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="python"> <span class="n" style="color: #333;">bins_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">],</span></span>
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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="python"> <span class="n" style="color: #333;">cell_name_pixels_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">],</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1237" 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">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">,</span></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="python"> <span class="n" style="color: #333;">dtypes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dtypes</span><span class="p">,</span></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span></span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="python"> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">assembly</span><span class="p">,</span></span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="python"> <span class="n" style="color: #333;">ordered</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ordered</span><span class="p">,</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="python"> <span class="n" style="color: #333;">symmetric_upper</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">symmetric_upper</span><span class="p">,</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a'</span><span class="p">,</span></span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="python"> <span class="n" style="color: #333;">boundscheck</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">boundscheck</span><span class="p">,</span></span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="python"> <span class="n" style="color: #333;">dupcheck</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dupcheck</span><span class="p">,</span></span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="python"> <span class="n" style="color: #333;">triucheck</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">triucheck</span><span class="p">,</span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="python"> <span class="n" style="color: #333;">ensure_sorted</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ensure_sorted</span><span class="p">,</span></span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="python"> <span class="n" style="color: #333;">h5opts</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5opts</span><span class="p">,</span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="python"> <span class="n" style="color: #333;">lock</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lock</span><span class="p">,</span></span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="python"> <span class="n" style="color: #333;">mergebuf</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mergebuf</span><span class="p">,</span></span>
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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="python"> <span class="n" style="color: #333;">delete_temp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">delete_temp</span><span class="p">,</span></span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="python"> <span class="n" style="color: #333;">temp_dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">temp_dir</span><span class="p">,</span></span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="python"> <span class="n" style="color: #333;">max_merge</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_merge</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="python"> <span class="n" style="color: #333;">append_scool</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="LC1255" class="line" lang="python"> <span class="n" style="color: #333;">scool_root_uri</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cool_uri</span></span>
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="python"> <span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#3a4d1f1256e0dbb60e09ee48c7d7daa042e6cd2e"><strong>cooler/fileops.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">@@ -19,7 +19,7 @@ import numpy as np</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">h5py</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">,</span> <span class="n" style="color: #333;">natsorted</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MAGIC</span><span class="p">,</span> <span class="n" style="color: #333;">URL</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MAGIC</span><span class="p">,</span> <span class="n" style="color: #333;">URL</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">MAGIC_SCOOL</span></span></span>
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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="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"is_cooler"</span><span class="p">,</span> <span class="s" style="color: #d14;">"is_multires_file"</span><span class="p">,</span> <span class="s" style="color: #d14;">"list_coolers"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mv"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ln"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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">@@ -104,8 +104,7 @@ def visititems(group, func, level=None):</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_cooler</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"format"</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="LC107" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"format-url"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fmt</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MAGIC</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">URL</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fmt</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MAGIC</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bins"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pixels"</span><span class="p">,</span> <span class="s" style="color: #d14;">"indexes"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">keys</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="n" style="color: #333;">keys</span><span class="p">):</span></span>
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111
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Cooler path {} appears to be corrupt"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" 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="116" 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">@@ -117,7 +116,7 @@ def is_cooler(uri):</td>
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117
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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118
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> Determine if a URI string references a cooler data collection.</span></span>
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119
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> Returns False if the file or group path doesn't exist.</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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121
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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122
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">grouppath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">(</span><span class="n" style="color: #333;">uri</span><span class="p">)</span></span>
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123
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122
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<pre style="margin: 0;"> <span id="LC122" 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;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">is_hdf5</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" 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="146" 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">@@ -147,6 +146,31 @@ def is_multires_file(filepath, min_version=1):</td>
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147
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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148
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>
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149
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_scool_file</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> Determine if a file is a single-cell cooler file.</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> Returns False if the file doesn't exist.</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" 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;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">is_hdf5</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">(</span><span class="s" style="color: #d14;">"'{}' is not an HDF5 file."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">filepath</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="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"format"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fmt</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">MAGIC_SCOOL</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"chroms"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bins"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cells"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">keys</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="n" style="color: #333;">keys</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="p">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Scooler path {} appears to be corrupt"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"cells"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cells</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" 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;">_is_cooler</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">[</span><span class="s" style="color: #d14;">"cells"</span><span class="p">][</span><span class="n" style="color: #333;">cells</span><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 class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></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;">return</span> <span class="bp" style="color: #999;">False</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"></span>
