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github-actions 2020-12-18 19:07:23 +00:00
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commit 2ba1a3411f
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dev/change-log/index.html
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</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="#next-release-030" class="md-nav__link">
next release (0.3.0)
</a>
</li>
<li class="md-nav__item">
<a href="#v023" class="md-nav__link">
v0.2.3
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</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="#next-release-030" class="md-nav__link">
next release (0.3.0)
</a>
</li>
<li class="md-nav__item">
<a href="#v023" class="md-nav__link">
v0.2.3
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<h1 id="change-log">Change Log<a class="headerlink" href="#change-log" title="Permanent link">&para;</a></h1>
<h2 id="next-release-030">next release (0.3.0)<a class="headerlink" href="#next-release-030" title="Permanent link">&para;</a></h2>
<ul>
<li>Update R and Python virtual environments</li>
</ul>
<h2 id="v023">v0.2.3<a class="headerlink" href="#v023" title="Permanent link">&para;</a></h2>
<ul>
<li>Fix participant IDS in the example analysis workflow</li>

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Remove packages
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</li>
<li class="md-nav__item">
<a href="#updating-all-packages" class="md-nav__link">
Updating all packages
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Remove packages
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<li class="md-nav__item">
<a href="#updating-all-packages_1" class="md-nav__link">
Updating all packages
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Remove packages
</a>
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<li class="md-nav__item">
<a href="#updating-all-packages" class="md-nav__link">
Updating all packages
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Remove packages
</a>
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<li class="md-nav__item">
<a href="#updating-all-packages_1" class="md-nav__link">
Updating all packages
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<p>Try to install any new package using <code>conda install -c CHANNEL PACKAGE_NAME</code> (you can use <code>pip</code> if the package is only available there). Make sure your Python virtual environment is active (<code>conda activate YOUR_ENV</code>).</p>
<h3 id="remove-packages">Remove packages<a class="headerlink" href="#remove-packages" title="Permanent link">&para;</a></h3>
<p>Uninstall packages using the same manager you used to install them <code>conda remove PACKAGE_NAME</code> or <code>pip uninstall PACKAGE_NAME</code></p>
<h3 id="updating-all-packages">Updating all packages<a class="headerlink" href="#updating-all-packages" title="Permanent link">&para;</a></h3>
<p>Make sure your Python virtual environment is active (<code>conda activate YOUR_ENV</code>), then run
<div class="highlight"><pre><span></span><code>conda update --all
</code></pre></div></p>
<h3 id="update-your-conda-environmentyaml">Update your conda <code>environment.yaml</code><a class="headerlink" href="#update-your-conda-environmentyaml" title="Permanent link">&para;</a></h3>
<p>After installing or removing a package you can use the following command in your terminal to update your <code>environment.yaml</code> before publishing your pipeline. Note that we ignore the package version for <code>libfortran</code> to keep compatibility with Linux:
<div class="highlight"><pre><span></span><code>conda env <span class="nb">export</span> --no-builds <span class="p">|</span> sed <span class="s1">&#39;s/^.*libgfortran.*$/ - libgfortran/&#39;</span> &gt; environment.yml
<p>After installing or removing a package you can use the following command in your terminal to update your <code>environment.yaml</code> before publishing your pipeline. Note that we ignore the package version for <code>libfortran</code> and <code>mkl</code> to keep compatibility with Linux:
<div class="highlight"><pre><span></span><code>conda env <span class="nb">export</span> --no-builds <span class="p">|</span> sed <span class="s1">&#39;s/^.*libgfortran.*$/ - libgfortran/&#39;</span> <span class="p">|</span> sed <span class="s1">&#39;s/^.*mkl=.*$/ - mkl/&#39;</span> &gt; environment.yml
</code></pre></div></p>
<h2 id="r-virtual-environment">R Virtual Environment<a class="headerlink" href="#r-virtual-environment" title="Permanent link">&para;</a></h2>
<h3 id="add-new-packages_1">Add new packages<a class="headerlink" href="#add-new-packages_1" title="Permanent link">&para;</a></h3>
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<li>Run <code>R</code> to open an R interactive session</li>
<li>Run <code>renv::remove("PACKAGE_NAME")</code></li>
</ol>
<h3 id="updating-all-packages_1">Updating all packages<a class="headerlink" href="#updating-all-packages_1" title="Permanent link">&para;</a></h3>
<ol>
<li>Open your terminal and navigate to RAPIDS&rsquo; root folder</li>
<li>Run <code>R</code> to open an R interactive session</li>
<li>Run <code>renv::update()</code></li>
</ol>
<h3 id="update-your-r-renvlock">Update your R <code>renv.lock</code><a class="headerlink" href="#update-your-r-renvlock" title="Permanent link">&para;</a></h3>
<p>After installing or removing a package you can use the following command in your terminal to update your <code>renv.lock</code> before publishing your pipeline.</p>
<ol>

