Browse Source

Migrate Auspice docs from docusaurus to RTD

As part of our migration of all nextstrain-docs to RTD and docs.nextstrain.org
this commit switches Auspice to using RTD.

There is further work needed in terms of organisation structure, using pages here
under docs.nextstrain.org's RTD page (as opposed to the Auspice subproject), but this
migration paves the way.

No content changes, but lots of syntax changes etc

See https://github.com/nextstrain/docs.nextstrain.org/issues/8 for context.
master
james hadfield 1 year ago
parent
commit
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CHANGELOG.md

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---
title: Changelog
---
# Changelog
## version 2.18.4 - 2020/09/28
* (Bugfix) Update dependencies to restore behavior of the leaflet-scroll overlay.

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DEV_DOCS.md

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---
title: Contributing to Auspice development
---
# Contributing to Auspice development
Thank you for helping us to improve Nextstrain!

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## docs
build/
i18n/

44
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# Auspice Documentation
This folder contains the static site generator and the markdown files which form the auspice documentation website, served via GitHub pages at [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice).
We are using [Docusaurus](https://docusaurus.io/) to generate the static site.
> Note that the code & content in this folder is used to generate the files in the `auspice/docs` directory, which are served by github pages.
Those files should not be modified, rather edit the contents of this directory & regenerate the documentation.
### Folder structure of `auspice/docs-src/`
* `README.md` this file
* `./docs/` contains the raw markdown files. The filenames (and directory names) will be used as URLs.
New pages here should also be added to `sidebars.json`.
* `./website/` the Docusaurus files needed to build the website.
* `./sidebars.json` define the links in the sidebar
* `./pages/index.js` the splash page
* `./siteConfig.js` docusarus configuration - [see docs here](https://docusaurus.io/docs/en/site-config)
## How to run
All commands run from this directory (`docs-src`).
#### Installing dependencies
```bash
npm install
# you must also have installed the dependencies from the parent directory (`auspice`)
```
#### Developing (live reloading etc):
```bash
npm run develop
```
#### (re-)build the static site
```bash
npm run build
```
> This command will modify the files in `../docs/` which is where the GitHub pages site is served from.
#### Deploy
Once changes are merged into the master branch and pushed to GitHub the changes will be live.

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---
title: Overview
hide_title: true
---
# Auspice: An Open-source Interactive Tool for Visualising Phylogenomic Data
![splash](assets/splash.png)
*Auspice being used to show the spread of influenza H7N9 virus across Asia.*
### Auspice is software to display beautiful, interactive visualisations of phylogenomic data.
Communicating scientific results while also allowing interrogation of the underlying data is an integral part of the scientific process.
Current scientific publishing practices hinder both the rapid dissemination of epidemiologically relevant results and the ability to easily interact with the data used to draw inferences.
These shortcomings motivated the [Nextstrain](https://nextstrain.org) project, for which Auspice was initially devloped.
Auspice can be run on your computer or integrated into websites.
It allows easy customisation of aesthetics and functionality, and powers the visualisations on [nextstrain.org](https://nextstrain.org).
For a more formal introduction to auspice & the wider nextstrain project, please see [Hadfield _et al.,_ Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018)](https://academic.oup.com/bioinformatics/article/34/23/4121/5001388).
![splash](assets/v2-pie-charts.gif)
*Exploring Enterovirus d68 by changing between three different colorings: clades, age-ranges & mutations at a certain genome position.*
## License and Copyright
Copyright © 2014-2020 Trevor Bedford and Richard Neher.
Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (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.

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../../../CHANGELOG.md

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docs-src/docs/tutorial/how-to-read-a-phylogenetic-tree.md

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---
title: How to read a phylogenetic tree
---
> TODO

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@ -1,5 +0,0 @@
---
title: Interpreting the entropy panel
---
> TODO

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docs-src/docs/tutorial/interpreting-frequencies.md

@ -1,5 +0,0 @@
---
title: Interpreting the frequencies panel
---
> TODO

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---
title: Interpreting the map
---
> TODO
* how are transmission lines created
* winner takes all -- uncertainty is not conveyed
* deme sizes

