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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/d993b066e9879c3f852b79a16221b748d9cdf615">d993b066</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-01-20T11:34:29+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.8+dfsg</pre>

</li>

</ul>

<h4>15 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>

</li>

<li class="file-stats">

<a href="#28e29f054410016d7f5a9b27dfc18d64f346fe67">

biom/cli/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#3b6a850229bcda1001a92fa24984fbc0677d4b9e">

<span class="new-file">

+

biom/cli/metadata_exporter.py

</span>

</a>

</li>

<li class="file-stats">

<a href="#23e2cf97b549b81a7a2a070c9887e017308dd1ee">

biom/cli/table_validator.py

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<li class="file-stats">

<a href="#7805345b6c8be3df5725771c493ce326d41d0f51">

biom/err.py

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<li class="file-stats">

<a href="#08a4e10076dcc2c977e4d3e580c33acd5b6eaaca">

biom/parse.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="#d5eff8e10cff8335bc068e36e27dbcfb6a245f3b">

biom/tests/test_cli/test_validate_table.py

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<a href="#0b315fcfbcf8da695790146349c415c7693f4f1a">

biom/tests/test_err.py

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<a href="#42b93e64b3f8c02a5184492da3b88a6643f2f148">

biom/tests/test_parse.py

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<li class="file-stats">

<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="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#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 class="idiff left right">/</span></span></span>

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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>

</pre>

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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=2.7 WITH_DOCTEST=False USE_CYTHON=True</span></span>

</pre>

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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=3.5 WITH_DOCTEST=True USE_CYTHON=True</span></span>

</pre>

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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=3.6 WITH_DOCTEST=True USE_CYTHON=True</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">PYTHON_VERSION=3.7 WITH_DOCTEST=True USE_CYTHON=True</span></span>

</pre>

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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>

</pre>

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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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">./miniconda.sh -b</span></span>

</pre>

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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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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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="13" 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="LC14" 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 <span class="idiff left right">scipy</span> pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(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="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="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">rm biom/*.c</span></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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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" 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="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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<td class="diff-line-num new_line old" 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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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "2.7" ]; then pip install pyqi; fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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="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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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "2.7" ]; then conda install --yes Sphinx=1.2.2; fi</span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "3.6" ]; then pip install sphinx==1.2.2; fi</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="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">

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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 coveralls</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">

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

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<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">

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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_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="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">

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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="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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="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="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="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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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [ ${PYTHON_VERSION} = "<span class="idiff left right">2.7</span>" ]; then make -C doc html; fi</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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} = "<span class="idiff left right">3.6</span>" ]; then make -C doc html; fi</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">

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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="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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<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="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">

27

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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>

</td>

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<br>

</li>

<li id="458e1d0f85716e3c7c27857fb05bfd41d637ba7c">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#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">

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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>

</td>

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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">

2

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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">

2

</td>

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

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

</pre>

</td>

</tr>

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

<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">

3

</td>

<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">

3

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></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="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">

</td>

<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">

4

</td>

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">biom 2.1.8</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="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">

</td>

<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

</td>

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

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

</td>

<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

</td>

<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>

</tr>

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

<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">

</td>

<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

</td>

<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 bug fixes, released on 6 January 2020.</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="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">

</td>

<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

</td>

<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>

</tr>

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

<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">

</td>

<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

</td>

<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>

</td>

</tr>

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

<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">

</td>

<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

</td>

<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>

</tr>

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

<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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Python 2.7 and 3.5 support has been dropped.</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="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">

</td>

<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

</td>

<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 class="p">*</span> Python 3.8 support has been added into Travis CI. </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="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">

</td>

<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

</td>

<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"><span class="p">*</span> A change to the defaults for <span class="sb" style="color: #d14;">`Table.nonzero_counts`</span> was performed such that the default now is to count the number of nonzero features. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #685</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/685</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="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">

</td>

<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">

14

</td>

<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 class="p">*</span> We now require a SciPy >= 1.3.1. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #816</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/816</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="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">

</td>

<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">

15

</td>

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></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="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">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">New Features:</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="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">

</td>

<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">

17

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></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="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">

</td>

<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

</td>

<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 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>

</td>

</tr>

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

<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">

</td>

<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">

19

</td>

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

<pre style="margin: 0;">+<span id="LC19" 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>

</td>

</tr>

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

<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">

</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC20" 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>

</td>

</tr>

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

<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">

</td>

<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

</td>

<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>

</tr>

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

<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">

</td>

<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>

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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">

</td>

<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">

</td>

<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">

24

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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="LC24" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.to_dataframe(dense=False)`</span> does now correctly produce sparse data frames (and not accidentally dense ones as before). See <span class="p">[</span><span class="nv" style="color: #008080;">issue #808</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/808</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">

</td>

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">*</span> Order of error evaluations was unstable in Python versions without implicit <span class="sb" style="color: #d14;">`OrderedDict`</span>. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #813</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/813</span><span class="p">)</span>. Thanks @gwarmstrong for identifying this bug.</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table._extract_data_from_tsv`</span> would fail if taxonomy was provided, and if the first row had the empty string for taxonomy. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #827</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/827</span><span class="p">)</span>. Thanks @KasperSkytte for identifying this bug.</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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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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="LC27" class="line" lang="markdown"></span>

</pre>

</td>

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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">

4

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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">

28

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="gh" style="color: #999;">biom 2.1.7</span></span>

</pre>

</td>

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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">

5

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<pre style="margin: 0;"> <span id="LC29" 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">

6

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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">

30

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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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">

31

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">New features and bug fixes, released on 28 September 2018.</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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="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">

32

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

<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">Important:<span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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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="LC33" class="line" lang="markdown">Important:</span>

</pre>

</td>

</tr>

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

<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">

10

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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">

34

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

<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<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">

35

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

<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="p">*</span> Python 3.4 support has been dropped. We now only support Python 2.7, 3.5, 3.6 and 3.7.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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

<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">*</span> We will be dropping Python 2.7 support on the next release.</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="13" 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">

13

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<td class="diff-line-num new_line old" data-linenumber="37" 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="LC13" class="line" lang="markdown"><span class="p">*</span> Pandas >= 0.20.0 is now the minimum required version.<span class="idiff left right"> </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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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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="LC37" class="line" lang="markdown"><span class="p">*</span> Pandas >= 0.20.0 is now the minimum required version.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

14

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<td class="diff-line-num 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">

38

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

<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="p">*</span> pytest is now used instead of nose.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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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">

39

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

<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<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">

16

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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">New Features:</span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>

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<td class="diff-line-num new_line old" data-linenumber="42" 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="markdown"><span class="p">*</span> Massive performance boost to <span class="sb" style="color: #d14;">`Table.collapse`</span> with the default collapse function. The difference was 10s of milliseconds vs. minutes stemming from prior use of <span class="sb" style="color: #d14;">`operator.add`</span>. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #761</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/761</span><span class="p">)</span>.<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">*</span> Massive performance boost to <span class="sb" style="color: #d14;">`Table.collapse`</span> with the default collapse function. The difference was 10s of milliseconds vs. minutes stemming from prior use of <span class="sb" style="color: #d14;">`operator.add`</span>. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #761</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/761</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new_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">

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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.align_to`</span> for aligning one table to another. This is useful in multi-omic analyses where multiple preparations have been performed on the sample physical samples. This is essentially a helper method around <span class="sb" style="color: #d14;">`Table.sort_order`</span>. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #747</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/747</span><span class="p">)</span>.</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="p">*</span> Added additional sanity checks when calling <span class="sb" style="color: #d14;">`Table.to_hdf5`</span>, see <span class="p">[</span><span class="nv" style="color: #008080;">PR #769</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/pull/769</span><span class="p">)</span>.</span>

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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"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.subsample()`</span> can optionally perform subsampling with replacement. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #774</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/774</span><span class="p">)</span>.</span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(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">@@ -38,7 +62,7 @@ New Features:</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.from_hdf5`</span> now supports a rapid subset in the event that metadata is</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown">   not needed. In benchmarking against the Earth Microbiome Project BIOM table,</span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown">   the reduction in runtime was multiple orders of magnitude while additionally</span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown">   preserving substantial memory.<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">   preserving substantial memory.</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.rankdata`</span> has been added to convert values to ranked abundances on</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">  either axis. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #645</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/639</span><span class="p">)</span>.</span>

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<td class="diff-line-num new_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="markdown"><span class="p">*</span> Format of numbers in <span class="sb" style="color: #d14;">``biom summarize-table``</span> output is now more readable and localized. See <span class="p">[</span><span class="nv" style="color: #008080;">issue #679</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/679</span><span class="p">)</span>.</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(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">@@ -96,8 +120,8 @@ Bug fixes:</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`biom --version`</span> now prints the software version (previously the individual</span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown">  commands did this, but not the base command).</span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`Table.vlen_list_of_str_formatter`</span> was considering a <span class="sb" style="color: #d14;">`str`</span> to be valid for</span>

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<td class="diff-line-num new_line old" data-linenumber="123" 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="LC99" class="line" lang="markdown">  formatting resulting in an obscure error when a <span class="sb" style="color: #d14;">`str`</span>, as opposed to a<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown">  <span class="sb" style="color: #d14;">`list`</span> of <span class="sb" style="color: #d14;">`str`</span>, was used for taxonomy. See<span class="idiff left right"> </span></span>

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<td class="diff-line-num new old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC123" class="line" lang="markdown">  formatting resulting in an obscure error when a <span class="sb" style="color: #d14;">`str`</span>, as opposed to a</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="124" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC124" class="line" lang="markdown">  <span class="sb" style="color: #d14;">`list`</span> of <span class="sb" style="color: #d14;">`str`</span>, was used for taxonomy. See</span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown">  <span class="p">[</span><span class="nv" style="color: #008080;">issue #709</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/biocore/biom-format/issues/709</span><span class="p">)</span>.</span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="gh" style="color: #999;">biom 2.1.4</span></span>