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150
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">list_coolers</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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151
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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152
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> List group paths to all cooler data collections in a file.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" 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="201" 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">@@ -177,6 +201,37 @@ def list_coolers(filepath):</td>
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177
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">natsorted</span><span class="p">(</span><span class="n" style="color: #333;">listing</span><span class="p">)</span></span>
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178
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"></span>
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179
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">list_scool_cells</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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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;">"""</span></span>
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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;"> List the paths to all single-cell cool matrices in a file scool file.</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"><span class="s" style="color: #d14;"> ----------</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> filepath : str</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> -------</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"> list</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> Cooler group paths of all cells in the file.</span></span>
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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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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_scool_file</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">):</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">listing</span> <span class="o" style="font-weight: 600;">=</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_cooler</span><span class="p">(</span><span class="n" style="color: #333;">pth</span><span class="p">,</span> <span class="n" style="color: #333;">grp</span><span class="p">):</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_is_cooler</span><span class="p">(</span><span class="n" style="color: #333;">grp</span><span class="p">):</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">listing</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pth</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pth</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">pth</span><span class="p">)</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">_check_cooler</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">visititems</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_check_cooler</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'/'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">listing</span><span class="p">:</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">listing</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">natsorted</span><span class="p">(</span><span class="n" style="color: #333;">listing</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;">else</span><span class="p">:</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">(</span><span class="s" style="color: #d14;">"'{}' is not a scool file."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">filepath</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;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></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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180
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ls</span><span class="p">(</span><span class="n" style="color: #333;">uri</span><span class="p">):</span></span>
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181
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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182
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;"> Get all groups and datasets in an HDF5 file.</span></span>
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<li id="666281ec0036892d1efe43a2eb0eacf61a8f5ad6">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#666281ec0036892d1efe43a2eb0eacf61a8f5ad6"><strong>cooler/reduce.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,6 +12,7 @@ import pandas as pd</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">h5py</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__format_version_mcool__</span></span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">._logging</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_logger</span></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.create</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ContactBinner</span><span class="p">,</span> <span class="n" style="color: #333;">create</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">parse_cooler_uri</span><span class="p">,</span> <span class="n" style="color: #333;">GenomeSegmentation</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="851" 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="852" 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">@@ -851,7 +852,10 @@ def zoomify_cooler(</td>
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851
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">"r+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">({</span><span class="s" style="color: #d14;">"format"</span><span class="p">:</span> <span class="s" style="color: #d14;">u"HDF5::MCOOL"</span><span class="p">,</span> <span class="s" style="color: #d14;">"format-version"</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">update</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;">"format"</span><span class="p">:</span> <span class="s" style="color: #d14;">u"HDF5::MCOOL"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="s" style="color: #d14;">"format-version"</span><span class="p">:</span> <span class="n" style="color: #333;">__format_version_mcool__</span></span>
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python"> <span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">legacy_zoomify</span><span class="p">(</span><span class="n" style="color: #333;">input_uri</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">nproc</span><span class="p">,</span> <span class="n" style="color: #333;">chunksize</span><span class="p">,</span> <span class="n" style="color: #333;">lock</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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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-cooler (0.8.10-1) UNRELEASED; 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 version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> TODO: Wait until</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> https://ftp-master.debian.org/new/python-pairix_0.3.7-1.html</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> will be accepted</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 29 Sep 2020 10:17:00 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">python-cooler (0.8.8-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#e91aac6c6631a5ed6134a791868d42a297bafbc0"><strong>docs/api.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">@@ -32,6 +32,7 @@ Creation/reduction</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> cooler.merge_coolers</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> cooler.coarsen_cooler</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> cooler.zoomify_cooler</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> cooler.create_scool</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Manipulation</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">~~~~~~~~~~~~</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="71" 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">@@ -70,6 +71,8 @@ cooler</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">.. autofunction:: cooler.zoomify_cooler</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">.. autofunction:: cooler.balance_cooler</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">.. autofunction:: cooler.rename_chroms</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.. autofunction:: cooler.create_scool</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">----</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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<br>
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<li id="e093c51fbebfff6c39e41d2b38d628df2de325a2">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#e093c51fbebfff6c39e41d2b38d628df2de325a2"><strong>docs/concepts.rst</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="213" 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">@@ -213,3 +213,25 @@ The experimental ``read_table`` function can be used to generate a dask datafram</td>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">Learn more about the `Dask <https://dask.org/>`_ project.</span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">Create a scool file</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">-------------------</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">The creation of a single-cell cooler file is similar to a regular cooler file. Each cell needs to have a name, bin table and a pixel table.</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">All cells must have the same dimensions, and the bins and pixels needs to be provided as two dicts with the cell names as keys.</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> >>> name_pixel_dict = {'cell1': pixels_cell1, 'cell2': pixels_cell2, 'cell3': pixels_cell3}</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> >>> name_bins_dict = {'cell1': bins_cell1, 'cell2': bins_cell2, 'cell3': bins_cell3}</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> >>> cooler.create_scool('single_cell_cool.scool', name_bins_dict, name_pixel_dict)</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">To read the content, each individual cell must be handled as a regular cool file.</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> >> content_of_scool = cooler.fileops.list_coolers('single_cell_cool.scool')</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> ['/', '/cells/cell1', '/cells/cell2', '/cells/cell3']</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> >>> c1 = cooler.Cooler('single_cell_cool.scool::cells/cell1')</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> >>> c2 = cooler.Cooler('single_cell_cool.scool::cells/cell2')</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> >>> c3 = cooler.Cooler('single_cell_cool.scool::cells/cell3')</span></pre>
