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<h1>Contributing</h1>
<!-- Table of contents -->
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<h2> Contents </h2>
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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 to <code class="docutils literal notranslate"><span class="pre">scDataset</span></code>! This document outlines how to contribute to the project.</p>
<section id="getting-started">
<h2>Getting Started<a class="headerlink" href="#getting-started" title="Link to this heading">#</a></h2>
<ol class="arabic">
<li><p><strong>Fork the repository</strong> on GitHub</p></li>
<li><p><strong>Clone your fork</strong> locally:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/yourusername/scDataset.git
<span class="nb">cd</span><span class="w"> </span>scDataset
</pre></div>
</div>
</li>
<li><p><strong>Create a development environment</strong>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span>-m<span class="w"> </span>venv<span class="w"> </span>venv
<span class="nb">source</span><span class="w"> </span>venv/bin/activate<span class="w"> </span><span class="c1"># On Windows: venv\Scripts\activate</span>
pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span><span class="s2">".[dev]"</span>
</pre></div>
</div>
</li>
<li><p><strong>Create a feature branch</strong>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>checkout<span class="w"> </span>-b<span class="w"> </span>feature/your-feature-name
</pre></div>
</div>
</li>
</ol>
</section>
<section id="development-setup">
<h2>Development Setup<a class="headerlink" href="#development-setup" title="Link to this heading">#</a></h2>
<p>Install development dependencies:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span><span class="s2">".[dev,test,docs]"</span>
</pre></div>
</div>
<p>This installs:</p>
<ul class="simple">
<li><p><strong>Core dependencies</strong>: <code class="docutils literal notranslate"><span class="pre">torch</span></code>, <code class="docutils literal notranslate"><span class="pre">numpy</span></code></p></li>
<li><p><strong>Development tools</strong>: <code class="docutils literal notranslate"><span class="pre">black</span></code>, <code class="docutils literal notranslate"><span class="pre">flake8</span></code>, <code class="docutils literal notranslate"><span class="pre">mypy</span></code></p></li>
<li><p><strong>Testing</strong>: <code class="docutils literal notranslate"><span class="pre">pytest</span></code>, <code class="docutils literal notranslate"><span class="pre">pytest-cov</span></code></p></li>
<li><p><strong>Documentation</strong>: <code class="docutils literal notranslate"><span class="pre">sphinx</span></code>, <code class="docutils literal notranslate"><span class="pre">sphinx-book-theme</span></code></p></li>
</ul>
</section>
<section id="code-style">
<h2>Code Style<a class="headerlink" href="#code-style" title="Link to this heading">#</a></h2>
<p>We use several tools to maintain code quality:</p>
<p><strong>Black</strong> for code formatting:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>black<span class="w"> </span>src/<span class="w"> </span>tests/
</pre></div>
</div>
<p><strong>Flake8</strong> for linting:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>flake8<span class="w"> </span>src/<span class="w"> </span>tests/
</pre></div>
</div>
<p><strong>MyPy</strong> for type checking:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mypy<span class="w"> </span>src/
</pre></div>
</div>
<p><strong>Pre-commit hooks</strong> (optional but recommended):</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pre-commit<span class="w"> </span>install
</pre></div>
</div>
</section>
<section id="testing">
<h2>Testing<a class="headerlink" href="#testing" title="Link to this heading">#</a></h2>
<p>Run the test suite:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pytest
</pre></div>
</div>
<p>Run with coverage:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pytest<span class="w"> </span>--cov<span class="o">=</span>scdataset<span class="w"> </span>--cov-report<span class="o">=</span>html
</pre></div>
</div>
<p>Test specific modules:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pytest<span class="w"> </span>tests/test_strategy.py
</pre></div>
</div>
<section id="writing-tests">
<h3>Writing Tests<a class="headerlink" href="#writing-tests" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Place tests in the <code class="docutils literal notranslate"><span class="pre">tests/</span></code> directory</p></li>
<li><p>Use descriptive test names: <code class="docutils literal notranslate"><span class="pre">test_streaming_strategy_returns_correct_indices</span></code></p></li>
<li><p>Test both success and failure cases</p></li>
<li><p>Add tests for any new functionality</p></li>
</ul>
</section>
</section>
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Link to this heading">#</a></h2>
<p>Build documentation locally:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>docs
make<span class="w"> </span>html
</pre></div>
</div>
<p>View the built documentation:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>open<span class="w"> </span>build/html/index.html<span class="w"> </span><span class="c1"># On macOS</span>
<span class="c1"># On Linux: xdg-open build/html/index.html</span>
</pre></div>
</div>
<section id="writing-documentation">
<h3>Writing Documentation<a class="headerlink" href="#writing-documentation" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p>Use <strong>reStructuredText</strong> format for documentation files</p></li>
<li><p>Add <strong>docstrings</strong> to all public functions and classes</p></li>
<li><p>Follow <strong>NumPy docstring style</strong></p></li>
<li><p>Include <strong>examples</strong> in docstrings when helpful</p></li>
</ul>
<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">my_function</span><span class="p">(</span><span class="n">param1</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">param2</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">"default"</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
<span class="w"> </span><span class="sd">"""</span>
<span class="sd"> Brief description of the function.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> param1 : int</span>
<span class="sd"> Description of param1.</span>
<span class="sd"> param2 : str, default="default"</span>
<span class="sd"> Description of param2.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> bool</span>
