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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-biom-format">Debian Med / python-biom-format</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403">29fca8e9</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-11-05T19:06:55+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.9</pre>

</li>

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<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#458e1d0f85716e3c7c27857fb05bfd41d637ba7c">

ChangeLog.md

</a>

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<li class="file-stats">

<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">

MANIFEST.in

</a>

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<li class="file-stats">

<a href="#96869f8ed2f2c71655a6cd6af01dd85f671d8118">

biom/__init__.py

</a>

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<li class="file-stats">

<a href="#9dd8fda12fdb52648464f77a09f12e329a75158d">

biom/table.py

</a>

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<li class="file-stats">

<a href="#42b93e64b3f8c02a5184492da3b88a6643f2f148">

biom/tests/test_parse.py

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<a href="#d7e3debefc34597187c86af589a0c55f4a8ff7e2">

biom/tests/test_table.py

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<li class="file-stats">

<a href="#a1915bee4c10d765761bc956a98de62711b346b4">

biom/util.py

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<li class="file-stats">

<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">

doc/conf.py

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<li class="file-stats">

<a href="#1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

doc/index.rst

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+

pyproject.toml

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Modified from https://github.com/biocore/scikit-bio</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.6 WITH_DOCTEST=True</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.7 WITH_DOCTEST=True</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.8 WITH_DOCTEST=True</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.6 WITH_DOCTEST=True</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.7 WITH_DOCTEST=True</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.8 WITH_DOCTEST=True</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">chmod +x miniconda.sh</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">@@ -11,15 +11,15 @@ before_install:</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH=/home/travis/miniconda3/bin:$PATH</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">conda create --yes -n env_name python=$PYTHON_VERSION pip click numpy "scipy>=1.3.1" pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">rm biom/*.c</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">source activate env_name</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" 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="15" 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="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "3.<span class="idiff left right">6" ]; then pip install sphinx==1.2.2</span>; fi</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "3.<span class="idiff left right">7" ]; then pip install sphinx==1.2.2 "docutils<0.14"</span>; fi</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install coveralls</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install anndata</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -e . --no-deps</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make test</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">make test</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">biom show-install-info</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "3.<span class="idiff left right">6</span>" ]; then make -C doc html; fi</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" 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="22" 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="LC22" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "3.<span class="idiff left right">7</span>" ]; then make -C doc html; fi</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># we can only validate the tables if we have H5PY</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">for table in examples/*hdf5.biom; do echo ${table}; biom validate-table -i ${table}; done</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># validate JSON formatted tables</span></span>

</pre>

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<br>

</li>

<li id="458e1d0f85716e3c7c27857fb05bfd41d637ba7c">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#458e1d0f85716e3c7c27857fb05bfd41d637ba7c"><strong>ChangeLog.md</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">BIOM-Format ChangeLog</span></span>

</pre>

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<td class="diff-line-num old_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="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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=====================</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" 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="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" 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="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 class="gh" style="color: #999;">biom 2.1.9</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</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="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">

6

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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="LC6" class="line" lang="markdown"></span>

</pre>

</td>

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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">

7

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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="LC7" class="line" lang="markdown">New features and support for Pandas >= 1.0, released on 5 November 2020.</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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>

</pre>

</td>

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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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">Important:</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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>

</pre>

</td>

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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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Cython and numpy are no more required to be present before building, see <span class="p">[</span><span class="nv" style="color: #008080;">PR #840</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/840</span><span class="p">)</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" 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="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">

13

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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="LC13" class="line" lang="markdown">New Features:</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" 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="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 support for the AnnData format, see <span class="p">[</span><span class="nv" style="color: #008080;">PR #845</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/845</span><span class="p">)</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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> Performance boost to <span class="sb" style="color: #d14;">`Table.remove_empty`</span>. For large tables this cuts the running time from 20 seconds to ~1.1 seconds, see <span class="p">[</span><span class="nv" style="color: #008080;">PR #847</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/847</span><span class="p">)</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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> A much faster way to merge tables (without metadata) has been added. For large tables, this was a few minutes rather than a few hours. This method is implicitly invoked when calling <span class="sb" style="color: #d14;">`Table.merge`</span> if unioning both axes, and the tables lack metadata. <span class="sb" style="color: #d14;">`Table.concat`</span> is still much faster, but assumes one axis is disjoint. See <span class="p">[</span><span class="nv" style="color: #008080;">PR #848</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/848</span><span class="p">)</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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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="LC18" class="line" lang="markdown"></span>

</pre>

</td>

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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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> Simplify interaction with the concatenation method, allowing for passing in an individual table and support for a general <span class="sb" style="color: #d14;">`biom.concat(tables)`</span> wrapper. See <span class="p">[</span><span class="nv" style="color: #008080;">PR #851</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/851</span><span class="p">)</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="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> Added support for parsing adjacency table structures, see <span class="p">[</span><span class="nv" style="color: #008080;">issue #823</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/823</span><span class="p">)</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="21" 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">

21

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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="LC21" class="line" lang="markdown"></span>

</pre>

</td>

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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="22" 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">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">Bug fixes:</span>

</pre>

</td>

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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="23" 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">

23

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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="LC23" class="line" lang="markdown"></span>

</pre>

</td>

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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="24" 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="LC24" class="line" lang="markdown"><span class="p">*</span> Support for pandas >= 1.0, see the comment and commits <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/837#issuecomment-721241751</span><span class="p">)</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="25" 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="LC25" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="gh" style="color: #999;">biom 2.1.8</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" 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="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" 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="29" 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="LC7" class="line" lang="markdown">New features and bug fixes, released on <span class="idiff left right">6</span> January 2020.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">New features and bug fixes, released on <span class="idiff left right">28</span> January 2020.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">Important:</span>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +40,7 @@ New Features:</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="p">*</span> The detailed report is no longer part of the table validator. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #378</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/378</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`load_table`</span> now accepts open file handles. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #481</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/481</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`biom export-metadata`</span> has been added to export metadata as TSV. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #820</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/820</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.to_tsv`</span> has been modified to allow for <span class="sb" style="color: #d14;">`direct_io`</span>. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #836</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/836</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown">Bug fixes:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>

</pre>

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<br>

</li>

<li id="8875df48c18030126ef5ef5a6f5c93b23451fb9f">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#8875df48c18030126ef5ef5a6f5c93b23451fb9f"><strong>MANIFEST.in</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,5 +14,6 @@ prune docs/_build</td>

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">global-exclude *.pyc</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">global-exclude *.pyo</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">global-exclude .git</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">global-exclude *.c</span>

</pre>

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17

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">global-exclude *.so</span>

</pre>

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18

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">global-exclude .*.swp</span></pre>

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<br>

</li>

<li id="96869f8ed2f2c71655a6cd6af01dd85f671d8118">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#96869f8ed2f2c71655a6cd6af01dd85f671d8118"><strong>biom/__init__.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="73" 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">@@ -73,5 +73,26 @@ example_table = Table([[0, 1, 2], [3, 4, 5]], ['O1', 'O2'],</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">                       <span class="p">{</span><span class="s" style="color: #d14;">'environment'</span><span class="p">:</span> <span class="s" style="color: #d14;">'A'</span><span class="p">}],</span> <span class="n" style="color: #333;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">concat</span><span class="p">(</span><span class="n" style="color: #333;">tables</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</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>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="s" style="color: #d14;">"""Wrapper for biom.Table.concat which requires a table instance</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="79" 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="LC79" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" 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="LC80" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="81" 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="LC81" class="line" lang="python"><span class="s" style="color: #d14;">    tables : iterable of biom.Table, or a single biom.Table instance</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="82" 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="LC82" class="line" lang="python"><span class="s" style="color: #d14;">        Tables to concatenate</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="83" 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="LC83" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="84" 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="LC84" class="line" lang="python"><span class="s" style="color: #d14;">    Raises</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="76" 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="85" 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="LC85" class="line" lang="python"><span class="s" style="color: #d14;">    ------</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="python"><span class="s" style="color: #d14;">    DisjointIDError</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;">        If IDs over the axis are not disjoint.</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;">    biom.Table</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;">        A table object reflecting the concatenation of the tables.</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tables</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">concat</span><span class="p">(</span><span class="n" style="color: #333;">tables</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="n" style="color: #333;">args</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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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"></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="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Table'</span><span class="p">,</span> <span class="s" style="color: #d14;">'example_table'</span><span class="p">,</span> <span class="s" style="color: #d14;">'parse_table'</span><span class="p">,</span> <span class="s" style="color: #d14;">'load_table'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">           <span class="s" style="color: #d14;">'__format_version__'</span><span class="p">,</span> <span class="s" style="color: #d14;">'__version__'</span><span class="p">]</span></span></pre>

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<br>

</li>

<li id="9dd8fda12fdb52648464f77a09f12e329a75158d">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#9dd8fda12fdb52648464f77a09f12e329a75158d"><strong>biom/table.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">@@ -179,7 +179,7 @@ from copy import deepcopy</td>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">json</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dumps</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">reduce</span><span class="p">,</span> <span class="n" style="color: #333;">partial</span></span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">operator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">itemgetter</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">operator</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">itemgetter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">or_</span></span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">future.builtins</span> <span class="kn" style="font-weight: 600;">import</span> <span class="nb" style="color: #0086b3;">zip</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">future.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">viewitems</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">,</span> <span class="n" style="color: #333;">Hashable</span><span class="p">,</span> <span class="n" style="color: #333;">Iterable</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="187" 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">@@ -187,7 +187,7 @@ from numpy import ndarray, asarray, zeros, newaxis</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.sparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">coo_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">csc_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">csr_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">isspmatrix</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">                          <span class="n" style="color: #333;">vstack</span><span class="p">,</span> <span class="n" style="color: #333;">hstack</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="191" 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="LC190" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">future.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">string_types</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_future_string_types</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.exception</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">TableException</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownAxisError</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownIDError</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1547" 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="1547" 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">@@ -1547,7 +1547,7 @@ class Table(object):</td>

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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">delimited_self</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">u'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">header_key</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">header_value</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="LC1549" class="line" lang="python">                       <span class="n" style="color: #333;">metadata_formatter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="1550" 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="LC1550" class="line" lang="python">                       <span class="n" style="color: #333;">observation_column_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">u'#OTU ID'</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="python">                       <span class="n" style="color: #333;">observation_column_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">u'#OTU ID'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">direct_io</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return self as a string in a delimited form</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1552" 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="diff-line-num new_line" data-linenumber="1552" 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">

1552

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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1553" 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">

1553

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<td class="diff-line-num new_line" data-linenumber="1553" 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">