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<li id="254a2da7a740675e537439eb88e32083b9ea4771">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.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">@@ -18,11 +18,14 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC18" 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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shlex</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Path setup --------------------------------------------------------------</span></span>
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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="c1" style="color: #998; font-style: italic;"># If extensions (or modules to document with autodoc) are in another directory,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add these directories to sys.path here. If the directory is relative to the</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documentation root, use os.path.abspath to make it absolute, like shown here.</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;">#sys.path.insert(0, os.path.abspath('.'))</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</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;">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="s" style="color: #d14;"><span class="idiff left right">'..'</span></span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>sys.path.insert(0, os.path.abspath('.'))</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</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;">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="s" style="color: #d14;"><span class="idiff left right">".."</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># autodoc_mock_imports = [</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'numpy',</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">@@ -33,293 +36,259 @@ sys.path.insert(0, os.path.abspath('..'))</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'cytoolz',</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ]</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">mock</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="n" style="color: #333;">MOCK_MODULES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'numpy'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'scipy'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'scipy.sparse'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'pandas'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'pandas.algos'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'pandas.api'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'pandas.api.types'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'h5py'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask.base'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask.array'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask.dataframe'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask.dataframe.core'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'dask.dataframe.utils'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'simplejson'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"numpy"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"scipy"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"scipy.sparse"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"pandas"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"pandas.algos"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"pandas.api"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"pandas.api.types"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"h5py"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask.base"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask.array"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask.dataframe"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask.dataframe.core"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"dask.dataframe.utils"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">"simplejson"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mod_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">MOCK_MODULES</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">modules</span><span class="p">[</span><span class="n" style="color: #333;">mod_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mock</span><span class="p">.</span><span class="n" style="color: #333;">Mock</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- General configuration ------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If your documentation needs a minimal Sphinx version, state it here.</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#needs_sphinx = '1.0'</span></span>
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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="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any Sphinx extension module names here, as strings. They can be</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># extensions coming with Sphinx (named 'sphinx.ext.*') or your custom</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ones.</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.autodoc'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.doctest'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.todo'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.coverage'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.mathjax'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.ifconfig'</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;">'sphinx.ext.viewcode'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.autosummary'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'sphinx.ext.napoleon'</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># 'numpydoc'</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>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">numpydoc_show_class_members</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="n" style="color: #333;">napoleon_use_rtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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="c1" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"><span class="n" style="color: #333;">templates_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_templates'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The suffix(es) of source filenames.</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You can specify multiple suffix as a list of string:</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"><span class="n" style="color: #333;">source_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'.rst'</span><span class="p">:</span> <span class="s" style="color: #d14;">'restructuredtext'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'.md'</span><span class="p">:</span> <span class="s" style="color: #d14;">'markdown'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"><span class="p">}</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="c1" style="color: #998; font-style: italic;"># The encoding of source files.</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#source_encoding = 'utf-8-sig'</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="n" style="color: #333;">source_parsers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'.md'</span><span class="p">:</span> <span class="s" style="color: #d14;">'recommonmark.parser.CommonMarkParser'</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The master toctree document.</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="n" style="color: #333;">master_doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'index'</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Project information -----------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'cooler'</span></span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'2016-2019, Nezar Abdennur'</span></span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"><span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'Nezar Abdennur'</span></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"cooler"</span></span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"2016-2019, Nezar Abdennur"</span></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"Nezar Abdennur"</span></span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># built documents.</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_version</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">init</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="s" style="color: #d14;"><span class="idiff left">'..'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'cooler'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'_version.py'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">init</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="s" style="color: #d14;"><span class="idiff left">".."</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"cooler"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"_version.py"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" 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="n" style="color: #333;">init</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</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="LC78" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">text</span><span class="p">,</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">MULTILINE</span><span class="p">).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]'</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">MULTILINE</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="p">).</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">version</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_version</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="c1" style="color: #998; font-style: italic;"># The short X.Y version.</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">release</span><span class="p">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'.'</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxsplit</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</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="LC88" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">release</span><span class="p">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"."</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxsplit</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</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="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This is also used if you do content translation via gettext catalogs.</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Usually you set "language" from the command line for these cases.</span></span>
