diff --git a/404.html b/404.html new file mode 100644 index 0000000..a0857c3 --- /dev/null +++ b/404.html @@ -0,0 +1,115 @@ + + + + + + + +Page not found (404) • BuildABiocWorkshop + + + + + + + + + + + +
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+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ + + +
+ + + + +
+ + + + + + + + diff --git a/LICENSE-text.html b/LICENSE-text.html new file mode 100644 index 0000000..e602d06 --- /dev/null +++ b/LICENSE-text.html @@ -0,0 +1,89 @@ + +License • BuildABiocWorkshop + + +
+
+ + + +
+
+
+

License

+
+ +
YEAR: 2020
+COPYRIGHT HOLDER: Sean Davis
+
+ +
+ + + +
+ + + +
+ + + + + + + + diff --git a/LICENSE.html b/LICENSE.html new file mode 100644 index 0000000..b11bd59 --- /dev/null +++ b/LICENSE.html @@ -0,0 +1,93 @@ + +MIT License • BuildABiocWorkshop + + +
+
+ + + +
+
+
+

MIT License

+
+ +
+ +

Copyright (c) 2020 Sean Davis

+

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

+

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

+

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

+
+ +
+ + + +
+ + + +
+ + + + + + + + diff --git a/articles/HOWTO_BUILD_WORKSHOP.html b/articles/HOWTO_BUILD_WORKSHOP.html new file mode 100644 index 0000000..87a6f83 --- /dev/null +++ b/articles/HOWTO_BUILD_WORKSHOP.html @@ -0,0 +1,244 @@ + + + + + + + +How To Build A Workshop Package • BuildABiocWorkshop + + + + + + + + + + + +
+
+ + + + +
+
+
+

How To Build A Workshop Package

+

In other words, how do I +use what’s here

+

Sean Davis1 +

+ + + Source: vignettes/HOWTO_BUILD_WORKSHOP.Rmd + + +
+ + + +

First, this package doesn’t do much except add a template Github +Action to build all the pieces necessary for a workshop.

+
+

Quickstart +

+
    +
  • + + +
    • +
  • + +
      +
      • +
      • +
      • +
      • +
      • +
    +
    • +
    • +
    • +
    • +
+
+
+

Details +

+

To accomplish this follow each of the 7 steps below. Once your edit +the yaml files, Github actions will run each time you commit to github +and will create for you:

+
    +
  • the pkgdown website
    • +
  • the docker image
    • +
+
+

1. Clone this repo +

+

Clone this repo, fork and rename it,

+

OR

+

(PREFERRED) create a repo from this template

+
+
+

2. Edit DESCRIPTION file +

+
    +
  • Change the package name to something identifiable and descriptive, +ideally something that will be somewhat unique.
    • +
  • Edit the title and description as per any normal R package.
    • +
  • Update authors (unless you want me to get credit for your +work).
    • +
  • Workshop packages are normal R packages, so dependencies work as +usual. Append libraries to the Depends/Suggests/Imports in this package +DESCRIPTION File, which includes;
    • +
+

Depends: Biobase Suggests: knitr, rmarkdown, pkgdown If your packages +depend on a github R repos, be sure to specify the correct repo +username/reponame. Installation will deal with this.

+
    +
  • Edit the last 3 lines of the DESCRIPTION FILE, URL, BugReports and +DockerImage (described in more detail below)
    • +
+
+
+

3. Set up a website (Github Pages) +

+

In your repository, click on settings or url https://github.com/*GITHUB_USERNAME*/*REPO_NAME*/settings. +Midway down the page, in the GitHub Pages section, select source +‘gh-pages branch’. If only ‘master branch’ is visible, select master for +now, but once Github actions runs, ‘gh-pages branch’ will be available +and is required to render the website.

+

In the DESCRIPTION file, update the URL: to the website url eg https://seandavi.github.io/BuildABiocWorkshop/ (but +substitute your own repo, etc.)

+
+
+

4. Edit _pkgdown.yml +

+

Edit the file _pkgdown.yml, updating the url:, title and href: which +should be your website url, title of your workshop and github repos url +respectively. You do not need to edit this file further. You do not need +to add menus or links to vignettes. GitHub Actions and pkgdown will do +this when it builds the website

+
+
+

5. Edit .github/workflows yaml as needed (likely no +need) +

+

You do not need to create a docker image manually. Github actions +will read Dockerfile located in this template, and using the yaml files +will create, build and push to the Github Container Registry an image +with the name (default) +ghcr.io/yourgithubuser/yourgithubreponame, all +lowercase.