1553

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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="python"><span class="s" style="color: #d14;">        Default str output for the Table is just row/col ids and table data</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1599" 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="1599" 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">@@ -1599,20 +1599,35 @@ class Table(object):</td>

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<td class="diff-line-num new_line" data-linenumber="1599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1599" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1600" 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="diff-line-num new_line" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="python">            <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'# Constructed from biom file'</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="1601" 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">

1601

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<td class="diff-line-num new_line" data-linenumber="1601" 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">

1601

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<pre style="margin: 0;"> <span id="LC1601" class="line" lang="python">                      <span class="s" style="color: #d14;">'%s%s%s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">observation_column_name</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">samp_ids</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1602" 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="1602" 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">

1602

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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1602" 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="1603" 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="LC1603" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direct_io</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1602" 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="1604" 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">

1604

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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="python">            <span class="n" style="color: #333;">direct_io</span><span class="p">.</span><span class="n" style="color: #333;">writelines</span><span class="p">([</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">output</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1602" 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="1605" 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="LC1605" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1602" 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">

1602

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<td class="diff-line-num new_line" data-linenumber="1606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="python">        <span class="n" style="color: #333;">obs_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1603" 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="1607" 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="LC1603" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">obs_values</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1604" 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="1607" 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="LC1607" class="line" lang="python">        <span class="n" style="color: #333;">iterable</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1604" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1608" 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">

1608

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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="python">        <span class="n" style="color: #333;">end_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direct_io</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1604" 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="1609" 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">

1609

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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1604" 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="1610" 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">

1610

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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">obs_values</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;">iterable</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1604" 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">

1604

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<td class="diff-line-num new_line" data-linenumber="1611" 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">

1611

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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="python">                                      <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter_obs</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1605" 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">

1605

</td>

<td class="diff-line-num new_line" data-linenumber="1612" 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">

1612

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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="python">            <span class="n" style="color: #333;">str_obs_vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">delim</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_to_dense</span><span class="p">(</span><span class="n" style="color: #333;">obs_values</span><span class="p">)))</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1606" 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">

1606

</td>

<td class="diff-line-num new_line old" data-linenumber="1613" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1606" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1607" 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">

1607

</td>

<td class="diff-line-num new_line" data-linenumber="1613" 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">

1613

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1613" class="line" lang="python">            <span class="n" style="color: #333;">obs_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_utf8</span><span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1608" 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">

1608

</td>

<td class="diff-line-num new_line" data-linenumber="1614" 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">

1614

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1614" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header_key</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">obs_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>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1609" 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">

1609

</td>

<td class="diff-line-num new_line" data-linenumber="1615" 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">

1615

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1615" class="line" lang="python">                <span class="n" style="color: #333;">md</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_metadata</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_obs_index</span><span class="p">[</span><span class="n" style="color: #333;">obs_id</span><span class="p">]]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1610" 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">

1610

</td>

<td class="diff-line-num new_line" data-linenumber="1616" 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">

1616

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1616" class="line" lang="python">                <span class="n" style="color: #333;">md_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata_formatter</span><span class="p">(</span><span class="n" style="color: #333;">md</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">header_key</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1611" 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">

1611

</td>

<td class="diff-line-num new_line old" data-linenumber="1617" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1611" class="line" lang="python">                <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1612" 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">

1612

</td>

<td class="diff-line-num new_line old" data-linenumber="1617" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1612" class="line" lang="python">                    <span class="s" style="color: #d14;">u'%s%s%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s'</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1613" 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">

1613

</td>

<td class="diff-line-num new_line old" data-linenumber="1617" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1613" class="line" lang="python">                    <span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">str_obs_vals</span><span class="p">,</span> <span class="n" style="color: #333;">md_out</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1617" 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">

1617

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1617" class="line" lang="python">                <span class="n" style="color: #333;">output_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'%s%s%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s%s'</span> <span class="o" style="font-weight: 600;">%</span> \</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1618" 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">

1618

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1618" class="line" lang="python">                    <span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">str_obs_vals</span><span class="p">,</span> <span class="n" style="color: #333;">md_out</span><span class="p">,</span> <span class="n" style="color: #333;">end_line</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1619" 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">

1619

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1619" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1620" 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">

1620

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1620" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direct_io</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1621" 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">

1621

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1621" class="line" lang="python">                    <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">output_row</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1622" 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">

1622

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1622" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1614" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1623" 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">

1623

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1623" class="line" lang="python">                    <span class="n" style="color: #333;">direct_io</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">output_row</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1614" 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">

1614

</td>

<td class="diff-line-num new_line" data-linenumber="1624" 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">

1624

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1624" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1615" 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">

1615

</td>

<td class="diff-line-num new_line old" data-linenumber="1625" 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="LC1615" class="line" lang="python">                <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">u'%s%s%s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">str_obs_vals</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1625" 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">

1625

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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="python">                <span class="n" style="color: #333;">output_row</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'%s%s%s%s'</span> <span class="o" style="font-weight: 600;">%</span> \</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1626" 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">

1626

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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="python">                            <span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">delim</span><span class="p">,</span> <span class="n" style="color: #333;">str_obs_vals</span><span class="p">,</span> <span class="n" style="color: #333;">end_line</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1627" 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">

1627

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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="LC1627" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direct_io</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1628" 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">

1628

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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="LC1628" class="line" lang="python">                    <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">output_row</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1629" 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">

1629

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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1616" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1630" 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">

1630

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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="python">                    <span class="n" style="color: #333;">direct_io</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">((</span><span class="n" style="color: #333;">output_row</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1616" 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">

1616

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<td class="diff-line-num new_line" data-linenumber="1631" 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">

1631

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1631" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1617" 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">

1617

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<td class="diff-line-num new_line" data-linenumber="1632" 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">

1632

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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1618" 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">

1618

</td>

<td class="diff-line-num new_line" data-linenumber="1633" 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">

1633

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1633" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3201" 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="3216" 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">@@ -3201,7 +3216,7 @@ class Table(object):</td>

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<td class="diff-line-num old_line" data-linenumber="3201" 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="diff-line-num new_line" data-linenumber="3216" 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">

3216

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<pre style="margin: 0;"> <span id="LC3216" class="line" lang="python">            <span class="n" style="color: #333;">axes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">axis</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3202" 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">

3202

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<td class="diff-line-num new_line" data-linenumber="3217" 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">

3217

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3217" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3203" 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">

3203

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<td class="diff-line-num new_line" data-linenumber="3218" 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">

3218

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<pre style="margin: 0;"> <span id="LC3218" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ax</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">axes</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3204" 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">

3204

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<td class="diff-line-num new_line old" data-linenumber="3219" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3204" class="line" lang="python">            <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">md</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">).</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3205" 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="3219" 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">

3219

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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="LC3219" class="line" lang="python">            <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">table</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ids</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">axis</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">ax</span></span><span class="p"><span class="idiff">)[</span></span><span class="n" style="color: #333;"><span class="idiff">table</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">sum</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">axis</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">ax</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ax</span><span class="p">)</span></span>

</pre>

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3205

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<td class="diff-line-num new_line" data-linenumber="3220" 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">

3220

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<pre style="margin: 0;"> <span id="LC3220" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3206" 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">

3206

</td>

<td class="diff-line-num new_line" data-linenumber="3221" 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">

3221

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<pre style="margin: 0;"> <span id="LC3221" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3207" 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">

3207

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<td class="diff-line-num new_line" data-linenumber="3222" 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">

3222

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3222" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3288" 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="3303" 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">@@ -3288,7 +3303,7 @@ class Table(object):</td>

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<td class="diff-line-num old_line" data-linenumber="3288" 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">

3288

</td>

<td class="diff-line-num new_line" data-linenumber="3303" 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">

3303

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3303" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3289" 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">

3289

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<td class="diff-line-num new_line" data-linenumber="3304" 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">

3304

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<pre style="margin: 0;"> <span id="LC3304" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3290" 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">

3290

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<td class="diff-line-num new_line" data-linenumber="3305" 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">

3305

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3305" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3291" 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">

3291

</td>

<td class="diff-line-num new_line old" data-linenumber="3306" 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="LC3291" class="line" lang="python"><span class="s" style="color: #d14;">        others : iterable of biom.Table</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3292" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3306" 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">

3306

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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="LC3306" class="line" lang="python"><span class="s" style="color: #d14;">        others : iterable of biom.Table<span class="idiff left right">, or a single biom.Table instance</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3292" 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">

3292

</td>

<td class="diff-line-num new_line" data-linenumber="3307" 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">

3307

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3307" class="line" lang="python"><span class="s" style="color: #d14;">            Tables to concatenate</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3293" 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">

3293

</td>

<td class="diff-line-num new_line" data-linenumber="3308" 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">

3308

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<pre style="margin: 0;"> <span id="LC3308" class="line" lang="python"><span class="s" style="color: #d14;">        axis : {'sample', 'observation'}, optional</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3294" 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">

3294

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<td class="diff-line-num new_line" data-linenumber="3309" 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">

3309

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<pre style="margin: 0;"> <span id="LC3309" class="line" lang="python"><span class="s" style="color: #d14;">            The axis to concatenate on. i.e., if axis is 'sample', then tables</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3332" 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="3347" 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">@@ -3332,6 +3347,9 @@ class Table(object):</td>

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<td class="diff-line-num old_line" data-linenumber="3332" 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">

3332

</td>

<td class="diff-line-num new_line" data-linenumber="3347" 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">

3347

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<pre style="margin: 0;"> <span id="LC3347" class="line" lang="python"><span class="s" style="color: #d14;">        O5     0.0     0.0     0.0     0.0     0.0     0.0     15.0    16.0    17.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3333" 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">

3333

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<td class="diff-line-num new_line" data-linenumber="3348" 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">

3348

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3348" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3334" 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">

3334

</td>

<td class="diff-line-num new_line" data-linenumber="3349" 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">

3349

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<pre style="margin: 0;"> <span id="LC3349" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3335" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3350" 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">

3350

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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="LC3350" 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;">others</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3335" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3351" 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">

3351

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<pre style="margin: 0;">+<span id="LC3351" class="line" lang="python">            <span class="n" style="color: #333;">others</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">others</span><span class="p">,</span> <span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3335" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3352" 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">

3352

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3352" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3335" 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">

3335

</td>

<td class="diff-line-num new_line" data-linenumber="3353" 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">

3353

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<pre style="margin: 0;"> <span id="LC3353" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># we grow along the opposite axis</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3336" 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">

3336

</td>

<td class="diff-line-num new_line" data-linenumber="3354" 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">