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<pre style="margin: 0;">-<span id="LC129" 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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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># There are two options for replacing |today|: either, you set today to some</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># non-false value, then it is used:</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#today = ''</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Else, today_fmt is used as the format for a strftime call.</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#today_fmt = '%B %d, %Y'</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- General configuration ------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># List of patterns, relative to source directory, that match files and</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directories to ignore when looking for source files.</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="n" style="color: #333;">exclude_patterns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_build'</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 class="c1" style="color: #998; font-style: italic;"># If your documentation needs a minimal Sphinx version, state it here.</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># needs_sphinx = '1.0'</span></span>
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140
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The reST default role (used for this markup: `text`) to use for all</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documents.</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#default_role = None</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any Sphinx extension module names here, as strings. They can be</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># extensions coming with Sphinx (named 'sphinx.ext.*') or your custom</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ones.</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <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="s" style="color: #d14;">"sphinx.ext.autodoc"</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="s" style="color: #d14;">"sphinx.ext.doctest"</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="s" style="color: #d14;">"sphinx.ext.todo"</span><span class="p">,</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;">"sphinx.ext.coverage"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"sphinx.ext.mathjax"</span><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="s" style="color: #d14;">"sphinx.ext.ifconfig"</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="s" style="color: #d14;">"sphinx.ext.viewcode"</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="s" style="color: #d14;">"sphinx.ext.autosummary"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"sphinx.ext.napoleon"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># 'numpydoc'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="s" style="color: #d14;">"recommonmark"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># If true, '()' will be appended to :func: etc. cross-reference text.</span></span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#add_function_parentheses = Tru</span>e</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">numpydoc_show_class_members</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">napoleon_use_rtype</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">Fals</span>e</span></span>
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147
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, the current module name will be prepended to all description</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># unit titles (such as .. function::).</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#add_module_names = True</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"><span class="n" style="color: #333;">templates_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"_templates"</span><span class="p">]</span></span>
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151
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, sectionauthor and moduleauthor directives will be shown in the</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># output. They are ignored by default.</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#show_authors = False</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># List of patterns, relative to source directory, that match files and</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directories to ignore when looking for source files.</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="n" style="color: #333;">exclude_patterns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"_build"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Thumbs.db"</span><span class="p">,</span> <span class="s" style="color: #d14;">".DS_Store"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The suffix(es) of source filenames.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># You can specify multiple suffix as a list of string:</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"><span class="n" style="color: #333;">source_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">".rst"</span><span class="p">:</span> <span class="s" style="color: #d14;">"restructuredtext"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">".md"</span><span class="p">:</span> <span class="s" style="color: #d14;">"markdown"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># source_parsers = {".md": "recommonmark.parser.CommonMarkParser"}</span></span>
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155
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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156
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of the Pygments (syntax highlighting) style to use.</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"><span class="n" style="color: #333;">pygments_style</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'sphinx'</span></span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"><span class="n" style="color: #333;">pygments_style</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"sphinx"</span></span></span>
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158
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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159
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># A list of ignored prefixes for module index sorting.</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#modindex_common_prefix = []</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>modindex_common_prefix = []</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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162
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, keep warnings as "system message" paragraphs in the built documents.</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#keep_warnings = False</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>keep_warnings = False</span></span>
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164
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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165
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, `todo` and `todoList` produce output, else they produce nothing.</span></span>
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166
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"><span class="n" style="color: #333;">todo_include_todos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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167
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"><span class="n" style="color: #333;">master_doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"index"</span></span>
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168
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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169
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Options for HTML output ----------------------------------------------</span></span>
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170
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The theme to use for HTML and HTML Help pages. See the documentation for</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># a list of builtin themes.</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"><span class="n" style="color: #333;">html_theme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'sphinx_rtd_theme'</span></span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="n" style="color: #333;">html_theme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"sphinx_rtd_theme"</span></span></span>
