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rebuild docs to reflect updated changelog

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james hadfield 2 years ago
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978cef97fa
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      docs/advanced-functionality/misc.html
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2
docs/advanced-functionality/misc.html

@ -62,4 +62,4 @@ Note that, if a discrete trait is selected, then a proportion of the pie-chart o
<p>If a trait is not set on a node it is considered missing, as well as if (after coersion to lower-case) it has one of the following values:</p>
<pre><code class="hljs css language-js">[<span class="hljs-string">"unknown"</span>, <span class="hljs-string">"?"</span>, <span class="hljs-string">"nan"</span>, <span class="hljs-string">"na"</span>, <span class="hljs-string">"n/a"</span>, <span class="hljs-string">""</span>, <span class="hljs-string">"unassigned"</span>]
</code></pre>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/24/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying mutliple trees</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/25/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying mutliple trees</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/misc/index.html

@ -62,4 +62,4 @@ Note that, if a discrete trait is selected, then a proportion of the pie-chart o
<p>If a trait is not set on a node it is considered missing, as well as if (after coersion to lower-case) it has one of the following values:</p>
<pre><code class="hljs css language-js">[<span class="hljs-string">"unknown"</span>, <span class="hljs-string">"?"</span>, <span class="hljs-string">"nan"</span>, <span class="hljs-string">"na"</span>, <span class="hljs-string">"n/a"</span>, <span class="hljs-string">""</span>, <span class="hljs-string">"unassigned"</span>]
</code></pre>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/24/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying mutliple trees</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/25/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev"></span><span>Displaying mutliple trees</span></a><a class="docs-next button" href="/auspice/customise-client/introduction"><span>Customising Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-auspice-handles-unknown-or-missing-data">How auspice handles unknown or missing data</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/second-trees.html

@ -73,4 +73,4 @@ Currently, the logic in <code>auspice view</code> is to match all datasets which
<li>have the same number of &quot;parts&quot; in the URL (parts are delimited by a <code>_</code> in the filename or a <code>/</code> in the URL).</li>
<li>differ from the currently selected dataset by only 1 part.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/advanced-functionality/second-trees/index.html

@ -73,4 +73,4 @@ Currently, the logic in <code>auspice view</code> is to match all datasets which
<li>have the same number of &quot;parts&quot; in the URL (parts are delimited by a <code>_</code> in the filename or a <code>/</code> in the URL).</li>
<li>differ from the currently selected dataset by only 1 part.</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/how-to-run"><span class="arrow-prev"></span><span>How to Run Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/misc"><span>Miscellaneous</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-load-multiple-trees">How to load multiple trees</a></li><li><a href="#showing-potential-datasets-in-the-sidebar">Showing potential datasets in the sidebar</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/contributing/overview.html

@ -62,4 +62,4 @@ Alternatively, you can <a href="mailto:hello@nextstrain.org">email us</a> with a
<p>We're very happy to have outside contributions to Auspice and see it grow.
If you are interested in contrubuting code then we would recommend that you create a <a href="https://github.com/nextstrain/auspice/issues/new">GitHub issue</a> before spending time in the codebase.
For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible -- thanks!</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 12/9/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-development">Contributing to Development</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 12/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-development">Contributing to Development</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/contributing/overview/index.html

@ -62,4 +62,4 @@ Alternatively, you can <a href="mailto:hello@nextstrain.org">email us</a> with a
<p>We're very happy to have outside contributions to Auspice and see it grow.
If you are interested in contrubuting code then we would recommend that you create a <a href="https://github.com/nextstrain/auspice/issues/new">GitHub issue</a> before spending time in the codebase.
For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible -- thanks!</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 12/9/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-development">Contributing to Development</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 12/10/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/v2"><span class="arrow-prev"></span><span>Auspice Version 2.0</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#contributing-to-documentation">Contributing to Documentation</a></li><li><a href="#contributing-to-development">Contributing to Development</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/api.html