</pre>

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<br>

</li>

<li id="28e29f054410016d7f5a9b27dfc18d64f346fe67">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#28e29f054410016d7f5a9b27dfc18d64f346fe67"><strong>biom/cli/__init__.py</strong></a>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +30,7 @@ def cli(ctx):</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.table_summarizer'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.metadata_adder'</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC33" class="line" lang="python"><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.metadata_exporter'</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="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.table_converter'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.installation_informer'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'biom.cli.table_subsetter'</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="3b6a850229bcda1001a92fa24984fbc0677d4b9e">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#3b6a850229bcda1001a92fa24984fbc0677d4b9e"><strong>biom/cli/metadata_exporter.py</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -----------------------------------------------------------------------------</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2011-2017, The BIOM Format Development Team.</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Distributed under the terms of the Modified BSD License.</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="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file COPYING.txt, distributed with this software.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -----------------------------------------------------------------------------</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">click</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom</span> <span class="kn" style="font-weight: 600;">import</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.cli</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cli</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">command</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'export-metadata'</span><span class="p">)</span></span>

</pre>

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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="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--input-fp'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="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="python">              <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</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;">dir_okay</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 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="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The input BIOM table'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--sample-metadata-fp'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">              <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</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;">dir_okay</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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">              <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The sample metadata output file.'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--observation-metadata-fp'</span><span class="p">,</span> <span class="n" style="color: #333;">required</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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">              <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">exists</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;">dir_okay</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 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="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The observation metadata output file.'</span><span class="p">)</span></span>

</pre>

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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="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">export_metadata</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">sample_metadata_fp</span><span class="p">,</span> <span class="n" style="color: #333;">observation_metadata_fp</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC26" class="line" lang="python">    <span class="s" style="color: #d14;">"""Export metadata as TSV.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">    Example usage:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">    Export metadata as TSV:</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">    $ biom export-metadata -i otu_table.biom</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">      --sample-metadata-fp sample.tsv</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">      --observation-metadata-fp observation.tsv</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" 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="36" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC36" class="line" lang="python">    <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC37" class="line" lang="python"></span>

</pre>

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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;">sample_metadata_fp</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">        <span class="n" style="color: #333;">_export_metadata</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample'</span><span class="p">,</span> <span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">sample_metadata_fp</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">observation_metadata_fp</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">        <span class="n" style="color: #333;">_export_metadata</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="s" style="color: #d14;">'observation'</span><span class="p">,</span> <span class="n" style="color: #333;">input_fp</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); 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="n" style="color: #333;">observation_metadata_fp</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_export_metadata</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="p">,</span> <span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">output_fp</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" 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="LC47" class="line" lang="python">        <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</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="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">        <span class="n" style="color: #333;">metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">output_fp</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</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>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</span><span class="s" style="color: #d14;">'File {} does not contain {} metadata'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">                                                                 <span class="n" style="color: #333;">axis</span><span class="p">))</span></span></pre>

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</table>

<br>

</li>

<li id="23e2cf97b549b81a7a2a070c9887e017308dd1ee">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#23e2cf97b549b81a7a2a070c9887e017308dd1ee"><strong>biom/cli/table_validator.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="29" style="width: 35px; color: rgba(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="29" style="width: 35px; color: rgba(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">@@ -29,9 +29,7 @@ from biom.util import HAVE_H5PY, biom_open, is_hdf5_file</td>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">                   <span class="s" style="color: #d14;">' specification'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--format-version'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="LC31" class="line" lang="python">              <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The specific format version to validate against'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="s" style="color: #d14;">'--detailed-report'</span><span class="p">,</span> <span class="n" style="color: #333;">is_flag</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;">default</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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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">              <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Include more details in the output report'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="p">,</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">):</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">    <span class="s" style="color: #d14;">"""Validate a BIOM-formatted file.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(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="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>

</pre>

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<td class="diff-line-num 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">

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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="s" style="color: #d14;">    Test a file for adherence to the Biological Observation Matrix (BIOM)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +44,7 @@ def validate_table(input_fp, format_version, detailed_report):</td>

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<td class="diff-line-num old_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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<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="python"><span class="s" style="color: #d14;">    $ biom validate-table -i table.biom</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(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="python"></span>

</pre>

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<td class="diff-line-num old_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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<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="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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="47" 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="LC49" class="line" lang="python">    <span class="n" style="color: #333;">valid</span><span class="p">,</span> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">detailed_report</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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 class="n" style="color: #333;">valid</span><span class="p">,</span> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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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<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;">click</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">echo</span><span class="p">(</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">report</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">valid</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(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="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="c1" style="color: #998; font-style: italic;"># apparently silence is too quiet to be golden.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(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">@@ -57,9 +55,8 @@ def validate_table(input_fp, format_version, detailed_report):</td>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" 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="58" 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="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</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;">detailed_report</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_line old" data-linenumber="58" 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="LC61" class="line" lang="python">    <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TableValidator</span><span class="p">()(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">format_version</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" 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="58" 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="LC62" class="line" lang="python">                              <span class="n" style="color: #333;">detailed_report</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">detailed_report</span><span class="p">)</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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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_table</span><span class="p">(</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="o" style="font-weight: 600;">=</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="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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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">    <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TableValidator</span><span class="p">()(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_fp</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">format_version</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'valid_table'</span><span class="p">],</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'report_lines'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(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="105" style="width: 35px; color: rgba(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">@@ -108,23 +105,15 @@ class TableValidator(object):</td>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"h5py is not installed, can only validate JSON "</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">                              <span class="s" style="color: #d14;">"tables"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(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="107" style="width: 35px; color: rgba(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="LC107" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="108" 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="LC111" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</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;">detailed_report</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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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">table</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;">format_version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">format_version</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" 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="108" 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="LC113" class="line" lang="python">                        <span class="n" style="color: #333;">detailed_report</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">detailed_report</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); 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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">format_version</span><span class="o" style="font-weight: 600;">=</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="114" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC109" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">table</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;">format_version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">format_version</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(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="LC111" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_validate_hdf5</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;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">        <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'table'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="114" 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="LC118" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Need to make this an attribute so that we have this info during</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># validation.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" 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="LC120" class="line" lang="python">        <span class="n" style="color: #333;">detailed_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'detailed_report'</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(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="LC114" class="line" lang="python">        <span class="n" style="color: #333;">report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">        <span class="n" style="color: #333;">valid_table</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="LC116" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" 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="LC125" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" 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="LC126" class="line" lang="python">            <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating BIOM table..."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" 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="LC127" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(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="LC117" class="line" lang="python">        <span class="n" style="color: #333;">required_attrs</span> <span class="o" style="font-weight: 600;">=</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">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">'format-url'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_valid_format_url</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_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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<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">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">'format-version'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_valid_hdf5_format_version</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,9 +143,6 @@ class TableValidator(object):</td>

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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="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing attribute: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">required_attr</span><span class="p">)</span></span>

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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">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'..."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">required_attr</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">            <span class="n" style="color: #333;">status_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attr_validator</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC148" 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;">status_msg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(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">@@ -166,20 +152,12 @@ class TableValidator(object):</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">required_groups</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">                <span class="n" style="color: #333;">valid_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python">                    <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing group: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">group</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dataset</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">required_datasets</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dataset</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">                <span class="n" style="color: #333;">valid_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python">                    <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing dataset: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">dataset</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'shape'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating 'shape' versus number of "</span></span>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python">                                    <span class="s" style="color: #d14;">"samples and observations..."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">            <span class="n" style="color: #333;">n_obs</span><span class="p">,</span> <span class="n" style="color: #333;">n_samp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'shape'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">            <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'observation/ids'</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="LC163" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'sample/ids'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</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">@@ -270,14 +248,10 @@ class TableValidator(object):</td>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Need to make this an attribute so that we have this info during</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># validation.</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_format_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'format_version'</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python">        <span class="n" style="color: #333;">detailed_report</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'detailed_report'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">        <span class="n" style="color: #333;">report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python">        <span class="n" style="color: #333;">valid_table</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="LC254" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python">            <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating BIOM table..."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python">        <span class="n" style="color: #333;">required_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">'format'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_valid_format</span><span class="p">),</span></span>

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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;">'format_url'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_valid_format_url</span><span class="p">),</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="299" style="width: 35px; color: rgba(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="273" style="width: 35px; color: rgba(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">@@ -299,9 +273,6 @@ class TableValidator(object):</td>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Missing field: '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">key</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'..."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">key</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python">            <span class="n" style="color: #333;">status_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">method</span><span class="p">(</span><span class="n" style="color: #333;">table_json</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC278" 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;">status_msg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(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="280" style="width: 35px; color: rgba(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">@@ -309,10 +280,6 @@ class TableValidator(object):</td>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">status_msg</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'shape'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table_json</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detailed_report</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python">                <span class="n" style="color: #333;">report_lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating 'shape' versus number of rows "</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python">                                    <span class="s" style="color: #d14;">"and columns..."</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="s" style="color: #d14;">'rows'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table_json</span> <span class="ow" style="font-weight: 600;">and</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">table_json</span><span class="p">[</span><span class="s" style="color: #d14;">'rows'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">table_json</span><span class="p">[</span><span class="s" style="color: #d14;">'shape'</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="LC285" class="line" lang="python">                <span class="n" style="color: #333;">valid_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<br>

