From 6809d6951f8d664868ee6b3981ba4a1acfc05205 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 19 Feb 2019 15:20:58 +0100 Subject: Fix NAMESPACE and rebuild docs --- ChangeLog | 6 ++ DESCRIPTION | 4 +- GNUmakefile | 4 +- NAMESPACE | 2 + R/install_PELMO.R | 1 + docs/authors.html | 47 +++++++---- docs/docsearch.css | 148 ++++++++++++++++++++++++++++++++++ docs/docsearch.js | 85 ++++++++++++++++++++ docs/index.html | 42 ++++++---- docs/jquery.sticky-kit.min.js | 9 --- docs/pkgdown.css | 60 +++++++++++--- docs/pkgdown.js | 165 +++++++++++++++++++++----------------- docs/pkgdown.yml | 5 ++ docs/reference/index.html | 101 ++++++++++++----------- docs/reference/install_PELMO.html | 51 ++++++++---- 15 files changed, 544 insertions(+), 186 deletions(-) create mode 100644 docs/docsearch.css create mode 100644 docs/docsearch.js delete mode 100644 docs/jquery.sticky-kit.min.js create mode 100644 docs/pkgdown.yml diff --git a/ChangeLog b/ChangeLog index 2a47aba..0c4d2d1 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,9 @@ +commit 4797fe2021dc0f05cc0da266e802c513ac543927 +Author: Johannes Ranke +Date: 2018-03-01 11:44:10 +0100 + + Update static docs using current pkdown + commit 5a60a334a61dde923a131d8798d6fa03f38525b2 Author: Johannes Ranke Date: 2017-03-15 09:50:29 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index 9d5be2a..d1558e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: PELMO.installeR Type: Package Title: Install FOCUS PELMO into an R library location Version: 0.1-1 -Date: 2018-03-01 +Date: 2019-02-19 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: The only function in this package downloads 'FOCUS PELMO' from the @@ -13,4 +13,4 @@ Imports: clipr License: GPL LazyLoad: yes LazyData: yes -RoxygenNote: 6.0.1 +RoxygenNote: 6.1.1 diff --git a/GNUmakefile b/GNUmakefile index 70d581b..213ecb2 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -34,8 +34,8 @@ $(TGZ): $(pkgfiles) build: $(TGZ) check: build - @echo "Running CRAN check..." - "$(R_HOME)/bin/R" CMD check --as-cran $(TGZ) + @echo "Running check..." + "$(R_HOME)/bin/R" CMD check $(TGZ) @echo "DONE." install: build diff --git a/NAMESPACE b/NAMESPACE index 46b7303..1975ddb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -2,3 +2,5 @@ export(install_PELMO) importFrom(clipr,write_clip) +importFrom(utils,download.file) +importFrom(utils,unzip) diff --git a/R/install_PELMO.R b/R/install_PELMO.R index 18efb81..beeecd1 100644 --- a/R/install_PELMO.R +++ b/R/install_PELMO.R @@ -1,6 +1,7 @@ #' Download FOCUS PELMO from the official site and unzip into the package installation directory #' #' @importFrom clipr write_clip +#' @importFrom utils download.file unzip #' @param version The FOCUS PELMO version to install #' @param local_zip Do not download, but use the local zip archive specified here #' @export diff --git a/docs/authors.html b/docs/authors.html index 46a2aa2..897f036 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,6 +1,6 @@ - + @@ -9,27 +9,34 @@ Authors • PELMO.installeR - + - - + + - + - + + + + - - - + + + + + + - + + @@ -75,8 +88,8 @@ -
-
+
+