@ -162,4 +162,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/api/index.html

@ -162,4 +162,4 @@ This can be changed by specifying <code>serverAddress</code> in the customisatio
<p>Note that currently you can't specify a different domain due to CORS headers.
This may well be a simple fix -- please get in touch if you can help here!</p>
</blockquote>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/introduction"><span class="arrow-prev"></span><span>Customising Auspice</span></a><a class="docs-next button" href="/auspice/customise-client/requests"><span>Requests Made from the Client</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#available-customisations">Available Customisations</a></li><li><a href="#sidebar-theme">Sidebar Theme</a></li><li><a href="#nav-bar-component">Nav-bar Component</a></li><li><a href="#splash-component">Splash component</a></li><li><a href="#specifying-the-api-server-address">Specifying the API server address</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/introduction.html

@ -63,4 +63,4 @@ This is how Auspice running locally and nextstrain.org look different, despite b
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/introduction/index.html

@ -63,4 +63,4 @@ This is how Auspice running locally and nextstrain.org look different, despite b
</code></pre>
<p><a href="https://github.com/nextstrain/nextstrain.org/blob/master/auspice/client/config.json">Here's</a> the file used by nextstrain.org to change the appearance of Auspice in the above image.</p>
<p>See the <a href="/auspice/customise-client/api">client customisation API</a> for the available options.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/misc"><span class="arrow-prev"></span><span>Miscellaneous</span></a><a class="docs-next button" href="/auspice/customise-client/api"><span>Client Customisation API</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/requests.html

@ -87,4 +87,4 @@ These are requested using our hardcoded access key, however this may change to a
<p>Auspice has the potential to include Google Analytics in a limited fashion.
See <a href="/auspice/customise-client/api#available-customisations">the client customisation API documentation</a> for how to set this.
Note that these requests are only made if you specify a Google Analytics key during build-time customisation of the client.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/customise-client/requests/index.html

@ -87,4 +87,4 @@ These are requested using our hardcoded access key, however this may change to a
<p>Auspice has the potential to include Google Analytics in a limited fashion.
See <a href="/auspice/customise-client/api#available-customisations">the client customisation API documentation</a> for how to set this.
Note that these requests are only made if you specify a Google Analytics key during build-time customisation of the client.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/api"><span class="arrow-prev"></span><span>Client Customisation API</span></a><a class="docs-next button" href="/auspice/server/introduction"><span>Auspice servers</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#requests-to-the-auspice-server">Requests to the Auspice Server</a><ul class="toc-headings"><li><a href="#auspice-client-javascript-code">Auspice Client JavaScript Code</a></li><li><a href="#quot-charon-quot-get-requests">&quot;Charon&quot; GET requests</a></li><li><a href="#image-requests">Image Requests</a></li></ul></li><li><a href="#external-requests">External Requests</a><ul class="toc-headings"><li><a href="#fonts">Fonts</a></li><li><a href="#leaflet">Leaflet</a></li><li><a href="#google-analytics-optional">Google Analytics (Optional)</a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/how-to-run.html

@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/13/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying mutliple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying mutliple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/how-to-run/index.html

@ -133,4 +133,4 @@ Using BEAST trees is possible, but you have to use Augur to convert them first.<
<li>You can download the narrative Markdown files by running <a href="https://github.com/nextstrain/auspice/blob/master/scripts/get-narratives.sh">this script</a> which will create a <code>./narratives</code> directory for you.</li>
</ul>
<p>You can then run <code>auspice view --datasetDir data --narrativeDir narratives</code> to visualise all of the <a href="https://nextstrain.org">nextstrain.org</a> datasets locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/13/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying mutliple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/install"><span class="arrow-prev"></span><span>Install Auspice</span></a><a class="docs-next button" href="/auspice/advanced-functionality/second-trees"><span>Displaying mutliple trees</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#how-to-get-an-example-dataset-up-and-running">How to Get an Example Dataset Up and Running</a></li><li><a href="#auspice-view"><code>auspice view</code></a></li><li><a href="#auspice-build"><code>auspice build</code></a></li><li><a href="#auspice-develop"><code>auspice develop</code></a></li><li><a href="#auspice-convert"><code>auspice convert</code></a></li><li><a href="#input-file-formats">Input File Formats</a><ul class="toc-headings"><li><a href="#dataset-jsons">Dataset JSONs</a></li><li><a href="#narratives">Narratives</a></li></ul></li><li><a href="#obtaining-a-set-of-input-files">Obtaining a Set of Input Files</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/install.html