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---
title: Interpreting data with Auspice
---
> We need some form of tutorials / explanation of what you can do in the app and (I hope) what biological insights can be gleamed.
Potentially, these could be done using narratives, or, since narratives are basically the same file format as these docs pages we could essentially use the same file for both.
It'd be great to also have a page focusing on a single dataset (WNV might be good for this).
>This is the content from nextstrain.org/docs:
Visualisation of bioinformatics results is an integral part of current phylodynamics, both for data exploration and communication.
We wanted to build a tool that was highly interactive, versatile and usable as communication platform to quickly disseminate results to the wider community.
Auspice is written in JavaScript and is the app that powers all the phylogenomic analysis on nextstrain.org (github repo [here](https://www.github.com/nextstrain/auspice)).
![mumps](assets/mumps.png)
*Auspice displaying Mumps genomes from North America. See [nextstrain.org/mumps/na](https://www.nextstrain.org/mumps/na)*
### General design overview
We wanted to build a powerful yet not overly complex visualisation tool.
Currently this is centered around a number of "panels".
These allow us to display relationships between isolates such as their phylogenetic relationships, putative transmissions on the map, variability across the genome.
Colour is used consistently throughout the app in order to link different panels.
The generator of the data controls which traits are able to be visualised - for instance, transmissions can be turned off if the data is not informative.
A number of controls are made available in a sidebar to control the time period viewed, the layout of the tree etc.
We are currently working on allowing scientists to author custom narratives which describe the data, and control how the data is visualised as one progresses through the narrative.
See [here](/docs/visualisation/narratives) for more information.

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{
"name": "auspice-documentation",
"version": "1.0.0",
"description": "source files for auspice documentation",
"author": "James Hadfield",
"license": "AGPL-3.0-only",
"scripts": {
"develop": "cd website && docusaurus-start",
"build": "cd website && docusaurus-build && npm run removeBuiltDocs && cp -r ./build/auspice/* ../../docs && npm run makeReadme",
"build-docs": "npm run build",
"removeBuiltDocs": "rimraf ../docs/*",
"makeReadme": "echo '# Auspice built documentation to be served by GitHub pages.\\n\\nFiles in this folder should not be modified by hand -- they are generated from within the `docs-src` directory.' > ../docs/README.md"
},
"devDependencies": {
"docusaurus": "^1.13.0",
"rimraf": "^2.6.3"
}
}

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docs-src/website/core/Footer.js

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const React = require('react');
class Footer extends React.Component {
docUrl(doc) {
return `${this.props.config.baseUrl}${doc}`;
}
pageUrl(doc, language) {
const baseUrl = this.props.config.baseUrl;
return baseUrl + (language ? `${language}/` : '') + doc;
}
render() {
return (
<footer className="nav-footer" id="footer">
<section className="sitemap">
<div>
<a href={this.props.config.baseUrl}>
<img
style={{paddingLeft: "20px"}}
src={this.props.config.baseUrl + this.props.config.footerIcon}
alt={this.props.config.title}
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 className="copyright">
Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a>
</section>
<section className="copyright">
If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a>
</section>
<section className="copyright">{this.props.config.copyright}</section>
</footer>
);
}
}
module.exports = Footer;