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174
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>
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175
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Theme options are theme-specific and customize the look and feel of a theme</span></span>
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176
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># further. For a list of options available for each theme, see the</span></span>
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177
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documentation.</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_theme_options = {}</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_theme_options = {}</span></span>
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179
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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180
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain custom themes here, relative to this directory.</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_theme_path = []</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_theme_path = []</span></span>
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182
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name for this set of Sphinx documents. If None, it defaults to</span></span>
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184
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># "<project> v<release> documentation".</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_title = None</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_title = None</span></span>
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186
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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187
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># A shorter title for the navigation bar. Default is the same as html_title.</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_short_title = None</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_short_title = None</span></span>
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189
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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190
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of an image file (relative to this directory) to place at the top</span></span>
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191
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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;"># of the sidebar.</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_logo = None</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_logo = None</span></span>
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193
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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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194
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of an image file (within the static path) to use as favicon of the</span></span>
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195
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32</span></span>
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196
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># pixels large.</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_favicon = None</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_favicon = None</span></span>
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198
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"></span>
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199
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain custom static files (such as style sheets) here,</span></span>
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200
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># relative to this directory. They are copied after the builtin static files,</span></span>
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201
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># so a file named "default.css" will overwrite the builtin "default.css".</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;">html_static_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left right">'_static'</span></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="n" style="color: #333;">html_static_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left right">"_static"</span></span><span class="p">]</span></span>
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203
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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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204
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any extra paths that contain custom files (such as robots.txt or</span></span>
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205
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># .htaccess) here, relative to this directory. These files are copied</span></span>
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206
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directly to the root of the documentation.</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_extra_path = []</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_extra_path = []</span></span>
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208
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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209
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If not '', a 'Last updated on:' timestamp is inserted at every page bottom,</span></span>
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210
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># using the given strftime format.</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;">#html_last_updated_fmt = '%b %d, %Y'</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_last_updated_fmt = '%b %d, %Y'</span></span>
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212
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></span>
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213
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, SmartyPants will be used to convert quotes and dashes to</span></span>
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214
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># typographically correct entities.</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_use_smartypants = True</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_use_smartypants = True</span></span>
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216
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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217
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Custom sidebar templates, maps document names to template names.</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_sidebars = {}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_sidebars = {}</span></span>
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219
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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220
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Additional templates that should be rendered to pages, maps page names to</span></span>
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221
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># template names.</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_additional_pages = {}</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_additional_pages = {}</span></span>
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223
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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224
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no module index is generated.</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_domain_indices = True</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_domain_indices = True</span></span>
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226
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"></span>
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227
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no index is generated.</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_use_index = True</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_use_index = True</span></span>
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229
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>
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230
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, the index is split into individual pages for each letter.</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_split_index = False</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_split_index = False</span></span>
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232
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>
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233
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, links to the reST sources are added to the pages.</span></span>
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234
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_show_sourcelink = True</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_show_sourcelink = True</span></span>
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235
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>
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236
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, "Created using Sphinx" is shown in the HTML footer. Default is True.</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_show_sphinx = True</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_show_sphinx = True</span></span>
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238
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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239
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_show_copyright = True</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_show_copyright = True</span></span>