3354

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<pre style="margin: 0;"> <span id="LC3354" class="line" lang="python">        <span class="n" style="color: #333;">invaxis</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_invert_axis</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3355" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'sample'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3442,6 +3460,67 @@ class Table(object):</td>

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<pre style="margin: 0;"> <span id="LC3460" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3461" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">concat</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3462" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3463" 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="LC3463" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fast_merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">others</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3464" 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="LC3464" class="line" lang="python">        <span class="s" style="color: #d14;">"""For simple merge operations it is faster to aggregate using pandas</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3465" 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="LC3465" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3466" 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="LC3466" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3467" 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="LC3467" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3468" 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="LC3468" class="line" lang="python"><span class="s" style="color: #d14;">        others : Table, or Iterable of Table</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3469" 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="LC3469" class="line" lang="python"><span class="s" style="color: #d14;">            If a Table, then merge with that table. If an iterable, then merge</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3470" 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="LC3470" class="line" lang="python"><span class="s" style="color: #d14;">            all of the tables</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3471" 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="LC3471" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3472" 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="LC3472" class="line" lang="python">        <span class="n" style="color: #333;">tables</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">others</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3473" 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="LC3473" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3474" 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="LC3474" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># gather all identifiers across tables</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3475" 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="LC3475" class="line" lang="python">        <span class="n" style="color: #333;">all_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">reduce</span><span class="p">(</span><span class="n" style="color: #333;">or_</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3476" 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="LC3476" class="line" lang="python">                                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tables</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3477" 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="LC3477" class="line" lang="python">        <span class="n" style="color: #333;">all_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">reduce</span><span class="p">(</span><span class="n" style="color: #333;">or_</span><span class="p">,</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">())</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tables</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3478" 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">

3478

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<pre style="margin: 0;">+<span id="LC3478" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3479" 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="LC3479" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># generate unique integer ids for the identifiers, and let's order</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3480" 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="LC3480" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># it to be polite</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="3481" 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="LC3481" class="line" lang="python">        <span class="n" style="color: #333;">feature_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">i</span><span class="p">:</span> <span class="n" style="color: #333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">all_features</span><span class="p">))}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3482" 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="LC3482" class="line" lang="python">        <span class="n" style="color: #333;">sample_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">i</span><span class="p">:</span> <span class="n" style="color: #333;">idx</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">all_samples</span><span class="p">))}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3483" 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">

3483

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<pre style="margin: 0;">+<span id="LC3483" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3484" 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">

3484

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<pre style="margin: 0;">+<span id="LC3484" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># produce a new stable order</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3485" 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">

3485

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<pre style="margin: 0;">+<span id="LC3485" class="line" lang="python">        <span class="n" style="color: #333;">get1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span>  <span class="c1" style="color: #998; font-style: italic;"># noqa</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3486" 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="LC3486" class="line" lang="python">        <span class="n" style="color: #333;">feature_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">feature_map</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get1</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3487" 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">

3487

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<pre style="margin: 0;">+<span id="LC3487" class="line" lang="python">        <span class="n" style="color: #333;">sample_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">sample_map</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get1</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3488" 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">

3488

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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="LC3488" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3489" 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="LC3489" class="line" lang="python">        <span class="n" style="color: #333;">mi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3490" 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="LC3490" class="line" lang="python">        <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3491" 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="LC3491" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">table</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tables</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3492" 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="LC3492" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># these data are effectively [((row_index, col_index), value), ]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3493" 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="LC3493" class="line" lang="python">            <span class="n" style="color: #333;">data_as_dok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span><span class="p">.</span><span class="n" style="color: #333;">todok</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3494" 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">

3494

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<pre style="margin: 0;">+<span id="LC3494" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3495" 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="LC3495" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># construct a map of the feature integer index to what it is in</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3496" 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="LC3496" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># the full table</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3497" 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="LC3497" class="line" lang="python">            <span class="n" style="color: #333;">feat_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3498" 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="LC3498" class="line" lang="python">            <span class="n" style="color: #333;">samp_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3499" 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="LC3499" class="line" lang="python">            <span class="n" style="color: #333;">table_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">idx</span><span class="p">:</span> <span class="n" style="color: #333;">feature_map</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3500" 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="LC3500" class="line" lang="python">                              <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">feat_ids</span><span class="p">)}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3501" 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">

3501

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<pre style="margin: 0;">+<span id="LC3501" class="line" lang="python">            <span class="n" style="color: #333;">table_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">idx</span><span class="p">:</span> <span class="n" style="color: #333;">sample_map</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3502" 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="LC3502" class="line" lang="python">                             <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">samp_ids</span><span class="p">)}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3503" 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">

3503

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<pre style="margin: 0;">+<span id="LC3503" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3504" 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">

3504

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<pre style="margin: 0;">+<span id="LC3504" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data_as_dok</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3505" 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">

3505

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<pre style="margin: 0;">+<span id="LC3505" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># collect the indices and values, adjusting the indices as we</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3506" 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="LC3506" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># go</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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="3507" 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="LC3507" class="line" lang="python">                <span class="n" style="color: #333;">mi</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">table_features</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">],</span> <span class="n" style="color: #333;">table_samples</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3508" 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="LC3508" class="line" lang="python">                <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3509" 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="LC3509" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3510" 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">

3510

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<pre style="margin: 0;">+<span id="LC3510" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># construct a multiindex of the indices where the outer index is the</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3511" 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">

3511

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<pre style="margin: 0;">+<span id="LC3511" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># feature and the inner index is the sample</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3512" 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">

3512

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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="LC3512" class="line" lang="python">        <span class="n" style="color: #333;">mi</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;">MultiIndex</span><span class="p">.</span><span class="n" style="color: #333;">from_tuples</span><span class="p">(</span><span class="n" style="color: #333;">mi</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3513" 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">

3513

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<pre style="margin: 0;">+<span id="LC3513" class="line" lang="python">        <span class="n" style="color: #333;">grouped</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;">Series</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mi</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3514" 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">

3514

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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="LC3514" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3515" 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">

3515

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<pre style="margin: 0;">+<span id="LC3515" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># aggregate the values where the outer and inner values in the</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3516" 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">

3516

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<pre style="margin: 0;">+<span id="LC3516" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># multiindex are the same</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3517" 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">

3517

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<pre style="margin: 0;">+<span id="LC3517" class="line" lang="python">        <span class="n" style="color: #333;">collapsed_rcv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grouped</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3518" 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">

3518

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<pre style="margin: 0;">+<span id="LC3518" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3519" 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">

3519

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<pre style="margin: 0;">+<span id="LC3519" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># convert into a representation understood by the Table constructor</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3520" 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">

3520

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<pre style="margin: 0;">+<span id="LC3520" class="line" lang="python">        <span class="n" style="color: #333;">list_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">),</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">collapsed_rcv</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3521" 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">

3521

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<pre style="margin: 0;">+<span id="LC3521" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3522" 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">

3522

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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="LC3522" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span><span class="p">(</span><span class="n" style="color: #333;">list_list</span><span class="p">,</span> <span class="n" style="color: #333;">feature_order</span><span class="p">,</span> <span class="n" style="color: #333;">sample_order</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3445" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="3523" 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">

3523

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<pre style="margin: 0;">+<span id="LC3523" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3445" 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">

3445

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<td class="diff-line-num new_line" data-linenumber="3524" 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">

3524

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<pre style="margin: 0;"> <span id="LC3524" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'union'</span><span class="p">,</span> <span class="n" style="color: #333;">observation</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'union'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3446" 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">

3446

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<td class="diff-line-num new_line" data-linenumber="3525" 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">

3525

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<pre style="margin: 0;"> <span id="LC3525" class="line" lang="python">              <span class="n" style="color: #333;">sample_metadata_f</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefer_self</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3447" 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">

3447

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<td class="diff-line-num new_line" data-linenumber="3526" 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">

3526

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<pre style="margin: 0;"> <span id="LC3526" class="line" lang="python">              <span class="n" style="color: #333;">observation_metadata_f</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefer_self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3458" 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="3537" 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">@@ -3458,8 +3537,9 @@ class Table(object):</td>

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<pre style="margin: 0;"> <span id="LC3537" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3459" 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="diff-line-num new_line" data-linenumber="3538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3538" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

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<td class="diff-line-num new_line" data-linenumber="3539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3539" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

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<td class="diff-line-num old old_line" data-linenumber="3461" 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="3540" 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="LC3461" class="line" lang="python"><span class="s" style="color: #d14;">        other : biom.Table</span></span>

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<td class="diff-line-num old old_line" data-linenumber="3462" 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="3540" 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="LC3462" class="line" lang="python"><span class="s" style="color: #d14;">            The other table to merge with this one</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3463" 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="LC3540" class="line" lang="python"><span class="s" style="color: #d14;">        other : biom.Table or Iterable of Table</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3463" 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="3541" 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="LC3541" class="line" lang="python"><span class="s" style="color: #d14;">            The other table to merge with this one. If an iterable, the tables</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3463" 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="3542" 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="LC3542" class="line" lang="python"><span class="s" style="color: #d14;">            are expected to not have metadata.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3543" class="line" lang="python"><span class="s" style="color: #d14;">        sample : {'union', 'intersection'}, optional</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3544" class="line" lang="python"><span class="s" style="color: #d14;">        observation : {'union', 'intersection'}, optional</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3545" class="line" lang="python"><span class="s" style="color: #d14;">        sample_metadata_f : function, optional</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3476" 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="3556" 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">@@ -3476,6 +3556,8 @@ class Table(object):</td>

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<td class="diff-line-num new_line" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3556" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3477" 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">

3477

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<td class="diff-line-num new_line" data-linenumber="3557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3557" class="line" lang="python"><span class="s" style="color: #d14;">        Notes</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3558" class="line" lang="python"><span class="s" style="color: #d14;">        -----</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3479" 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="3559" 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="LC3559" class="line" lang="python"><span class="s" style="color: #d14;">        - If ``sample_metadata_f`` and ``observation_metadata_f`` are None,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3479" 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="3560" 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="LC3560" class="line" lang="python"><span class="s" style="color: #d14;">            then a fast merge is applied.</span></span>

</pre>

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3479

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<td class="diff-line-num new_line" data-linenumber="3561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3561" class="line" lang="python"><span class="s" style="color: #d14;">        - There is an implicit type conversion to ``float``.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3480" 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="diff-line-num new_line" data-linenumber="3562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3562" class="line" lang="python"><span class="s" style="color: #d14;">        - The return type is always that of ``self``</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3563" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3587" class="line" lang="python"><span class="s" style="color: #d14;">        O3     10.0    10.0</span></span>