281
docs-src/website/pages/en/index.js

@ -1,281 +0,0 @@
const React = require('react'); // eslint-disable-line
const CompLibrary = require('../../core/CompLibrary.js'); // eslint-disable-line
const siteConfig = require(`${process.cwd()}/siteConfig.js`); // eslint-disable-line
/* https://docusaurus.io/docs/en/api-pages#complibrarymarkdownblock */
const MarkdownBlock = CompLibrary.MarkdownBlock;
/* https://docusaurus.io/docs/en/api-pages#complibrarycontainer */
const Container = CompLibrary.Container;
const mainIntroduction = `
Communicating scientific results while also allowing interrogation of the underlying data is an integral part of the scientific process.
Current scientific publishing practices hinder both the rapid dissemination of epidemiologically relevant results and the ability to easily interact with the data which was used to draw the inferences.
These shortcomings motivated the [nextstrain](https://nextstrain.org) project, for which auspice was initially devloped.
Auspice is software to display beautiful interactive visualisations of phylogenomic data.
It can be run on your computer or integrated into websites.
It allows easy customisation of aesthetics and functionality, and powers the visualisations on [nextstrain.org](https://nextstrain.org).
`;
function imgUrl(img) {
return `${siteConfig.baseUrl}img/${img}`;
}
function docUrl(doc) {
return `${siteConfig.baseUrl}${doc}`;
}
const RenderLogos = () => (
<Container padding={['bottom', 'top']}>
<div className="iconsRow">
<a key={1} href="https://nextstrain.org/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="50" src={imgUrl("nextstrain.png")}/>
</a>
<a key={1} href="http://www.fredhutch.org/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="75" src={imgUrl("fred-hutch-logo-small.png")}/>
</a>
<a key={2} href="http://www.eb.tuebingen.mpg.de/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="65" src={imgUrl("max-planck-logo.png")}/>
</a>
<a key={3} href="https://www.nih.gov/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="52" src={imgUrl("nih-logo.jpg")}/>
</a>
<a key={4} href="https://erc.europa.eu/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="60" src={imgUrl("erc-logo.jpg")}/>
</a>
<a key={5} href="https://www.openscienceprize.org/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="82" src={imgUrl("osp-logo-small.png")}/>
</a>
<a key={6} href="http://biozentrum.org/" target="_blank" rel="noopener noreferrer">
<img alt="logo" width="85" src={imgUrl("bz-logo.png")} />
</a>
</div>
</Container>
);
class Button extends React.Component { // eslint-disable-line
render() {
return (
<div className="pluginWrapper buttonWrapper" style={{paddingTop: "30px"}}>
<a className={`button ${this.props.className}`} href={this.props.href} target={this.props.target}>
{this.props.children}
</a>
</div>
);
}
}
Button.defaultProps = {
target: '_self'
};
const SplashImage = () => (
<img className="splashImage" alt="splash image" src={imgUrl("splash.png")}/>
);
const SplashContainer = (props) => (
<div className="homeContainer">
<div className="homeSplashFade">
<div className="wrapper homeWrapper">{props.children}</div>
</div>
</div>
);
const Logo = (props) => (
<div className="projectLogo" style={{bottom: "auto", top: "100px"}}>
<img src={props.img_src} style={{maxHeight: "100px"}} alt="Project Logo" />
</div>
);
const ProjectTitle = () => (
<h2 className="projectTitle">
{siteConfig.title}
<small>{siteConfig.tagline}</small>
</h2>
);
const PromoSection = (props) => (
<div className="section promoSection">
<div className="promoRow">
<div className="pluginRowBlock">{props.children}</div>
</div>
</div>
);
const BlockContainer = (props) => (
<Container
padding={['bottom', 'top']}
id={props.id}
background={props.background}
>
<div className="gridBlock">
{props.children}
</div>
{props.footer || null}
</Container>
);
const Block = ({title, content, buttonText=false, buttonLink=false}) => (
<div className="blockElement alignCenter fourByGridBlock" key={title}>
<div className="blockContent">
<h2>{title}</h2>
<MarkdownBlock>
{content}
</MarkdownBlock>
{buttonText && buttonLink ? (
<Button href={buttonLink}>{buttonText}</Button>
) : null}
</div>
</div>
);
/**
* The contents of the "blocks" to be displayed on the splash page.
