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Commit 66198e69 authored by Pauline Maury Laribière's avatar Pauline Maury Laribière
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Merge branch 'documentation' into 'master' 

Documentation

See merge request !7
parents a16529dd 5a6af494
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.Rbuildignore
View file @ 66198e69
...@@ -15,3 +15,6 @@ example.Rmd ...@@ -15,3 +15,6 @@ example.Rmd
install.R install.R
requirements.txt requirements.txt
^_pkgdown\.yml$
^docs$
^pkgdown$
.gitignore
View file @ 66198e69
...@@ -377,4 +377,4 @@ tags ...@@ -377,4 +377,4 @@ tags
# Renku # Renku
.renku.lock .renku.lock
.renku/tmp .renku/tmp
.renku/cache .renku/cache
\ No newline at end of file
.gitlab-ci.yml
View file @ 66198e69
...@@ -5,6 +5,7 @@ variables: ...@@ -5,6 +5,7 @@ variables:
stages: stages:
- build - build
- deploy
image_build: image_build:
stage: build stage: build
...@@ -14,4 +15,21 @@ image_build: ...@@ -14,4 +15,21 @@ image_build:
script: | script: |
CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7) CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 . docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 .
docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7
\ No newline at end of file tags:
- image-build
except:
variables:
- $CI_PROJECT_URL == "https://gitlab.com/d6538/fso-metadata-r"
pages:
stage: deploy
image: alpine:latest
script:
- echo 'Nothing to do...'
artifacts:
paths:
- docs
only:
variables:
- $CI_PROJECT_URL == "https://gitlab.com/d6538/fso-metadata-r"
_pkgdown.yml 0 → 100644
View file @ 66198e69
template:
bootstrap: 5
docs/404.html 0 → 100644
View file @ 66198e69
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Page not found (404) • fso.metadata</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="bootstrap-toc.css">
<script src="bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script>
<meta property="og:title" content="Page not found (404)" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-title-body">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">fso.metadata</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Page not found (404)</h1>
</div>
Content not found. Please use links in the navbar.
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Pauline Maury Laribiere.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
docs/authors.html 0 → 100644
View file @ 66198e69
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Authors • fso.metadata</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="bootstrap-toc.css">
<script src="bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script>
<meta property="og:title" content="Authors" />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-authors">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">fso.metadata</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.0.1</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Authors</h1>
</div>
<ul class="list-unstyled">
<li>
<p><strong>Pauline Maury Laribiere</strong>. Author, maintainer.
</p>
</li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Pauline Maury Laribiere.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
docs/bootstrap-toc.css 0 → 100644
View file @ 66198e69
/*!
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
* Copyright 2015 Aidan Feldman
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
/* All levels of nav */
nav[data-toggle='toc'] .nav > li > a {
display: block;
padding: 4px 20px;
font-size: 13px;
font-weight: 500;
color: #767676;
}
nav[data-toggle='toc'] .nav > li > a:hover,
nav[data-toggle='toc'] .nav > li > a:focus {
padding-left: 19px;
color: #563d7c;
text-decoration: none;
background-color: transparent;
border-left: 1px solid #563d7c;
}
nav[data-toggle='toc'] .nav > .active > a,
nav[data-toggle='toc'] .nav > .active:hover > a,
nav[data-toggle='toc'] .nav > .active:focus > a {
padding-left: 18px;
font-weight: bold;
color: #563d7c;
background-color: transparent;
border-left: 2px solid #563d7c;
}
/* Nav: second level (shown on .active) */
nav[data-toggle='toc'] .nav .nav {
display: none; /* Hide by default, but at >768px, show it */
padding-bottom: 10px;
}
nav[data-toggle='toc'] .nav .nav > li > a {
padding-top: 1px;
padding-bottom: 1px;
padding-left: 30px;
font-size: 12px;
font-weight: normal;
}
nav[data-toggle='toc'] .nav .nav > li > a:hover,
nav[data-toggle='toc'] .nav .nav > li > a:focus {
padding-left: 29px;
}
nav[data-toggle='toc'] .nav .nav > .active > a,
nav[data-toggle='toc'] .nav .nav > .active:hover > a,
nav[data-toggle='toc'] .nav .nav > .active:focus > a {
padding-left: 28px;
font-weight: 500;
}
/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */
nav[data-toggle='toc'] .nav > .active > ul {
display: block;
}
docs/bootstrap-toc.js 0 → 100644
View file @ 66198e69
/*!
* Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
* Copyright 2015 Aidan Feldman
* Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
(function() {
'use strict';
window.Toc = {
helpers: {
// return all matching elements in the set, or their descendants
findOrFilter: function($el, selector) {
// http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
// http://stackoverflow.com/a/12731439/358804
var $descendants = $el.find(selector);
return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])');
},
generateUniqueIdBase: function(el) {
var text = $(el).text();
var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-');
return anchor || el.tagName.toLowerCase();
},
generateUniqueId: function(el) {
var anchorBase = this.generateUniqueIdBase(el);
for (var i = 0; ; i++) {
var anchor = anchorBase;
if (i > 0) {
// add suffix
anchor += '-' + i;
}
// check if ID already exists
if (!document.getElementById(anchor)) {
return anchor;
}
}
},
generateAnchor: function(el) {
if (el.id) {
return el.id;
} else {
var anchor = this.generateUniqueId(el);
el.id = anchor;
return anchor;
}
},
createNavList: function() {
return $('<ul class="nav"></ul>');
},
createChildNavList: function($parent) {
var $childList = this.createNavList();
$parent.append($childList);
return $childList;
},
generateNavEl: function(anchor, text) {
var $a = $('<a></a>');
$a.attr('href', '#' + anchor);
$a.text(text);
var $li = $('<li></li>');
$li.append($a);
return $li;
},
generateNavItem: function(headingEl) {
var anchor = this.generateAnchor(headingEl);
var $heading = $(headingEl);
var text = $heading.data('toc-text') || $heading.text();
return this.generateNavEl(anchor, text);
},
// Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
getTopLevel: function($scope) {
for (var i = 1; i <= 6; i++) {
var $headings = this.findOrFilter($scope, 'h' + i);
if ($headings.length > 1) {
return i;
}
}
return 1;
},
// returns the elements for the top level, and the next below it
getHeadings: function($scope, topLevel) {
var topSelector = 'h' + topLevel;
var secondaryLevel = topLevel + 1;
var secondarySelector = 'h' + secondaryLevel;
return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
},
getNavLevel: function(el) {
return parseInt(el.tagName.charAt(1), 10);
},
populateNav: function($topContext, topLevel, $headings) {
var $context = $topContext;
var $prevNav;
var helpers = this;
$headings.each(function(i, el) {
var $newNav = helpers.generateNavItem(el);
var navLevel = helpers.getNavLevel(el);
// determine the proper $context
if (navLevel === topLevel) {
// use top level
$context = $topContext;
} else if ($prevNav && $context === $topContext) {
// create a new level of the tree and switch to it
$context = helpers.createChildNavList($prevNav);
} // else use the current $context
$context.append($newNav);
$prevNav = $newNav;
});
},
parseOps: function(arg) {
var opts;
if (arg.jquery) {
opts = {
$nav: arg
};
} else {
opts = arg;
}
opts.$scope = opts.$scope || $(document.body);
return opts;
}
},
// accepts a jQuery object, or an options object
init: function(opts) {
opts = this.helpers.parseOps(opts);
// ensure that the data attribute is in place for styling
opts.$nav.attr('data-toggle', 'toc');
var $topContext = this.helpers.createChildNavList(opts.$nav);
var topLevel = this.helpers.getTopLevel(opts.$scope);
var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
this.helpers.populateNav($topContext, topLevel, $headings);
}
};
$(function() {
$('nav[data-toggle="toc"]').each(function(i, el) {
var $nav = $(el);
Toc.init($nav);
});
});
})();
docs/docsearch.css 0 → 100644
View file @ 66198e69
/* Docsearch -------------------------------------------------------------- */
/*
Source: https://github.com/algolia/docsearch/
License: MIT
*/
.algolia-autocomplete {
display: block;
-webkit-box-flex: 1;
-ms-flex: 1;
flex: 1
}
.algolia-autocomplete .ds-dropdown-menu {
width: 100%;
min-width: none;
max-width: none;
padding: .75rem 0;
background-color: #fff;
background-clip: padding-box;
border: 1px solid rgba(0, 0, 0, .1);
box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
}
@media (min-width:768px) {
.algolia-autocomplete .ds-dropdown-menu {
width: 175%
}
}
.algolia-autocomplete .ds-dropdown-menu::before {
display: none
}
.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
padding: 0;
background-color: rgb(255,255,255);
border: 0;
max-height: 80vh;
}
.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
margin-top: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion {
padding: 0;
overflow: visible
}
.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
padding: .125rem 1rem;
margin-top: 0;
font-size: 1.3em;
font-weight: 500;
color: #00008B;
border-bottom: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
float: none;
padding-top: 0