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<pre style="margin: 0;"> <span id="LC3588" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3589" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3590" 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="LC3590" class="line" lang="python">        <span class="n" style="color: #333;">s_md</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3591" 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="LC3591" class="line" lang="python">        <span class="n" style="color: #333;">o_md</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3592" 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="LC3592" class="line" lang="python">        <span class="n" style="color: #333;">no_md</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s_md</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">o_md</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3593" 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="LC3593" class="line" lang="python">        <span class="n" style="color: #333;">ignore_md</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sample_metadata_f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3594" 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="LC3594" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">observation_metadata_f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3595" 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="LC3595" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3596" 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="LC3596" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no_md</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ignore_md</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3508" 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="3597" 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="LC3597" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'union'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">observation</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'union'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3598" 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="LC3598" 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;">other</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3599" 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="LC3599" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_fast_merge</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3508" 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="3600" 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="LC3600" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3601" 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="LC3601" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_fast_merge</span><span class="p">([</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3602" 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="LC3602" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3603" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># determine the sample order in the resulting table</span></span>

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<pre style="margin: 0;"> <span id="LC3604" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'union'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3510" 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="diff-line-num new_line" data-linenumber="3605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3605" class="line" lang="python">            <span class="n" style="color: #333;">new_samp_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_union_id_order</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">(),</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">ids</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3972" 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="4067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC4067" class="line" lang="python">                                     <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keep</span><span class="p">])</span></span>

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<td class="diff-line-num old_line" data-linenumber="3973" 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="diff-line-num new_line" data-linenumber="4068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4068" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Create the new indptr</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3974" 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="diff-line-num new_line" data-linenumber="4069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4069" class="line" lang="python">            <span class="n" style="color: #333;">indptr_subset</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="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span></span>

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<td class="diff-line-num new_line old" data-linenumber="4070" 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="LC3975" class="line" lang="python">                                     <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indptr_indices</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3976" 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="4070" 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="LC4070" class="line" lang="python">                                     <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indptr_indices</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3976" 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="diff-line-num new_line" data-linenumber="4071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4071" class="line" lang="python">            <span class="n" style="color: #333;">indptr</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;">empty</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keep</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 class="n" style="color: #333;">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 class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3977" 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="diff-line-num new_line" data-linenumber="4072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4072" class="line" lang="python">            <span class="n" style="color: #333;">indptr</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="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3978" 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="diff-line-num new_line" data-linenumber="4073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4073" class="line" lang="python">            <span class="n" style="color: #333;">indptr</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="n" style="color: #333;">indptr_subset</span><span class="p">.</span><span class="n" style="color: #333;">cumsum</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4045" 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="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="diff-line-num new_line" data-linenumber="4140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4140" class="line" lang="python">            <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span><span class="p">.</span><span class="n" style="color: #333;">toarray</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4046" 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="diff-line-num new_line" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4141" class="line" lang="python">            <span class="n" style="color: #333;">constructor</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4047" 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="diff-line-num new_line" data-linenumber="4142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4142" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4048" 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="4143" 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="LC4048" class="line" lang="python">            <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4049" 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="4143" 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="LC4049" class="line" lang="python">            <span class="n" style="color: #333;">constructor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">SparseDataFrame</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4050" class="line" lang="python">                                  <span class="n" style="color: #333;">default_fill_value</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4051" class="line" lang="python">                                  <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4143" class="line" lang="python">            <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4144" 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="LC4144" class="line" lang="python">            <span class="n" style="color: #333;">constructor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</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 class="n" style="color: #333;">sparse</span><span class="p">.</span><span class="n" style="color: #333;">from_spmatrix</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4145" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4146" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">constructor</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <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>

</pre>

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<pre style="margin: 0;"> <span id="LC4147" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4148" 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="LC4148" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_anndata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"float32"</span><span class="p">,</span> <span class="n" style="color: #333;">transpose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4149" 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="LC4149" class="line" lang="python">        <span class="s" style="color: #d14;">"""Convert Table to AnnData format</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4150" 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="LC4150" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4151" 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="LC4151" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4152" 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="LC4152" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4153" 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="LC4153" class="line" lang="python"><span class="s" style="color: #d14;">        dense : bool, optional</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4154" 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="LC4154" class="line" lang="python"><span class="s" style="color: #d14;">            If True, set adata.X as np.ndarray instead of sparse matrix.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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="4155" 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="LC4155" class="line" lang="python"><span class="s" style="color: #d14;">        dtype: str, optional</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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="4156" 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="LC4156" class="line" lang="python"><span class="s" style="color: #d14;">            dtype used for storage in anndata object.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4157" 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="LC4157" class="line" lang="python"><span class="s" style="color: #d14;">        tranpose: bool, optional</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4158" class="line" lang="python"><span class="s" style="color: #d14;">            If True, transpose the anndata so that observations are columns</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4159" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4160" 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">

4160

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<pre style="margin: 0;">+<span id="LC4160" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4161" 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">

4161

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<pre style="margin: 0;">+<span id="LC4161" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4162" 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">

4162

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<pre style="margin: 0;">+<span id="LC4162" class="line" lang="python"><span class="s" style="color: #d14;">        anndata.AnnData</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4163" 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">

4163

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<pre style="margin: 0;">+<span id="LC4163" class="line" lang="python"><span class="s" style="color: #d14;">            AnnData with matrix data and associated observation and</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4164" 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">

4164

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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="LC4164" class="line" lang="python"><span class="s" style="color: #d14;">            sample metadata.</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4165" 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">

4165

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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="LC4165" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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="4166" 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">

4166

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<pre style="margin: 0;">+<span id="LC4166" class="line" lang="python"><span class="s" style="color: #d14;">        Notes</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4167" 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">

4167

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<pre style="margin: 0;">+<span id="LC4167" class="line" lang="python"><span class="s" style="color: #d14;">        -----</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4168" 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">

4168

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<pre style="margin: 0;">+<span id="LC4168" class="line" lang="python"><span class="s" style="color: #d14;">        Nested metadata are not included.</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="4169" 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">

4169

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<pre style="margin: 0;">+<span id="LC4169" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4170" 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">

4170

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<pre style="margin: 0;">+<span id="LC4170" class="line" lang="python"><span class="s" style="color: #d14;">        Examples</span></span>

</pre>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4171" 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">

4171

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<pre style="margin: 0;">+<span id="LC4171" class="line" lang="python"><span class="s" style="color: #d14;">        --------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4172" 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">

4172

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<pre style="margin: 0;">+<span id="LC4172" class="line" lang="python"><span class="s" style="color: #d14;">        >>> from biom import example_table</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4173" 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">

4173

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<pre style="margin: 0;">+<span id="LC4173" class="line" lang="python"><span class="s" style="color: #d14;">        >>> adata = example_table.to_anndata()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4174" 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">

4174

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<pre style="margin: 0;">+<span id="LC4174" class="line" lang="python"><span class="s" style="color: #d14;">        >>> adata</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4175" 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">

4175

</td>

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<pre style="margin: 0;">+<span id="LC4175" class="line" lang="python"><span class="s" style="color: #d14;">        AnnData object with n_obs × n_vars = 3 × 2</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4176" 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">

4176

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<pre style="margin: 0;">+<span id="LC4176" class="line" lang="python"><span class="s" style="color: #d14;">            obs: 'environment'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4177" 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">

4177

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4177" class="line" lang="python"><span class="s" style="color: #d14;">            var: 'taxonomy_0', 'taxonomy_1'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4178" 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">

4178

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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="LC4178" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4179" 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">

4179

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<pre style="margin: 0;">+<span id="LC4179" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4180" 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">

4180

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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="LC4180" class="line" lang="python">            <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">anndata</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4181" 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">

4181

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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="LC4181" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4182" 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">

4182

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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="LC4182" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">(</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4183" 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">

4183

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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="LC4183" class="line" lang="python">                <span class="s" style="color: #d14;">"Please install anndata package -- `pip install anndata`"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4184" 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">

4184

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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="LC4184" class="line" lang="python">            <span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4185" 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">

4185

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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="LC4185" class="line" lang="python">        <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4186" 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">

4186

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4186" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4187" 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">

4187

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4187" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dense</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4188" 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">

4188

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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="LC4188" class="line" lang="python">            <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mat</span><span class="p">.</span><span class="n" style="color: #333;">toarray</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4189" 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">

4189

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4189" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4190" 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">

4190

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4190" class="line" lang="python">        <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata_to_dataframe</span><span class="p">(</span><span class="s" style="color: #d14;">"sample"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4191" 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">

4191

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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="LC4191" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata_to_dataframe</span><span class="p">(</span><span class="s" style="color: #d14;">"observation"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4192" 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">

4192

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4192" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4193" 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">

4193

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4193" class="line" lang="python">        <span class="n" style="color: #333;">adata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">anndata</span><span class="p">.</span><span class="n" style="color: #333;">AnnData</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">obs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dtype</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4194" 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">

4194

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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="LC4194" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Convention for scRNA-seq analysis in Python</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4195" 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">

4195

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4195" class="line" lang="python">        <span class="n" style="color: #333;">adata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adata</span><span class="p">.</span><span class="n" style="color: #333;">transpose</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4196" 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">

4196

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4196" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4197" 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">

4197

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4197" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">adata</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4055" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4198" 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">

4198

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<pre style="margin: 0;">+<span id="LC4198" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4199" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">metadata_to_dataframe</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4200" class="line" lang="python">        <span class="s" style="color: #d14;">"""Convert axis metadata to a Pandas DataFrame</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4201" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4740" 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">@@ -4596,6 +4740,103 @@ html</td>

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<pre style="margin: 0;"> <span id="LC4740" class="line" lang="python">                                      <span class="n" style="color: #333;">matrix_element_type</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4597" 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="diff-line-num new_line" data-linenumber="4741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4741" class="line" lang="python">                                      <span class="s" style="color: #d14;">u''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">),</span> <span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4742" 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">

4742

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<pre style="margin: 0;"> <span id="LC4742" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4743" 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="LC4743" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4744" 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="LC4744" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_adjacency</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4745" 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="LC4745" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parse an adjacency format into BIOM</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4746" 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">

4746

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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="LC4746" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4747" 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">

4747

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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="LC4747" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4748" 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">

4748

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<pre style="margin: 0;">+<span id="LC4748" class="line" lang="python"><span class="s" style="color: #d14;">        ----------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4749" 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="LC4749" class="line" lang="python"><span class="s" style="color: #d14;">        lines : list, str, or file-like object</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4750" 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="LC4750" class="line" lang="python"><span class="s" style="color: #d14;">            The tab delimited data to parse</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4751" 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">

