🔄 Synced file(s) with jhudsl/AnVIL_Template

.github/workflows/check-url.yml

@@ -0,0 +1,107 @@
+name: Periodic URL Check
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  set-up:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/[email protected]
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+  url-check:
+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr:main
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
+    - name: Find issues
+      id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        echo "$GITHUB_REPOSITORY"
+        curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
+        issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+        echo URL issue exists: $issue_exists
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+      uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-spell-error || echo "No branch to delete"

.github/workflows/pull_request.yml

@@ -52,7 +52,7 @@ jobs:
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      
+
   build-collection:
     name: Build Collection
     needs: yaml-check

_output.yml

@@ -1,5 +1,6 @@
 bookdown::gitbook:
-  css: assets/AnVIL_style/style.css
+  # When using multiple css files, the default file path will be the first one #
+  css: [assets/style.css, assets/AnVIL_style/anvil.css]
   includes:
     in_header: GA_Script.html
     before_body: assets/AnVIL_style/big-image_anvil.html
@@ -16,5 +17,6 @@ bookdown::gitbook:
        <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
-       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/AK12iVXTjsB7yCUUA"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
-
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=your+course"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.

assets/AnVIL_style/anvil.css

@@ -0,0 +1,48 @@
+
+/* AnVIL style */
+/* Things below this comment are AnVIL customizations */
+
+.trapezoid {
+  width: 132px;
+  text-align: center;
+  position: relative;
+    left: 10px;
+  border-right: 50px solid #012d72;
+  border-bottom: 50px solid #dbdbdb;
+  border-left: 50px solid #012d72;
+  box-sizing: content-box;
+}
+.trapezoid span {
+  position: absolute;
+  top: 8px;
+  bottom: 5px;
+  left: 5%;
+  color: #dbdbdb;
+}
+
+/* Module chunk shading --------------------------------------------*/
+div.borrowed_chunk {
+  padding: 1em;
+  margin: 1em 0;
+  min-height: 120px;
+  background-repeat: no-repeat;
+  background-color: #eff7fe;
+}
+
+.hero-image-container {
+  height: 100px;
+}
+
+.page-inner {
+  padding-top: 60px !important;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal h1,
+.book .book-body .page-wrapper .page-inner section.normal h2,
+.book .book-body .page-wrapper .page-inner section.normal h3,
+.book .book-body .page-wrapper .page-inner section.normal h4,
+.book .book-body .page-wrapper .page-inner section.normal h5,
+.book .book-body .page-wrapper .page-inner section.normal h6 {
+    margin-top: 1em;
+    margin-bottom: 1em;
+}

assets/GDSCN_style/gdscn.css

@@ -0,0 +1,99 @@
+
+/* GDSCN style */
+/* Change colors to match GDSCN logo */
+/* Things below this comment are GDSCN customizations */
+
+.hero-image-container {
+  height: 100px;
+}
+
+.page-inner {
+  padding-top: 60px !important;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal h1,
+.book .book-body .page-wrapper .page-inner section.normal h2,
+.book .book-body .page-wrapper .page-inner section.normal h3,
+.book .book-body .page-wrapper .page-inner section.normal h4,
+.book .book-body .page-wrapper .page-inner section.normal h5,
+.book .book-body .page-wrapper .page-inner section.normal h6 {
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+:root {
+  --highlight-txt-color: #73b263;
+  --main-txt-color: #274731;
+}
+
+.trapezoid {
+  width: 132px;
+  text-align: center;
+  position: relative;
+    left: 10px;
+  border-right: 50px solid --main-txt-color;
+  border-bottom: 50px solid #dbdbdb;
+  border-left: 50px solid --main-txt-color;
+  box-sizing: content-box;
+}
+.trapezoid span {
+  position: absolute;
+  top: 8px;
+  bottom: 5px;
+  left: 5%;
+  color: #dbdbdb;
+}
+
+/* Module chunk shading --------------------------------------------*/
+div.borrowed_chunk {
+  padding: 1em;
+  margin: 1em 0;
+  min-height: 120px;
+  background-repeat: no-repeat;
+  background-color: #eff7fe;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal a {
+  color: var(--highlight-txt-color);
+}
+
+.title {
+  color: var(--main-txt-color);
+}
+
+.section.level1 > p:first-of-type:first-letter { /*drop cap for first p beneath level 1 headers only within class .section*/
+  color: var(--main-txt-color);
+}
+
+.book .book-summary a {
+  color: var(--main-txt-color);
+}
+
+/* all TOC list items, basically */
+.book .book-summary ul.summary li a,
+.book .book-summary ul.summary li span {
+  color: var(--main-txt-color);
+}
+
+.summary a:hover {
+  color: var(--highlight-txt-color) !important;
+}
+
+.book .book-summary ul.summary li.active>a { /*active TOC links*/
+  color: var(--highlight-txt-color) !important;
+  border-color: var(--highlight-txt-color);
+}
+
+.trapezoid {
+  border-right: 50px solid var(--main-txt-color);
+  border-left: 50px solid var(--main-txt-color);
+}
+
+div.notice, div.dictionary, div.reflection {
+  border: 4px var(--highlight-txt-color);
+  border-style: solid;
+}
+
+.footer {
+  color: var(--main-txt-color);
+}