<span class="sd"> Description of return value.</span>
<span class="sd"> Examples</span>
<span class="sd"> --------</span>
<span class="sd"> >>> my_function(42, "test")</span>
<span class="sd"> True</span>
<span class="sd"> """</span>
</pre></div>
</div>
</section>
</section>
<section id="types-of-contributions">
<h2>Types of Contributions<a class="headerlink" href="#types-of-contributions" title="Link to this heading">#</a></h2>
<section id="bug-reports">
<h3>Bug Reports<a class="headerlink" href="#bug-reports" title="Link to this heading">#</a></h3>
<p>When reporting bugs, please include:</p>
<ul class="simple">
<li><p><strong>Clear description</strong> of the problem</p></li>
<li><p><strong>Minimal example</strong> to reproduce the issue</p></li>
<li><p><strong>System information</strong> (OS, Python version, package versions)</p></li>
<li><p><strong>Expected vs actual behavior</strong></p></li>
</ul>
</section>
<section id="feature-requests">
<h3>Feature Requests<a class="headerlink" href="#feature-requests" title="Link to this heading">#</a></h3>
<p>For new features:</p>
<ul class="simple">
<li><p><strong>Describe the use case</strong> and motivation</p></li>
<li><p><strong>Provide examples</strong> of how it would be used</p></li>
<li><p><strong>Consider backwards compatibility</strong></p></li>
</ul>
</section>
<section id="code-contributions">
<h3>Code Contributions<a class="headerlink" href="#code-contributions" title="Link to this heading">#</a></h3>
<ul class="simple">
<li><p><strong>Start with an issue</strong> to discuss the change</p></li>
<li><p><strong>Keep changes focused</strong> - one feature/fix per PR</p></li>
<li><p><strong>Add tests</strong> for new functionality</p></li>
<li><p><strong>Update documentation</strong> as needed</p></li>
<li><p><strong>Follow code style</strong> guidelines</p></li>
</ul>
</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 an issue</strong> first (unless it’s a small fix)</p></li>
<li><p><strong>Fork and clone</strong> the repository</p></li>
<li><p><strong>Create a feature branch</strong></p></li>
<li><p><strong>Make your changes</strong>:</p>
<ul class="simple">
<li><p>Write code</p></li>
<li><p>Add tests</p></li>
<li><p>Update documentation</p></li>
<li><p>Run tests and style checks</p></li>
</ul>
</li>
<li><p><strong>Commit your changes</strong>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>add<span class="w"> </span>.
git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">"feat: add new sampling strategy"</span>
</pre></div>
</div>
</li>
<li><p><strong>Push to your fork</strong>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>push<span class="w"> </span>origin<span class="w"> </span>feature/your-feature-name
</pre></div>
</div>
</li>
<li><p><strong>Create a Pull Request</strong> on GitHub</p></li>
</ol>
</section>
<section id="commit-message-guidelines">
<h2>Commit Message Guidelines<a class="headerlink" href="#commit-message-guidelines" title="Link to this heading">#</a></h2>
<p>We follow <a class="reference external" href="https://www.conventionalcommits.org/">Conventional Commits</a>:</p>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">feat:</span></code>: New feature</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">fix:</span></code>: Bug fix</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">docs:</span></code>: Documentation changes</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">test:</span></code>: Adding tests</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">refactor:</span></code>: Code refactoring</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">style:</span></code>: Code style changes</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">ci:</span></code>: CI/CD changes</p></li>
</ul>
<p>Examples:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>feat:<span class="w"> </span>add<span class="w"> </span>weighted<span class="w"> </span>sampling<span class="w"> </span>strategy
fix:<span class="w"> </span>resolve<span class="w"> </span>memory<span class="w"> </span>leak<span class="w"> </span><span class="k">in</span><span class="w"> </span>block<span class="w"> </span>shuffling
docs:<span class="w"> </span>improve<span class="w"> </span>quickstart<span class="w"> </span>examples
test:<span class="w"> </span>add<span class="w"> </span>integration<span class="w"> </span>tests<span class="w"> </span><span class="k">for</span><span class="w"> </span>scDataset
</pre></div>
</div>
</section>
<section id="review-process">
<h2>Review Process<a class="headerlink" href="#review-process" title="Link to this heading">#</a></h2>
<p>All submissions require review. We use GitHub pull requests for this purpose.</p>
<ul class="simple">
<li><p><strong>Automated checks</strong> must pass (tests, linting, etc.)</p></li>
<li><p><strong>At least one maintainer</strong> must approve</p></li>
<li><p><strong>All conversations</strong> must be resolved</p></li>
<li><p><strong>Documentation</strong> must be updated if needed</p></li>
</ul>
</section>
<section id="release-process">
<h2>Release Process<a class="headerlink" href="#release-process" title="Link to this heading">#</a></h2>
<p>Releases are handled by maintainers:</p>
<ol class="arabic simple">
<li><p><strong>Version bump</strong> following semantic versioning</p></li>
<li><p><strong>Update changelog</strong></p></li>
<li><p><strong>Create GitHub release</strong></p></li>
<li><p><strong>Publish to PyPI</strong></p></li>
</ol>
</section>
<section id="community-guidelines">
<h2>Community Guidelines<a class="headerlink" href="#community-guidelines" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p><strong>Be respectful</strong> and inclusive</p></li>
<li><p><strong>Follow the code of conduct</strong></p></li>
<li><p><strong>Help others</strong> and share knowledge</p></li>
<li><p><strong>Stay on topic</strong> in discussions</p></li>
</ul>
</section>
<section id="getting-help">
<h2>Getting Help<a class="headerlink" href="#getting-help" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p><strong>GitHub Issues</strong>: Bug reports and feature requests</p></li>
<li><p><strong>GitHub Discussions</strong>: Questions and general discussion</p></li>
<li><p><strong>Documentation</strong>: Check the docs first!</p></li>
</ul>
<p>Thank you for contributing to <code class="docutils literal notranslate"><span class="pre">scDataset</span></code>! 🎉</p>
</section>
</section>
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