* Note that most of these are currently unused, but remain here as we hope to use them in the future.
*/
const blockContent = {
tutorial: {
title: 'Why interactive visualisation?',
content: "What can you learn by interacting with the data? Follow these guides to learn about what auspice helped us understand about Zika in the Americas",
buttonText: "tutorial",
buttonLink: docUrl("tutorial/overview")
},
getStarted: {
title: "Get started",
content: "Learn how to install auspice locally get up and running visualising phylogenomic data",
buttonText: "Installation",
buttonLink: docUrl("introduction/install")
},
build: {
title: "Build your own website",
content: "Learn how to use auspice to build customised websites -- either backed by a server or staticallly genenerated (e.g. for GitHub pages).",
buttonText: "build using github-pages",
buttonLink: docUrl("build-static/introduction")
},
augur: {
title: "Bioinformatics",
content: "Augur is our seperate toolkit for phylodynamic analysis with a focus on pathgen and outbreak tracking. It's designed to work seamlessly with auspice. See the [nextstrain documentation](https://nextstrain.org/docs/bioinformatics/introduction) to find out more.",
buttonText: "go to augur docs",
buttonLink: "https://nextstrain.org/docs/bioinformatics/introduction/"
},
narratives: {
title: "Narratives",
content: "Instead of simply presenting the data for someone to explore, use auspice to tell a story where _you_ control what visualisation is presented.",
buttonText: "writing narratives",
buttonLink: docUrl("narratives/introduction")
},
auspiceUs: {
title: "Drag & Drop data",
content: "auspice.us is a customised build of auspice designed to allow users to drag Newick files & metadata on and visualise their data. It's that simple.",
buttonText: "go to auspice.us",
buttonLink: "https://auspice.us"
},
version: {
title: "What's new?",
content: "We've just released version 2 of auspice with lots of new things (this website being one of them!) Click here for the release notes.",
buttonText: "Version 2",
buttonLink: docUrl("releases/v2")
}
};
class Index extends React.Component { // eslint-disable-line
render() {
return (
<div>
<SplashContainer>
<div className="splashTitle">
<Logo img_src={imgUrl('logo-light.svg')} />
<ProjectTitle />
<PromoSection>
<div style={{fontSize: "90%", lineHeight: "140%"}}>
<MarkdownBlock>
{mainIntroduction}
</MarkdownBlock>
</div>
</PromoSection>
</div>
<SplashImage/>
<BlockContainer background="highlight">
<Block {...blockContent.getStarted}/>
<Block {...blockContent.narratives}/>
<Block {...blockContent.version}/>
</BlockContainer>
<div style={{minHeight: "80px"}} />
<RenderLogos/>
</SplashContainer>
</div>
);
}
}
module.exports = Index;
/* UNUSED COMPONENTS
These were removed for v2 release as they are incomplete, however they should reappear
as we fill out the documentation & examples.
const showcaseUsers = {
nextstrain: {
name: "Nextstrain",
link: "https://nextstrain.org",
caption: "Real-time tracking of pathogen evolution",
image: "img/nextstrain.png"
},
auspiceUs: {
name: "auspice.us",
link: "https://auspice-us.herokuapp.com",
caption: "drag & drop viusualisation",
image: "img/logo-dark.svg"
},
ghana: {
name: "ARTIC workshop",
link: "https://artic-network.github.io/artic-workshop",
caption: "Simulated viral outbreak for a ARTIC workshop in Ghana, built using auspice as a static site generator",
image: "img/artic-logo.png"
}
};
const Showcase = (props) => (
<Container padding={['top', 'bottom']}>
<h2>Auspice is behind:</h2>
<div className="gridBlock">
{props.children}
</div>
</Container>
);
const ShowcaseItem = ({name, link, image, caption}) => (
<div className="blockElement alignCenter fourByGridBlock showcaseItem" key={name}>
<a href={link} target="_blank" rel="noopener noreferrer">
<h3 style={{marginTop: "0px"}}>
{name}
</h3>
<img src={image} alt={name} style={{maxHeight: "100px"}}/>
<p>{caption}</p>
</a>
</div>
);
<Showcase>
<ShowcaseItem {...showcaseUsers.nextstrain}/>
<ShowcaseItem {...showcaseUsers.auspiceUs}/>
<ShowcaseItem {...showcaseUsers.ghana}/>
</Showcase>
<div className="soloButtons">
<Button href={docUrl("introduction/overview")}>Read the docs</Button>
<Button href={docUrl("tutorial/overview")}>Learn how to interpret datasets</Button>
</div>
*/

