Merge pull request #833 from nextstrain/contributing-documentation

Contributing documentation

CONTRIBUTING.md

@@ -0,0 +1,19 @@
+---
+title: Contributing to Auspice
+---
+
+
+Auspice is developed via GitHub and issues and comments are very welcome -- [click here](https://github.com/nextstrain/auspice/issues/new) to create a new issue.
+Alternatively, you can [email us](mailto:hello@nextstrain.org) with any questions or comments you may have.
+
+
+## Contributing to Documentation
+
+This documentation is all contained within the Auspice GitHub repo -- see [the README](https://github.com/nextstrain/auspice/tree/master/docs-src) within the `docs-src` directory for more details and instructions on how to contribute.
+
+
+## Contributing to Development
+
+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 [GitHub issue](https://github.com/nextstrain/auspice/issues/new) before spending time in the codebase.
+For pull requests, please use [eslint](https://eslint.org/) as much as possible -- thanks!

docs-src/docs/contributing/overview.md

@@ -0,0 +1 @@
+../../../CONTRIBUTING.md

docs/advanced-functionality/misc.html

@@ -62,4 +62,4 @@
 <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 10/25/2019</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>
+</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>

docs/advanced-functionality/misc/index.html

@@ -62,4 +62,4 @@
 <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 10/25/2019</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>
+</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>

docs/advanced-functionality/second-trees.html

@@ -73,4 +73,4 @@ <h2><a class="anchor" aria-hidden="true" id="showing-potential-datasets-in-the-s
 <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 10/15/2019</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>
+</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>

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

@@ -73,4 +73,4 @@ <h2><a class="anchor" aria-hidden="true" id="showing-potential-datasets-in-the-s
 <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 10/15/2019</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>
+</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>