</li>

<li id="7805345b6c8be3df5725771c493ce326d41d0f51">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#7805345b6c8be3df5725771c493ce326d41d0f51"><strong>biom/err.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,8 @@ OBSMDSIZE = "Size of observation metadata differs from matrix size!"</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="n" style="color: #333;">SAMPMDSIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Size of sample metadata differs from matrix size!"</span></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_test_empty</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># _zz_ so the sort order places this test last</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_zz_test_empty</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    <span class="s" style="color: #d14;">"""Check if t is empty"""</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="250" style="width: 35px; color: rgba(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="251" style="width: 35px; color: rgba(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">@@ -250,8 +251,9 @@ class ErrorProfile(object):</td>

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<pre style="margin: 0;"> <span id="LC251" 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;">args</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">            <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">errtype</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">args</span></span><span class="p">:</span></span>

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<td class="diff-line-num new old_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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">errtype</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python">            <span class="n" style="color: #333;">test</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_test</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">errtype</span><span class="p">,</span> <span class="k" style="font-weight: 600;">lambda</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="LC256" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_handle_error</span><span class="p">(</span><span class="n" style="color: #333;">errtype</span><span class="p">,</span> <span class="n" style="color: #333;">item</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(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">@@ -318,7 +320,7 @@ class ErrorProfile(object):</td>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"><span class="n" style="color: #333;">__errprof</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ErrorProfile</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"><span class="n" style="color: #333;">__errprof</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="n" style="color: #333;">EMPTY</span><span class="p">,</span> <span class="s" style="color: #d14;">'ignore'</span><span class="p">,</span> <span class="n" style="color: #333;">_test_empty</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"><span class="n" style="color: #333;">__errprof</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="s" style="color: #d14;">'empty'</span><span class="p">,</span> <span class="n" style="color: #333;">EMPTY</span><span class="p">,</span> <span class="s" style="color: #d14;">'ignore'</span><span class="p">,</span> <span class="n" style="color: #333;">_<span class="idiff left right">zz_</span>test_empty</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">                   <span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">TableException</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"><span class="n" style="color: #333;">__errprof</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="s" style="color: #d14;">'obssize'</span><span class="p">,</span> <span class="n" style="color: #333;">OBSSIZE</span><span class="p">,</span> <span class="s" style="color: #d14;">'raise'</span><span class="p">,</span> <span class="n" style="color: #333;">_test_obssize</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python">                   <span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">TableException</span><span class="p">)</span></span>

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<li id="08a4e10076dcc2c977e4d3e580c33acd5b6eaaca">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#08a4e10076dcc2c977e4d3e580c33acd5b6eaaca"><strong>biom/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">@@ -12,6 +12,8 @@ from __future__ import division</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">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="LC14" 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>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">h5py</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>

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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;">biom.exception</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BiomParseException</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownAxisError</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.table</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Table</span></span>

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<pre style="margin: 0;"> <span id="LC343" 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;">data</span><span class="p">,</span> <span class="n" style="color: #333;">observation_ids</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">observation_ids</span><span class="p">,</span> <span class="n" style="color: #333;">sample_ids</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sample_ids</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_biom_table</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="n" style="color: #333;">ids</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;">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;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python">    <span class="s" style="color: #d14;">r"""Parses the biom table stored in <span class="idiff left right">the filepath `fp</span>`</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_biom_table</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="n" style="color: #333;">ids</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;">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;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python">    <span class="s" style="color: #d14;">r"""Parses the biom table stored in <span class="idiff left right">`file_obj</span>`</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"><span class="s" style="color: #d14;">    fp : file like</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;">        File alike object storing the BIOM table</span></span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"><span class="s" style="color: #d14;">    file_obj : file-like object, or list</span></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;">        file-like object storing the BIOM table (tab-delimited or JSON), or</span></span>

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<td class="diff-line-num new old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); 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="353" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC353" class="line" lang="python"><span class="s" style="color: #d14;">        a list of lines of the BIOM table in tab-delimited or JSON format</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"><span class="s" style="color: #d14;">    ids : iterable</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"><span class="s" style="color: #d14;">        The sample/observation ids of the samples/observations that we need</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"><span class="s" style="color: #d14;">        to retrieve from the biom table</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="360" style="width: 35px; color: rgba(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="363" style="width: 35px; color: rgba(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">@@ -360,7 +363,7 @@ def parse_biom_table(fp, ids=None, axis='sample', input_is_dense=False):</td>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;">    Table</span></span>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"><span class="s" style="color: #d14;">        The BIOM table stored at f<span class="idiff left right">p</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;">        The BIOM table stored at f<span class="idiff left right">ile_obj</span></span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"><span class="s" style="color: #d14;">    Raises</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" 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="391" style="width: 35px; color: rgba(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="394" style="width: 35px; color: rgba(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">@@ -391,34 +394,36 @@ def parse_biom_table(fp, ids=None, axis='sample', input_is_dense=False):</td>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">        <span class="n" style="color: #333;">UnknownAxisError</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="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

395

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(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="396" style="width: 35px; color: rgba(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="LC396" 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 old old_line" data-linenumber="394" 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">

394

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<td class="diff-line-num new_line old" data-linenumber="397" 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="LC394" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_hdf5</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">axis</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); 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="397" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC397" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_hdf5</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">axis</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

395

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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(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="399" style="width: 35px; color: rgba(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="LC399" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="400" style="width: 35px; color: rgba(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="LC400" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

401

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="399" 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="402" 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="LC399" 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;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'read'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="400" 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="402" 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="LC400" class="line" lang="python">        <span class="n" style="color: #333;">old_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tell</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); 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="402" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC402" 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;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'read'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" style="width: 35px; color: rgba(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="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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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="LC403" class="line" lang="python">        <span class="n" style="color: #333;">old_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tell</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="401" style="width: 35px; color: rgba(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="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

404

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Read in characters until first non-whitespace</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="405" style="width: 35px; color: rgba(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="LC405" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If it is a {, then this is (most likely) JSON</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="406" 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="LC403" class="line" lang="python">        <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); 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="406" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC406" class="line" lang="python">        <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

404

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<td class="diff-line-num new_line" data-linenumber="407" style="width: 35px; color: rgba(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="LC407" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isspace</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="408" 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="LC405" class="line" lang="python">            <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC408" class="line" lang="python">            <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'{'</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python">            <span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">old_pos</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">object_pairs_hook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC410" class="line" lang="python">            <span class="n" style="color: #333;">file_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">old_pos</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC411" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">file_obj</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC412" class="line" lang="python">                                          <span class="n" style="color: #333;">object_pairs_hook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="413" style="width: 35px; color: rgba(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="LC413" class="line" lang="python">                                <span class="n" style="color: #333;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_is_dense</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="414" style="width: 35px; color: rgba(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="LC414" 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_line old" data-linenumber="415" 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="LC411" class="line" lang="python">            <span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">old_pos</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="415" 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="LC412" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</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>

</pre>

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); 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="415" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC415" class="line" lang="python">            <span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">old_pos</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC416" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC417" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python">                                           <span class="n" style="color: #333;">object_pairs_hook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">                                <span class="n" style="color: #333;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_is_dense</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</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>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python">            <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_tsv</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ile_obj</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</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>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python">        <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">object_pairs_hook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python">        <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_json</span><span class="p">(</span><span class="n" style="color: #333;">json</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">file_obj</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python">                                       <span class="n" style="color: #333;">object_pairs_hook</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">OrderedDict</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">                            <span class="n" style="color: #333;">input_is_dense</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_is_dense</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">subset_ids</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">md</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">@@ -632,7 +637,8 @@ def load_table(f):</td>

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"><span class="s" style="color: #d14;">    Parameters</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python"><span class="s" style="color: #d14;">    ----------</span></span>

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<td class="diff-line-num new_line old" data-linenumber="640" 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="LC635" class="line" lang="python"><span class="s" style="color: #d14;">    f : str</span></span>

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<td class="diff-line-num new old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC640" class="line" lang="python"><span class="s" style="color: #d14;">    f : str or file-like object</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python"><span class="s" style="color: #d14;">        The entity to parse</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"><span class="s" style="color: #d14;">    Returns</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"><span class="s" style="color: #d14;">    -------</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="655" style="width: 35px; color: rgba(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">@@ -655,9 +661,15 @@ def load_table(f):</td>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"><span class="s" style="color: #d14;">    >>> table = load_table('path/to/table.biom') # doctest: +SKIP</span></span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python">    <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">biom_open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC664" class="line" lang="python">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</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">io</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">IOBase</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">h5py</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">File</span></span><span class="p"><span class="idiff right">))</span>:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC665" 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="LC660" class="line" lang="python">            <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_biom_table</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">p</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python">            <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_biom_table</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="667" style="width: 35px; color: rgba(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="LC667" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="662" style="width: 35px; color: rgba(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="668" style="width: 35px; color: rgba(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="LC668" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not appear to be a BIOM file!"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC669" 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="663" style="width: 35px; color: rgba(0,0,0,0.3); 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="670" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC670" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">biom_open</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC671" 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 new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC672" class="line" lang="python">                <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_biom_table</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC673" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC674" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not appear to be a BIOM file!"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span></pre>

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<br>

</li>

<li id="9dd8fda12fdb52648464f77a09f12e329a75158d">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#9dd8fda12fdb52648464f77a09f12e329a75158d"><strong>biom/table.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(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="178" style="width: 35px; color: rgba(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">@@ -178,7 +178,7 @@ import scipy.stats</td>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>

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<pre style="margin: 0;"> <span id="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>

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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="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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">partial</span></span></span>

</pre>

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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="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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2822" style="width: 35px; color: rgba(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="2822" style="width: 35px; color: rgba(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">@@ -2822,7 +2822,7 @@ class Table(object):</td>

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<pre style="margin: 0;"> <span id="LC2822" 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="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2823

