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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/umap-learn">Debian Med / umap-learn</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f">3fa8c8d1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-10T08:05:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.1+dfsg</pre>
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<h4>9 changed files:</h4>
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<li class="file-stats">
<a href="#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">
azure-pipelines.yml
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#17be97c2caf7e4c303eda35f22db8ed3f6e417da">
umap/__init__.py
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<li class="file-stats">
<a href="#10ae44f0c5823e4912f0f49b238766ad43e6523d">
umap/layouts.py
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<li class="file-stats">
<a href="#d98e262ae612f6d2b2eb6910f0176a5eb7511874">
umap/plot.py
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<li class="file-stats">
<a href="#e9fc11a14bec2d71d2e943771ceff8603a91b6b7">
umap/sparse.py
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<li class="file-stats">
<a href="#c79d62f5eef209460979f658832439f421faa1a0">
umap/spectral.py
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<li class="file-stats">
<a href="#c8d53af80c731323988aef4615fdf83f01302be1">
umap/tests/test_umap_metrics.py
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<li class="file-stats">
<a href="#0463e74cf9e81602454d0f8d49ea9170a8bb70b1">
umap/umap_.py
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<h4>Changes:</h4>
<li id="40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">
<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,6 @@</td>
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"></span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">trigger</span><span class="pi">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">master</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;">0.5dev</span></span>
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<td class="old_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s" style="color: #d14;">Linux</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ def readme():</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="n" style="color: #333;">configuration</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"name"</span><span class="p">:</span> <span class="s" style="color: #d14;">"umap-learn"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num 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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<td class="new_line diff-line-num 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="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">0</span>"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" 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="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">1</span>"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"description"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Uniform Manifold Approximation and Projection"</span><span class="p">,</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"long_description"</span><span class="p">:</span> <span class="n" style="color: #333;">readme</span><span class="p">(),</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"long_description_content_type"</span><span class="p">:</span> <span class="s" style="color: #d14;">"text/x-rst"</span><span class="p">,</span></span>
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<li id="17be97c2caf7e4c303eda35f22db8ed3f6e417da">
<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#17be97c2caf7e4c303eda35f22db8ed3f6e417da"><strong>umap/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,27 @@ try:</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">simplefilter</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="LC7" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.parametric_umap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ParametricUMAP</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Tensorflow not installed; ParametricUMAP will be unavailable"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">warn</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">"Tensorflow not installed; ParametricUMAP will be unavailable"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">category</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">ImportWarning</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add a dummy class to raise an error</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ParametricUMAP</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</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;">kwds</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">warn</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"""The umap.parametric_umap package requires Tensorflow > 2.0 to be installed.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> You can install Tensorflow at https://www.tensorflow.org/install</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> or you can install the CPU version of Tensorflow using </span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> pip install umap-learn[parametric_umap]</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"umap.parametric_umap requires Tensorflow >= 2.0"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.aligned_umap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AlignedUMAP</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></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;"># Workaround: https://github.com/numba/numba/issues/3341</span></span>
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<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#10ae44f0c5823e4912f0f49b238766ad43e6523d"><strong>umap/layouts.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">@@ -33,7 +33,7 @@ def clip(val):</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="nb" style="color: #0086b3;">locals</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"result"</span><span class="p">:</span> <span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">types</span><span class="p">.</span><span class="n" style="color: #333;">float32</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"diff"</span><span class="p">:</span> <span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">types</span><span class="p">.</span><span class="n" style="color: #333;">float32</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"dim"</span><span class="p">:</span> <span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">types</span><span class="p">.</span><span class="n" style="color: #333;">int<span class="idiff left right">32</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"dim"</span><span class="p">:</span> <span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">types</span><span class="p">.</span><span class="n" style="color: #333;">int<span class="idiff left right">p</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rdist</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#d98e262ae612f6d2b2eb6910f0176a5eb7511874"><strong>umap/plot.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">@@ -42,6 +42,7 @@ from matplotlib.patches import Patch</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">umap.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">submatrix</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bokeh.plotting</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">show</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">show_interactive</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bokeh.plotting</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_notebook</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bokeh.layouts</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">column</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bokeh.models</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CustomJS</span><span class="p">,</span> <span class="n" style="color: #333;">TextInput</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">matplotlib.pyplot</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">show</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">show_static</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">@@ -1385,7 +1386,7 @@ def interactive(</td>
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="python"> <span class="n" style="color: #333;">tooltip_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC1387" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hover_data</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">col_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hover_data</span><span class="p">[</span><span class="n" style="color: #333;">col_name</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="python"> <span class="n" style="color: #333;">tooltip_dict</span><span class="p">[</span><span class="n" style="color: #333;">col_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">col_name</span></span>
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="python"> <span class="n" style="color: #333;">tooltip_dict</span><span class="p">[</span><span class="n" style="color: #333;">col_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"@<span class="idiff left">{</span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">col_name</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"}"</span></span></span>