@ -100,4 +100,4 @@ auspice --<span class="hljs-built_in">help</span>
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/install/index.html

@ -100,4 +100,4 @@ auspice --<span class="hljs-built_in">help</span>
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/overview.html

@ -69,4 +69,4 @@ It allows easy customisation of aesthetics and functionality, and powers the vis
<h2><a class="anchor" aria-hidden="true" id="license-and-copyright"></a><a href="#license-and-copyright" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>License and Copyright</h2>
<p>Copyright © 2014-2019 Trevor Bedford and Richard Neher.</p>
<p>Source code to Nextstrain is made available under the terms of the <a href="LICENSE.txt">GNU Affero General Public License</a> (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/20/2019</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/introduction/overview/index.html

@ -69,4 +69,4 @@ It allows easy customisation of aesthetics and functionality, and powers the vis
<h2><a class="anchor" aria-hidden="true" id="license-and-copyright"></a><a href="#license-and-copyright" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>License and Copyright</h2>
<p>Copyright © 2014-2019 Trevor Bedford and Richard Neher.</p>
<p>Source code to Nextstrain is made available under the terms of the <a href="LICENSE.txt">GNU Affero General Public License</a> (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/20/2019</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-next button" href="/auspice/introduction/install"><span>Install Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#license-and-copyright">License and Copyright</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/create-pdf.html

@ -95,4 +95,4 @@ decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see &quot;Printed 11 slides&quot; or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/create-pdf/index.html

@ -95,4 +95,4 @@ decktape generic --load-pause 3000 --key ArrowDown --size 1600x900 \
</code></pre>
<p>You'll see a lot of bad-looking warning messages printed in the terminal 😱, but as long as you see &quot;Printed 11 slides&quot; or similar then the command has worked.
You should now be able to view a static PDF of the narrative, in this case at <code>example.pdf</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/how-to-write"><span class="arrow-prev"></span><span>Writing a Narrative</span></a><a class="docs-next button" href="/auspice/releases/changelog"><span>Changelog</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#saving-an-online-narrative-to-pdf">Saving an online narrative to PDF</a></li><li><a href="#saving-a-local-narrative-to-pdf">Saving a local narrative to PDF</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/how-to-write.html

@ -151,4 +151,4 @@ For instance, let's assume your GitHub username is &quot;yourname&quot; and your
</code></pre>
<p>Then, by uploading the repo to GitHub it will be available to everyone at nextstrain.org/narratives/yourname/auspice-narrative-example.</p>
<p>This is how the narrative file at <a href="https://github.com/emmahodcroft/tb/blob/master/narratives/tb_crispell.md">GitHub &gt; emmahodcroft &gt; tb &gt; narratives</a> can be accessed via <a href="https://nextstrain.org/community/narratives/emmahodcroft/tb/crispell">nextstrain.org/community/narratives/emmahodcroft/tb/crispell</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/how-to-write/index.html