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<pre style="margin: 0;"> <span id="LC2823" 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="2824" style="width: 35px; color: rgba(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="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2824

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<pre style="margin: 0;"> <span id="LC2824" class="line" lang="python"><span class="s" style="color: #d14;">        inplace : bool, optional</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2825" 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">

2825

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<td class="diff-line-num new_line old" data-linenumber="2825" 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="LC2825" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to ``<span class="idiff left right">Fals</span>e``</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2826" style="width: 35px; color: rgba(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="2825" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2825" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to ``<span class="idiff left right">Tru</span>e``</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2826

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<td class="diff-line-num new_line" data-linenumber="2826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2826

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<pre style="margin: 0;"> <span id="LC2826" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2827" style="width: 35px; color: rgba(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="2827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2827

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<pre style="margin: 0;"> <span id="LC2827" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2828" style="width: 35px; color: rgba(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="2828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2828

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<pre style="margin: 0;"> <span id="LC2828" class="line" lang="python"><span class="s" style="color: #d14;">        -------</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3103" style="width: 35px; color: rgba(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="3103" style="width: 35px; color: rgba(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 old_line" data-linenumber="3103" style="width: 35px; color: rgba(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="3103" style="width: 35px; color: rgba(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="LC3103" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indices</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">end</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3104

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<td class="diff-line-num new_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3104

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<pre style="margin: 0;"> <span id="LC3104" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">obs_id</span><span class="p">,</span> <span class="n" style="color: #333;">samp_ids</span><span class="p">[</span><span class="n" style="color: #333;">col_idx</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3105

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<td class="diff-line-num new_line" data-linenumber="3105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3105

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

<pre style="margin: 0;"> <span id="LC3105" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3106" 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">

3106

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<td class="diff-line-num new_line old" data-linenumber="3106" 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="LC3106" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nonzero_counts</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 class="n" style="color: #333;">binary</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">Fals</span>e</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); 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="3106" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3106" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nonzero_counts</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 class="n" style="color: #333;">binary</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;"><span class="idiff left right">Tru</span>e</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3107

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<td class="diff-line-num new_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3107

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<pre style="margin: 0;"> <span id="LC3107" class="line" lang="python">        <span class="s" style="color: #d14;">"""Get nonzero summaries about an axis</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3108" style="width: 35px; color: rgba(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="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3108

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

<pre style="margin: 0;"> <span id="LC3108" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3109

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<td class="diff-line-num new_line" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3109

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<pre style="margin: 0;"> <span id="LC3109" class="line" lang="python"><span class="s" style="color: #d14;">        Parameters</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3111" style="width: 35px; color: rgba(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="3111" style="width: 35px; color: rgba(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">@@ -3111,7 +3111,7 @@ class Table(object):</td>

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<td class="diff-line-num old_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3111

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<td class="diff-line-num new_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3111

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<pre style="margin: 0;"> <span id="LC3111" class="line" lang="python"><span class="s" style="color: #d14;">        axis : {'sample', 'observation', 'whole'}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3112

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<td class="diff-line-num new_line" data-linenumber="3112" style="width: 35px; color: rgba(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="LC3112" class="line" lang="python"><span class="s" style="color: #d14;">            The axis on which to count nonzero entries</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3113

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<td class="diff-line-num new_line" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3113

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<pre style="margin: 0;"> <span id="LC3113" class="line" lang="python"><span class="s" style="color: #d14;">        binary : bool, optional</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3114" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to ``<span class="idiff left right">Fals</span>e``. If ``True``, return number of nonzero</span></span>

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<pre style="margin: 0;">+<span id="LC3114" class="line" lang="python"><span class="s" style="color: #d14;">            Defaults to ``<span class="idiff left right">Tru</span>e``. If ``True``, return number of nonzero</span></span>

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<pre style="margin: 0;"> <span id="LC3115" class="line" lang="python"><span class="s" style="color: #d14;">            entries. If ``False``, sum the values of the entries.</span></span>

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<pre style="margin: 0;"> <span id="LC3116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3117" class="line" lang="python"><span class="s" style="color: #d14;">        Returns</span></span>

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<pre style="margin: 0;"> <span id="LC3252" class="line" lang="python">        <span class="n" style="color: #333;">alignable_o</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self_o</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other_o</span></span>

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<pre style="margin: 0;"> <span id="LC3253" class="line" lang="python">        <span class="n" style="color: #333;">alignable_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self_s</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other_s</span></span>

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<pre style="margin: 0;"> <span id="LC3254" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC3255" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'both'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">alignable_o</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC3255" 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 class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'both'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">alignable_o</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC3256" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">DisjointIDError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot align both axes"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC3257" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'sample'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC3257" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'sample'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3258" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">DisjointIDError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot align samples"</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="3259" 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="LC3259" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'observation'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignable_o</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC3259" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'observation'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">alignable_o</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3260" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">DisjointIDError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot align observations"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3261" 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">

3261

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<td class="diff-line-num new_line old" data-linenumber="3261" 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>

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<pre style="margin: 0;">-<span id="LC3261" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'detect'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">alignable_o</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3262" style="width: 35px; color: rgba(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="3261" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3261" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'detect'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">alignable_o</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3262

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<td class="diff-line-num new_line" data-linenumber="3262" style="width: 35px; color: rgba(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="LC3262" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">DisjointIDError</span><span class="p">(</span><span class="s" style="color: #d14;">"Neither axis appears alignable"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3263

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<td class="diff-line-num new_line" data-linenumber="3263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3263

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<pre style="margin: 0;"> <span id="LC3263" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3264" 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="3264" 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="LC3264" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'both'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3265" style="width: 35px; color: rgba(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="3264" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3264" 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 class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'both'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3265

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<td class="diff-line-num new_line" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3265

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<pre style="margin: 0;"> <span id="LC3265" class="line" lang="python">            <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'observation'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3266" 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">

3266

</td>

<td class="diff-line-num new_line old" data-linenumber="3266" 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="LC3266" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'detect'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3267" style="width: 35px; color: rgba(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="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3266

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<pre style="margin: 0;">+<span id="LC3266" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'detect'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3267

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<td class="diff-line-num new_line" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3267

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<pre style="margin: 0;"> <span id="LC3267" class="line" lang="python">            <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3268

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<td class="diff-line-num new_line" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3268

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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alignable_s</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3269

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<td class="diff-line-num new_line" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3269

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<pre style="margin: 0;"> <span id="LC3269" class="line" lang="python">                <span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3270" style="width: 35px; color: rgba(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="3270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3270

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<pre style="margin: 0;"> <span id="LC3270" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">alignable_o</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3271

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<td class="diff-line-num new_line" data-linenumber="3271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3271

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<pre style="margin: 0;"> <span id="LC3271" class="line" lang="python">                <span class="n" style="color: #333;">order</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'observation'</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="3272" 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">

3272

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<td class="diff-line-num new_line old" data-linenumber="3272" 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="LC3272" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></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="3273" style="width: 35px; color: rgba(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="3272" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3272" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'sample'</span><span class="p">:</span></span>

</pre>

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3273

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<td class="diff-line-num new_line" data-linenumber="3273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3273

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<pre style="margin: 0;"> <span id="LC3273" class="line" lang="python">            <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'sample'</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC3274" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'observation'</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC3274" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'observation'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3275" class="line" lang="python">            <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'observation'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC3276" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3277" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownAxisError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized axis: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">axis</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC3506" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3507" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC3508" 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="LC3509" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'union'</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC3509" 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 class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'union'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3510" 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="o" style="font-weight: 600;">.</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</span><span class="p">(),</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</span><span class="p">())</span></span>

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<td class="diff-line-num new_line old" data-linenumber="3511" 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="LC3511" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'intersection'</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC3511" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'intersection'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3512" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_intersect_id_order</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</span><span class="p">(),</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC3513" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC3514" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">TableException</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown sample merge type: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">sample</span><span class="p">)</span></span>

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3515

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<pre style="margin: 0;"> <span id="LC3515" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3516

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<td class="diff-line-num new_line" data-linenumber="3516" style="width: 35px; color: rgba(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="LC3516" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># determine the observation order in the resulting table</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3517" 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="3517" 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="LC3517" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">observation</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></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 old_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">

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<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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">observation</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></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="3518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3518

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<td class="diff-line-num new_line" data-linenumber="3518" style="width: 35px; color: rgba(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="LC3518" class="line" lang="python">            <span class="n" style="color: #333;">new_obs_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_union_id_order</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3519

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<td class="diff-line-num new_line" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3519

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<pre style="margin: 0;"> <span id="LC3519" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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 class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</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>

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<td class="diff-line-num old old_line" data-linenumber="3520" 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">

3520

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<td class="diff-line-num new_line old" data-linenumber="3520" 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="LC3520" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">observation</span> <span class="ow" style="font-weight: 600;"><span class="idiff left right">is</span></span> <span class="s" style="color: #d14;">'intersection'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">observation</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span> <span class="s" style="color: #d14;">'intersection'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3521

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<td class="diff-line-num new_line" data-linenumber="3521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3521

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<pre style="margin: 0;"> <span id="LC3521" class="line" lang="python">            <span class="n" style="color: #333;">new_obs_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_intersect_id_order</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3522

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<td class="diff-line-num new_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3522

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<pre style="margin: 0;"> <span id="LC3522" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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 class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</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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3523

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<td class="diff-line-num new_line" data-linenumber="3523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3523

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<pre style="margin: 0;"> <span id="LC3523" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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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="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>

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<pre style="margin: 0;"> <span id="LC4045" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matrix_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toarray</span><span class="p">()</span></span>

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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="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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<pre style="margin: 0;"> <span id="LC4046" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span></span>

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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="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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<pre style="margin: 0;"> <span id="LC4047" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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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">