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241
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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242
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, an OpenSearch description file will be output, and all pages will</span></span>
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243
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># contain a <link> tag referring to it. The value of this option must be the</span></span>
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># base URL from which the finished HTML is served.</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_use_opensearch = ''</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_use_opensearch = ''</span></span>
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246
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"></span>
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247
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This is the file name suffix for HTML files (e.g. ".xhtml").</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_file_suffix = None</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_file_suffix = None</span></span>
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249
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"></span>
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250
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Language to be used for generating the HTML full-text search index.</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Sphinx supports the following languages:</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_search_language = 'en'</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_search_language = 'en'</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># A dictionary with options for the search language support, empty by default.</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Now only 'ja' uses this config value</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_search_options = {'type': 'default'}</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_search_options = {'type': 'default'}</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of a javascript file (relative to the configuration directory) that</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># implements a search results scorer. If empty, the default will be used.</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#html_search_scorer = 'scorer.js'</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>html_search_scorer = 'scorer.js'</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Output file base name for HTML help builder.</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"><span class="n" style="color: #333;">htmlhelp_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'coolerdoc'</span></span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="n" style="color: #333;">htmlhelp_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"coolerdoc"</span></span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Options for LaTeX output ---------------------------------------------</span></span>
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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 class="n" style="color: #333;">latex_elements</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The paper size ('letterpaper' or 'a4paper').</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#'papersize': 'letterpaper',</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The font size ('10pt', '11pt' or '12pt').</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#'pointsize': '10pt',</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Additional stuff for the LaTeX preamble.</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#'preamble': '',</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Latex figure (float) alignment</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#'figure_align': 'htbp',</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The paper size ('letterpaper' or 'a4paper').</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#'papersize': 'letterpaper',</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The font size ('10pt', '11pt' or '12pt').</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#'pointsize': '10pt',</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Additional stuff for the LaTeX preamble.</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#'preamble': '',</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Latex figure (float) alignment</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#'figure_align': 'htbp',</span></span>
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281
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"><span class="p">}</span></span>
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282
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>
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283
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Grouping the document tree into LaTeX files. List of tuples</span></span>
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284
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, target name, title,</span></span>
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285
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># author, documentclass [howto, manual, or own class]).</span></span>
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286
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"><span class="n" style="color: #333;">latex_documents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">master_doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler.tex'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler Documentation'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">'Nezar Abdennur'</span><span class="p">,</span> <span class="s" style="color: #d14;">'manual'</span><span class="p">),</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">master_doc</span><span class="p">,</span> <span class="s" style="color: #d14;">"cooler.tex"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cooler Documentation"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Nezar Abdennur"</span><span class="p">,</span> <span class="s" style="color: #d14;">"manual"</span><span class="p">),</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"><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>
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291
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of an image file (relative to this directory) to place at the top of</span></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># the title page.</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_logo = None</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_logo = None</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># For "manual" documents, if this is true, then toplevel headings are parts,</span></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># not chapters.</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_use_parts = False</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_use_parts = False</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, show page references after internal links.</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_show_pagerefs = False</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_show_pagerefs = False</span></span>
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301
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"></span>
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302
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, show URL addresses after external links.</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_show_urls = False</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_show_urls = False</span></span>
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304
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>
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305
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Documents to append as an appendix to all manuals.</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_appendices = []</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_appendices = []</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no module index is generated.</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#latex_domain_indices = True</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>latex_domain_indices = True</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Options for manual page output ---------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># One entry per manual page. List of tuples</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, name, description, authors, manual section).</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"><span class="n" style="color: #333;">man_pages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">master_doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler Documentation'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">author</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"><span class="n" style="color: #333;">man_pages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">master_doc</span><span class="p">,</span> <span class="s" style="color: #d14;">"cooler"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cooler Documentation"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">author</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, show URL addresses after external links.</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#man_show_urls = False</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>man_show_urls = False</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Options for Texinfo output -------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="297" 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">@@ -328,19 +297,25 @@ man_pages = [</td>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, target name, title, author,</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># dir menu entry, description, category)</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"><span class="n" style="color: #333;">texinfo_documents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">master_doc</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler Documentation'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="p">,</span> <span class="s" style="color: #d14;">'cooler'</span><span class="p">,</span> <span class="s" style="color: #d14;">'One line description of project.