4751

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<pre style="margin: 0;">+<span id="LC4751" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4752" 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">

4752

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<pre style="margin: 0;">+<span id="LC4752" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4753" 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">

4753

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<pre style="margin: 0;">+<span id="LC4753" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4754" 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="LC4754" class="line" lang="python"><span class="s" style="color: #d14;">        biom.Table</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4755" 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">

4755

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<pre style="margin: 0;">+<span id="LC4755" class="line" lang="python"><span class="s" style="color: #d14;">            A BIOM ``Table`` object</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4756" 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">

4756

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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="LC4756" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4757" 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">

4757

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<pre style="margin: 0;">+<span id="LC4757" class="line" lang="python"><span class="s" style="color: #d14;">        Notes</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4758" 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">

4758

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<pre style="margin: 0;">+<span id="LC4758" class="line" lang="python"><span class="s" style="color: #d14;">        -----</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4759" 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">

4759

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<pre style="margin: 0;">+<span id="LC4759" class="line" lang="python"><span class="s" style="color: #d14;">        The input is expected to be of the form: observation, sample, value. A</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4760" 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">

4760

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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="LC4760" class="line" lang="python"><span class="s" style="color: #d14;">        header is not required, but if present, it must be of the form:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4761" 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">

4761

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4761" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4762" 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">

4762

</td>

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<pre style="margin: 0;">+<span id="LC4762" class="line" lang="python"><span class="s" style="color: #d14;">        #OTU ID<tab>SampleID<tab>value</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4763" 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">

4763

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4763" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4764" 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">

4764

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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="LC4764" class="line" lang="python"><span class="s" style="color: #d14;">        Raises</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4765" 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">

4765

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<pre style="margin: 0;">+<span id="LC4765" class="line" lang="python"><span class="s" style="color: #d14;">        ------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4766" 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">

4766

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<pre style="margin: 0;">+<span id="LC4766" class="line" lang="python"><span class="s" style="color: #d14;">        ValueError</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4767" 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">

4767

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<pre style="margin: 0;">+<span id="LC4767" class="line" lang="python"><span class="s" style="color: #d14;">            If the input is not an iterable or file-like object.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4768" 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">

4768

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4768" class="line" lang="python"><span class="s" style="color: #d14;">        ValueError</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4769" 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">

4769

</td>

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<pre style="margin: 0;">+<span id="LC4769" class="line" lang="python"><span class="s" style="color: #d14;">            If the data is incorrectly formatted.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4770" 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">

4770

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4770" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4771" 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">

4771

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4771" class="line" lang="python"><span class="s" style="color: #d14;">        Examples</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4772" 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">

4772

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4772" class="line" lang="python"><span class="s" style="color: #d14;">        --------</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4773" 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">

4773

</td>

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<pre style="margin: 0;">+<span id="LC4773" class="line" lang="python"><span class="s" style="color: #d14;">        Parse tab separated adjacency data into a table:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4774" 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">

4774

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4774" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4775" 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">

4775

</td>

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<pre style="margin: 0;">+<span id="LC4775" class="line" lang="python"><span class="s" style="color: #d14;">        >>> from biom.table import Table</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4776" 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">

4776

</td>

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<pre style="margin: 0;">+<span id="LC4776" class="line" lang="python"><span class="s" style="color: #d14;">        >>> from io import StringIO</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4777" 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="LC4777" class="line" lang="python"><span class="s" style="color: #d14;">        >>> data = 'a</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tb</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t1</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">na</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tc</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t2</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">nd</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">tc</span><span class="se" style="color: #d14;">\\</span><span class="s" style="color: #d14;">t3'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4778" 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="LC4778" class="line" lang="python"><span class="s" style="color: #d14;">        >>> data_fh = StringIO(data)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4779" 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="LC4779" class="line" lang="python"><span class="s" style="color: #d14;">        >>> test_table = Table.from_adjacency(data_fh)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4780" 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="LC4780" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4781" 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="LC4781" 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;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4782" 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="LC4782" 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;">lines</span><span class="p">,</span> <span class="s" style="color: #d14;">'readlines'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4783" 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">

4783

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<pre style="margin: 0;">+<span id="LC4783" class="line" lang="python">                <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4784" 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">

4784

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<pre style="margin: 0;">+<span id="LC4784" 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;">lines</span><span class="p">,</span> <span class="s" style="color: #d14;">'splitlines'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4785" 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">

4785

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<pre style="margin: 0;">+<span id="LC4785" class="line" lang="python">                <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4786" 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="LC4786" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4787" 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="LC4787" 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;">"Not sure how to handle this input"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4788" 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="LC4788" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4789" 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="LC4789" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_num</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4790" 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="LC4790" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># from https://stackoverflow.com/a/23059703</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4791" 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="LC4791" class="line" lang="python">            <span class="n" style="color: #333;">numeric</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'(?=.)([+-]?([0-9]*)(\.([0-9]+))?)([eE][+-]?\d+)?'</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># noqa</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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="4792" 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="LC4792" class="line" lang="python">            <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numeric</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4793" 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="LC4793" class="line" lang="python">            <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">span</span><span class="p">()</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="4794" 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">

4794

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<pre style="margin: 0;">+<span id="LC4794" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</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;">item</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4795" 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">

4795

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<pre style="margin: 0;">+<span id="LC4795" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4796" 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">

4796

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<pre style="margin: 0;">+<span id="LC4796" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4797" 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">

4797

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<pre style="margin: 0;">+<span id="LC4797" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4798" 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">

4798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4798" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4799" 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">

4799

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<pre style="margin: 0;">+<span id="LC4799" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># sanity check and determine if we have a header or not</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4800" 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">

4800

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<pre style="margin: 0;">+<span id="LC4800" class="line" lang="python">        <span class="n" style="color: #333;">lh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">strip</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="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4801" 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">

4801

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<pre style="margin: 0;">+<span id="LC4801" 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;">lh</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4802" 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">

4802

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<pre style="margin: 0;">+<span id="LC4802" 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;">"Does not appear to be an adjacency format"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4803" 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">

4803

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<pre style="margin: 0;">+<span id="LC4803" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">lh</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'#OTU ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SampleID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'value'</span><span class="p">]:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4804" 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">

4804

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<pre style="margin: 0;">+<span id="LC4804" class="line" lang="python">            <span class="n" style="color: #333;">include_line_zero</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4805" 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">

4805

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4805" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">is_num</span><span class="p">(</span><span class="n" style="color: #333;">lh</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4806" 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">

4806

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4806" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># allow anything for columns 1 and 2, but test that column 3 is</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4807" 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">

4807

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4807" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># numeric</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4808" 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">

4808

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4808" class="line" lang="python">            <span class="n" style="color: #333;">include_line_zero</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4809" 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">

4809

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4809" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4810" 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">

4810

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4810" 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;">"Does not appear to be an adjacency format"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4811" 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">

4811

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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="LC4811" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4812" 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">

4812

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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="LC4812" 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;">include_line_zero</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4813" 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">

4813

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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="LC4813" class="line" lang="python">            <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4814" 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">

4814

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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="LC4814" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4815" 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">

4815

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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="LC4815" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># extract the entities</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4816" 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">

4816

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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="LC4816" class="line" lang="python">        <span class="n" style="color: #333;">observations</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4817" 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">

4817

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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="LC4817" class="line" lang="python">        <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4818" 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">

4818

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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="LC4818" class="line" lang="python">        <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4819" 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">

4819

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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="LC4819" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4820" 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">

4820

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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="LC4820" class="line" lang="python">            <span class="n" style="color: #333;">parts</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4821" 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">

4821

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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="LC4821" 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;">parts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4822" 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">

4822

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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="LC4822" class="line" lang="python">            <span class="n" style="color: #333;">observations</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4823" 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">

4823

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4823" class="line" lang="python">            <span class="n" style="color: #333;">samples</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4824" 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">

4824

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4824" class="line" lang="python">            <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4825" 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">

4825

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4825" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4826" 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">

4826

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4826" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># determine a stable order and index positioning for the identifiers</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4827" 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">

4827

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4827" class="line" lang="python">        <span class="n" style="color: #333;">obs_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">observations</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4599" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4828" 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">

4828

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4828" class="line" lang="python">        <span class="n" style="color: #333;">samp_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="4829" 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="LC4829" class="line" lang="python">        <span class="n" style="color: #333;">obs_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">o</span><span class="p">:</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">o</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">obs_order</span><span class="p">)}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4830" 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="LC4830" class="line" lang="python">        <span class="n" style="color: #333;">samp_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">samp_order</span><span class="p">)}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4831" 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="LC4831" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4832" 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="LC4832" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># fill the matrix</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4833" 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="LC4833" class="line" lang="python">        <span class="n" style="color: #333;">row</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="n" style="color: #333;">obs_index</span><span class="p">[</span><span class="n" style="color: #333;">obs</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">obs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">observations</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="4834" 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="LC4834" class="line" lang="python">        <span class="n" style="color: #333;">col</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="n" style="color: #333;">samp_index</span><span class="p">[</span><span class="n" style="color: #333;">samp</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">samp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="4835" 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="LC4835" class="line" lang="python">        <span class="n" style="color: #333;">data</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;">asarray</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4836" 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="LC4836" class="line" lang="python">        <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coo_matrix</span><span class="p">((</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4837" 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="LC4837" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4838" 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="LC4838" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">obs_order</span><span class="p">,</span> <span class="n" style="color: #333;">samp_order</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4839" 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="LC4839" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4840" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4841" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">,</span> <span class="n" style="color: #333;">obs_mapping</span><span class="p">,</span> <span class="n" style="color: #333;">sample_mapping</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4601" 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="diff-line-num new_line" data-linenumber="4842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4842" class="line" lang="python">                 <span class="n" style="color: #333;">process_func</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>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4629,7 +4870,7 @@ html</td>

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<pre style="margin: 0;"> <span id="LC4870" class="line" lang="python"><span class="s" style="color: #d14;">        >>> test_table = Table.from_tsv(tsv_fh, None, None, func)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4871" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4631" 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">

4631

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<td class="diff-line-num new_line" data-linenumber="4872" 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">

4872

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<pre style="margin: 0;"> <span id="LC4872" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">sample_ids</span><span class="p">,</span> <span class="n" style="color: #333;">obs_ids</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">t_md</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4632" 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">

4632

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<td class="diff-line-num new_line old" data-linenumber="4873" 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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4632" class="line" lang="python">         <span class="idiff left right">   </span><span class="n" style="color: #333;">t_md_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">_extract_data_from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">lines</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4633" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4873" 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">