4048

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<td class="diff-line-num new_line old" 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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<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="p">[</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SparseSeries</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toarray</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">squeeze</span><span class="p">())</span></span>

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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="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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<pre style="margin: 0;">-<span id="LC4049" class="line" lang="python">                   <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matrix_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tocsr</span><span class="p">()]</span></span>

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<td class="diff-line-num old old_line" data-linenumber="4050" 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="LC4050" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SparseDataFrame</span></span>

</pre>

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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matrix_data</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SparseDataFrame</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4051" style="width: 35px; color: rgba(0,0,0,0.3); 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="4050" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="diff-line-num new new_line" data-linenumber="4051" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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4052

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<pre style="margin: 0;"> <span id="LC4052" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4053" style="width: 35px; color: rgba(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="LC4053" 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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<td class="diff-line-num new_line" data-linenumber="4054" style="width: 35px; color: rgba(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="LC4054" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4689" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4690" style="width: 35px; color: rgba(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="LC4690" class="line" lang="python"><span class="s" style="color: #d14;">        .. shownumpydoc</span></span>

</pre>

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4691

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<pre style="margin: 0;"> <span id="LC4691" 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="4692" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4692" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isfloat</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4693" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4693" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># see https://stackoverflow.com/a/20929881</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4694" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4694" 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 new_line" data-linenumber="4695" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4695" class="line" lang="python">                <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4696" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4696" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="4697" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC4697" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4698" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4699" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4691

</td>

<td class="diff-line-num new_line" data-linenumber="4700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4700

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

<pre style="margin: 0;"> <span id="LC4700" 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="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4692

</td>

<td class="diff-line-num new_line" data-linenumber="4701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4701

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

<pre style="margin: 0;"> <span id="LC4701" 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 old_line" data-linenumber="4693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4693

</td>

<td class="diff-line-num new_line" data-linenumber="4702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4702

</td>

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

<pre style="margin: 0;"> <span id="LC4702" class="line" lang="python">                <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;">'seek'</span><span class="p">)</span></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="4706" style="width: 35px; color: rgba(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="4715" style="width: 35px; color: rgba(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">@@ -4706,37 +4715,28 @@ html</td>

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<td class="diff-line-num old_line" data-linenumber="4706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4706

</td>

<td class="diff-line-num new_line" data-linenumber="4715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4715

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

<pre style="margin: 0;"> <span id="LC4715" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># Covers the case where the first line is the header</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4707

</td>

<td class="diff-line-num new_line" data-linenumber="4716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4716

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

<pre style="margin: 0;"> <span id="LC4716" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># and there is no indication of it (no comment character)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4708

</td>

<td class="diff-line-num new_line" data-linenumber="4717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4717

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

<pre style="margin: 0;"> <span id="LC4717" 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;">header</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="4709" 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">

4709

</td>

<td class="diff-line-num new_line old" data-linenumber="4718" 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="LC4709" class="line" lang="python">                    <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</span><span class="p">)[</span><span class="mi" style="color: #099;">1</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="4710" style="width: 35px; color: rgba(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="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4718

</td>

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

<pre style="margin: 0;">+<span id="LC4718" class="line" lang="python">                    <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">r</span>strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</span><span class="p">)[</span><span class="mi" style="color: #099;">1</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="4710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4710

</td>

<td class="diff-line-num new_line" data-linenumber="4719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4719

</td>

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

<pre style="margin: 0;"> <span id="LC4719" class="line" lang="python">                    <span class="n" style="color: #333;">data_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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="4711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4711

</td>

<td class="diff-line-num new_line" data-linenumber="4720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4720

</td>

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

<pre style="margin: 0;"> <span id="LC4720" 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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4712

</td>

<td class="diff-line-num new_line" data-linenumber="4721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4721

</td>

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

<pre style="margin: 0;"> <span id="LC4721" class="line" lang="python">                    <span class="n" style="color: #333;">data_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_index</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4713

</td>

<td class="diff-line-num new_line" data-linenumber="4722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4722

</td>

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

<pre style="margin: 0;"> <span id="LC4722" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</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="4714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4714

</td>

<td class="diff-line-num new_line" data-linenumber="4723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4723

</td>

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

<pre style="margin: 0;"> <span id="LC4723" class="line" lang="python">            <span class="n" style="color: #333;">list_index</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</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="4715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4715

</td>

<td class="diff-line-num new_line" data-linenumber="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4724

</td>

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

<pre style="margin: 0;"> <span id="LC4724" class="line" lang="python">            <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</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 old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4716" 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">

4716

</td>

<td class="diff-line-num new_line old" data-linenumber="4725" 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="LC4716" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If the first line is the header, then we need to get the next</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="4717" style="width: 35px; color: rgba(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="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4725

</td>

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

<pre style="margin: 0;">+<span id="LC4725" 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="4717" style="width: 35px; color: rgba(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="4726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4726

</td>

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

<pre style="margin: 0;">+<span id="LC4726" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If the first line is the header, then we need to get the data lines</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4717

</td>

<td class="diff-line-num new_line" data-linenumber="4727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4727

</td>

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

<pre style="margin: 0;"> <span id="LC4727" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># line for the "last column" check</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4718

</td>

<td class="diff-line-num new_line" data-linenumber="4728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4728

</td>

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

<pre style="margin: 0;"> <span id="LC4728" 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;">lines</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</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="4719" 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">

4719

</td>

<td class="diff-line-num new_line old" data-linenumber="4729" 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="LC4719" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">data_start</span></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="4720" style="width: 35px; color: rgba(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="4729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4729

</td>

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

<pre style="margin: 0;">+<span id="LC4729" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">value_checks</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">data_start</span></span><span class="p"><span class="idiff right">:</span>]</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="4720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4720

</td>

<td class="diff-line-num new_line" data-linenumber="4730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4730

</td>

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

<pre style="margin: 0;"> <span id="LC4730" 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" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="4721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4721

</td>

<td class="diff-line-num new_line" data-linenumber="4731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4731

</td>

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

<pre style="margin: 0;"> <span id="LC4731" 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;">seek</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 old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4722" 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">

4722

</td>

<td class="diff-line-num new_line old" data-linenumber="4732" 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="LC4722" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">data_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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="4723" 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">

4723

</td>

<td class="diff-line-num new_line old" data-linenumber="4732" 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="LC4723" class="line" lang="python">                <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readline</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="4724" style="width: 35px; color: rgba(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="4732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4732

</td>

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

<pre style="margin: 0;">+<span id="LC4732" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">data_start</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="4724" style="width: 35px; color: rgba(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="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4733

</td>

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

<pre style="margin: 0;">+<span id="LC4733" 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;">readline</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="4724" style="width: 35px; color: rgba(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="4734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4734

</td>

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

<pre style="margin: 0;">+<span id="LC4734" class="line" lang="python">            <span class="n" style="color: #333;">value_checks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</span> <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>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4724

</td>

<td class="diff-line-num new_line" data-linenumber="4735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4735

</td>

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

<pre style="margin: 0;"> <span id="LC4735" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4725

</td>

<td class="diff-line-num new_line" data-linenumber="4736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4736

</td>

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

<pre style="margin: 0;"> <span id="LC4736" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># attempt to determine if the last column is non-numeric, ie, metadata</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="4726" 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">

4726

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4726" class="line" lang="python">        <span class="n" style="color: #333;">first_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</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="4727" 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">

4727

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4727" class="line" lang="python">        <span class="n" style="color: #333;">last_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_values</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>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="4728" 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">

4728

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4728" class="line" lang="python">        <span class="n" style="color: #333;">last_column_is_numeric</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 old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4729" 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">

4729

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4729" class="line" lang="python"></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="4730" 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">

4730

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4730" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'.'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">last_value</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="4731" 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">

4731

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4731" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</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="4732" 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">

4732

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4732" class="line" lang="python">                <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">last_value</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="4733" 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">

4733

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4733" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</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="4734" 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">

4734

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4734" class="line" lang="python">                <span class="n" style="color: #333;">last_column_is_numeric</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4735" 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">

4735

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4735" 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 old old_line" data-linenumber="4736" 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">

4736

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4736" 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 old old_line" data-linenumber="4737" 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">

4737

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4737" class="line" lang="python">                <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">last_value</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4738" 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">

4738

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4738" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4739" 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">

4739

</td>

<td class="diff-line-num new_line old" data-linenumber="4737" 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="LC4739" class="line" lang="python">                <span class="n" style="color: #333;">last_column_is_numeric</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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="4740" style="width: 35px; color: rgba(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="4737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4737

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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="LC4737" class="line" lang="python">        <span class="n" style="color: #333;">last_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="n" style="color: #333;">delim</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="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4740" style="width: 35px; color: rgba(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="4738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4738

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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="LC4738" 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;">value_checks</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="4740" style="width: 35px; color: rgba(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="4739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4739

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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="LC4739" class="line" lang="python">        <span class="n" style="color: #333;">last_column_is_numeric</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">([</span><span class="n" style="color: #333;">isfloat</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</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;">last_values</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num old_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">

4740

</td>

<td class="diff-line-num 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">

4740

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

<pre style="margin: 0;"> <span id="LC4740" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_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">

4741

</td>

<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">

4741

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

<pre style="margin: 0;"> <span id="LC4741" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># determine sample ids</span></span>

</pre>

</td>

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<td class="diff-line-num old_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

</td>

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

<pre style="margin: 0;"> <span id="LC4742" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_column_is_numeric</span><span class="p">:</span></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="4761" style="width: 35px; color: rgba(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="4761" style="width: 35px; color: rgba(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">@@ -4761,13 +4761,13 @@ html</td>

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<td class="diff-line-num old_line" data-linenumber="4761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4761

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<td class="diff-line-num new_line" data-linenumber="4761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4761

