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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-epimodels/-/commit/86e060f7e3a8d918efa9b763c194e94e478f2740">86e060f7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-02-22T16:28:35+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream has tagged release

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-epimodels/-/commit/5c49f65dd61af0998209ca621bc1d128cfad5234">5c49f65d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-02-22T16:29:01+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.18</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-epimodels/-/commit/c6159d65cf646a29e23b79f17dfb3734d5db6b5c">c6159d65</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-02-22T16:29:02+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.3.18'

Update to upstream version '0.3.18'

with Debian dir 7b867a0718e1d0a659d427b4b00f2c792de0d709</pre>

</li>

</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#b77754b27a55c2c13c65a0269c3c4d77027aa611">

<span class="deleted-file">

−

.github/workflows/python-package.yml

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</a>

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<li class="file-stats">

<a href="#15af4b3d30054104e85f65a444b1db188c5deefb">

Pipfile

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

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<a href="#440d72257dadecfd1bd1f8e065e09681a5d1fb2e">

src/epimodels/continuous/models.py

</a>

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<li class="file-stats">

<a href="#69813e36ae3f36f222a06b3462cf570748823c8f">

src/epimodels/discrete/models.py

</a>

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<li class="file-stats">

<a href="#5c9bdb6a850e51fc64db3f13ef8dfe223a1a71b2">

tests/test_continuous_models.py

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<h4>Changes:</h4>

<li id="b77754b27a55c2c13c65a0269c3c4d77027aa611">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#b77754b27a55c2c13c65a0269c3c4d77027aa611"><strong>.github/workflows/python-package.yml</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># This workflow will install Python dependencies, run tests and lint with a variety of Python versions</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Python package</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml">  <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">  <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>

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

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">        <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.5</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">      <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">      <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">        <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install dependencies</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml">        <span class="s" style="color: #d14;">python -m pip install --upgrade pip</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml">        <span class="s" style="color: #d14;">pip install flake8 pytest</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml">        <span class="s" style="color: #d14;">if [ -f requirements.txt ]; then pip install -r requirements.txt; fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Lint with flake8</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml">        <span class="s" style="color: #d14;"># stop the build if there are Python syntax errors or undefined names</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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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml">        <span class="s" style="color: #d14;">flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml">        <span class="s" style="color: #d14;"># exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml">        <span class="s" style="color: #d14;">flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test with pytest</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" 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="LC39" class="line" lang="yaml">        <span class="s" style="color: #d14;">pytest</span></span></pre>

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<br>

</li>

<li id="15af4b3d30054104e85f65a444b1db188c5deefb">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#15af4b3d30054104e85f65a444b1db188c5deefb"><strong>Pipfile</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@ matplotlib = "*"</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="toml"><span class="py">mypy</span> <span class="p">=</span> <span class="s" style="color: #d14;">"*"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="toml"><span class="py">sphinx</span> <span class="p">=</span> <span class="s" style="color: #d14;">"*"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="toml"><span class="py">pyitlib</span> <span class="p">=</span> <span class="s" style="color: #d14;">"*"</span></span>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="toml"><span class="py">numba</span> <span class="p">=</span> <span class="s" style="color: #d14;">"*"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="toml"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="toml"><span class="nn" style="color: #555;">[dev-packages]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="toml"></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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

1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">python-epimodels (0.<span class="idiff left right">0+git20201022.2c49b90</span>-1) UNRELEASED; urgency=medium</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-epimodels (0.<span class="idiff left right">3.18</span>-1) UNRELEASED; urgency=medium</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * Initial release (Closes: #<bug>)</span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="mode=git,pretty=0.0+git%cd.%h" \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">    https://github.com/fccoelho/epimodels.git HEAD</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" 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">

5

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"># Issue asking for release tags:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># https://github.com/fccoelho/epimodels/issues/3</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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<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="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">#https://github.com/fccoelho/epimodels/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>

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

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  https://github.com/fccoelho/epimodels/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>

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<br>

</li>

<li id="440d72257dadecfd1bd1f8e065e09681a5d1fb2e">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#440d72257dadecfd1bd1f8e065e09681a5d1fb2e"><strong>src/epimodels/continuous/models.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">@@ -9,6 +9,7 @@ from epimodels import BaseModel</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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<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;">logging</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</span></span>

</pre>

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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;">from</span> <span class="nn" style="color: #555;">functools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">lru_cache</span></span>

</pre>

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<td class="diff-line-num new old_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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<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;">import</span> <span class="nn" style="color: #555;">numba</span></span>

</pre>

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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 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="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="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'epimodels.log'</span><span class="p">,</span> <span class="n" style="color: #333;">filemode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">)</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="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="python"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,13 +60,13 @@ class SIR(ContinuousModel):</td>

