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Notebooks, link to notebooks in gh-pages docs
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yinchi committed May 5, 2024
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20 changes: 0 additions & 20 deletions Makefile

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build-docs() {
pushd `git rev-parse --show-toplevel`
poetry run sphinx-apidoc -fe -o docs/apidoc/ histopath_bim_des/
cd docs
pushd docs
rm -rf html
poetry run make html
cp -r _build/html html
cp -r _build/html .
popd
popd
}

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<li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul>
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config
simulation
processes
`Jupyter notebooks <https://github.com/yinchi/histopath-bim-des/tree/main/notebooks>`_

.. toctree::
:maxdepth: 2
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<li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="../config.html">Model Configuration</a></li>
<li class="toctree-l1"><a class="reference internal" href="../simulation.html">Simulation and KPI extraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../processes.html">Histopathology processes</a></li>
<li class="toctree-l1"><a class="reference external" href="`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_">`Jupyter notebooks &lt;https://github.com/yinchi/histopath-bim-des/tree/main/notebooks&gt;`_</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">API reference:</span></p>
<ul class="current">
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