+

In the DESCRIPTION file, the DockerImage: should match your +the docker image name (should be lowercase).

+
+
+

6. Edit README.md, add vignettes to vignettes folder +

+

Edit the README.md. and add one or more Rmd vignettes that will +constitute the workshop materials. It is normal R package that should +pass rcmdcheck::rcmdcheck(), and be installed using regular +R package install commands.

+
+
+
+
+
    +

  1. ↩︎

    2. +
+
+
+ + + +
+ + + + +
+ + + + + + + + diff --git a/articles/index.html b/articles/index.html new file mode 100644 index 0000000..3a7e030 --- /dev/null +++ b/articles/index.html @@ -0,0 +1,88 @@ + +Articles • BuildABiocWorkshop + + +
+
+ + + +
+
+
+

Articles

+
+ +
+

All vignettes

+

+ +
How To Build A Workshop Package
+
+
An Example Workshop
+
+
+
+
+ + +
+ + + + + + + + diff --git a/articles/workshop_example.html b/articles/workshop_example.html new file mode 100644 index 0000000..77e9d45 --- /dev/null +++ b/articles/workshop_example.html @@ -0,0 +1,252 @@ + + + + + + + +An Example Workshop • BuildABiocWorkshop + + + + + + + + + + + +
+
+ + + + +
+
+
+

An Example Workshop

+

Sean Davis1 +

+ + + Source: vignettes/workshop_example.Rmd + + +
+ + + +
+

Workshop Title +

+

Authors: Author Name2, Another Author3.
Last modified: +14 May, 2018.

+
+

Overview +

+
+

Description +

+

Along with the topic of your workshop, include how students can +expect to spend their time. For the description may also include +information about what type of workshop it is (e.g. instructor-led live +demo, lab, lecture + lab, etc.). Instructors are strongly recommended to +provide completely worked examples for lab sessions, and a set of +stand-alone notes that can be read and understood outside of the +workshop.

+
+
+

Pre-requisites +

+

List any workshop prerequisites, for example:

+
    +
  • Basic knowledge of R syntax
    • +
  • Familiarity with the GenomicRanges class
    • +
  • Familiarity with xyz vignette (provide link)
    • +
+

List relevant background reading for the workshop, including any +theoretical background you expect students to have.

+
    +
  • List any textbooks, papers, or other reading that students should be +familiar with. Include direct links where possible.
    • +
+
+
+

Participation +

+

Describe how students will be expected to participate in the +workshop.

+
+
+

+R / Bioconductor packages used +

+

List any R / Bioconductor packages that will be +explicitly covered.

+
+
+

Time outline +

+

An example for a 45-minute workshop:

+ + + + + + + + + + + + + + + + + + + + + + + +
ActivityTime
Packages15m
Package Development15m
Contributing to Bioconductor5m
Best Practices10m
+
+
+

Workshop goals and objectives +

+

List “big picture” student-centered workshop goals and learning +objectives. Learning goals and objectives are related, but not the same +thing. These goals and objectives will help some people to decide +whether to attend the conference for training purposes, so please make +these as precise and accurate as possible.

+

Learning goals are high-level descriptions of what +participants will learn and be able to do after the workshop is over. +Learning objectives, on the other hand, describe in very +specific and measurable terms specific skills or knowledge attained. The +Bloom’s Taxonomy may be a useful framework for +defining and describing your goals and objectives, although there are +others.

+
+
+

Learning goals +

+

Some examples:

+
    +
  • describe how to…
    • +
  • identify methods for…
    • +
  • understand the difference between…
    • +
+
+
+

Learning objectives +

+
    +
  • analyze xyz data to produce…
    • +
  • create xyz plots
    • +
  • evaluate xyz data for artifacts
    • +
+
+
+
+

Workshop +

+

Divide the workshop into sections (## A Section). +Include fully-evaluated R code chunks. Develop exercises and +solutions, and anticipate that your audience will walk through the code +with you, or work on the code independently – do not be too ambitious in +the material that you present.

