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  <section id="contributing">
<h1>Contributing<a class="headerlink" href="#contributing" title="Link to this heading">#</a></h1>
<p>We welcome contributions from the community! This guide will help you get started with contributing to GeomFuM.</p>
<section id="getting-started">
<h2>Getting Started<a class="headerlink" href="#getting-started" title="Link to this heading">#</a></h2>
<section id="development-setup">
<h3>Development Setup<a class="headerlink" href="#development-setup" title="Link to this heading">#</a></h3>
<p>The instructions in this section detail the step-by-step
process on setting up your development environment before
contribution.</p>
<p>We recommend using  <cite>Git</cite> for source control to allow collaboration. Typical interaction with the project involves using <cite>git</cite> to pull/push code and
submitting bugs/feature requests to the <a class="reference external" href="https://github.com/DiG-AIR/geomfum">GeomFuM repository</a>.</p>
<p>Be sure to follow the Git installation and configuration instructions for your
respective operating system from the
<a class="reference external" href="https://git-scm.com/book/en/v2/Getting-Started-Installing-Git">official Git documentation</a>,
before you follow along the next section of this documentation.</p>
<ol class="arabic">
<li><p><strong>Fork the repository</strong>:
Visit <cite>https://github.com/DiG-AIR/geomfum</cite> and click “Fork”</p></li>
<li><p><strong>Clone your fork</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p>git clone <a class="github reference external" href="https://github.com">github</a>/&lt;your-username&gt;/geomfum.git
cd geomfum</p>
</div></blockquote>
</li>
<li><p><strong>Install in development mode</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p>pip install -e .[test,,plotting-all]</p>
</div></blockquote>
</li>
</ol>
</section>
<section id="development-environment">
<h3>Development Environment<a class="headerlink" href="#development-environment" title="Link to this heading">#</a></h3>
<p>We recommend using a virtual environment to manage dependencies:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Create virtual environment</span>
python<span class="w"> </span>-m<span class="w"> </span>venv<span class="w"> </span>geomfum_env
<span class="nb">source</span><span class="w"> </span>geomfum_env/bin/activate<span class="w">  </span><span class="c1"># On Windows: geomfum_env\Scripts\activate</span>

<span class="c1"># Install development dependencies</span>
pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.<span class="o">[</span>test,test-scripts,plotting-all<span class="o">]</span>
</pre></div>
</div>
</section>
</section>
<section id="code-style">
<h2>Code Style<a class="headerlink" href="#code-style" title="Link to this heading">#</a></h2>
<p>We follow PEP 8 and use several tools to maintain code quality:</p>
<section id="formatting">
<h3>Formatting<a class="headerlink" href="#formatting" title="Link to this heading">#</a></h3>
<p>We use <cite>ruff</cite> for code formatting and linting. We recommend downloading the extension for your preferred IDE editor.</p>
</section>
<section id="documentation">
<h3>Documentation<a class="headerlink" href="#documentation" title="Link to this heading">#</a></h3>
<p>The documentation is written in <cite>rst</cite> format and is located in the <cite>docs/</cite> directory.
The documentation is built using <cite>sphinx</cite> and is located in <cite>https://DiG-AIR.github.io/geomfum.github.io/</cite> directory.
The documentation is viewable in a web browser.</p>
</section>
<section id="writing-documentation">
<h3>Writing Documentation<a class="headerlink" href="#writing-documentation" title="Link to this heading">#</a></h3>
<ol class="arabic simple">
<li><p><strong>API Documentation</strong>: Add docstrings to all public functions</p></li>
<li><p><strong>Tutorials</strong>: Create Jupyter notebooks in <cite>notebooks/</cite></p></li>
<li><p><strong>Concept Documentation</strong>: Add theoretical explanations in <cite>docs/concepts/</cite></p></li>
</ol>
<p>Example docstring:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="k">def</span><span class="w"> </span><span class="nf">zoomout_refinement</span><span class="p">(</span>
    <span class="n">functional_map</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
    <span class="n">mesh1</span><span class="p">:</span> <span class="n">Mesh</span><span class="p">,</span>
    <span class="n">mesh2</span><span class="p">:</span> <span class="n">Mesh</span><span class="p">,</span>
    <span class="n">iterations</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">5</span>
<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
<span class="w">    </span><span class="sd">&quot;&quot;&quot;Apply ZoomOut refinement to functional map.</span>