37
docs-src/website/sidebars.json

@ -1,37 +0,0 @@
{
"docs": {
"Introduction": [
"introduction/overview",
"introduction/install",
"introduction/how-to-run"
],
"Advanced Functionality": [
"advanced-functionality/second-trees",
"advanced-functionality/view-settings",
"advanced-functionality/drag-drop-csv-tsv",
"advanced-functionality/misc"
],
"Customising Auspice": [
"customise-client/introduction",
"customise-client/api",
"customise-client/requests"
],
"Using a Custom Server": [
"server/introduction",
"server/api",
"server/authentication"
],
"Narratives": [
"narratives/introduction",
"narratives/how-to-write",
"narratives/create-pdf"
],
"Release Notes": [
"releases/changelog",
"releases/v2"
],
"Contributing": [
"contributing/overview"
]
}
}

85
docs-src/website/siteConfig.js

@ -1,85 +0,0 @@
/**
* Copyright (c) 2017-present, Facebook, Inc.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
// See https://docusaurus.io/docs/site-config for all the possible site configuration options.
const siteConfig = {
title: 'Auspice', // Title for your website.
tagline: 'Interactive exploration of phylodynamic & phylogenomic data.',
projectName: 'auspice',
organizationName: 'nextstrain',
url: 'https://nextstrain.github.io', // Your website URL
baseUrl: '/auspice/', // Base URL for your project */
// Header links in the top nav bar
headerLinks: [
{doc: 'introduction/overview', label: 'Docs'},
// {doc: 'tutorial/overview', label: 'Tutorial'}
],
/* path to images for header/footer */
headerIcon: 'img/logo-light.svg',
footerIcon: 'img/logo-light.svg',
favicon: 'img/favicon.ico',
colors: {
primaryColor: '#30353F', /* header navigation bar and sidebars */
secondaryColor: '#5DA8A3' /* second row of the header navigation bar when the site window is narrow */
},
/* Custom fonts for website */
/*
fonts: {
myFont: [
"Times New Roman",
"Serif"
],
myOtherFont: [
"-apple-system",
"system-ui"
]
},
*/
// This copyright info is used in /core/Footer.js and blog RSS/Atom feeds.
copyright: `Copyright © 2014-${new Date().getFullYear()} Richard Neher & Trevor Bedford`,
highlight: {
// The name of the theme used by Highlight.js when highlighting code.
// You can find the list of supported themes here:
// https://github.com/isagalaev/highlight.js/tree/master/src/styles
theme: 'solarized-dark'
},
// Add custom scripts here that would be placed in <script> tags.
scripts: ['https://buttons.github.io/buttons.js'],
// On page navigation for the current documentation page.
onPageNav: 'separate',
// No .html extensions for paths.
cleanUrl: true,
// Open Graph and Twitter card images.
ogImage: 'img/icon.svg',
twitterImage: 'img/icon.svg',
// Show documentation's last contributor's name.
// enableUpdateBy: true,
// Show documentation's last update time.
enableUpdateTime: true,
// disableHeaderTitle: true, /* don't automatically add title to top of page */
docsUrl: '' /* no /docs/ in URL */
// You may provide arbitrary config keys to be used as needed by your
// template. For example, if you need your repo's URL...
// repoUrl: 'https://github.com/facebook/test-site',
};
module.exports = siteConfig;

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docs-src/website/static/img/logo-dark.svg

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<?xml version="1.0" encoding="UTF-8"?>
<svg width="200px" height="200px" viewBox="0 0 200 200" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<!-- Generator: Sketch 52.5 (67469) - http://www.bohemiancoding.com/sketch -->
<title>icon copy</title>
<desc>Created with Sketch.</desc>
<defs>
<rect id="path-1" x="0" y="0" width="200" height="201"></rect>
</defs>
<g id="icon-copy" stroke="none" stroke-width="1" fill="none" fill-rule="evenodd">
<mask id="mask-2" fill="white">
<use xlink:href="#path-1"></use>
</mask>
<g id="Rectangle"></g>
<path d="M7.5,201 L99,1" id="Line" stroke="#30353F" stroke-width="15" stroke-linecap="square" mask="url(#mask-2)"></path>
<path d="M192.5,201 L100,2" id="Line" stroke="#30353F" stroke-width="15" stroke-linecap="square" mask="url(#mask-2)"></path>
<path d="M134.525012,72.3545577 C131.898763,91.9778105 123.664754,107.369579 109.822982,118.529862 C95.9812106,129.690145 82.0210413,134.431118 67.9424742,132.75278" id="Path-3" stroke="#30353F" stroke-width="15" mask="url(#mask-2)"></path>
<path d="M92.8033327,150.437802 C87.2580617,145.075444 82.3123172,141.421674 77.9660992,139.476492 C73.6198812,137.53131 68.6741366,136.016933 63.1288656,134.933362 C66.7380359,132.976705 70.3641768,130.208064 74.0072883,126.627438 C77.6503997,123.046812 81.0761669,117.593413 84.2845899,110.26724" id="Path-3" stroke="#30353F" stroke-width="10" stroke-linecap="round" mask="url(#mask-2)"></path>
</g>
</svg>