+
+
+
+
+
    +

  1. ↩︎

    2. +

  2. Institution↩︎

    3. +

  3. Another Institution↩︎

    4. +
+
+
+ + + +
+ + + + +
+ + + + + + + + diff --git a/authors.html b/authors.html new file mode 100644 index 0000000..1fa8e0e --- /dev/null +++ b/authors.html @@ -0,0 +1,108 @@ + +Authors and Citation • BuildABiocWorkshop + + +
+
+ + + +
+
+
+
+

Authors and Citation

+
+ + +
  • +

    Sean Davis. Author, maintainer. +

    +
    • +
+
+
+

Citation

+ Source: DESCRIPTION +
+
+ + +

Davis S (2024). +BuildABiocWorkshop: Bioconductor or R Workshop Template and Github Actions. +R package version 2.0.1, https://seandavi.github.io/BuildABiocWorkshop/. +

+ 
@Manual{,
+  title = {BuildABiocWorkshop: Bioconductor or R Workshop Template and Github Actions},
+  author = {Sean Davis},
+  year = {2024},
+  note = {R package version 2.0.1},
+  url = {https://seandavi.github.io/BuildABiocWorkshop/},
+}
+ +
+ +
+ + + +
+ + + + + + + + diff --git a/bootstrap-toc.css b/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * 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; +} diff --git a/bootstrap-toc.js b/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * 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 $(''); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $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 (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + 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); + }); + }); +})(); diff --git a/docsearch.css b/docsearch.css new file mode 100644 index 0000000..e5f1fe1 --- /dev/null +++ b/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/docsearch.js b/docsearch.js new file mode 100644 index 0000000..b35504c --- /dev/null +++ b/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/index.html b/index.html new file mode 100644 index 0000000..8ede347 --- /dev/null +++ b/index.html @@ -0,0 +1,194 @@ + + + + + + + +BuildABiocWorkshop • BuildABiocWorkshop + + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    BuildABiocWorkshop +

    +

    This package is a template for building a Bioconductor workshop. The package includes Github actions to:

    +
      +
    1. Set up bioconductor/bioconductor_docker:devel on Github resources
      2. +
    2. Install package dependencies for your package (based on the DESCRIPTION file)
      3. +
    3. Run rcmdcheck::rcmdcheck +
      4. +
    4. Build a pkgdown website and push it to github pages
      5. +
    5. Build a docker image with the installed package and dependencies and deploy to the Github Container Repository at the name ghcr.io/gihub_user/repo_name, all lowercase.
      6. +
    +
    +

    Responsibilities +

    +

    Package authors are primarily responsible for:

    +
      +
    1. Creating a landing site of their choosing for their workshops (a website). This website should be listed in the DESCRIPTION file as the URL.
      2. +
    2. Creating a docker image that will contain workshop materials and the installed packages necessary to run those materials. The name of the resulting docker image, including “tag” if desired, should be listed in a non-standard tag, DockerImage: in the DESCRIPTION file.
      3. +
    +

    Both of those tasks can be accomplished using the Github actions included in this template package. The vignette accompanying this package describes how to accomplish both of these tasks.

    +
    +
    +

    Details +

    +

    For detailed instructions, see the How to build a workshop article/vignette.

    +
    +
    +

    Results of successful deployment +

    +
      +
    • A working docker image that contains the installed package and dependencies.
      • +
    • An up-to-date pkgdown website at https://YOURUSERNAME.github.io/YOURREPOSITORYNAME/ +
      • +
    • Docker image will be tagged with latest, sha-XXXXXX where XXXXXX is the hash of the current master commit, and master.
      • +
    +
    +
    +

    To use the resulting image: +

    +
    docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME
    +

    Once running, navigate to http://localhost:8787/ and then login with rstudio:yourchosenpassword.

    +

    To try with this repository docker image:

    +
    docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/bioconductor/buildabiocworkshop
    +

    NOTE: Running docker that uses the password in plain text like above exposes the password to others in a multi-user system (like a shared workstation or compute node). In practice, consider using an environment variable instead of plain text to pass along passwords and other secrets in docker command lines.

    +
    +
    +

    Whatcha get +

    + +
    +
    +
    + + +
    + + +
    +

    +

    Developed by Sean Davis.

    +
    + +
    +

    +

    Site built with pkgdown 2.1.1.