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<pre style="margin: 0;"> <span id="LC4761" 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;">data_start</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4762

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<td class="diff-line-num new_line" data-linenumber="4762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4762

</td>

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

<pre style="margin: 0;"> <span id="LC4762" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4763" style="width: 35px; color: rgba(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="LC4763" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lineno</span><span class="p">,</span> <span class="n" style="color: #333;">line</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;">lines</span><span class="p">,</span> <span class="n" style="color: #333;">data_start</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4764" 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>

<td class="diff-line-num new_line old" data-linenumber="4764" 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="LC4764" class="line" lang="python">            <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</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="4765" 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">

4765

</td>

<td class="diff-line-num new_line old" data-linenumber="4764" 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>

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<pre style="margin: 0;">-<span id="LC4765" 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;">line</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_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">

</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">

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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="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">():</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4766

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<td class="diff-line-num new_line" data-linenumber="4765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC4765" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4767

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<td class="diff-line-num new_line" data-linenumber="4766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC4766" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'#'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4768

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<td class="diff-line-num new_line" data-linenumber="4767" style="width: 35px; color: rgba(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="LC4767" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4769" style="width: 35px; color: rgba(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="4768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4768

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

<pre style="margin: 0;"> <span id="LC4768" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4770" 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">

4770

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<td class="diff-line-num new_line old" data-linenumber="4769" 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="LC4770" class="line" lang="python">            <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC4769" class="line" lang="python">            <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">delim</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="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">

</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">

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<pre style="margin: 0;">+<span id="LC4770" class="line" lang="python">            <span class="n" style="color: #333;">fields</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4771

</td>

<td class="diff-line-num new_line" data-linenumber="4771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4771

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<pre style="margin: 0;"> <span id="LC4771" class="line" lang="python">            <span class="n" style="color: #333;">obs_ids</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fields</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_line" data-linenumber="4772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4772

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<pre style="margin: 0;"> <span id="LC4772" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4773" style="width: 35px; color: rgba(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="4773" style="width: 35px; color: rgba(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="LC4773" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_column_is_numeric</span><span class="p">:</span></span>

</pre>

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</table>

<br>

</li>

<li id="d5eff8e10cff8335bc068e36e27dbcfb6a245f3b">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#d5eff8e10cff8335bc068e36e27dbcfb6a245f3b"><strong>biom/tests/test_cli/test_validate_table.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="121" style="width: 35px; color: rgba(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="121" style="width: 35px; color: rgba(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">@@ -121,9 +121,8 @@ class TableValidatorTests(TestCase):</td>

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(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="LC121" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(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="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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

<pre style="margin: 0;"> <span id="LC122" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_remove</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'valid_test3'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC124" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'valid_test3'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">detailed_report</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC124" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmd</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'valid_test3'</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="s" style="color: #d14;">'valid_table'</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">[</span><span class="s" style="color: #d14;">'report_lines'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(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="LC127" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid</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="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">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">        <span class="s" style="color: #d14;">"""Correctly invalidates a table that is... invalid."""</span></span>

</pre>

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<br>

</li>

<li id="0b315fcfbcf8da695790146349c415c7693f4f1a">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#0b315fcfbcf8da695790146349c415c7693f4f1a"><strong>biom/tests/test_err.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -11,12 +11,14 @@</td>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">unittest</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestCase</span><span class="p">,</span> <span class="n" style="color: #333;">main</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="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="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="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="python"></span>

</pre>

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<td class="diff-line-num 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">

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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="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;">Table</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.exception</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TableException</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="18" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.err</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">_<span class="idiff left">test_empty</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_test_obssize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_test_sampsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_test_obsdup</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC17" class="line" lang="python">                      <span class="n" style="color: #333;">_test_<span class="idiff left">sampdup</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_test_obsmdsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_test_samp</span>mdsize</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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="18" 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="n" style="color: #333;"><span class="idiff left">errstate</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">geterr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seterr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">geterrcall</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span>eterrcall</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">                      <span class="n" style="color: #333;">errcheck</span><span class="p">,</span> <span class="n" style="color: #333;">__errprof</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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;">biom.err</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">_<span class="idiff left">zz_test_empty</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_test_obssize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_test_sampsize</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">                      <span class="n" style="color: #333;">_test_<span class="idiff left">obsdup</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_test_sampdup</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_test_obs</span>mdsize</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">                      <span class="n" style="color: #333;"><span class="idiff left">_test_sampmdsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">errstate</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">geterr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seterr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g</span>eterrcall</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">                      <span class="n" style="color: #333;"><span class="idiff left">seterrcall</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">errcheck</span><span class="p">,</span> <span class="n" style="color: #333;">__errprof</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

</pre>

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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="python"></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="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="python"><span class="n" style="color: #333;">runtime_ep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__errprof</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,8 +32,8 @@ class ErrModeTests(TestCase):</td>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ex_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example_table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_test_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 new_line old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">_test_empty</span><span class="p">(</span><span class="n" style="color: #333;">Table</span><span class="p">([],</span> <span class="p">[],</span> <span class="p">[])))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertFalse</span><span class="p">(</span><span class="n" style="color: #333;">_test_empty</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ex_table</span><span class="p">))</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">_<span class="idiff left right">zz_</span>test_empty</span><span class="p">(</span><span class="n" style="color: #333;">Table</span><span class="p">([],</span> <span class="p">[],</span> <span class="p">[])))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertFalse</span><span class="p">(</span><span class="n" style="color: #333;">_<span class="idiff left right">zz_</span>test_empty</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ex_table</span><span class="p">))</span></span>

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<td class="diff-line-num new_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">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_test_obssize</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_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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertFalse</span><span class="p">(</span><span class="n" style="color: #333;">_test_obssize</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ex_table</span><span class="p">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" style="width: 35px; color: rgba(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="89" style="width: 35px; color: rgba(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">@@ -87,6 +89,17 @@ class ErrorProfileTests(TestCase):</td>

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87

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ex_table</span><span class="p">,</span> <span class="s" style="color: #d14;">'obssize'</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">                                   <span class="n" style="color: #333;">TableException</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(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="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="92" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC92" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_test_evaluation_order</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="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="93" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC93" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># issue 813</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="94" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC94" class="line" lang="python">        <span class="n" style="color: #333;">tab</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</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="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="p">[</span><span class="s" style="color: #d14;">'C'</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="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="95" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC95" class="line" lang="python">        <span class="n" style="color: #333;">tab</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_observation_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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;">'object'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC96" class="line" lang="python">        <span class="n" style="color: #333;">tab</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_sample_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="s" style="color: #d14;">'B'</span><span class="p">,</span> <span class="s" style="color: #d14;">'B'</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;">'object'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="97" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC97" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="98" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC98" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="s" style="color: #d14;">'obsdup'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sampdup'</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="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="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="99" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC99" class="line" lang="python">                         <span class="s" style="color: #d14;">'Duplicate observation IDs'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">test</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="s" style="color: #d14;">'sampdup'</span><span class="p">,</span> <span class="s" style="color: #d14;">'obsdup'</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="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="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC101" class="line" lang="python">                         <span class="s" style="color: #d14;">'Duplicate observation IDs'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_state</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_line" data-linenumber="104" style="width: 35px; color: rgba(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="LC104" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'all'</span><span class="p">:</span> <span class="s" style="color: #d14;">'ignore'</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_state</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">'ignore'</span><span class="p">]))</span></span>

</pre>

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<br>

</li>

<li id="42b93e64b3f8c02a5184492da3b88a6643f2f148">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#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">@@ -16,7 +16,8 @@ from unittest import TestCase, main</td>

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<pre style="margin: 0;"> <span id="LC16" 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="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">npt</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.parse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">generatedby</span><span class="p">,</span> <span class="n" style="color: #333;">MetadataMap</span><span class="p">,</span> <span class="n" style="color: #333;">parse_biom_table</span><span class="p">,</span> <span class="n" style="color: #333;">parse_uc</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.parse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">generatedby</span><span class="p">,</span> <span class="n" style="color: #333;">MetadataMap</span><span class="p">,</span> <span class="n" style="color: #333;">parse_biom_table</span><span class="p">,</span> <span class="n" style="color: #333;">parse_uc</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">                        <span class="n" style="color: #333;">load_table</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">

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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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.table</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Table</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">

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HAVE_H5PY</span><span class="p">,</span> <span class="n" style="color: #333;">__version__</span></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="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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">biom.tests.long_lines</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">uc_empty</span><span class="p">,</span> <span class="n" style="color: #333;">uc_invalid_id</span><span class="p">,</span> <span class="n" style="color: #333;">uc_minimal</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">@@ -237,6 +238,32 @@ class ParseTests(TestCase):</td>

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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_hdf5</span><span class="p">(</span><span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="s" style="color: #d14;">'test_data/test.biom'</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">cwd</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dec</span><span class="o" style="font-weight: 600;">.</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="LC242" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_load_table_filepath</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="LC243" class="line" lang="python">        <span class="n" style="color: #333;">cwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'/'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">__file__</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="LC245" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</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="LC246" class="line" lang="python">        <span class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="s" style="color: #d14;">'test_data/test.biom'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">cwd</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dec</span><span class="o" style="font-weight: 600;">.</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="LC250" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_load_table_inmemory</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="LC251" class="line" lang="python">        <span class="n" style="color: #333;">cwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'/'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">__file__</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="LC253" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</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 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="n" style="color: #333;">load_table</span><span class="p">(</span><span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="s" style="color: #d14;">'test_data/test.biom'</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="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">cwd</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>

</pre>

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<td class="diff-line-num new old_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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<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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_load_table_inmemory_json</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="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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<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="n" style="color: #333;">cwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'/'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">__file__</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</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 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 class="n" style="color: #333;">load_table</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'test_data/test.json'</span><span class="p">))</span></span>