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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="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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">state_variables</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">({</span><span class="s" style="color: #d14;">'S'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Susceptible'</span><span class="p">,</span> <span class="s" style="color: #d14;">'I'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Infectious'</span><span class="p">,</span> <span class="s" style="color: #d14;">'R'</span><span class="p">:</span> <span class="s" style="color: #d14;">'Removed'</span><span class="p">})</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">({</span><span class="s" style="color: #d14;">'beta'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\beta$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gamma'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\gamma$'</span><span class="p">})</span></span>

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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 class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SIR'</span></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" 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;">jit</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;">        SIR Model.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;">        :param t:</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">        :param y:</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;">        :param params:</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">        :param t:<span class="idiff left right"> time step</span></span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;">        :param y:<span class="idiff left right"> state of the model at time t</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="s" style="color: #d14;">        :param params:<span class="idiff left right"> parameter dictionary</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;">        :return:</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">        <span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">I</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;">y</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">@@ -85,6 +86,7 @@ class SIS(ContinuousModel):</td>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SIS'</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @lru_cache(1000)</span></span>

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<pre style="margin: 0;">+<span id="LC89" 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;">jit</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>

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<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 class="s" style="color: #d14;">"""</span></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;">        SIS Model.</span></span>

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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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,6 +110,7 @@ class SIRS(ContinuousModel):</td>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">({</span><span class="s" style="color: #d14;">'beta'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\beta$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gamma'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\gamma$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'xi'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\xi$'</span><span class="p">})</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SIRS'</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">numba</span><span class="p">.</span><span class="n" style="color: #333;">jit</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>

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<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="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;">        SIR Model.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,6 +135,7 @@ class SEIR(ContinuousModel):</td>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">({</span><span class="s" style="color: #d14;">'beta'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\beta$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gamma'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\gamma$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'epsilon'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\epsilon$'</span><span class="p">})</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SEIR'</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC137" class="line" lang="python"></span>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" 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;">jit</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">        <span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="n" style="color: #333;">I</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;">y</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">        <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">epsilon</span><span class="p">,</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="s" style="color: #d14;">'beta'</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="s" style="color: #d14;">'gamma'</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="s" style="color: #d14;">'epsilon'</span><span class="p">],</span> <span class="n" style="color: #333;">params</span><span class="p">[</span><span class="s" style="color: #d14;">'N'</span><span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="160" style="width: 35px; color: rgba(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">@@ -156,6 +160,7 @@ class SEQIAHR(ContinuousModel):</td>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">                                       <span class="p">})</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SEQIAHR'</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC163" 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;">jit</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">        <span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="n" style="color: #333;">I</span><span class="p">,</span> <span class="n" style="color: #333;">A</span><span class="p">,</span> <span class="n" style="color: #333;">H</span><span class="p">,</span> <span class="n" style="color: #333;">R</span><span class="p">,</span> <span class="n" style="color: #333;">C</span><span class="p">,</span> <span class="n" style="color: #333;">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">y</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">        <span class="n" style="color: #333;">chi</span><span class="p">,</span> <span class="n" style="color: #333;">phi</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">rho</span><span class="p">,</span> <span class="n" style="color: #333;">delta</span><span class="p">,</span> <span class="n" style="color: #333;">gamma</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="p">,</span> <span class="n" style="color: #333;">mu</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span></span>

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</li>

<li id="69813e36ae3f36f222a06b3462cf570748823c8f">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#69813e36ae3f36f222a06b3462cf570748823c8f"><strong>src/epimodels/discrete/models.py</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,12 +8,15 @@ License: GPL-v3</td>

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fccoelho'</span></span>

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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>

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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="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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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.stats.distributions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">poisson</span><span class="p">,</span> <span class="n" style="color: #333;">nbinom</span></span>

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12

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<td class="diff-line-num new_line old" data-linenumber="11" 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;">from</span> <span class="nn" style="color: #555;">numpy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">inf</span><span class="p">,</span> <span class="n" style="color: #333;">nan</span><span class="p">,</span> <span class="n" style="color: #333;">nan_to_num</span></span>

</pre>

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<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">

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<td class="diff-line-num new_line old" data-linenumber="11" 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="LC13" 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 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="11" 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="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>from scipy.stats.distributions import poisson, nbinom</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="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="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>from numpy import inf, nan, nan_to_num</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="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>import sys</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="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="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>import logging</span></span>

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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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OrderedDict</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;">cython</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import cython</span></span>

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

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<td class="diff-line-num new new_line" data-linenumber="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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Dict</span><span class="p">,</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">Iterable</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span></span>

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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="c1" style="color: #998; font-style: italic;"># import numba</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="c1" style="color: #998; font-style: italic;"># from numba.experimental import jitclass</span></span>

