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Update documentation
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svniemeijer committed Oct 31, 2022
1 parent e50df77 commit 65532d4
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Showing 512 changed files with 3,010 additions and 1,856 deletions.
6 changes: 3 additions & 3 deletions DEVELOPER
Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@ get regenerated (all using the autotools build system):

Run 'make doc' to regenerate the documentation.
Current versions used for generating the documentation are:
- Sphinx 4.4.0
- Sphinx 5.3.0
- sphinx-autobuild 2021.3.14
- sphinx-rtd-theme 1.0.0
- breathe 4.33.0
- doxygen 1.9.2
- breathe 4.34.0
- doxygen 1.9.5
A conda-forge environment file can be found in `doc/environment.yml`

Run 'make dist' to have config.h.cmake.in and harp.h.cmake.in updated to be
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2 changes: 1 addition & 1 deletion doc/html/.buildinfo
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@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 8084bf475fee59f3ead594d615898e59
config: edfa8b8d22bf0dd0a6a741bcac236376
tags: 645f666f9bcd5a90fca523b33c5a78b7
6 changes: 4 additions & 2 deletions doc/html/R.html
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Expand Up @@ -4,7 +4,7 @@
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>R interface &mdash; HARP 1.15 documentation</title>
<title>R interface &mdash; HARP 1.16 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
Expand All @@ -15,7 +15,9 @@
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/sphinx_highlight.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="next" title="Command line tools" href="tools.html" />
Expand All @@ -30,7 +32,7 @@
<a href="index.html" class="icon icon-home"> HARP
</a>
<div class="version">
1.15
1.16
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul class="current">
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134 changes: 134 additions & 0 deletions doc/html/_static/_sphinx_javascript_frameworks_compat.js
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@@ -0,0 +1,134 @@
/*
* _sphinx_javascript_frameworks_compat.js
* ~~~~~~~~~~
*
* Compatability shim for jQuery and underscores.js.
*
* WILL BE REMOVED IN Sphinx 6.0
* xref RemovedInSphinx60Warning
*
*/

/**
* select a different prefix for underscore
*/
$u = _.noConflict();


/**
* small helper function to urldecode strings
*
* See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
*/
jQuery.urldecode = function(x) {
if (!x) {
return x
}
return decodeURIComponent(x.replace(/\+/g, ' '));
};

/**
* small helper function to urlencode strings
*/
jQuery.urlencode = encodeURIComponent;

/**
* This function returns the parsed url parameters of the
* current request. Multiple values per key are supported,
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
if (typeof s === 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
for (var i = 0; i < parts.length; i++) {
var tmp = parts[i].split('=', 2);
var key = jQuery.urldecode(tmp[0]);
var value = jQuery.urldecode(tmp[1]);
if (key in result)
result[key].push(value);
else
result[key] = [value];
}
return result;
};

/**
* highlight a given string on a jquery object by wrapping it in
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
function highlight(node, addItems) {
if (node.nodeType === 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 &&
!jQuery(node.parentNode).hasClass(className) &&
!jQuery(node.parentNode).hasClass("nohighlight")) {
var span;
var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
if (isInSVG) {
span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
} else {
span = document.createElement("span");
span.className = className;
}
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
addItems.push({
"parent": node.parentNode,
"target": rect});
}
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
highlight(this, addItems);
});
}
}
var addItems = [];
var result = this.each(function() {
highlight(this, addItems);
});
for (var i = 0; i < addItems.length; ++i) {
jQuery(addItems[i].parent).before(addItems[i].target);
}
return result;
};

/*
* backward compatibility for jQuery.browser
* This will be supported until firefox bug is fixed.
*/
if (!jQuery.browser) {
jQuery.uaMatch = function(ua) {
ua = ua.toLowerCase();

var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
/(webkit)[ \/]([\w.]+)/.exec(ua) ||
/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
/(msie) ([\w.]+)/.exec(ua) ||
ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
[];

return {
browser: match[ 1 ] || "",
version: match[ 2 ] || "0"
};
};
jQuery.browser = {};
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
}
13 changes: 3 additions & 10 deletions doc/html/_static/basic.css
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Expand Up @@ -222,7 +222,7 @@ table.modindextable td {
/* -- general body styles --------------------------------------------------- */

div.body {
min-width: 450px;
min-width: 360px;
max-width: 800px;
}

Expand All @@ -236,7 +236,6 @@ div.body p, div.body dd, div.body li, div.body blockquote {
a.headerlink {
visibility: hidden;
}

a.brackets:before,
span.brackets > a:before{
content: "[";
Expand All @@ -247,6 +246,7 @@ span.brackets > a:after {
content: "]";
}


h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
Expand Down Expand Up @@ -334,13 +334,11 @@ aside.sidebar {
p.sidebar-title {
font-weight: bold;
}

div.admonition, div.topic, blockquote {
clear: left;
}

/* -- topics ---------------------------------------------------------------- */

div.topic {
border: 1px solid #ccc;
padding: 7px;
Expand Down Expand Up @@ -428,10 +426,6 @@ table.docutils td, table.docutils th {
border-bottom: 1px solid #aaa;
}

table.footnote td, table.footnote th {
border: 0 !important;
}

th {
text-align: left;
padding-right: 5px;
Expand Down Expand Up @@ -614,7 +608,6 @@ ol.simple p,
ul.simple p {
margin-bottom: 0;
}

dl.footnote > dt,
dl.citation > dt {
float: left;
Expand Down Expand Up @@ -643,11 +636,11 @@ dl.field-list > dt {
padding-left: 0.5em;
padding-right: 5px;
}

dl.field-list > dt:after {
content: ":";
}


dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
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