19
docs-src/website/static/img/logo-light.svg

@ -1,19 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<svg width="200px" height="200px" viewBox="0 0 200 200" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<!-- Generator: Sketch 52.5 (67469) - http://www.bohemiancoding.com/sketch -->
<title>icon</title>
<desc>Created with Sketch.</desc>
<defs>
<rect id="path-1" x="0" y="0" width="200" height="201"></rect>
</defs>
<g id="icon" stroke="none" stroke-width="1" fill="none" fill-rule="evenodd">
<mask id="mask-2" fill="white">
<use xlink:href="#path-1"></use>
</mask>
<g id="Rectangle"></g>
<path d="M7.5,201 L99,1" id="Line" stroke="#5DA8A3" stroke-width="15" stroke-linecap="square" mask="url(#mask-2)"></path>
<path d="M192.5,201 L100,2" id="Line" stroke="#5DA8A3" stroke-width="15" stroke-linecap="square" mask="url(#mask-2)"></path>
<path d="M134.525012,72.3545577 C131.898763,91.9778105 123.664754,107.369579 109.822982,118.529862 C95.9812106,129.690145 82.0210413,134.431118 67.9424742,132.75278" id="Path-3" stroke="#5DA8A3" stroke-width="15" mask="url(#mask-2)"></path>
<path d="M92.8033327,150.437802 C87.2580617,145.075444 82.3123172,141.421674 77.9660992,139.476492 C73.6198812,137.53131 68.6741366,136.016933 63.1288656,134.933362 C66.7380359,132.976705 70.3641768,130.208064 74.0072883,126.627438 C77.6503997,123.046812 81.0761669,117.593413 84.2845899,110.26724" id="Path-3" stroke="#5DA8A3" stroke-width="10" stroke-linecap="round" mask="url(#mask-2)"></path>
</g>
</svg>

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130
docs-src/website/static/styles.css

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/* see https://docusaurus.io/docs/en/api-pages#styles
This CSS file will get concatenated to the end of Docusaurus'
provided styles, allowing you to add to or override Docusaurus default styles as you wish.
Here is the docusaurus CSS:
https://github.com/facebook/docusaurus/blob/master/packages/docusaurus-1.x/lib/static/css/main.css
*/
:root {
--aqua: #5DA8A3;
--dark: #30353F;
}
.highlightBackground {
background-color: var(--aqua);
}
.darkBackground {
background-color: var(--dark);
}
/* .lightBackground {
background-color: rgb(186, 193, 224);
} */
a {
color: var(--aqua);
font-weight: 400;
}
a:hover {
color: var(--dark);
text-decoration: underline;
}
.nav-footer a:hover {
color: var(--aqua);
}
button:hover {
background-color: var(--dark);
}
header a:hover {
color: var(--aqua);
}
/* Showcase items */
.showcaseItem {
color: var(--dark);
cursor: pointer;
border: 1px solid white;
}
.showcaseItem a {
color: var(--dark);
}
.showcaseItem a:hover {
text-decoration: none;
}
.showcaseItem:hover {
border: 1px solid #e0e0e0;
border-radius: 10px;
}
.container.paddingTop {
padding-top: 0px;
}
.container.paddingBottom {
padding-bottom: 40px;
}
.blockContent {
height: 100%;
display: flex;
flex-direction: column;
flex-wrap: wrap;
justify-content: space-between
}
.container.highlightBackground h2 {
margin-top: 40px;
}
.iconsRow {
display: flex;
flex-direction: row;
flex-wrap: nowrap;
justify-content: space-between;
}
.navWrapper.wrapper {
border-right: 1px solid #e0e0e0;
}
/* add padding to splashTitle for non-mobile views */
@media (min-width: 500px) {
.splashTitle {
padding-top: 100px;
padding-bottom: 40px;
}
}
.soloButtons {
padding-bottom: 60px;
display: flex;
justify-content: space-around;
flex-direction: column;
}
.soloButtons a {
background: var(--aqua);
color: white;
border-color: var(--aqua);
}
.soloButtons a:hover {
border-color: var(--dark);
}
/* splash image */
.splashImage {
max-width: 800px;
padding-bottom: 40px;
}
@media (min-width: 800px) {
.splashImage {
width: 90%;
padding-bottom: 20px;
}
}

4
docs/.gitignore

@ -0,0 +1,4 @@
# read the docs generated files
_templates
_static
_build

20
docs/Makefile

@ -0,0 +1,20 @@
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

10
docs/README.md

@ -1,3 +1,9 @@
# Auspice built documentation to be served by GitHub pages.
# Auspice 'Read The Docs' Documentation.
Files in this folder should not be modified by hand -- they are generated from within the `docs-src` directory.
Very much a work-in-progress!
```
make clean
make html
open _build/html/index.html
```

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@ -1,6 +1,4 @@
---
title: "Adding extra metadata via CSV/TSV"
---
# Adding extra metadata via CSV/TSV
Auspice datasets can define a number of colorings -- e.g. "country", "age" -- which you can switch between via the dropdown in the left-hand sidebar.
By dragging CSV / TSV files onto the browser you can add in extra colorings.
@ -31,7 +29,7 @@ For instance, if we save the above example as a TSV file and drag it onto the br
This allows you to change the coloring (via the drop-down in the sidebar) to "secret" to reveal the information attached to those 4 USVI strains.
The tree will now look like:
![auspice with extra data shown via csv](assets/csv-extra-data.png)
![auspice with extra data shown via csv](../assets/csv-extra-data.png)
### Gotchas