Authors

@@ -99,11 +112,13 @@
-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

-
+ + + diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 0000000..e5f1fe1 --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,148 @@ +/* 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 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { + float: none; + width: auto; + padding: 0; + text-align: left +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content { + float: none; + width: auto; + padding: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content::before { + display: none +} + +.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { + padding-top: .75rem; + margin-top: .75rem; + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { + display: block; + padding: .1rem 1rem; + margin-bottom: 0.1; + font-size: 1.0em; + font-weight: 400 + /* display: none */ +} + +.algolia-autocomplete .algolia-docsearch-suggestion--title { + display: block; + padding: .25rem 1rem; + margin-bottom: 0; + font-size: 0.9em; + font-weight: 400 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--text { + padding: 0 1rem .5rem; + margin-top: -.25rem; + font-size: 0.8em; + font-weight: 400; + line-height: 1.25 +} + +.algolia-autocomplete .algolia-docsearch-footer { + width: 110px; + height: 20px; + z-index: 3; + margin-top: 10.66667px; + float: right; + font-size: 0; + line-height: 0; +} + +.algolia-autocomplete .algolia-docsearch-footer--logo { + background-image: url("data:image/svg+xml;utf8,"); + background-repeat: no-repeat; + background-position: 50%; + background-size: 100%; + overflow: hidden; + text-indent: -9000px; + width: 100%; + height: 100%; + display: block; + transform: translate(-8px); +} + +.algolia-autocomplete .algolia-docsearch-suggestion--highlight { + color: #FF8C00; + background: rgba(232, 189, 54, 0.1) +} + + +.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { + box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) +} + +.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { + background-color: rgba(192, 192, 192, .15) +} diff --git a/docs/docsearch.js b/docs/docsearch.js new file mode 100644 index 0000000..b35504c --- /dev/null +++ b/docs/docsearch.js @@ -0,0 +1,85 @@ +$(function() { + + // register a handler to move the focus to the search bar + // upon pressing shift + "/" (i.e. "?") + $(document).on('keydown', function(e) { + if (e.shiftKey && e.keyCode == 191) { + e.preventDefault(); + $("#search-input").focus(); + } + }); + + $(document).ready(function() { + // do keyword highlighting + /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ + var mark = function() { + + var referrer = document.URL ; + var paramKey = "q" ; + + if (referrer.indexOf("?") !== -1) { + var qs = referrer.substr(referrer.indexOf('?') + 1); + var qs_noanchor = qs.split('#')[0]; + var qsa = qs_noanchor.split('&'); + var keyword = ""; + + for (var i = 0; i < qsa.length; i++) { + var currentParam = qsa[i].split('='); + + if (currentParam.length !== 2) { + continue; + } + + if (currentParam[0] == paramKey) { + keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); + } + } + + if (keyword !== "") { + $(".contents").unmark({ + done: function() { + $(".contents").mark(keyword); + } + }); + } + } + }; + + mark(); + }); +}); + +/* Search term highlighting ------------------------------*/ + +function matchedWords(hit) { + var words = []; + + var hierarchy = hit._highlightResult.hierarchy; + // loop to fetch from lvl0, lvl1, etc. + for (var idx in hierarchy) { + words = words.concat(hierarchy[idx].matchedWords); + } + + var content = hit._highlightResult.content; + if (content) { + words = words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/index.html b/docs/index.html index 9d7b5cd..79c106c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,19 +1,19 @@ - + Install FOCUS PELMO into an R library location • PELMO.installeR - - - - + + + + - @@ -23,13 +23,18 @@
-
+

PELMO.installeR

The R package PELMO.installeR provides a way to install FOCUS PELMO in a standardised way on Linux/Unix systems for use with wine.

@@ -70,27 +75,34 @@
- +

Developed by Johannes Ranke.

-

Site built with pkgdown.

+

Site built with pkgdown 1.3.0.