<span class="sd">    ZoomOut is a spectral upsampling technique that improves</span>
<span class="sd">    correspondence quality by iteratively refining the functional map.</span>

<span class="sd">    Parameters</span>
<span class="sd">    ----------</span>
<span class="sd">    functional_map : np.ndarray</span>
<span class="sd">        Input functional map matrix</span>
<span class="sd">    mesh1 : Mesh</span>
<span class="sd">        First mesh</span>
<span class="sd">    mesh2 : Mesh</span>
<span class="sd">        Second mesh</span>
<span class="sd">    iterations : int, optional</span>
<span class="sd">        Number of refinement iterations, by default 5</span>

<span class="sd">    Returns</span>
<span class="sd">    -------</span>
<span class="sd">    np.ndarray</span>
<span class="sd">        Refined functional map</span>

<span class="sd">    References</span>
<span class="sd">    ----------</span>
<span class="sd">    .. [1] Melzi, S., et al. &quot;ZoomOut: Spectral Upsampling for Efficient</span>
<span class="sd">           Shape Correspondence.&quot; ACM TOG 38.6 (2019): 155.</span>
<span class="sd">    &quot;&quot;&quot;</span>
    <span class="k">pass</span>
</pre></div>
</div>
</section>
</section>
<section id="pull-request-process">
<h2>Pull Request Process<a class="headerlink" href="#pull-request-process" title="Link to this heading">#</a></h2>
<ol class="arabic">
<li><p><strong>Create a feature branch</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p>git checkout -b feature/your-feature-name</p>
</div></blockquote>
</li>
<li><p><strong>Make your changes</strong>:
- Write code following our style guidelines
- Add tests for new functionality
- Update documentation</p></li>
<li><p><strong>Run tests and checks</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p># Run tests
pytest</p>
</div></blockquote>
</li>
<li><p><strong>Commit your changes</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p>git add .
git commit -m “Add feature: brief description”</p>
<p># Use conventional commit format:
# feat: add new functional map refinement
# fix: resolve memory leak in laplacian computation
# docs: update installation instructions</p>
</div></blockquote>
</li>
<li><p><strong>Push and create PR</strong>:
.. code-block:: bash</p>
<blockquote>
<div><p>git push origin feature/your-feature-name</p>
</div></blockquote>
</li>
<li><p><strong>Create Pull Request</strong>:
- Use the PR template
- Describe your changes clearly
- Link related issues
- Request reviews from maintainers</p></li>
<li><p><strong>Wait for review</strong>:
- Address feedback from maintainers
- Make changes as requested
- Re-request review when ready
- Ensure all checks pass before merging
- Merge when approved</p></li>
</ol>
</section>
<section id="code-review">
<h2>Code Review<a class="headerlink" href="#code-review" title="Link to this heading">#</a></h2>
<section id="review-process">
<h3>Review Process<a class="headerlink" href="#review-process" title="Link to this heading">#</a></h3>
<ol class="arabic simple">
<li><p><strong>Automated checks</strong> must pass:
- Tests
- Code style
- Documentation build
- Type checking</p></li>
<li><p><strong>Manual review</strong> by maintainers:
- Code quality
- Algorithm correctness
- Performance considerations
- Documentation quality</p></li>
<li><p><strong>Address feedback</strong>:
- Respond to review comments
- Make requested changes
- Re-request review when ready</p></li>
</ol>
</section>
<section id="review-guidelines">
<h3>Review Guidelines<a class="headerlink" href="#review-guidelines" title="Link to this heading">#</a></h3>
<p>When reviewing code:</p>
<ol class="arabic simple">
<li><p><strong>Check correctness</strong>: Is the algorithm implemented correctly?</p></li>
<li><p><strong>Check performance</strong>: Are there performance issues?</p></li>
<li><p><strong>Check style</strong>: Does the code follow our conventions?</p></li>