    +
    + +
    +
    + + + + + + + + diff --git a/link.svg b/link.svg new file mode 100644 index 0000000..88ad827 --- /dev/null +++ b/link.svg @@ -0,0 +1,12 @@ + + + + + + diff --git a/pkgdown.css b/pkgdown.css new file mode 100644 index 0000000..80ea5b8 --- /dev/null +++ b/pkgdown.css @@ -0,0 +1,384 @@ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> 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 { + position: relative; +} + +body > .container { + display: flex; + height: 100%; + flex-direction: column; +} + +body > .container .row { + flex: 1 0 auto; +} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; + color: #666; + display: flex; + flex-shrink: 0; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; +} +footer p { + margin-bottom: 0; +} + +img.icon { + float: right; +} + +/* Ensure in-page images don't run outside their container */ +.contents img { + max-width: 100%; + height: auto; +} + +/* Fix bug in bootstrap (only seen in firefox) */ +summary { + display: list-item; +} + +/* Typographic tweaking ---------------------------------*/ + +.contents .page-header { + margin-top: calc(-60px + 1em); +} + +dd { + margin-left: 3em; +} + +/* Section anchors ---------------------------------*/ + +a.anchor { + display: none; + margin-left: 5px; + width: 20px; + height: 20px; + + background-image: url(./link.svg); + background-repeat: no-repeat; + background-size: 20px 20px; + background-position: center center; +} + +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; +} + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -40px; +} + +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} + +/* Sidebar --------------------------*/ + +#pkgdown-sidebar { + margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; +} + +#pkgdown-sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#pkgdown-sidebar h2:first-child { + margin-top: 0; +} + +#pkgdown-sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +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: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* 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-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +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: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + +.orcid { + font-size: 16px; + color: #A6CE39; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; + vertical-align: middle; +} + +/* Reference index & topics ----------------------------------------------- */ + +.ref-index th {font-weight: normal;} + +.ref-index td {vertical-align: top; min-width: 100px} +.ref-index .icon {width: 40px;} +.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;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} +.ref-arguments .name {width: 20%;} +.ref-arguments .desc {width: 80%;} + +/* Nice scrolling for wide elements --------------------------------------- */ + +table { + display: block; + overflow: auto; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +pre, code, pre code { + background-color: #f8f8f8; + color: #333; +} +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} + +pre { + border: 1px solid #eee; +} + +pre .img, pre .r-plt { + margin: 5px 0; +} + +pre .img img, pre .r-plt img { + background-color: #fff; +} + +code a, pre a { + color: #375f84; +} + +a.sourceLine:hover { + text-decoration: none; +} + +.fl {color: #1514b5;} +.fu {color: #000000;} /* function */ +.ch,.st {color: #036a07;} /* string */ +.kw {color: #264D66;} /* keyword */ +.co {color: #888888;} /* comment */ + +.error {font-weight: bolder;} +.warning {font-weight: bolder;} + +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} + +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + +/* 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; +} + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/pkgdown.js b/pkgdown.js new file mode 100644 index 0000000..6f0eee4 --- /dev/null +++ b/pkgdown.js @@ -0,0 +1,108 @@ +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $('.navbar-fixed-top').headroom(); + + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); + }); + + $('[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; + } + } + + // 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 / + + 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); + + // 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(i); + } + + return(haystack.length); + } + + /* 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); + } + + if(ClipboardJS.isSupported()) { + $(document).ready(function() { + var copyButton = ""; + + $("div.sourceCode").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); + } +})(window.jQuery || window.$) diff --git a/pkgdown.yml b/pkgdown.yml new file mode 100644 index 0000000..343f141 --- /dev/null +++ b/pkgdown.yml @@ -0,0 +1,10 @@ +pandoc: '3.4' +pkgdown: 2.1.1 +pkgdown_sha: ~ +articles: + HOWTO_BUILD_WORKSHOP: HOWTO_BUILD_WORKSHOP.html + workshop_example: workshop_example.html +last_built: 2024-10-31T04:19Z +urls: + reference: https://seandavi.github.io/BuildABiocWorkshop/reference + article: https://seandavi.github.io/BuildABiocWorkshop/articles diff --git a/reference/index.html b/reference/index.html new file mode 100644 index 0000000..46daef4 --- /dev/null +++ b/reference/index.html @@ -0,0 +1,83 @@ + + • BuildABiocWorkshop + + +
    +
    + + + +
    +
    +
    +

    Reference

    +
    + +
    + + +
    + + +
    +

    Developed by Sean Davis.

    +
    + +
    +

    Site built with pkgdown 2.1.1.

    +
    + +
    + + + + + + + + diff --git a/sitemap.xml b/sitemap.xml new file mode 100644 index 0000000..c63a696 --- /dev/null +++ b/sitemap.xml @@ -0,0 +1,12 @@ + +https://seandavi.github.io/BuildABiocWorkshop/404.html +https://seandavi.github.io/BuildABiocWorkshop/LICENSE-text.html +https://seandavi.github.io/BuildABiocWorkshop/LICENSE.html +https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html +https://seandavi.github.io/BuildABiocWorkshop/articles/index.html +https://seandavi.github.io/BuildABiocWorkshop/articles/workshop_example.html +https://seandavi.github.io/BuildABiocWorkshop/authors.html +https://seandavi.github.io/BuildABiocWorkshop/index.html +https://seandavi.github.io/BuildABiocWorkshop/reference/index.html + +