4873

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<pre style="margin: 0;">+<span id="LC4873" class="line" lang="python">         <span class="n" style="color: #333;">t_md_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">_extract_data_from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">lines</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4633" 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">

4633

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<td class="diff-line-num new_line" data-linenumber="4874" 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">

4874

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4874" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4634" 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">

4634

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<td class="diff-line-num new_line" data-linenumber="4875" 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">

4875

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<pre style="margin: 0;"> <span id="LC4875" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if we have it, keep it</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4635" 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">

4635

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<td class="diff-line-num new_line" data-linenumber="4876" 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">

4876

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<pre style="margin: 0;"> <span id="LC4876" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">t_md</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4797" 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="5038" 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">@@ -4797,7 +5038,9 @@ html</td>

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<td class="diff-line-num old_line" data-linenumber="4797" 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">

4797

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<td class="diff-line-num new_line" data-linenumber="5038" 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">

5038

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<pre style="margin: 0;"> <span id="LC5038" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samp_ids</span><span class="p">,</span> <span class="n" style="color: #333;">obs_ids</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">md_name</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4798" 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">

4798

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<td class="diff-line-num new_line" data-linenumber="5039" 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">

5039

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5039" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4799" 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">

4799

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<td class="diff-line-num new_line" data-linenumber="5040" 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">

5040

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<pre style="margin: 0;"> <span id="LC5040" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_tsv</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">header_key</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">header_value</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4800" 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">

4800

</td>

<td class="diff-line-num new_line old" data-linenumber="5041" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4800" class="line" lang="python">               <span class="n" style="color: #333;">metadata_formatter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">observation_column_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'#OTU ID'</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5041" 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">

5041

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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="LC5041" class="line" lang="python">               <span class="n" style="color: #333;">metadata_formatter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5042" 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">

5042

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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="LC5042" class="line" lang="python">               <span class="n" style="color: #333;">observation_column_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'#OTU ID'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4801" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5043" 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">

5043

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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="LC5043" class="line" lang="python">               <span class="n" style="color: #333;">direct_io</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4801" 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">

4801

</td>

<td class="diff-line-num new_line" data-linenumber="5044" 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">

5044

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<pre style="margin: 0;"> <span id="LC5044" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return self as a string in tab delimited form</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4802" 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">

4802

</td>

<td class="diff-line-num new_line" data-linenumber="5045" 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">

5045

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5045" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4803" 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">

4803

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<td class="diff-line-num new_line" data-linenumber="5046" 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">

5046

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<pre style="margin: 0;"> <span id="LC5046" class="line" lang="python"><span class="s" style="color: #d14;">        Default ``str`` output for the ``Table`` is just row/col ids and table</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4815" 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="5058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC5058" class="line" lang="python"><span class="s" style="color: #d14;">        observation_column_name : str, optional</span></span>

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<td class="diff-line-num new_line" data-linenumber="5059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5059" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to "#OTU ID". The name of the first column in the output</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5060" class="line" lang="python"><span class="s" style="color: #d14;">            table, corresponding to the observation IDs.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="5061" 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="LC5061" class="line" lang="python"><span class="s" style="color: #d14;">        direct_io : file or file-like object, optional</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5062" 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="LC5062" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to ``None``. Must implement a ``write`` function. If</span></span>

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<td class="diff-line-num new new_line" data-linenumber="5063" 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="LC5063" class="line" lang="python"><span class="s" style="color: #d14;">            `direct_io` is not ``None``, the final output is written directly</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5064" 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="LC5064" class="line" lang="python"><span class="s" style="color: #d14;">            to `direct_io` during processing.</span></span>

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<td class="diff-line-num new_line" data-linenumber="5065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5065" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4819" 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="diff-line-num new_line" data-linenumber="5066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5066" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

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<pre style="margin: 0;"> <span id="LC5067" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4838" 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="5085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<pre style="margin: 0;"> <span id="LC5085" class="line" lang="python"><span class="s" style="color: #d14;">        #OTU ID        S1      S2      S3</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="5086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5086" class="line" lang="python"><span class="s" style="color: #d14;">        O1     0.0     0.0     1.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4840" 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="diff-line-num new_line" data-linenumber="5087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5087" class="line" lang="python"><span class="s" style="color: #d14;">        O2     1.0     3.0     42.0</span></span>

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<td class="diff-line-num new old_line" data-linenumber="4841" 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="5088" 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="LC5088" class="line" lang="python"><span class="s" style="color: #d14;">        >>> with open("result.tsv", "w") as f:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5089" 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="LC5089" class="line" lang="python"><span class="s" style="color: #d14;">                table.to_tsv(direct_io=f)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="5090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5090" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="diff-line-num old_line" data-linenumber="4842" 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="diff-line-num new_line" data-linenumber="5091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5091" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">delimited_self</span><span class="p">(</span><span class="s" style="color: #d14;">u'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">header_key</span><span class="p">,</span> <span class="n" style="color: #333;">header_value</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5092" class="line" lang="python">                                   <span class="n" style="color: #333;">metadata_formatter</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4844" 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="LC4844" class="line" lang="python">                                   <span class="n" style="color: #333;">observation_column_name</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5093" 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="LC5093" class="line" lang="python">                                   <span class="n" style="color: #333;">observation_column_name</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5094" 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="LC5094" class="line" lang="python">                                   <span class="n" style="color: #333;">direct_io</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">direct_io</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC5095" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC5096" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC5097" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">coo_arrays_to_sparse</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">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;">float64</span><span class="p">,</span> <span class="n" style="color: #333;">shape</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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<br>

</li>

<li id="42b93e64b3f8c02a5184492da3b88a6643f2f148">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#42b93e64b3f8c02a5184492da3b88a6643f2f148"><strong>biom/tests/test_parse.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">@@ -229,6 +229,51 @@ class ParseTests(TestCase):</td>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(),</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</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="LC231" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_adjacency_weird_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Not sure"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python">            <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">({</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bar'</span><span class="p">})</span></span>

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<td class="diff-line-num new new_line" data-linenumber="235" 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="LC235" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="236" 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="LC236" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_adjacency_bad_input</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Does not appear"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="238" 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="LC238" class="line" lang="python">            <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">([</span><span class="s" style="color: #d14;">'a</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">b</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">c</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">'d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">e</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">])</span></span>

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<td class="diff-line-num new new_line" data-linenumber="239" 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="LC239" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="240" 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="LC240" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Does not appear"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="241" 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="LC241" class="line" lang="python">            <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">([</span><span class="s" style="color: #d14;">'a</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">b</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">'d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="242" 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="LC242" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="243" 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="LC243" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="244" 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="LC244" class="line" lang="python">            <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">([</span><span class="s" style="color: #d14;">'a</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">b</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="s" style="color: #d14;">'d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="245" 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="LC245" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="246" 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="LC246" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_adjacency_table_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="247" 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="LC247" class="line" lang="python">        <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'#OTU ID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SampleID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">value</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="248" 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="LC248" class="line" lang="python">                 <span class="s" style="color: #d14;">'O1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">10</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="249" 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="LC249" class="line" lang="python">                 <span class="s" style="color: #d14;">'O4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="250" 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="LC250" class="line" lang="python">                 <span class="s" style="color: #d14;">'O3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="251" 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="LC251" class="line" lang="python">                 <span class="s" style="color: #d14;">'O4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="252" 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="LC252" class="line" lang="python">                 <span class="s" style="color: #d14;">'O2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="253" 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="LC253" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</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;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="254" 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="LC254" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="255" 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="LC255" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="256" 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="LC256" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="257" 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="LC257" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O4'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="258" 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="LC258" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="260" 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">

260

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="261" 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="LC261" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="262" 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="LC262" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_adjacency_table_no_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="263" 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="LC263" class="line" lang="python">        <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'O1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">10</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="264" 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="LC264" class="line" lang="python">                 <span class="s" style="color: #d14;">'O4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="265" 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="LC265" class="line" lang="python">                 <span class="s" style="color: #d14;">'O3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">2</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="266" 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="LC266" class="line" lang="python">                 <span class="s" style="color: #d14;">'O4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">5</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="232" 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="267" 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="LC267" class="line" lang="python">                 <span class="s" style="color: #d14;">'O2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">S2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="268" 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="LC268" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</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;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="269" 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">

269

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="270" 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="LC270" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="271" 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="LC271" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</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="LC272" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O4'</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">.</span><span class="n" style="color: #333;">from_adjacency</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">npt</span><span class="p">.</span><span class="n" style="color: #333;">dec</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_H5PY</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'H5PY is not installed'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_biom_table_hdf5</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">        <span class="s" style="color: #d14;">"""Make sure we can parse a HDF5 table through the same loader"""</span></span>

</pre>

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<br>

</li>

<li id="d7e3debefc34597187c86af589a0c55f4a8ff7e2">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#d7e3debefc34597187c86af589a0c55f4a8ff7e2"><strong>biom/tests/test_table.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,8 +19,9 @@ from scipy.sparse import lil_matrix, csr_matrix, csc_matrix</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;">scipy.sparse</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas.util.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">example_table</span><span class="p">,</span> <span class="n" style="color: #333;">load_table</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">example_table</span><span class="p">,</span> <span class="n" style="color: #333;">load_table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">concat</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.exception</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">UnknownAxisError</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownIDError</span><span class="p">,</span> <span class="n" style="color: #333;">TableException</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">                            <span class="n" style="color: #333;">DisjointIDError</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unzip</span><span class="p">,</span> <span class="n" style="color: #333;">HAVE_H5PY</span><span class="p">,</span> <span class="n" style="color: #333;">H5PY_VLEN_STR</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="38" 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">@@ -37,6 +38,13 @@ np.random.seed(1234)</td>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">HAVE_H5PY</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" 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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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="41" 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="LC41" 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 old_line" data-linenumber="40" 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="LC42" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">anndata</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="LC43" class="line" lang="python">    <span class="n" style="color: #333;">anndata</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span></span>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="44" 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="LC44" class="line" lang="python">    <span class="n" style="color: #333;">HAVE_ANNDATA</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="46" 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="LC46" class="line" lang="python">    <span class="n" style="color: #333;">HAVE_ANNDATA</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="47" 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="LC47" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" 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;">"Daniel McDonald"</span></span>

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" 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;">"Copyright 2011-2017, The BIOM Format Development Team"</span></span>