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="s" style="color: #d14;">'Miscellaneous'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">master_doc</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"cooler"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="s" style="color: #d14;">"cooler Documentation"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="s" style="color: #d14;">"cooler"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="s" style="color: #d14;">"One line description of project."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="s" style="color: #d14;">"Miscellaneous"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Documents to append as an appendix to all manuals.</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#texinfo_appendices = []</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>texinfo_appendices = []</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If false, no module index is generated.</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#texinfo_domain_indices = True</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>texinfo_domain_indices = True</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># How to display URL addresses: 'footnote', 'no', or 'inline'.</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#texinfo_show_urls = 'footnote'</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>texinfo_show_urls = 'footnote'</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, do not generate a @detailmenu in the "Top" node's menu.</span></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#texinfo_no_detailmenu = False</span></span></pre>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>texinfo_no_detailmenu = False</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#f34e53c7c5195ebd7026b508f17382e09de4d2e7"><strong>docs/schema_v3.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">@@ -279,3 +279,73 @@ In addition, a multi-resolution cooler file may indicate to clients that it is u</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext"> .. versionchanged:: 0.8</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext"> Both the legacy layout and the new mcool layout are supported by `HiGlass <http://higlass.io/app/>`_. Prior to cooler 0.8, the new layout was produced only when requesting a specific list of resolutions. As of cooler 0.8, the new layout is always produced by the :command:`cooler zoomify` command unless the ``--legacy`` option is given. Files produced by :py:func:`cooler.zoomify_cooler`, `hic2cool <https://github.com/4dn-dcic/hic2cool/>`_, and the mcools from the `4DN data portal <https://data.4dnucleome.org/>`_ also follow the new layout.</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">Single-cell (single-resolution)</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">-------------------------------</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">A single-cell cooler file contains all the matrices of a single-cell Hi-C data set. All cells are stored under a group called ``/cells``, and all cells share the primary bin table columns </span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">i.e. ``bins['chrom']``, ``bins['start']`` and ``bins['end']`` which are `hardlinked <http://docs.h5py.org/en/stable/high/group.html#hard-links>`_ to the root-level bin table. Any individual cell can be accessed using the regular :class:`cooler.Cooler` interface.</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">Conventional file extension: ``.scool``.</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">:: </span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> XYZ.scool</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> ├── bins</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> ├── chroms</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> └── cells</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> ├── cell_id1</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> │ ├── bins</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> │ ├── chroms</span>
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> │ ├── pixels</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> │ └── indexes</span>
</pre>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> ├── cell_id2</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> │ ├── bins</span>
</pre>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> │ ├── chroms</span>
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<td class="diff-line-num new new_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> │ ├── pixels</span>
</pre>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> │ └── indexes</span>
</pre>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> ├── cell_id3</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> │ ├── bins</span>
</pre>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> │ ├── chroms</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> │ ├── pixels</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> │ └── indexes</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> ├── cell_id4</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> │ ├── bins</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> │ ├── chroms</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> │ ├── pixels</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> │ └── indexes</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> .</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> .</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">In addition, a single-cell single-resolution cooler file may indicate to clients that it is using this layout with the following ``/``-level attributes:</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">.. describe:: format : string (constant)</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> "HDF5::SCOOL"</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">.. describe:: format-version : int</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> 1</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">.. describe:: bin-type : { "fixed", "variable" }</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> Indicates whether the resolution is constant along both axes.</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">.. describe:: bin-size : int</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> The bin resolution</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">.. describe:: nbins : int</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> The number of bins </span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">.. describe:: nchroms : int</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"> The number of chromosomes of the cells</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">.. describe:: ncells : int</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> The number of stored cells</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#f4fb69164b97e1b6f17984369c9c382573a3f919"><strong>requirements-dev.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-r requirements.txt</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">biopython<1.77</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">dask[array,dataframe]</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">pytest</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ipytree</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">matplotlib</span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">mock</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">psutil</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">pysam</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">pytest</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">pytest-flake8</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">pytest-cov</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</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">@@ -4,7 +4,7 @@ scipy>=0.16</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pandas" rel="nofollow noreferrer noopener" target="_blank">pandas</a></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/h5py" rel="nofollow noreferrer noopener" target="_blank">h5py</a>>=2.5</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/click" rel="nofollow noreferrer noopener" target="_blank">click</a>>=7</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/cytoolz" rel="nofollow noreferrer noopener" target="_blank">cytoolz</a></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/cytoolz" rel="nofollow noreferrer noopener" target="_blank">cytoolz</a><span class="idiff left right"><0.11</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/multiprocess" rel="nofollow noreferrer noopener" target="_blank">multiprocess</a></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pyfaidx" rel="nofollow noreferrer noopener" target="_blank">pyfaidx</a></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/pypairix" rel="nofollow noreferrer noopener" target="_blank">pypairix</a></span>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#1b0c5863423edca6f8335bfcfddd08c62e72cb0c"><strong>tests/data/scool_test_file.scool</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">@@ -432,3 +432,42 @@ def test_create_cooler_from_dask():</td>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pixels,</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ordered=False</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># )</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="s" style="color: #d14;">"fp"</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">datadir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hg19.GM12878-MboI.matrix.2000kb.cool"</span><span class="p">)]</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_create_scool</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cooler</span><span class="p">.