-
+ + diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js deleted file mode 100644 index e2a3c6d..0000000 --- a/docs/jquery.sticky-kit.min.js +++ /dev/null @@ -1,9 +0,0 @@ -/* - Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net -*/ -(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); -if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("
"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, -u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),eb&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), -a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", -y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + body > .container { display: flex; - padding-top: 60px; - min-height: calc(100vh); + height: 100%; flex-direction: column; + + padding-top: 60px; } body > .container .row { - flex: 1; + flex: 1 0 auto; } footer { @@ -16,6 +35,7 @@ footer { border-top: 1px solid #e5e5e5; color: #666; display: flex; + flex-shrink: 0; } footer p { margin-bottom: 0; @@ -38,6 +58,17 @@ img { max-width: 100%; } +/* Fix bug in bootstrap (only seen in firefox) */ +summary { + display: list-item; +} + +/* Typographic tweaking ---------------------------------*/ + +.contents .page-header { + margin-top: calc(-60px + 1em); +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -68,7 +99,7 @@ a.anchor { .contents h1, .contents h2, .contents h3, .contents h4 { padding-top: 60px; - margin-top: -60px; + margin-top: -40px; } /* Static header placement on mobile devices */ @@ -108,13 +139,11 @@ a.anchor { /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} -.ref-index h2 {font-size: 20px;} .ref-index td {vertical-align: top;} +.ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} -.ref-index .title {width: 60%;} - -.ref-index .alias {width: 40%;} +.ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} @@ -192,3 +221,16 @@ a.sourceLine:hover { .hasCopyButton:hover button.btn-copy-ex { visibility: visible; } + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 64b20df..eb7e83d 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,94 +1,115 @@ -$(function() { - - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $("#sidebar") + .stick_in_parent({offset_top: 40}) + .on('sticky_kit:bottom', function(e) { + $(this).parent().css('position', 'static'); + }) + .on('sticky_kit:unbottom', function(e) { + $(this).parent().css('position', 'relative'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); + + var length = prefix_length(nav_path, cur_path); + if (length > max_length) { + max_length = length; + pos = i; + } + } - var cur_path = paths(location.pathname); - $("#navbar ul li a").each(function(index, value) { - if (value.text == "Home") - return; - if (value.getAttribute("href") === "#") - return; - - var path = paths(value.pathname); - if (is_prefix(cur_path, path)) { - // Add class to parent
  • , and enclosing
  • if in dropdown - var menu_anchor = $(value); + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); menu_anchor.parent().addClass("active"); menu_anchor.closest("li.dropdown").addClass("active"); } }); -}); -function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); -} + // Returns -1 if not found + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(-1); -function is_prefix(needle, haystack) { - if (needle.length > haystack.lengh) - return(false); + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 0 : -1); + } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(false); - } + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } - return(true); -} + return(haystack.length); + } -/* Clipboard --------------------------*/ + /* Clipboard --------------------------*/ -function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-original-title'); - element.setAttribute('data-original-title', msg); - $(element).tooltip('show'); - element.setAttribute('data-original-title', tooltipOriginalTitle); -} + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } -if(Clipboard.isSupported()) { - $(document).ready(function() { - var copyButton = ""; + if(ClipboardJS.isSupported()) { + $(document).ready(function() { + var copyButton = ""; - $(".examples").addClass("hasCopyButton"); + $(".examples, div.sourceCode").addClass("hasCopyButton"); - // Insert copy buttons: - $(copyButton).prependTo(".hasCopyButton"); + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); - // Initialize tooltips: - $('.btn-copy-ex').tooltip({container: 'body'}); + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); - // Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { - text: function(trigger) { - return trigger.parentNode.textContent; - } - }); + // Initialize clipboard: + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); - clipboardBtnCopies.on('success', function(e) { - changeTooltipMessage(e.trigger, 'Copied!'); - e.clearSelection(); - }); + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); - clipboardBtnCopies.on('error', function() { - changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); }); - }); -} - + } +})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 0000000..1dc6ec1 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,5 @@ +pandoc: 2.2.1 +pkgdown: 1.3.0 +pkgdown_sha: ~ +articles: [] + diff --git a/docs/reference/index.html b/docs/reference/index.html index 98764f7..126ac9f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,6 +1,6 @@ - + @@ -9,27 +9,34 @@ Function reference • PELMO.installeR - + - - + + - + - + + + + - - - + + + + + + - + +
    • @@ -75,40 +88,36 @@ -
    -
    +
    +
    -

    - Reference - version 0.1-1 -

    +

    Reference

    -
    - - - - - - - - - - - - - - - - - -
    -

    All functions

    -

    -
    -

    install_PELMO

    -

    Download FOCUS PELMO from the official site and unzip into the package installation directory

    -
    + + + + + + + + + + + + + + + + + + +
    +

    All functions

    +

    +
    +

    install_PELMO()

    +

    Download FOCUS PELMO from the official site and unzip into the package installation directory

    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.3.0.

    -
    + + + diff --git a/docs/reference/install_PELMO.html b/docs/reference/install_PELMO.html index c2a9feb..6750418 100644 --- a/docs/reference/install_PELMO.html +++ b/docs/reference/install_PELMO.html @@ -1,6 +1,6 @@ - + @@ -9,30 +9,37 @@ Download FOCUS PELMO from the official site and unzip into the package installation directory — install_PELMO • PELMO.installeR - + - - + + - + - + + + + - - - + + + + + + - + +
    @@ -78,19 +91,23 @@ -
    +

    Download FOCUS PELMO from the official site and unzip into the package installation directory

    + +
    +

    Download FOCUS PELMO from the official site and unzip into the package installation directory

    + 
    install_PELMO(version = "5.5.3", local_zip = NULL)
    -

    Arguments

    +

    Arguments

    @@ -120,11 +137,13 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown 1.3.0.

    - + + + -- cgit v1.2.1