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docs/advanced-functionality/index.rst

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======================================
Advanced Functionality
======================================
This page shouldn't be rendered & should jump to the first TOC entry instead. TODO.
.. toctree::
:hidden:
:maxdepth: 0
:titlesonly:
second-trees
view-settings
drag-drop-csv-tsv
misc

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docs-src/docs/advanced-functionality/misc.md → docs/advanced-functionality/misc.md

@ -1,6 +1,5 @@
---
title: "Miscellaneous"
---
# Miscellaneous
## How auspice handles unknown or missing data

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@ -1,6 +1,4 @@
---
title: "Displaying multiple trees"
---
# Displaying multiple trees
Auspice has the ability to display two trees side-by-side, and to draw lines between tips with the same name (aka tanglegrams).
This is useful to compare the shape of different trees, especially when they are from the same organism -- for instance comparing phylogenies constructed from different
@ -12,7 +10,7 @@ You can compare any two datasets which you have available -- for instance if you
A toggle is made available in the sidebar to turn off the lines drawn between tips.
![two-trees](assets/tangle.png)
![two-trees](../assets/tangle.png)
*Comparing epitope mutations between HA and NA (worldwide influena H3N2).*
*Notice how the segments can differ drastically in how many epitope mutations they acquire!*
*While the crossing of the lines between the tips doesn't always prove reassortment, it's usually a good indication that reassortment is present.*

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---
title: "View Settings"
---
# View Settings
View settings refer to things such as how we display the tree (radal? root-to-tip?), what panels we display (map? tree? both?), what colouring we are using etcetera.
There are three ways these can be controlled:

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# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- Project information -----------------------------------------------------
project = 'Auspice'
copyright = '2020, James Hadfield, Trevor Bedford and Richard Neher'
author = 'James Hadfield, Trevor Bedford and Richard Neher'
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'recommonmark',
'sphinx.ext.intersphinx',
'sphinx_markdown_tables',
'sphinxarg.ext',
'sphinx.ext.autodoc'
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'README.md']
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'nextstrain-sphinx-theme'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_theme_options = {
'display_version': False,
'logo_only': True,
'collapse_navigation': False,
'titles_only': True,
}

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======================================
Contributing
======================================
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.. toctree::
:hidden:
:maxdepth: 0
:titlesonly:
overview

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../../DEV_DOCS.md

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*
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*
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* @author Lea Verou
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---
title: Client Customisation API
---
# Client Customisation API
> The functionality detailed in this page needs more attention, both in terms of testing and code development.
We expect there to be some bugs and possible API changes.

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======================================
Customising the Auspice Client
======================================
This page shouldn't be rendered & should jump to the first TOC entry instead. TODO.
.. toctree::
:hidden:
:maxdepth: 0
:titlesonly:
introduction
api
requests

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---
title: Customising Auspice
---
# Customising the Auspice Client
Auspice allows you to customise the appearance and functionality of Auspice [when the client is built](introduction/how-to-run.md#auspice-build).
This is how Auspice running locally and nextstrain.org look different, despite both using "Auspice".
![mumps](assets/auspice-vs-nextstrain.png)
![mumps](../assets/auspice-vs-nextstrain.png)
*Notice the difference? Default Auspice (left) and nextstrain.org's customised version (right)*
@ -19,7 +17,7 @@ auspice build --extend <JSON>
[Here's](https://github.com/nextstrain/nextstrain.org/blob/master/auspice-client/customisations/config.json) the file used by nextstrain.org to change the appearance of Auspice in the above image.
See the [client customisation API](customise-client/api.md) for the available options.
See the [client customisation API](api.md) for the available options.