</pre>

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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="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">cwd</span><span class="p">)</span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num new old_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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<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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_load_table_inmemory_stringio</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 new old_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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<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="n" style="color: #333;">load_table</span><span class="p">(</span><span class="n" style="color: #333;">StringIO</span><span class="p">(</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">classic_otu_table1_no_tax</span><span class="p">)))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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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<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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(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="LC267" 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</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_line" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="python">        <span class="s" style="color: #d14;">"""tests for parse_biom_table when we do not have h5py"""</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(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="LC269" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># This is a TSV as a list of lines</span></span>

</pre>

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<br>

</li>

<li id="d7e3debefc34597187c86af589a0c55f4a8ff7e2">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#d7e3debefc34597187c86af589a0c55f4a8ff7e2"><strong>biom/tests/test_table.py</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC1475" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SparseDataFrame</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</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>

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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>

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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>

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<pre style="margin: 0;"> <span id="LC1480" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="python">        <span class="n" style="color: #333;">pdt</span><span class="o" style="font-weight: 600;">.</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>

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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC1483" 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>

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<pre style="margin: 0;">+<span id="LC1484" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_dataframe</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC1485" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matrix_data</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getnnz</span><span class="p">())</span> <span class="o" style="font-weight: 600;">/</span></span>

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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="python">                   <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prod</span><span class="p">(</span><span class="n" style="color: #333;">example_table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">shape</span><span class="p">))</span></span>

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<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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">.</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>

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<pre style="margin: 0;">+<span id="LC1488" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC1489" 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 new_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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<pre style="margin: 0;"> <span id="LC1490" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</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 new_line" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1491

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<pre style="margin: 0;"> <span id="LC1491" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2228" style="width: 35px; color: rgba(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="2235" style="width: 35px; color: rgba(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">@@ -2228,9 +2235,9 @@ class SparseTableTests(TestCase):</td>

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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="python">        <span class="n" style="color: #333;">exp_obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">15</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_line" data-linenumber="2236" style="width: 35px; color: rgba(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="LC2236" class="line" lang="python">        <span class="n" style="color: #333;">exp_whole</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">29</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2237" style="width: 35px; color: rgba(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="LC2237" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2231" 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="2238" 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="LC2231" 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;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</span><span class="s" style="color: #d14;">'sample'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2232" 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="2238" 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="LC2232" 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;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</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="2233" 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="2238" 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="LC2233" class="line" lang="python">        <span class="n" style="color: #333;">obs_whole</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</span><span class="s" style="color: #d14;">'whole'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); 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="2238" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2238" 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;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</span><span class="s" style="color: #d14;">'sample'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">binary</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2234" style="width: 35px; color: rgba(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="2239" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2239" 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;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</span><span class="s" style="color: #d14;">'observation'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">binary</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); 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="2240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2240" class="line" lang="python">        <span class="n" style="color: #333;">obs_whole</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonzero_counts</span><span class="p">(</span><span class="s" style="color: #d14;">'whole'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">binary</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2234

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<td class="diff-line-num new_line" data-linenumber="2241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2241

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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2235

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<td class="diff-line-num new_line" data-linenumber="2242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2242

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<pre style="margin: 0;"> <span id="LC2242" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assert_equal</span><span class="p">(</span><span class="n" style="color: #333;">obs_samp</span><span class="p">,</span> <span class="n" style="color: #333;">exp_samp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2236" style="width: 35px; color: rgba(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="2243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2243

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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3771,6 +3778,47 @@ class SparseTableTests(TestCase):</td>

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<pre style="margin: 0;"> <span id="LC3778" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_extract_data_from_tsv</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</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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<pre style="margin: 0;"> <span id="LC3779" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</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;">exp</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC3780" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="3781" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3781" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_extract_data_from_tsv_bad_metadata</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="diff-line-num new new_line" data-linenumber="3782" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3782" class="line" lang="python">        <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">legacy_otu_table_bad_metadata</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3783" class="line" lang="python">        <span class="n" style="color: #333;">samp_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'Fing'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Key'</span><span class="p">,</span> <span class="s" style="color: #d14;">'NA'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3784" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3784" class="line" lang="python">        <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'3'</span><span class="p">,</span> <span class="s" style="color: #d14;">'4'</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3785" class="line" lang="python">        <span class="n" style="color: #333;">metadata</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 new_line" data-linenumber="3786" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3786" class="line" lang="python">            <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="3787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3787

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<pre style="margin: 0;">+<span id="LC3787" class="line" lang="python">            <span class="s" style="color: #d14;">'Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillal'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3788

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<pre style="margin: 0;">+<span id="LC3788" class="line" lang="python">            <span class="s" style="color: #d14;">'es; Lactobacillales; Streptococcaceae; Streptococcus'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3789

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<pre style="margin: 0;">+<span id="LC3789" class="line" lang="python">            <span class="s" style="color: #d14;">'Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Coryneb'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3790

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<pre style="margin: 0;">+<span id="LC3790" class="line" lang="python">            <span class="s" style="color: #d14;">'acteriaceae'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3791

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<pre style="margin: 0;">+<span id="LC3791" class="line" lang="python">            <span class="s" style="color: #d14;">'Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococca'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3792

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<pre style="margin: 0;">+<span id="LC3792" class="line" lang="python">            <span class="s" style="color: #d14;">'ceae'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3793

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<pre style="margin: 0;">+<span id="LC3793" class="line" lang="python">            <span class="s" style="color: #d14;">'Bacteria; Cyanobacteria; Chloroplasts; vectors'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3794" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3794" class="line" lang="python">        <span class="n" style="color: #333;">md_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Consensus Lineage'</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="3795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3795

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<pre style="margin: 0;">+<span id="LC3795" 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;">19111</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;">44536</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;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">42</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3796

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<pre style="margin: 0;">+<span id="LC3796" class="line" lang="python">                <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;">1216</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;">3500</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;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">],</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="3797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3797

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<pre style="margin: 0;">+<span id="LC3797" class="line" lang="python">                <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;">1803</span><span class="p">],</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 class="mi" style="color: #099;">1184</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="3798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3798

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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="LC3798" 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;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1722</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">4903</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">17</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3799

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<pre style="margin: 0;">+<span id="LC3799" class="line" lang="python">                <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">589</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2074</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">34</span><span class="p">]]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3800

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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="LC3800" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3801

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<pre style="margin: 0;">+<span id="LC3801" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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 class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3802

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<pre style="margin: 0;">+<span id="LC3802" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_extract_data_from_tsv</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3803

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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="LC3803" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</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;">exp</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3804

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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="LC3804" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3805

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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="LC3805" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># and assert the exact identified bug in #827 is resolved</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3806

</td>

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

<pre style="margin: 0;">+<span id="LC3806" class="line" lang="python">        <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extract_tsv_bug</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">splitlines</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3807

</td>

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

<pre style="margin: 0;">+<span id="LC3807" class="line" lang="python">        <span class="n" style="color: #333;">samp_ids</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3808

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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="LC3808" class="line" lang="python">        <span class="n" style="color: #333;">obs_ids</span> <span class="o" style="font-weight: 600;">=</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>

</td>

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</td>

<td class="diff-line-num new new_line" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3809

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<pre style="margin: 0;">+<span id="LC3809" class="line" lang="python">        <span class="n" style="color: #333;">metadata</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 new_line" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3810

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<pre style="margin: 0;">+<span id="LC3810" class="line" lang="python">            <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="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3811

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<pre style="margin: 0;">+<span id="LC3811" class="line" lang="python">            <span class="s" style="color: #d14;">'k__test;p__test'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3812

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<pre style="margin: 0;">+<span id="LC3812" class="line" lang="python">            <span class="s" style="color: #d14;">'k__test;p__test'</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3813

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<pre style="margin: 0;">+<span id="LC3813" class="line" lang="python">        <span class="n" style="color: #333;">md_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'taxonomy'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3814

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<pre style="margin: 0;">+<span id="LC3814" 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;">123</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;">32</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3815

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<pre style="margin: 0;">+<span id="LC3815" class="line" lang="python">                <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;">315</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;">3</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3816

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<pre style="margin: 0;">+<span id="LC3816" class="line" lang="python">                <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 class="mi" style="color: #099;">22</span><span class="p">]]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3817

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<pre style="margin: 0;">+<span id="LC3817" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3818

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<pre style="margin: 0;">+<span id="LC3818" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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 class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3819

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<pre style="margin: 0;">+<span id="LC3819" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_extract_data_from_tsv</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3820

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<pre style="margin: 0;">+<span id="LC3820" class="line" lang="python">        <span class="n" style="color: #333;">npt</span><span class="o" style="font-weight: 600;">.</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;">exp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3774" style="width: 35px; color: rgba(0,0,0,0.3); 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="3821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3821

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<pre style="margin: 0;">+<span id="LC3821" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3774" style="width: 35px; color: rgba(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="3822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3822

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<pre style="margin: 0;"> <span id="LC3822" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_identify_bad_value</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="3775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3775

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<td class="diff-line-num new_line" data-linenumber="3823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3823

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<pre style="margin: 0;"> <span id="LC3823" class="line" lang="python">        <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3776

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<td class="diff-line-num new_line" data-linenumber="3824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3824

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<pre style="margin: 0;"> <span id="LC3824" class="line" lang="python">        <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</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="4116" style="width: 35px; color: rgba(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="4164" style="width: 35px; color: rgba(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">@@ -4116,6 +4164,21 @@ ae; Corynebacteriaceae</td>

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4116

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<td class="diff-line-num new_line" data-linenumber="4164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4164