@ -151,4 +151,4 @@ For instance, let's assume your GitHub username is &quot;yourname&quot; and your
</code></pre>
<p>Then, by uploading the repo to GitHub it will be available to everyone at nextstrain.org/narratives/yourname/auspice-narrative-example.</p>
<p>This is how the narrative file at <a href="https://github.com/emmahodcroft/tb/blob/master/narratives/tb_crispell.md">GitHub &gt; emmahodcroft &gt; tb &gt; narratives</a> can be accessed via <a href="https://nextstrain.org/community/narratives/emmahodcroft/tb/crispell">nextstrain.org/community/narratives/emmahodcroft/tb/crispell</a>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 11/15/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/introduction"><span class="arrow-prev"></span><span>Communicating Results Using Narratives</span></a><a class="docs-next button" href="/auspice/narratives/create-pdf"><span>Converting a narrative to PDF</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#step-1-get-the-underlying-datasets">Step 1: Get the Underlying Datasets</a></li><li><a href="#step-2-start-a-simple-narrative">Step 2: Start a Simple Narrative</a></li><li><a href="#step-3-view-the-narrative-so-far">Step 3: View the Narrative so Far</a></li><li><a href="#step-4-adding-a-paragraph">Step 4: Adding a Paragraph</a></li><li><a href="#step-5-adding-more-paragraphs">Step 5: Adding More Paragraphs</a></li><li><a href="#step-6-upload-your-example-to-the-nextstrain-community-to-share-with-everyone">Step 6: Upload Your Example to the Nextstrain Community to Share with Everyone</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/introduction.html

@ -96,4 +96,4 @@ This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/narratives/introduction/index.html

@ -96,4 +96,4 @@ This limits what views can be defined by paragraphs in the narratives.</p></li>
<li><p>The frontmatter parsing will be extended to allow arrays of authors (etc).</p></li>
</ul>
<p>Take a look at the <a href="https://github.com/nextstrain/auspice/labels/narratives">GitHub issues tagged as related to narrative functionality</a> for a potentially more up-to-date list of these.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/authentication"><span class="arrow-prev"></span><span>Authentication</span></a><a class="docs-next button" href="/auspice/narratives/how-to-write"><span>Writing a Narrative</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#examples">Examples</a></li><li><a href="#how-to-write-a-narrative">How to Write a Narrative</a></li><li><a href="#sharing-narratives">Sharing Narratives</a></li><li><a href="#known-bugs-limitations">Known Bugs / Limitations</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

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@ -206,4 +206,4 @@ We have now generalised this, and the <a href="/auspice/server/api#charon-getava
<p>It's possible to use <code>auspice build</code> to <a href="/auspice/customise-client/introduction">build a custom auspice client</a>.
If this has been done, then running <code>auspice view</code> will serve it -- before you had to run <code>auspice view --customBuild</code>.
This streamlines generating custom auspice bundles and serving them locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/20/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
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@ -206,4 +206,4 @@ We have now generalised this, and the <a href="/auspice/server/api#charon-getava
<p>It's possible to use <code>auspice build</code> to <a href="/auspice/customise-client/introduction">build a custom auspice client</a>.
If this has been done, then running <code>auspice view</code> will serve it -- before you had to run <code>auspice view --customBuild</code>.
This streamlines generating custom auspice bundles and serving them locally.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/20/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/21/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/releases/changelog"><span class="arrow-prev"></span><span>Changelog</span></a><a class="docs-next button" href="/auspice/contributing/overview"><span>Contributing to Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#whats-new">What's New</a></li><li><a href="#backstory">Backstory</a></li><li><a href="#i-dont-want-to-upgrade-how-can-i-continue-to-use-auspice-v1">I don't want to upgrade - how can I continue to use Auspice v1?</a></li><li><a href="#pie-charts-to-represent-discrete-variables-on-a-map">Pie charts to represent discrete variables on a map</a></li><li><a href="#new-dataset-json-format">New dataset JSON format</a></li><li><a href="#more-information-in-tree-info-boxes">More information in tree info boxes</a></li><li><a href="#display-of-second-trees">Display of second trees</a></li><li><a href="#display-better-dates-on-the-tree-axis">Display better dates on the tree axis</a></li><li><a href="#map-quot-reset-zoom-quot-button-zooms-to-include-all-demes">Map &quot;reset zoom&quot; button zooms to include all demes</a></li><li><a href="#consistent-colouring-of-missing-data-in-the-tree">Consistent colouring of missing data in the tree</a></li><li><a href="#removal-of-twitter-amp-google-analytics">Removal of Twitter &amp; Google Analytics</a></li><li><a href="#improvements-in-the-entropy-panel">Improvements in the entropy panel</a></li><li><a href="#auspice-responds-to-server-redirects-for-datasets">Auspice responds to server redirects for datasets</a></li><li><a href="#importing-server-code-from-auspice">Importing (server) code from Auspice</a></li><li><a href="#new-auspice-subcommand-auspice-convert">New Auspice subcommand: <code>auspice convert</code></a></li><li><a href="#ability-to-show-a-quot-build-quot-source-url-in-the-sidebar">Ability to show a &quot;build&quot; source URL in the sidebar</a></li><li><a href="#auspice-view-uses-a-custom-auspice-client-if-present"><code>auspice view</code> uses a custom Auspice client if present</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