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Daniel McDonald"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jai Ram Rideout"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Justin Kuczynski"</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="156" 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">@@ -148,11 +156,37 @@ class SupportTests(TestCase):</td>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table1</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">([</span><span class="n" style="color: #333;">table2</span><span class="p">,</span> <span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="158" 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">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="159" 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="LC159" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_concat_single_table_nonlist</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="python">        <span class="n" style="color: #333;">table2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="161" 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">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">        <span class="n" style="color: #333;">table2</span><span class="p">.</span><span class="n" style="color: #333;">update_ids</span><span class="p">({</span><span class="s" style="color: #d14;">'S1'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S6'</span><span class="p">})</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="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">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="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">

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="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">

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">]]),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="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">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="166" 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="LC166" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S6'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="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">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">                    <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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">

</td>

<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">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">())</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="169" 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">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">(</span><span class="n" style="color: #333;">table2</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="170" 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="LC170" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" 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="171" 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">

171

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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="LC171" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="151" 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">

151

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<td class="diff-line-num new_line" data-linenumber="172" 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">

172

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_concat_empty</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" 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="diff-line-num new_line" data-linenumber="173" 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">

173

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">concat</span><span class="p">([])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="175" 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">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" 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="diff-line-num new_line" data-linenumber="176" 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">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="177" 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="LC177" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_concat_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="178" 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="LC178" class="line" lang="python">        <span class="n" style="color: #333;">table2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="179" 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="LC179" class="line" lang="python">        <span class="n" style="color: #333;">table2</span><span class="p">.</span><span class="n" style="color: #333;">update_ids</span><span class="p">({</span><span class="s" style="color: #d14;">'S1'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S6'</span><span class="p">})</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="180" 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="LC180" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="181" 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="LC181" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="182" 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="LC182" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">]]),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="183" 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="LC183" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="184" 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="LC184" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S6'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="185" 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="LC185" class="line" lang="python">                    <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="186" 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="LC186" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">())</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="187" 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="LC187" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">concat</span><span class="p">([</span><span class="n" style="color: #333;">example_table</span><span class="p">,</span> <span class="n" style="color: #333;">table2</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="156" 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="188" 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="LC188" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="189" 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="LC189" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_concat_samples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">        <span class="n" style="color: #333;">table2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">        <span class="n" style="color: #333;">table2</span><span class="p">.</span><span class="n" style="color: #333;">update_ids</span><span class="p">({</span><span class="s" style="color: #d14;">'S1'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">:</span> <span class="s" style="color: #d14;">'S6'</span><span class="p">})</span></span>

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<pre style="margin: 0;"> <span id="LC1507" class="line" lang="python">             <span class="s" style="color: #d14;">'tree'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'newick'</span><span class="p">,</span> <span class="s" style="color: #d14;">'((4:0.1,5:0.1):0.2,(6:0.1,7:0.1):0.2):0.3;'</span><span class="p">)})</span></span>

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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_dataframe</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC1476" class="line" lang="python">        <span class="n" style="color: #333;">exp</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;">SparseDataFrame</span><span class="p">(</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="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">3.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">,</span> <span class="mf" style="color: #099;">5.0</span><span class="p">]]),</span></span>

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<pre style="margin: 0;">-<span id="LC1477" class="line" lang="python">                                 <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC1478" class="line" lang="python">                                 <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;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1510" 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="LC1479" class="line" lang="python">                                 <span class="n" style="color: #333;">default_fill_value</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="python">        <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csr_matrix</span><span class="p">(</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="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1511" class="line" lang="python">                                   <span class="p">[</span><span class="mf" style="color: #099;">3.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">,</span> <span class="mf" style="color: #099;">5.0</span><span class="p">]]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1480" 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="1512" 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="LC1512" class="line" lang="python">        <span class="n" style="color: #333;">exp</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 class="n" style="color: #333;">sparse</span><span class="p">.</span><span class="n" style="color: #333;">from_spmatrix</span><span class="p">(</span><span class="n" style="color: #333;">mat</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1513" class="line" lang="python">                                                <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'O1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'O2'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="python">                                                <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;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1481" 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">

1481

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<td class="diff-line-num new_line old" data-linenumber="1516" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1481" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1516" 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">

1516

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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="LC1516" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1517" 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">

1517

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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># assert frame equal between sparse and dense frames wasn't working</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1518" 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">

1518

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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="LC1518" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># as expected</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1519" 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">

1519

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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="LC1519" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="p">.</span><span class="n" style="color: #333;">assert_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1520" 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">

1520

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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="LC1520" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1482" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1521" 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">

1521

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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="LC1521" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">exp</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1482" 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">

1482

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<td class="diff-line-num new_line" data-linenumber="1522" 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">

1522

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1522" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1483" 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">

1483

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<td class="diff-line-num new_line" data-linenumber="1523" 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">

1523

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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_dataframe_is_sparse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1484" 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">

1484

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<td class="diff-line-num new_line" data-linenumber="1524" 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">

1524

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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="python">        <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1485" 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">

1485

</td>

<td class="diff-line-num new_line" data-linenumber="1525" 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">

1525

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1525" class="line" lang="python">        <span class="n" style="color: #333;">density</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span><span class="p">.</span><span class="n" style="color: #333;">getnnz</span><span class="p">())</span> <span class="o" style="font-weight: 600;">/</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1486" 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">

1486

</td>

<td class="diff-line-num new_line" data-linenumber="1526" 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">

1526

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1526" class="line" lang="python">                   <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">prod</span><span class="p">(</span><span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1487" 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">

1487

</td>

<td class="diff-line-num new_line old" data-linenumber="1527" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1487" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">density</span><span class="p">,</span> <span class="n" style="color: #333;">density</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1488" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1527" 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">

1527

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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="LC1527" class="line" lang="python">        <span class="n" style="color: #333;">df_density</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">().</span><span class="nb" style="color: #0086b3;">sum</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;">prod</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1488" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1528" 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">

1528

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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="LC1528" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">df_density</span><span class="p">,</span> <span class="n" style="color: #333;">density</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1488" 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">

1488

</td>

<td class="diff-line-num new_line" data-linenumber="1529" 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">

1529

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1529" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1489" 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">

1489

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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_dataframe_dense</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1490" 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="diff-line-num new_line" data-linenumber="1531" 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">

1531

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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="python">        <span class="n" style="color: #333;">exp</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 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="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">2.0</span><span class="p">],</span> <span class="p">[</span><span class="mf" style="color: #099;">3.0</span><span class="p">,</span> <span class="mf" style="color: #099;">4.0</span><span class="p">,</span> <span class="mf" style="color: #099;">5.0</span><span class="p">]]),</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1493" 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="1534" 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">@@ -1493,6 +1534,28 @@ class TableTests(TestCase):</td>

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<td class="diff-line-num new_line" data-linenumber="1534" 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">

1534

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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1494" 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="diff-line-num new_line" data-linenumber="1535" 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">

1535

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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1495" 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">

1495

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<td class="diff-line-num new_line" data-linenumber="1536" 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">

1536

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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1537" 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">

1537

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<pre style="margin: 0;">+<span id="LC1537" 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;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">HAVE_ANNDATA</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"anndata not installed"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1538" 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">

1538

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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_anndata_dense</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1539" 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">

1539

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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1540" 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">

1540

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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="python">        <span class="n" style="color: #333;">adata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_anndata</span><span class="p">(</span><span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float64'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1541" 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">

1541

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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="LC1541" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">adata</span><span class="p">.</span><span class="n" style="color: #333;">transpose</span><span class="p">().</span><span class="n" style="color: #333;">to_df</span><span class="p">(),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1542" 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">

1542

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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="LC1542" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1543" 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">

1543

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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="LC1543" 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;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">HAVE_ANNDATA</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"anndata not installed"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1544" 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">

1544

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<pre style="margin: 0;">+<span id="LC1544" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_anndata_sparse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1545" 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">

1545

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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="python">        <span class="n" style="color: #333;">adata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_anndata</span><span class="p">(</span><span class="n" style="color: #333;">dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1546" 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">

1546

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<pre style="margin: 0;">+<span id="LC1546" class="line" lang="python">        <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">matrix_data</span><span class="p">.</span><span class="n" style="color: #333;">toarray</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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="1547" 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">

1547

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<pre style="margin: 0;">+<span id="LC1547" class="line" lang="python">        <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">testing</span><span class="p">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span><span class="n" style="color: #333;">adata</span><span class="p">.</span><span class="n" style="color: #333;">transpose</span><span class="p">().</span><span class="n" style="color: #333;">X</span><span class="p">.</span><span class="n" style="color: #333;">toarray</span><span class="p">(),</span> <span class="n" style="color: #333;">mat</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1548" 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">

1548

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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="LC1548" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1549" 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">

1549

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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="LC1549" 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;">skipif</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">HAVE_ANNDATA</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"anndata not installed"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1550" 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">

1550

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<pre style="margin: 0;">+<span id="LC1550" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_to_anndata_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1551" 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">

1551

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<pre style="margin: 0;">+<span id="LC1551" class="line" lang="python">        <span class="n" style="color: #333;">adata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">to_anndata</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1552" 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">

1552

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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="LC1552" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1553" 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">

1553

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<pre style="margin: 0;">+<span id="LC1553" class="line" lang="python">        <span class="n" style="color: #333;">obs_samp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata_to_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1554" 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">

1554

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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="python">        <span class="n" style="color: #333;">obs_obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="p">.</span><span class="n" style="color: #333;">metadata_to_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1555" 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">

1555

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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="LC1555" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1556" 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">

1556

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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">adata</span><span class="p">.</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">obs_samp</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1557" 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">

1557

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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">adata</span><span class="p">.</span><span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">obs_obs</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1496" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1558" 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">

1558

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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="LC1558" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1496" 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">

1496

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<td class="diff-line-num new_line" data-linenumber="1559" 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">

1559

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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_metadata_to_dataframe</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1497" 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">

1497

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<td class="diff-line-num new_line" data-linenumber="1560" 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">

1560

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<pre style="margin: 0;"> <span id="LC1560" class="line" lang="python">        <span class="n" style="color: #333;">exp_samp</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 class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">],</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'S1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S3'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1498" 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">

1498

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<td class="diff-line-num new_line" data-linenumber="1561" 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">

1561

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<pre style="margin: 0;"> <span id="LC1561" class="line" lang="python">                                <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;">'environment'</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2262" 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="2325" 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">@@ -2262,6 +2325,30 @@ class SparseTableTests(TestCase):</td>

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2262

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<td class="diff-line-num new_line" data-linenumber="2325" 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">

2325

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<pre style="margin: 0;"> <span id="LC2325" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="p">.</span><span class="n" style="color: #333;">assert_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs_obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_obs</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2263" 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">

