update so docs/ is where output is

.github/workflows/pull_request.yml

@@ -37,7 +37,7 @@ jobs:
           git checkout -b $branch_name || echo branch exists
           git push --set-upstream origin $branch_name
         shell: bash
-        
+
     outputs:
       public_repository: "${{ steps.public_repository.outputs.public }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
@@ -140,7 +140,7 @@ jobs:
         id: build-components
         run: |
           course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
-          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/index.html")
+          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           echo ::set-output name=website_link::$website_link
           echo ::set-output name=time::$(date +'%Y-%m-%d')
           echo ::set-output name=commit_id::$GITHUB_SHA

.github/workflows/render-site.yml

@@ -15,7 +15,6 @@ on:
       - '**.Rmd'
       - styles.css
       - _site.yml
-      - subdir_html/*.Rmd
       - resources/images/*.png
       - resources/images/favicon.ico
       - site_libs/*
@@ -63,11 +62,6 @@ jobs:
         id: site
         run: Rscript -e "rmarkdown::render_site()"
 
-      # We may have html files that we want to render to add as links on the pages -these will be stored in a dir called subdir_html
-      - name: Render subdir_html
-        id: subdir_html
-        run: Rscript -e "for (i in list.files(path = './subdir_html', pattern = 'Rmd$', recursive = TRUE, full.names = TRUE)){rmarkdown::render(i)}"
-
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
       - name: Check on render steps
@@ -82,8 +76,7 @@ jobs:
           git config --system --add safe.directory $GITHUB_WORKSPACE
           git config --local user.email "actions@github.com"
           git config --local user.name "GitHub Actions"
-          git add --force *.html
-          git add --force subdir_html/*.html
+          git add --force docs/*
           git add --force site_libs/*
           git commit -m 'Render site' || echo "No changes to commit"
           git push origin main || echo "No changes to push"

_site.yml

@@ -1,5 +1,5 @@
 name: OTTR Template Website
-output_dir: '.'
+output_dir: 'docs'
 navbar:
   title: OTTR Web
   left:

docs/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 jhudsl
+
+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.

docs/config_automation.yml

@@ -0,0 +1,24 @@
+
+##### Checks run at pull request #####
+# Check quiz formatting
+check-quizzes: no
+# Check that urls in the content are not broken
+url-checker: yes
+# Render preview of content with changes (Rmd's and md's are checked)
+render-preview: yes
+# Spell check Rmds and quizzes
+spell-check: yes
+# Style any R code
+style-code: yes
+# Test build the docker image if any docker-relevant files have been changed
+docker-test: no
+
+##### Renderings run upon merge to main branch #####
+# Rendering each platform's content
+render-bookdown: yes
+render-leanpub: yes
+render-coursera: no
+
+# What docker image should be used for rendering?
+# The default is jhudsl/base_ottr:main
+rendering-docker-image: 'jhudsl/base_ottr:main'

contact.html → docs/contact.html

@@ -13,8 +13,8 @@
 
 <title>Contact Us</title>
 
-<script src="site_libs/header-attrs-2.10/header-attrs.js"></script>
-<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
+<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
+<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1" />
 <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
 <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
@@ -32,8 +32,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
 <link rel="shortcut icon" href="resources/images/favicon.ico" />
  <!--- go to https://favicon.io/favicon-converter/ to upload an image to make a new favicon.io. You will need to replace the current favicon.io image with the one in the downloaded directory from the website. The current image is in the resources/images/ directory --->
 
@@ -61,6 +61,7 @@
 
 
 
+
 <link rel="stylesheet" href="styles.css" type="text/css" />
 
 
@@ -86,6 +87,9 @@
 summary {
   display: list-item;
 }
+details > summary > p:only-child {
+  display: inline;
+}
 pre code {
   padding: 0;
 }
@@ -142,11 +146,15 @@
     href = "index.html";
   var menuAnchor = $('a[href="' + href + '"]');
 
-  // mark it active
-  menuAnchor.tab('show');
-
-  // if it's got a parent navbar menu mark it active as well
-  menuAnchor.closest('li.dropdown').addClass('active');
+  // mark the anchor link active (and if it's in a dropdown, also mark that active)
+  var dropdown = menuAnchor.closest('li.dropdown');
+  if (window.bootstrap) { // Bootstrap 4+
+    menuAnchor.addClass('active');
+    dropdown.find('> .dropdown-toggle').addClass('active');
+  } else { // Bootstrap 3
+    menuAnchor.parent().addClass('active');
+    dropdown.addClass('active');
+  }
 
   // Navbar adjustments
   var navHeight = $(".navbar").first().height() + 15;
@@ -175,25 +183,18 @@
   border-radius: 4px;
 }
 
-.tabset-dropdown > .nav-tabs > li.active:before {
-  content: "";
+.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
+  content: "\e259";
   font-family: 'Glyphicons Halflings';
   display: inline-block;
   padding: 10px;
   border-right: 1px solid #ddd;
 }
 
 .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
-  content: "&#xe258;";
-  border: none;
-}
-
-.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
-  content: "";
+  content: "\e258";
   font-family: 'Glyphicons Halflings';
-  display: inline-block;
-  padding: 10px;
-  border-right: 1px solid #ddd;
+  border: none;
 }
 
 .tabset-dropdown > .nav-tabs > li.active {
@@ -237,7 +238,7 @@
 <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">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
@@ -250,33 +251,26 @@
   <a href="index.html">
     <span class="fa fa-home"></span>
 
-    Home
+
   </a>
 </li>
 <li>
-  <a href="setup.html">Setup</a>
+  <a href="setup.html">1. Setup</a>
 </li>
 <li>
-  <a href="hosting.html">Hosting</a>
+  <a href="hosting.html">2. Hosting</a>
 </li>
 <li>
   <a href="editing.html">Editing</a>
 </li>
 <li>
-  <a href="style.html">Style</a>
+  <a href="style.html">3. Style</a>
 </li>
 <li>
-  <a href="git_actions.html">Git Actions</a>
+  <a href="git_actions.html">4. Git Actions</a>
 </li>
 <li>
-  <a href="docker.html">Docker</a>
-</li>
-<li>
-  <a href="contact.html">
-    <span class="fa fa-envelope"></span>
-
-    Contact
-  </a>
+  <a href="https://www.ottrproject.org/">More ottr docs</a>
 </li>
       </ul>
       <ul class="nav navbar-nav navbar-right">
@@ -297,7 +291,8 @@ <h1 class="title toc-ignore"><strong>Contact Us</strong></h1>
 
 <p>If you have questions please contact:</p>
 <ul>
-<li>Carrie Wright (<a href="mailto:cwrigh60@jhu.edu" class="email">cwrigh60@jhu.edu</a>)</li>
+<li>Carrie Wright (<a href="mailto:cwrigh60@jhu.edu"
+class="email">cwrigh60@jhu.edu</a>)</li>
 </ul>