</span><span class="n" style="color: #333;">Cooler</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># chromsizes = c.chromsizes</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bins</span><span class="p">()[:]</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">pixels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">pixels</span><span class="p">()[:]</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># random and different content to prove only chrom, start, end is linked and the rest is independent for each cell</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">bins</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">'weight'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell2</span><span class="p">[</span><span class="s" style="color: #d14;">'weight'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell3</span><span class="p">[</span><span class="s" style="color: #d14;">'weight'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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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="LC455" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">'KR'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell2</span><span class="p">[</span><span class="s" style="color: #d14;">'KR'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">bins_cell3</span><span class="p">[</span><span class="s" style="color: #d14;">'KR'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bins_cell1</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">name_pixel_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'cell1'</span><span class="p">:</span> <span class="n" style="color: #333;">pixels</span><span class="p">,</span> <span class="s" style="color: #d14;">'cell2'</span><span class="p">:</span> <span class="n" style="color: #333;">pixels</span><span class="p">,</span> <span class="s" style="color: #d14;">'cell3'</span><span class="p">:</span> <span class="n" style="color: #333;">pixels</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">name_bins_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'cell1'</span><span class="p">:</span> <span class="n" style="color: #333;">bins_cell1</span><span class="p">,</span> <span class="s" style="color: #d14;">'cell2'</span><span class="p">:</span> <span class="n" style="color: #333;">bins_cell2</span><span class="p">,</span> <span class="s" style="color: #d14;">'cell3'</span><span class="p">:</span> <span class="n" style="color: #333;">bins_cell3</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">isolated_filesystem</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">cooler</span><span class="p">.</span><span class="n" style="color: #333;">create_scool</span><span class="p">(</span><span class="s" style="color: #d14;">'outfile_test.scool'</span><span class="p">,</span> <span class="n" style="color: #333;">name_bins_dict</span><span class="p">,</span> <span class="n" style="color: #333;">name_pixel_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">content_of_scool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cooler</span><span class="p">.</span><span class="n" style="color: #333;">fileops</span><span class="p">.</span><span class="n" style="color: #333;">list_scool_cells</span><span class="p">(</span><span class="s" style="color: #d14;">'outfile_test.scool'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">content_expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/cells/cell1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/cell2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/cell3'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">content</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">content_expected</span><span class="p">:</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">content</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">content_of_scool</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">cooler</span><span class="p">.</span><span class="n" style="color: #333;">create_scool</span><span class="p">(</span><span class="s" style="color: #d14;">'outfile_test.scool'</span><span class="p">,</span> <span class="n" style="color: #333;">bins</span><span class="p">,</span> <span class="n" style="color: #333;">name_pixel_dict</span><span class="p">)</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">content_of_scool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cooler</span><span class="p">.</span><span class="n" style="color: #333;">fileops</span><span class="p">.</span><span class="n" style="color: #333;">list_scool_cells</span><span class="p">(</span><span class="s" style="color: #d14;">'outfile_test.scool'</span><span class="p">)</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">content_expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/cells/cell1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/cell2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/cell3'</span><span class="p">]</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">content</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">content_expected</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">content</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">content_of_scool</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#1a2cd0b041cec9088c0e4ed03ab86524f36b6fbe"><strong>tests/test_create_ingest.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="256" 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">@@ -256,6 +256,11 @@ def test_cload_pairix(bins_path, pairs_path, ref_path):</td>
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256
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy.bins.var.bed"</span><span class="p">),</span></span>
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257
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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;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy_hash.pairs"</span><span class="p">),</span></span>
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258
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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;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy.symm.upper.var.cool"</span><span class="p">),</span></span>
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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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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="p">(</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy.bins.var.bed"</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;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy_hash.pairs.gz"</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="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"toy.symm.upper.var.cool"</span><span class="p">),</span></span>
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259
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="p">)</span></span>
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260
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="p">],</span></span>
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261
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"><span class="p">)</span></span>
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<li id="54ecd4202f00a30f9544f03cd0738f9ed6038a56">
<a href="https://salsa.debian.org/med-team/python-cooler/-/compare/20cc09f8adfee06f8268a8395182c4a7738f7151...3961764f28a3241b31f363ef73f84b742ab66061#54ecd4202f00a30f9544f03cd0738f9ed6038a56"><strong>tests/test_fileops.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="150" 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="150" 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">@@ -150,3 +150,20 @@ def test_print_trees():</td>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">src_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileops</span><span class="p">.</span><span class="n" style="color: #333;">TreeViewer</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">_ipython_display_</span><span class="p">()</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_is_scool_file</span><span class="p">():</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">src_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">'scool_test_file.scool'</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fileops</span><span class="p">.</span><span class="n" style="color: #333;">is_scool_file</span><span class="p">(</span><span class="n" style="color: #333;">src_file</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_list_scool_cells</span><span class="p">():</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">src_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">testdir</span><span class="p">,</span> <span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="s" style="color: #d14;">'scool_test_file.scool'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'/cells/GSM2687248_41669_ACAGTG-R1-DpnII.100000.cool'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/GSM2687249_41670_GGCTAC-R1-DpnII.100000.cool'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">'/cells/GSM2687250_41671_TTAGGC-R1-DpnII.100000.cool'</span><span class="p">,</span> <span class="s" style="color: #d14;">'/cells/GSM2687251_41672_AGTTCC-R1-DpnII.100000.cool'</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="s" style="color: #d14;">'/cells/GSM2687252_41673_CCGTCC-R1-DpnII.100000.cool'</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">cell_paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fileops</span><span class="p">.</span><span class="n" style="color: #333;">list_scool_cells</span><span class="p">(</span><span class="n" style="color: #333;">src_file</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cell_paths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cell</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">paths</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cell</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cell_paths</span><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 class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">False</span></span></pre>
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