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<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 2A10 10 0 002 12c0 4.42 2.87 8.17 6.84 9.5.5.08.66-.23.66-.5v-1.69c-2.77.6-3.36-1.34-3.36-1.34-.46-1.16-1.11-1.47-1.11-1.47-.91-.62.07-.6.07-.6 1 .07 1.53 1.03 1.53 1.03.87 1.52 2.34 1.07 2.91.83.09-.65.35-1.09.63-1.34-2.22-.25-4.55-1.11-4.55-4.92 0-1.11.38-2 1.03-2.71-.1-.25-.45-1.29.1-2.64 0 0 .84-.27 2.75 1.02.79-.22 1.65-.33 2.5-.33.85 0 1.71.11 2.5.33 1.91-1.29 2.75-1.02 2.75-1.02.55 1.35.2 2.39.1 2.64.65.71 1.03 1.6 1.03 2.71 0 3.82-2.34 4.66-4.57 4.91.36.31.69.92.69 1.85V21c0 .27.16.59.67.5C19.14 20.16 22 16.42 22 12A10 10 0 0012 2z"/></svg></span> Bugs and feature requests should be posted on <a href="https://github.com/carissalow/rapids/issues">Github</a>. </p>
<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M139.61 35.5a12 12 0 00-17 0L58.93 98.81l-22.7-22.12a12 12 0 00-17 0L3.53 92.41a12 12 0 000 17l47.59 47.4a12.78 12.78 0 0017.61 0l15.59-15.62L156.52 69a12.09 12.09 0 00.09-17zm0 159.19a12 12 0 00-17 0l-63.68 63.72-22.7-22.1a12 12 0 00-17 0L3.53 252a12 12 0 000 17L51 316.5a12.77 12.77 0 0017.6 0l15.7-15.69 72.2-72.22a12 12 0 00.09-16.9zM64 368c-26.49 0-48.59 21.5-48.59 48S37.53 464 64 464a48 48 0 000-96zm432 16H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16v-32a16 16 0 00-16-16zm0-320H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16V80a16 16 0 00-16-16zm0 160H208a16 16 0 00-16 16v32a16 16 0 0016 16h288a16 16 0 0016-16v-32a16 16 0 00-16-16z"/></svg></span> Join our discussions on our algorithms and assumptions for feature <a href="https://github.com/carissalow/rapids/issues?q=is%3Aissue+is%3Aopen+label%3Adiscussion">processing</a>.</p>
<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><path d="M424.4 214.7L72.4 6.6C43.8-10.3 0 6.1 0 47.9V464c0 37.5 40.7 60.1 72.4 41.3l352-208c31.4-18.5 31.5-64.1 0-82.6z"/></svg></span> Ready to start? Go to <a href="setup/installation/">Installation</a>, then to <a href="setup/configuration/">Configuration</a>, and then to <a href="setup/execution/">Execution</a></p>
<p><span class="twemoji"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M370.72 133.28C339.458 104.008 298.888 87.962 255.848 88c-77.458.068-144.328 53.178-162.791 126.85-1.344 5.363-6.122 9.15-11.651 9.15H24.103c-7.498 0-13.194-6.807-11.807-14.176C33.933 94.924 134.813 8 256 8c66.448 0 126.791 26.136 171.315 68.685L463.03 40.97C478.149 25.851 504 36.559 504 57.941V192c0 13.255-10.745 24-24 24H345.941c-21.382 0-32.09-25.851-16.971-40.971l41.75-41.749zM32 296h134.059c21.382 0 32.09 25.851 16.971 40.971l-41.75 41.75c31.262 29.273 71.835 45.319 114.876 45.28 77.418-.07 144.315-53.144 162.787-126.849 1.344-5.363 6.122-9.15 11.651-9.15h57.304c7.498 0 13.194 6.807 11.807 14.176C478.067 417.076 377.187 504 256 504c-66.448 0-126.791-26.136-171.315-68.685L48.97 471.03C33.851 486.149 8 475.441 8 454.059V320c0-13.255 10.745-24 24-24z"/></svg></span> Are you upgrading from RAPIDS <a href="https://rapidspitt.readthedocs.io/en/latest/">beta</a>? Follow this <a href="migrating-from-old-versions">guide</a></p>
</div>
<h2 id="how-does-it-work">How does it work?<a class="headerlink" href="#how-does-it-work" title="Permanent link">&para;</a></h2>
<p>RAPIDS is formed by R and Python scripts orchestrated by <a href="https://snakemake.readthedocs.io/en/stable/">Snakemake</a>. We suggest you read Snakemake&rsquo;s docs but in short: every link in the analysis chain is atomic and has files as input and output. Behavioral features are processed per sensor and per participant.</p>

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