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@ -173,4 +173,4 @@ Each object has properties</p>
<li><code>dataset</code> -- the dataset associated with this block</li>
<li><code>query</code> -- the query associated with this block</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

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docs/server/api/index.html

@ -173,4 +173,4 @@ Each object has properties</p>
<li><code>dataset</code> -- the dataset associated with this block</li>
<li><code>query</code> -- the query associated with this block</li>
</ul>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/introduction"><span class="arrow-prev"></span><span>Auspice servers</span></a><a class="docs-next button" href="/auspice/server/authentication"><span>Authentication</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-client-requests">Auspice client requests</a><ul class="toc-headings"><li><a href="#charon-getavailable"><code>/charon/getAvailable</code></a></li><li><a href="#charon-getdataset"><code>/charon/getDataset</code></a></li><li><a href="#charon-getnarrative"><code>/charon/getNarrative</code></a></li></ul></li><li><a href="#suppling-custom-handlers-to-the-auspice-server">Suppling custom handlers to the Auspice server</a></li><li><a href="#importing-code-from-auspice">Importing code from Auspice</a><ul class="toc-headings"><li><a href="#convertfromv1"><code>convertFromV1</code></a></li><li><a href="#parsenarrativefile"><code>parseNarrativeFile</code></a></li></ul></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/server/authentication.html

@ -73,4 +73,4 @@ This allows the server to examine the cookie and:</p>
<p>It is this custom authentication page which can process a login and set a cookie appropriately.
As Auspice is served from the same domain, the cookie should remain with all requests.</p>
<p>Implementing authentication is beyond the scope of this documentation, but we can recommend <a href="http://www.passportjs.org">PassportJS</a> and <a href="https://auth0.com/">Auth0</a>, the latter of which allows you to easily use single sign-on strategies.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/16/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/api"><span class="arrow-prev"></span><span>Server API</span></a><a class="docs-next button" href="/auspice/narratives/introduction"><span>Communicating Results Using Narratives</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#using-the-server-to-verify-cookies">Using the Server to Verify Cookies</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/server/api"><span class="arrow-prev"></span><span>Server API</span></a><a class="docs-next button" href="/auspice/narratives/introduction"><span>Communicating Results Using Narratives</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#using-the-server-to-verify-cookies">Using the Server to Verify Cookies</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2019 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

2
docs/server/authentication/index.html

@ -73,4 +73,4 @@ This allows the server to examine the cookie and:</p>
<p>It is this custom authentication page which can process a login and set a cookie appropriately.
As Auspice is served from the same domain, the cookie should remain with all requests.</p>
<p>Implementing authentication is beyond the scope of this documentation, but we can recommend <a href="http://www.passportjs.org">PassportJS</a> and <a href="https://auth0.com/">Auth0</a>, the latter of which allows you to easily use single sign-on strategies.</p>