<li><p><strong>Check documentation</strong>: Is the documentation clear and complete?</p></li>
<li><p><strong>Check tests</strong>: Are there adequate tests?</p></li>
</ol>
</section>
</section>
<section id="areas-for-contribution">
<h2>Areas for Contribution<a class="headerlink" href="#areas-for-contribution" title="Link to this heading">#</a></h2>
<p>We welcome contributions in these areas:</p>
<section id="algorithms">
<h3>Algorithms<a class="headerlink" href="#algorithms" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>New functional map algorithms</p></li>
<li><p>Improved refinement techniques</p></li>
<li><p>Novel shape descriptors</p></li>
<li><p>Deep learning approaches</p></li>
</ul>
</section>
<section id="performance">
<h3>Performance<a class="headerlink" href="#performance" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>GPU acceleration</p></li>
<li><p>Parallel processing</p></li>
<li><p>Memory optimization</p></li>
<li><p>Sparse matrix operations</p></li>
</ul>
</section>
<section id="id1">
<h3>Documentation<a class="headerlink" href="#id1" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Tutorials and examples</p></li>
<li><p>API documentation</p></li>
<li><p>Theoretical explanations</p></li>
<li><p>Performance benchmarks</p></li>
</ul>
</section>
<section id="testing">
<h3>Testing<a class="headerlink" href="#testing" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Unit tests</p></li>
<li><p>Integration tests</p></li>
<li><p>Performance tests</p></li>
<li><p>Documentation tests</p></li>
</ul>
</section>
<section id="tools-and-utilities">
<h3>Tools and Utilities<a class="headerlink" href="#tools-and-utilities" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Visualization tools</p></li>
<li><p>Data processing utilities</p></li>
<li><p>Evaluation metrics</p></li>
<li><p>Benchmarking tools</p></li>
</ul>
</section>
</section>
<section id="getting-help">
<h2>Getting Help<a class="headerlink" href="#getting-help" title="Link to this heading">#</a></h2>
<p>If you need help:</p>
<ol class="arabic simple">
<li><p><strong>Check existing issues</strong>: Search for similar problems</p></li>
<li><p><strong>Join Discord</strong>: <cite>https://discord.gg/6sYmEbUp</cite></p></li>
<li><p><strong>Create an issue</strong>: For bugs or feature requests</p></li>
<li><p><strong>Ask questions</strong>: In GitHub Discussions</p></li>
</ol>
</section>
<section id="community-guidelines">
<h2>Community Guidelines<a class="headerlink" href="#community-guidelines" title="Link to this heading">#</a></h2>
<p>We are committed to providing a welcoming and inclusive environment:</p>
<ol class="arabic simple">
<li><p><strong>Be respectful</strong>: Treat everyone with respect</p></li>
<li><p><strong>Be helpful</strong>: Help others learn and contribute</p></li>
<li><p><strong>Be patient</strong>: Everyone learns at their own pace</p></li>
<li><p><strong>Be constructive</strong>: Provide constructive feedback</p></li>
</ol>
<section id="code-of-conduct">
<h3>Code of Conduct<a class="headerlink" href="#code-of-conduct" title="Link to this heading">#</a></h3>
<p>We follow the Contributor Covenant Code of Conduct. Please read it at:
<cite>https://www.contributor-covenant.org/version/2/0/code_of_conduct.html</cite></p>
</section>
</section>
<section id="recognition">
<h2>Recognition<a class="headerlink" href="#recognition" title="Link to this heading">#</a></h2>
<p>Contributors are recognized in:</p>
<ol class="arabic simple">
<li><p><strong>GitHub contributors list</strong></p></li>
<li><p><strong>Documentation acknowledgments</strong></p></li>
<li><p><strong>Release notes</strong></p></li>
<li><p><strong>Academic citations</strong> (for significant contributions)</p></li>
</ol>
<p>Thank you for contributing to GeomFuM! 🎉</p>
</section>
</section>


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