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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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">epimodels</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BaseModel</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">model_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(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">@@ -76,7 +79,6 @@ class DiscreteModel(BaseModel):</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># args = self.get_args_from_redis()</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">        <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run</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>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">traces</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># return res</span></span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="s" style="color: #d14;">'time'</span><span class="p">:</span> <span class="n" style="color: #333;">tspan</span><span class="p">,</span> <span class="s" style="color: #d14;">'S'</span><span class="p">:</span> <span class="n" style="color: #333;">S</span><span class="p">,</span> <span class="s" style="color: #d14;">'I'</span><span class="p">:</span> <span class="n" style="color: #333;">I</span><span class="p">,</span> <span class="s" style="color: #d14;">'E'</span><span class="p">:</span> <span class="n" style="color: #333;">E</span><span class="p">,</span> <span class="s" style="color: #d14;">'R'</span><span class="p">:</span> <span class="n" style="color: #333;">R</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># from numba.types import unicode_type, pyobject</span></span>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># spec = [</span></span>

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     ('model_type', unicode_type),</span></span>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     ('state_variables', pyobject),</span></span>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     ('parameters', pyobject),</span></span>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     ('run', pyobject)</span></span>

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<pre style="margin: 0;">+<span id="LC522" 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="LC523" 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="LC524" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># @jitclass(spec)</span></span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SIRS</span><span class="p">(</span><span class="n" style="color: #333;">DiscreteModel</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC526" 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>

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'beta'</span><span class="p">:</span> <span class="sa">r</span><span class="s" style="color: #d14;">'$\beta$'</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="s" style="color: #d14;">'w'</span><span class="p">:</span> <span class="s" style="color: #d14;">'w'</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model</span></span>

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inits</span><span class="p">,</span> <span class="n" style="color: #333;">trange</span><span class="p">,</span> <span class="n" style="color: #333;">totpop</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># @numba.jit</span></span>

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inits</span><span class="p">:</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">trange</span><span class="p">:</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">totpop</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">:</span> <span class="n" style="color: #333;">Dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Dict</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="s" style="color: #d14;">        calculates the model SIRS, and return its values (no demographics)</span></span>

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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;">        - inits = (E,I,S)</span></span>

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"><span class="s" style="color: #d14;">        - theta = infectious individuals from neighbor sites</span></span>

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python"><span class="s" style="color: #d14;">        :param inits: (E,I,S)</span></span>

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"><span class="s" style="color: #d14;">        :param trange:</span></span>

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"><span class="s" style="color: #d14;">        :param totpop:</span></span>

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python"><span class="s" style="color: #d14;">        :param params:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"><span class="s" style="color: #d14;">        :return:</span></span>

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528

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<td class="diff-line-num new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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529

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<td class="diff-line-num new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">        <span class="n" style="color: #333;">S</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</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;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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530

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<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python">        <span class="n" style="color: #333;">I</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</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;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trange</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 unfold js-unfold old_line" data-linenumber="565" style="width: 35px; color: rgba(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="580" style="width: 35px; color: rgba(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">@@ -565,7 +580,7 @@ class SEQIAHR(DiscreteModel):</td>

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565

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"></span>

</pre>

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566

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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">model</span></span>

</pre>

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567

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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" 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">

568

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<td class="diff-line-num new_line old" data-linenumber="583" 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="LC568" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inits</span><span class="p">,</span> <span class="n" style="color: #333;">trange</span><span class="p">,</span> <span class="n" style="color: #333;">totpop</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">lis</span>t</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); 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="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">model</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inits</span><span class="p">,</span> <span class="n" style="color: #333;">trange</span><span class="p">,</span> <span class="n" style="color: #333;">totpop</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">dic</span>t</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

569

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<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python">        <span class="n" style="color: #333;">S</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</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;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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570

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<td class="diff-line-num new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

585

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python">        <span class="n" style="color: #333;">E</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</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;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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571

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<td class="diff-line-num new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python">        <span class="n" style="color: #333;">I</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</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;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trange</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<li id="5c9bdb6a850e51fc64db3f13ef8dfe223a1a71b2">

<a href="https://salsa.debian.org/med-team/python-epimodels/-/compare/a8b54ee7b8268f0c3564989393d52b55e378ae71...c6159d65cf646a29e23b79f17dfb3734d5db6b5c#5c9bdb6a850e51fc64db3f13ef8dfe223a1a71b2"><strong>tests/test_continuous_models.py</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,6 @@ def test_SIR_with_t_eval():</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">traces</span><span class="p">[</span><span class="s" style="color: #d14;">'S'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">500</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># assert len(model.traces['time']) == 50</span></span>

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>

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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;">test_SIS</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SIS</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">model</span><span class="p">([</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">50</span><span class="p">],</span> <span class="mi" style="color: #099;">1001</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'beta'</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">'gamma'</span><span class="p">:</span> <span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">})</span></span>

</pre>

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