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<pre style="margin: 0;"> <span id="LC4164" class="line" lang="python"><span class="s" style="color: #d14;">aphylococcaceae</span></span>

</pre>

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4117

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<td class="diff-line-num new_line" data-linenumber="4165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4165

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<pre style="margin: 0;"> <span id="LC4165" class="line" lang="python"><span class="s" style="color: #d14;">4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">589</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">2074</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Cyanobacteria; Chloroplasts; vectors</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4118

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<td class="diff-line-num new_line" data-linenumber="4166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4166

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<pre style="margin: 0;"> <span id="LC4166" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4167" class="line" lang="python"><span class="n" style="color: #333;">legacy_otu_table_bad_metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"""# some comment goes here</span></span>

</pre>

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</td>

<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

</td>

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

<pre style="margin: 0;">+<span id="LC4168" class="line" lang="python"><span class="s" style="color: #d14;">#OTU id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Fing</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Key</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Consensus Lineage</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4169" class="line" lang="python"><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">19111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">44536</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">42 </span><span class="se" style="color: #d14;">\t</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4170" class="line" lang="python"><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1216</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">3500</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">6</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; La</span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC4172" class="line" lang="python"><span class="s" style="color: #d14;">7</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1803</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1184</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Actinobacteria; Actinobacteridae; Gordoniace</span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4173" class="line" lang="python"><span class="s" style="color: #d14;">ae; Corynebacteriaceae</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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

</td>

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

<pre style="margin: 0;">+<span id="LC4174" class="line" lang="python"><span class="s" style="color: #d14;">3</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1722</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">4903</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">17</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; St</span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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

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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="LC4175" class="line" lang="python"><span class="s" style="color: #d14;">aphylococcaceae</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(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="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

</td>

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

<pre style="margin: 0;">+<span id="LC4176" class="line" lang="python"><span class="s" style="color: #d14;">4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">589</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">2074</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">34</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Cyanobacteria; Chloroplasts; vectors</span></span>

</pre>

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</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

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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="LC4177" 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="4119" style="width: 35px; color: rgba(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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<pre style="margin: 0;">+<span id="LC4178" class="line" lang="python"><span class="n" style="color: #333;">extract_tsv_bug</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""#OTU ID       s1      s2      taxonomy</span></span>

</pre>

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</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

</td>

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

<pre style="margin: 0;">+<span id="LC4179" class="line" lang="python"><span class="s" style="color: #d14;">1      123     32</span><span class="se" style="color: #d14;">\t</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4119" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;">+<span id="LC4180" class="line" lang="python"><span class="s" style="color: #d14;">2      315     3       k__test;p__test</span></span>

</pre>

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<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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<pre style="margin: 0;">+<span id="LC4181" class="line" lang="python"><span class="s" style="color: #d14;">3      0       22      k__test;p__test"""</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4182" style="width: 35px; color: rgba(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="LC4182" class="line" lang="python"><span class="n" style="color: #333;">otu_table1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u"""# Some comment</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4120" style="width: 35px; color: rgba(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="4183" style="width: 35px; color: rgba(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="LC4183" class="line" lang="python"><span class="s" style="color: #d14;">#OTU ID</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Fing</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Key</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Consensus Lineage</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4121" style="width: 35px; color: rgba(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="4184" style="width: 35px; color: rgba(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="LC4184" class="line" lang="python"><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">19111</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">44536</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">42</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Bacteria; Actinobacteria; Actinobacteridae; </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<br>

</li>

<li id="a1915bee4c10d765761bc956a98de62711b346b4">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#a1915bee4c10d765761bc956a98de62711b346b4"><strong>biom/util.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,6 @@</td>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">contextmanager</span></span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,12 +26,8 @@ try:</td>

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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="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">h5py</span></span>

</pre>

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<td class="diff-line-num old_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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<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="n" style="color: #333;">HAVE_H5PY</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(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="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="30" 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="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">major</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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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="LC31" class="line" lang="python">        <span class="n" style="color: #333;">H5PY_VLEN_STR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">unicode</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># noqa</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python">        <span class="n" style="color: #333;">H5PY_VLEN_UNICODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">unicode</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># noqa</span></span>

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<pre style="margin: 0;">-<span id="LC33" 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_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="LC34" class="line" lang="python">        <span class="n" style="color: #333;">H5PY_VLEN_STR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

</pre>

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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="LC35" class="line" lang="python">        <span class="n" style="color: #333;">H5PY_VLEN_UNICODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

</pre>

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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="python">    <span class="n" style="color: #333;">H5PY_VLEN_STR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="n" style="color: #333;">H5PY_VLEN_UNICODE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h5py</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">special_dtype</span><span class="p">(</span><span class="n" style="color: #333;">vlen</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">)</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC32" 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_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">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">    <span class="n" style="color: #333;">HAVE_H5PY</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 unfold js-unfold old_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">...</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">@@ -50,7 +45,7 @@ __url__ = "http://biom-format.org"</td>

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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>

</pre>

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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="LC53" 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">7</span>"</span></span>

</pre>

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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>

</pre>

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(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="385" style="width: 35px; color: rgba(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">@@ -390,7 +385,8 @@ def is_gzip(fp):</td>

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"><span class="s" style="color: #d14;">    project, but we obtained permission from the authors of this function to</span></span>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"><span class="s" style="color: #d14;">    port it to the BIOM Format project (and keep it under BIOM's BSD license).</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="diff-line-num new_line old" data-linenumber="388" 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="LC393" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x1f\x8b</span><span class="s" style="color: #d14;">'</span></span>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC389" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x1f\x8b</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(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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392

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">contextmanager</span></span>

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<br>

</li>

<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(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="66" style="width: 35px; color: rgba(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">@@ -66,8 +66,8 @@ copyright = u'2011-2018 The BIOM Format Development Team'</td>

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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>

</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">7</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">7</span>"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="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>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

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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>

</td>

</tr>

</table>

<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-biom-format/commit/d993b066e9879c3f852b79a16221b748d9cdf615#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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="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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,6 @@</td>

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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="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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full license is in the file COPYING.txt, distributed with this software.</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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="12" 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="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(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="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="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>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +20,13 @@ try:</td>

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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">

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

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

<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 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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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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="python"></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

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

<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 old_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">

</td>

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

<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>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); 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="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>

</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); 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="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>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC28" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC30" 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>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># in multiprocessing/util.py _exit_function when running `python</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># setup.py test` (see</span></span>

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +43,7 @@ __copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"</td>

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<pre style="margin: 0;"> <span id="LC43" 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>

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<pre style="margin: 0;"> <span id="LC44" 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>

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<pre style="margin: 0;"> <span id="LC45" 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>

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<pre style="margin: 0;">-<span id="LC40" 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">7</span>"</span></span>

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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>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" 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>

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<pre style="margin: 0;"> <span id="LC48" 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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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(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="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,10 +98,9 @@ classes = """</td>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    Topic :: Software Development :: Libraries :: Application Frameworks</span></span>

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="python"><span class="s" style="color: #d14;">    Topic :: Software Development :: Libraries :: Python Modules</span></span>

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(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="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python</span></span>

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<td class="diff-line-num new_line old" data-linenumber="101" 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="LC95" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 2.7</span></span>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.4</span></span>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.5</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.6</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.7</span></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: 3.8</span></span>

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(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="LC104" class="line" lang="python"><span class="s" style="color: #d14;">    Programming Language :: Python :: Implementation :: CPython</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;">    Operating System :: OS Independent</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;">    Operating System :: POSIX :: Linux</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(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">@@ -104,8 +109,7 @@ classes = """</td>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"><span class="n" style="color: #333;">classifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">classes</span><span class="o" style="font-weight: 600;">.</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;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Dealing with Cython</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"><span class="n" style="color: #333;">USE_CYTHON</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">environ</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'USE_CYTHON'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.pyx'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">USE_CYTHON</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'.c'</span></span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.pyx'</span></span>

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(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="LC113" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"biom._filter"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(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="LC114" class="line" lang="python">                        <span class="p">[</span><span class="s" style="color: #d14;">"biom/_filter"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ext</span><span class="p">],</span></span>

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(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="LC115" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_include</span><span class="p">()]),</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,22 +119,15 @@ extensions = [Extension("biom._filter",</td>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">              <span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"biom._subsample"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">                        <span class="p">[</span><span class="s" style="color: #d14;">"biom/_subsample"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ext</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_include</span><span class="p">()])]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">USE_CYTHON</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC120" 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="LC121" class="line" lang="python">    <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(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="LC124" 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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<td class="diff-line-num new_line old" data-linenumber="125" 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="LC124" class="line" lang="python">                    <span class="s" style="color: #d14;">"scipy >= <span class="idiff left right">0.13.0</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">'pandas >= 0.20.0'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python">                    <span class="s" style="color: #d14;">"six >= 1.10.0"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); 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="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC125" class="line" lang="python">                    <span class="s" style="color: #d14;">"scipy >= <span class="idiff left right">1.3.1</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">'pandas >= 0.20.0'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); 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="126" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC126" class="line" lang="python">                    <span class="s" style="color: #d14;">"six >= 1.10.0"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"cython >= 0.29"</span></span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(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="LC127" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" 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="128" 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="LC127" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># HACK: for backward-compatibility with QIIME 1.9.x, pyqi must be installed.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" 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="LC128" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># pyqi is not used anymore in this project.</span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" 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="129" 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="LC130" 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;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"pyqi"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" 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="LC131" class="line" lang="python">    <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python">    <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Python 2.7 support will be removed on the next release"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python">                  <span class="nb" style="color: #0086b3;">DeprecationWarning</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC129" 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>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"></span>

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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>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'biom-format'</span><span class="p">,</span></span>

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<td class="diff-line-num old_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="LC133" class="line" lang="python">      <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span></span>

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