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---
title: Requests Made from the Client
---
# Requests Made from the Client
The Auspice client will make a number of requests to various endpoints, which this document aims to provide an overview of.
Some of these are dependent on the [build-time customisations](customise-client/introduction.md) in use, and we plan to allow more flexibility here using this mechanism.
Some of these are dependent on the [build-time customisations](../customise-client/introduction.md) in use, and we plan to allow more flexibility here using this mechanism.
## Requests to the Auspice Server
@ -24,7 +22,7 @@ When a dataset, narrative, or listing of available datasets is to be displayed i
* `/charon/getDataset` -- return the requested dataset
* `/charon/getNarrative` -- return the requested narrative
See [the server API documentation](server/api.md) for more details about the requests, or the [client customisation API](api.md) for the ability to change "/charon" to a different value.
See [the server API documentation](../server/api.md) for more details about the requests, or the [client customisation API](api.md) for the ability to change "/charon" to a different value.
### Image Requests

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<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Auspice · Interactive exploration of phylodynamic &amp; phylogenomic data.</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="Interactive exploration of phylodynamic &amp; phylogenomic data."/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Auspice · Interactive exploration of phylodynamic &amp; phylogenomic data."/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="Interactive exploration of phylodynamic &amp; phylogenomic data."/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class=""><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div><div class="homeContainer"><div class="homeSplashFade"><div class="wrapper homeWrapper"><div class="splashTitle"><div class="projectLogo" style="bottom:auto;top:100px"><img src="/auspice/img/logo-light.svg" style="max-height:100px" alt="Project Logo"/></div><h2 class="projectTitle">Auspice<small>Interactive exploration of phylodynamic &amp; phylogenomic data.</small></h2><div class="section promoSection"><div class="promoRow"><div class="pluginRowBlock"><div style="font-size:90%;line-height:140%"><div><span><p>Communicating scientific results while also allowing interrogation of the underlying data is an integral part of the scientific process.
Current scientific publishing practices hinder both the rapid dissemination of epidemiologically relevant results and the ability to easily interact with the data which was used to draw the inferences.
These shortcomings motivated the <a href="https://nextstrain.org">nextstrain</a> project, for which auspice was initially devloped.</p>
<p>Auspice is software to display beautiful interactive visualisations of phylogenomic data.
It can be run on your computer or integrated into websites.
It allows easy customisation of aesthetics and functionality, and powers the visualisations on <a href="https://nextstrain.org">nextstrain.org</a>.</p>
</span></div></div></div></div></div></div><img class="splashImage" alt="splash image" src="/auspice/img/splash.png"/><div class="container highlightBackground paddingBottom paddingTop"><div class="wrapper"><div class="gridBlock"><div class="blockElement alignCenter fourByGridBlock"><div class="blockContent"><h2>Get started</h2><div><span><p>Learn how to install auspice locally get up and running visualising phylogenomic data</p>
</span></div><div class="pluginWrapper buttonWrapper" style="padding-top:30px"><a class="button undefined" href="/auspice/introduction/install" target="_self">Installation</a></div></div></div><div class="blockElement alignCenter fourByGridBlock"><div class="blockContent"><h2>Narratives</h2><div><span><p>Instead of simply presenting the data for someone to explore, use auspice to tell a story where <em>you</em> control what visualisation is presented.</p>
</span></div><div class="pluginWrapper buttonWrapper" style="padding-top:30px"><a class="button undefined" href="/auspice/narratives/introduction" target="_self">writing narratives</a></div></div></div><div class="blockElement alignCenter fourByGridBlock"><div class="blockContent"><h2>What&#x27;s new?</h2><div><span><p>We've just released version 2 of auspice with lots of new things (this website being one of them!) Click here for the release notes.</p>
</span></div><div class="pluginWrapper buttonWrapper" style="padding-top:30px"><a class="button undefined" href="/auspice/releases/v2" target="_self">Version 2</a></div></div></div></div></div></div><div style="min-height:80px"></div><div class="container paddingBottom paddingTop"><div class="wrapper"><div class="iconsRow"><a href="https://nextstrain.org/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="50" src="/auspice/img/nextstrain.png"/></a><a href="http://www.fredhutch.org/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="75" src="/auspice/img/fred-hutch-logo-small.png"/></a><a href="http://www.eb.tuebingen.mpg.de/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="65" src="/auspice/img/max-planck-logo.png"/></a><a href="https://www.nih.gov/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="52" src="/auspice/img/nih-logo.jpg"/></a><a href="https://erc.europa.eu/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="60" src="/auspice/img/erc-logo.jpg"/></a><a href="https://www.openscienceprize.org/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="82" src="/auspice/img/osp-logo-small.png"/></a><a href="http://biozentrum.org/" target="_blank" rel="noopener noreferrer"><img alt="logo" width="85" src="/auspice/img/bz-logo.png"/></a></div></div></div></div></div></div></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 © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

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