rebuild docs

docs/advanced-functionality/view-settings.html

@@ -109,6 +109,7 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 <tr><td><code>r</code></td><td>Geographic resolution</td><td><code>r=region</code></td></tr>
 <tr><td><code>m</code></td><td>Phylogeny x-axis measure</td><td><code>m=div</code></td></tr>
 <tr><td><code>l</code></td><td>Phylogeny layout</td><td><code>l=clock</code></td></tr>
+<tr><td><code>lang</code></td><td>Language</td><td><code>lang=ja</code> (Japanese)</td></tr>
 <tr><td><code>dmin</code></td><td>Temporal range (minimum)</td><td><code>dmin=2008-05-13</code></td></tr>
 <tr><td><code>dmax</code></td><td>Temporal range (maximum)</td><td><code>dmax=2010-05-13</code></td></tr>
 <tr><td><code>f_&lt;name&gt;</code></td><td>Data filter. Multiple values per key are <code>,</code> separated.</td><td><code>f_region=Oceania</code></td></tr>
@@ -129,4 +130,4 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 </table>
 <p><strong>See this in action:</strong></p>
 <p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/27/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</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:[email protected]">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 © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</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:[email protected]">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 © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

docs/advanced-functionality/view-settings/index.html

@@ -109,6 +109,7 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 <tr><td><code>r</code></td><td>Geographic resolution</td><td><code>r=region</code></td></tr>
 <tr><td><code>m</code></td><td>Phylogeny x-axis measure</td><td><code>m=div</code></td></tr>
 <tr><td><code>l</code></td><td>Phylogeny layout</td><td><code>l=clock</code></td></tr>
+<tr><td><code>lang</code></td><td>Language</td><td><code>lang=ja</code> (Japanese)</td></tr>
 <tr><td><code>dmin</code></td><td>Temporal range (minimum)</td><td><code>dmin=2008-05-13</code></td></tr>
 <tr><td><code>dmax</code></td><td>Temporal range (maximum)</td><td><code>dmax=2010-05-13</code></td></tr>
 <tr><td><code>f_&lt;name&gt;</code></td><td>Data filter. Multiple values per key are <code>,</code> separated.</td><td><code>f_region=Oceania</code></td></tr>
@@ -129,4 +130,4 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 </table>
 <p><strong>See this in action:</strong></p>
 <p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/27/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</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:[email protected]">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 © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</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:[email protected]">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 © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

docs/contributing/overview.html

@@ -61,8 +61,12 @@
 <p>This project strictly adheres to the <a href="https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md">Contributor Covenant Code of Conduct</a>.</p>
 <p>Please see the <a href="https://github.com/orgs/nextstrain/projects">project boards</a> for currently available issues.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-code"></a><a href="#contributing-code" 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>Contributing code</h2>
-<p><a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice locally.</p>
-<p>For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible (via <code>npm run lint</code>).</p>
+<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
+<p>Please comment on an open issue if you are working on it.
+For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
+<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
+In the future we will make this a requirement for PRs or commits.</p>
+<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" 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>Contributing to Documentation</h2>
 <p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
 <p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>

docs/contributing/overview/index.html

@@ -61,8 +61,12 @@
 <p>This project strictly adheres to the <a href="https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md">Contributor Covenant Code of Conduct</a>.</p>
 <p>Please see the <a href="https://github.com/orgs/nextstrain/projects">project boards</a> for currently available issues.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-code"></a><a href="#contributing-code" 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>Contributing code</h2>
-<p><a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice locally.</p>
-<p>For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible (via <code>npm run lint</code>).</p>
+<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
+<p>Please comment on an open issue if you are working on it.
+For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
+<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
+In the future we will make this a requirement for PRs or commits.</p>
+<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" 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>Contributing to Documentation</h2>
 <p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
 <p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>