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="python"> <span class="n" style="color: #333;">tooltips</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">tooltip_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC1391" 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="LC1392" class="line" lang="python"> <span class="n" style="color: #333;">tooltips</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#e9fc11a14bec2d71d2e943771ceff8603a91b6b7"><strong>umap/sparse.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">@@ -288,15 +288,17 @@ def sparse_canberra(ind1, data1, ind2, data2):</td>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">njit</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sparse_bray_curtis</span><span class="p">(</span><span class="n" style="color: #333;">ind1</span><span class="p">,</span> <span class="n" style="color: #333;">data1</span><span class="p">,</span> <span class="n" style="color: #333;">ind2</span><span class="p">,</span> <span class="n" style="color: #333;">data2</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># pragma: no cover</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">abs_data1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">data1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">abs_data2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">data2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">denom_inds</span><span class="p">,</span> <span class="n" style="color: #333;">denom_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparse_sum</span><span class="p">(</span><span class="n" style="color: #333;">ind1</span><span class="p">,</span> <span class="n" style="color: #333;">abs_data1</span><span class="p">,</span> <span class="n" style="color: #333;">ind2</span><span class="p">,</span> <span class="n" style="color: #333;">abs_data2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">denom_inds</span><span class="p">,</span> <span class="n" style="color: #333;">denom_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparse_sum</span><span class="p">(</span><span class="n" style="color: #333;">ind1</span><span class="p">,</span> <span class="n" style="color: #333;">data1</span><span class="p">,</span> <span class="n" style="color: #333;">ind2</span><span class="p">,</span> <span class="n" style="color: #333;">data2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">denom_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">denom_data</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">denom_data</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">denominator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">denom_data</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">denominator</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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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">numer_inds</span><span class="p">,</span> <span class="n" style="color: #333;">numer_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sparse_diff</span><span class="p">(</span><span class="n" style="color: #333;">ind1</span><span class="p">,</span> <span class="n" style="color: #333;">data1</span><span class="p">,</span> <span class="n" style="color: #333;">ind2</span><span class="p">,</span> <span class="n" style="color: #333;">data2</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;">numer_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">numer_data</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -589,7 +591,7 @@ sparse_named_distances = {</td>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Other distances</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"canberra"</span><span class="p">:</span> <span class="n" style="color: #333;">sparse_canberra</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="s" style="color: #d14;">"ll_dirichlet"</span><span class="p">:</span> <span class="n" style="color: #333;">sparse_ll_dirichlet</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>'braycurtis': sparse_bray_curtis,</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="s" style="color: #d14;">'braycurtis'</span><span class="p">:</span> <span class="n" style="color: #333;">sparse_bray_curtis</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Binary distances</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"> <span class="s" style="color: #d14;">"hamming"</span><span class="p">:</span> <span class="n" style="color: #333;">sparse_hamming</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <span class="s" style="color: #d14;">"jaccard"</span><span class="p">:</span> <span class="n" style="color: #333;">sparse_jaccard</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">@@ -207,7 +207,7 @@ def multi_component_layout(</td>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">distances</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pairwise_distances</span><span class="p">([</span><span class="n" style="color: #333;">meta_embedding</span><span class="p">[</span><span class="n" style="color: #333;">label</span><span class="p">]],</span> <span class="n" style="color: #333;">meta_embedding</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">data_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">distances</span><span class="p">[</span><span class="n" style="color: #333;">distances</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">].</span><span class="nb" style="color: #0086b3;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">2.0</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">component_graph</span><span class="p">.</span><span class="n" style="color: #333;">shape</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;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dim</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">component_graph</span><span class="p">.</span><span class="n" style="color: #333;">shape</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;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dim</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">component_graph</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">shape</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dim</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">component_labels</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">label</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">random_state</span><span class="p">.</span><span class="n" style="color: #333;">uniform</span><span class="p">(</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">low</span><span class="o" style="font-weight: 600;">=-</span><span class="n" style="color: #333;">data_range</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/umap-learn/-/commit/3fa8c8d10c98a37d885fcd40590f1e53bf43734f#c8d53af80c731323988aef4615fdf83f01302be1"><strong>umap/tests/test_umap_metrics.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">@@ -270,6 +270,9 @@ def test_sparse_correlation(sparse_spatial_data):</td>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">sparse_spatial_check</span><span class="p">(</span><span class="s" style="color: #d14;">"correlation"</span><span class="p">,</span> <span class="n" style="color: #333;">sparse_spatial_data</span><span class="p">)</span></span>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_sparse_braycurtis</span><span class="p">(</span><span class="n" style="color: #333;">sparse_spatial_data</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">sparse_spatial_check</span><span class="p">(</span><span class="s" style="color: #d14;">"braycurtis"</span><span class="p">,</span> <span class="n" style="color: #333;">sparse_spatial_data</span><span class="p">)</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="LC276" 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="LC277" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Sparse Binary Metric Tests</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ---------------------------</span></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">@@ -1283,7 +1283,6 @@ def init_graph_transform(graph, embedding):</td>
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="python"><span class="s" style="color: #d14;"> new_embedding: array of shape (n_new_samples, dim)</span></span>
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="python"><span class="s" style="color: #d14;"> An initial embedding of the new sample points.</span></span>
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"inside function</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">graph</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1286" 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;">np</span><span class="p">.</span><span class="n" style="color: #333;">zeros</span><span class="p">((</span><span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">embedding</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float32</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row_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="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]):</span></span>
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