2263

</td>

<td class="diff-line-num new_line" data-linenumber="2326" 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">

2326

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2326" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="p">.</span><span class="n" style="color: #333;">assert_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs_whole</span><span class="p">,</span> <span class="n" style="color: #333;">exp_whole</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2264" 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">

2264

</td>

<td class="diff-line-num new_line" data-linenumber="2327" 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">

2327

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2327" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2328" 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">

2328

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2328" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fast_merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2329" 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">

2329

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2329" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="p">(</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 class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="mi" style="color: #099;">16</span><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2330" 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">

2330

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2330" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2'</span><span class="p">],</span> <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2331" 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">

2331

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2331" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">.</span><span class="n" style="color: #333;">_fast_merge</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2332" 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">

2332

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2332" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2333" 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">

2333

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2333" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2334" 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">

2334

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2334" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fast_merge_multiple</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2335" 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">

2335

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2335" class="line" lang="python">        <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="mi" style="color: #099;">24</span><span class="p">,</span> <span class="p">(</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 class="mi" style="color: #099;">28</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span> <span class="mi" style="color: #099;">32</span><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2336" 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">

2336

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2336" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2'</span><span class="p">],</span> <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2337" 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">

2337

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2337" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">.</span><span class="n" style="color: #333;">_fast_merge</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2338" 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">

2338

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2338" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2339" 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">

2339

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2339" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2340" 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">

2340

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<pre style="margin: 0;">+<span id="LC2340" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fast_merge_nonoverlapping</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2341" 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="LC2341" class="line" lang="python">        <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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="2342" 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="LC2342" class="line" lang="python">        <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">update_ids</span><span class="p">({</span><span class="s" style="color: #d14;">'a'</span><span class="p">:</span> <span class="s" style="color: #d14;">'d'</span><span class="p">},</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">strict</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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="2343" 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="LC2343" class="line" lang="python">        <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">update_ids</span><span class="p">({</span><span class="s" style="color: #d14;">'2'</span><span class="p">:</span> <span class="s" style="color: #d14;">'3'</span><span class="p">},</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'observation'</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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="2344" 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="LC2344" class="line" lang="python">                      <span class="n" style="color: #333;">strict</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2345" 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="LC2345" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="p">(</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="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2346" 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="LC2346" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2347" 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="LC2347" class="line" lang="python">                              <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">]]),</span> <span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2348" 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">

2348

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<pre style="margin: 0;">+<span id="LC2348" class="line" lang="python">                    <span class="p">[</span><span class="s" style="color: #d14;">'a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'d'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2349" 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">

2349

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<pre style="margin: 0;">+<span id="LC2349" class="line" lang="python">        <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t2</span><span class="p">.</span><span class="n" style="color: #333;">_fast_merge</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">st1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2350" 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">

2350

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<pre style="margin: 0;">+<span id="LC2350" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2265" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2351" 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">

2351

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<pre style="margin: 0;">+<span id="LC2351" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2265" 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">

2265

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<td class="diff-line-num new_line" data-linenumber="2352" 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">

2352

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<pre style="margin: 0;"> <span id="LC2352" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2266" 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="diff-line-num new_line" data-linenumber="2353" 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">

2353

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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="python">        <span class="s" style="color: #d14;">"""Merge two tables"""</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2267" 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="diff-line-num new_line" data-linenumber="2354" 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">

2354

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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="python">        <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'union'</span></span>

</pre>

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</table>

<br>

</li>

<li id="a1915bee4c10d765761bc956a98de62711b346b4">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#a1915bee4c10d765761bc956a98de62711b346b4"><strong>biom/util.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="45" 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">@@ -45,7 +45,7 @@ __url__ = "http://biom-format.org"</td>

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<td class="diff-line-num old_line" data-linenumber="45" 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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45

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Daniel McDonald"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"daniel.mcdonald@colorado.edu"</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">__format_version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</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="LC48" 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;">"2.1.<span class="idiff left right">8</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC48" 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;">"2.1.<span class="idiff left right">9</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_subsamples</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample'</span><span class="p">,</span> <span class="n" style="color: #333;">by_id</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -202,9 +202,9 @@ def prefer_self(x, y):</td>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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="n" style="color: #333;">y</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index_list</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">l</span></span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index_list</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">item</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">    <span class="s" style="color: #d14;">"""Takes a list and returns {l[idx]:idx}"""</span></span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">id_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">l</span></span><span class="p">)])</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">id_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">item</span></span><span class="p">)])</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_biom_config</span><span class="p">():</span></span>

</pre>

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<br>

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<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/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">@@ -59,15 +59,15 @@ master_doc = 'index'</td>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" 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;">u'biom-format'</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" 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;">u'2011-20<span class="idiff left right">18</span> The BIOM Format Development Team'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="63" 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="LC62" 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;">u'2011-20<span class="idiff left right">20</span> The BIOM Format Development Team'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" 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="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC64" 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="LC65" 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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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># built documents.</span></span>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" 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="LC69" 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;">"2.1.<span class="idiff left right">8</span>"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1.<span class="idiff left right">8</span>"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" 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;">"2.1.<span class="idiff left right">9</span>"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.1.<span class="idiff left right">9</span>"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" 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>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>

</pre>

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</li>

<li id="1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.rst</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,7 @@ To enable Bash tab completion of ``biom`` commands, add the following line to ``</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">Citing the BIOM project</span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">=======================</span>

</pre>

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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">You can cite the BIOM format as follows (`link <http<span class="idiff left right">://www.gigasciencejournal.com/content/1/1/7</span>>`_):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">You can cite the BIOM format as follows (`link <http<span class="idiff left right">s://academic.oup.com/gigascience/article/1/1/2047-217X-1-7/2656152</span>>`_):</span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">| The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">| Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.</span>

</pre>

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<br>

</li>

<li id="5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="toml"><span class="nn" style="color: #555;">[build-system]</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="toml"><span class="py">requires</span> <span class="p">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"setuptools"</span><span class="p">,</span><span class="s" style="color: #d14;">"wheel"</span><span class="p">,</span> <span class="s" style="color: #d14;">"numpy"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cython"</span><span class="p">]</span></span></pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-biom-format/-/commit/29fca8e932fbf74620831f1cde788bb1dd0ae403#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -14,18 +14,8 @@ import sys</td>

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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;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">find_packages</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;">setuptools.extension</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Extension</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;">setuptools.command.test</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">test</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">TestCommand</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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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;">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="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC21" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">(</span><span class="s" style="color: #d14;">"numpy must be installed prior to installing biom"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" 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="17" 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="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" 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="17" 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="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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="17" 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="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC25" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cythonize</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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="17" 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="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">(</span><span class="s" style="color: #d14;">"cython must be installed prior to installing biom"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC28" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" 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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cythonize</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Hack to prevent stupid "TypeError: 'NoneType' object is not callable" error</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># in multiprocessing/util.py _exit_function when running `python</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="33" 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">@@ -43,7 +33,7 @@ __copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">__credits__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Greg Caporaso"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Daniel McDonald"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jose Clemente"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">               <span class="s" style="color: #d14;">"Jai Ram Rideout"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Jorge Cañardo Alastuey"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Michael Hall"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">__license__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BSD"</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="36" 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="LC46" 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;">"2.1.<span class="idiff left right">8</span>"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" 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;">"2.1.<span class="idiff left right">9</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="n" style="color: #333;">__maintainer__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Daniel McDonald"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">__email__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"mcdonadt@colorado.edu"</span></span>

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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="65" 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">@@ -75,7 +65,6 @@ class PyTest(TestCommand):</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># import here, cause outside the eggs aren't loaded</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">        <span class="n" style="color: #333;">errno</span> <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;">main</span><span class="p">(</span><span class="n" style="color: #333;">shlex</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pytest_args</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" 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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,7 +112,8 @@ extensions = cythonize(extensions)</td>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"><span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"click"</span><span class="p">,</span> <span class="s" style="color: #d14;">"numpy >= 1.9.2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"future >= 0.16.0"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">                    <span class="s" style="color: #d14;">"scipy >= 1.3.1"</span><span class="p">,</span> <span class="s" style="color: #d14;">'pandas >= 0.20.0'</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;">"six >= 1.10.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cython >= 0.29"</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;">"six >= 1.10.0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cython >= 0.29"</span><span class="p">,</span> <span class="s" style="color: #d14;">"h5py"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python">                    <span class="s" style="color: #d14;">"cython"</span><span class="p">]</span></span>

</pre>

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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="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</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="mi" style="color: #099;">3</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="129" 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">

129

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<td class="diff-line-num new_line" data-linenumber="119" 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">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Python 2.7 is no longer supported"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="130" 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">@@ -140,7 +130,7 @@ setup(name='biom-format',</td>

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<td class="diff-line-num old_line" data-linenumber="140" 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="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">      <span class="n" style="color: #333;">maintainer_email</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__email__</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" 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="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" 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;">'http://www.biom-format.org'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" 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="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">      <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" 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="133" 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="LC143" class="line" lang="python">      <span class="n" style="color: #333;">tests_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pytest'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="144" 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="133" 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="LC133" class="line" lang="python">      <span class="n" style="color: #333;">tests_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'pytest<span class="idiff left right"> < 5.3.4</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" 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">

144

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<td class="diff-line-num new_line" data-linenumber="134" 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">

134

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">                     <span class="s" style="color: #d14;">'pytest-cov'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" 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="diff-line-num new_line" data-linenumber="135" 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">

135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">                     <span class="s" style="color: #d14;">'flake8'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">                     <span class="s" style="color: #d14;">'nose'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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="138" 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">@@ -148,7 +138,8 @@ setup(name='biom-format',</td>

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<td class="diff-line-num old_line" data-linenumber="148" 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="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python">      <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" 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="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">      <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">get_include</span><span class="p">()],</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="140" 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">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">      <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">install_requires</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" 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="141" 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="LC151" class="line" lang="python">      <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'hdf5'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"h5py >= 2.2.0"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" 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="141" 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="LC141" class="line" lang="python">      <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'hdf5'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"h5py >= 2.2.0"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" 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="142" 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="LC142" class="line" lang="python">                      <span class="s" style="color: #d14;">'anndata'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"anndata"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" 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="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python">                      <span class="p">},</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" 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="diff-line-num new_line" data-linenumber="144" 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">

144

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python">      <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">classifiers</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" 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">

154

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<td class="diff-line-num new_line" data-linenumber="145" 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">

145

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python">      <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"pytest"</span><span class="p">:</span> <span class="n" style="color: #333;">PyTest</span><span class="p">},</span></span>

</pre>

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