diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
new file mode 100644
index 0000000..a437049
--- /dev/null
+++ b/.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/yaml-env-action@v1.0.0
+ 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"
diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
index afd658a..faa83cc 100644
--- a/.github/workflows/delete-preview.yml
+++ b/.github/workflows/delete-preview.yml
@@ -18,7 +18,7 @@ jobs:
# Check out current repository
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index b9bb17a..d4d2515 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -14,9 +14,10 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
+ token: ${{ secrets.GH_PAT }}
# Use the yaml-env-action action.
- name: Load environment from YAML
@@ -31,15 +32,17 @@ jobs:
# Make the branch fresh
- name: Make the branch fresh
run: |
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ git config --global --add safe.directory $GITHUB_WORKSPACE
+ git config --global user.name 'github-actions[bot]'
+ git config --global user.email 'github-actions[bot]@users.noreply.github.com'
branch_name='preview-${{ github.event.pull_request.number }}'
echo branch doesnt exist
git checkout -b $branch_name || echo branch exists
- git push --set-upstream origin $branch_name
+ git push --set-upstream origin $branch_name || echo echo branch exists remotely
shell: bash
+
outputs:
toggle_spell_check: "${{ env.SPELL_CHECK }}"
toggle_style_code: "${{ env.STYLE_CODE }}"
@@ -47,7 +50,6 @@ jobs:
toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
- render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
########################## Make the error reports ##############################
spell-check:
@@ -59,6 +61,7 @@ jobs:
check_type: spelling
error_min: 3
gh_pat: secrets.GH_PAT
+ branch_name: ${GITHUB_HEAD_REF}
url-check:
name: Check URLs
@@ -69,6 +72,7 @@ jobs:
check_type: urls
error_min: 0
gh_pat: secrets.GH_PAT
+ branch_name: ${GITHUB_HEAD_REF}
quiz-check:
name: Check quiz formatting
@@ -79,6 +83,7 @@ jobs:
check_type: quiz_format
error_min: 0
gh_pat: secrets.GH_PAT
+ branch_name: ${GITHUB_HEAD_REF}
############################# Style the code ###################################
style-code:
@@ -91,7 +96,7 @@ jobs:
steps:
- name: Checkout files
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
@@ -117,16 +122,16 @@ jobs:
steps:
- name: Checkout files
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
# Set up git checkout
- name: Set up git checkout
run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ git config --global --add safe.directory $GITHUB_WORKSPACE
+ git config --global user.name 'github-actions[bot]'
+ git config --global user.email 'github-actions[bot]@users.noreply.github.com'
branch_name='preview-${{ github.event.pull_request.number }}'
git fetch --all
@@ -134,11 +139,16 @@ jobs:
git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
shell: bash
+ # Make sure the link for AnVIL feedback is prepopulated for the specific course
+ - name: Set up feedback link
+ id: feedback
+ run: bash scripts/AnVIL_Feedback_Script.sh
+
# Run bookdown rendering
- name: Run bookdown render
id: bookdown
run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-
+
# Render a student guide if specified. This is a bit clunky because
# Bookdown does not work well if the files aren't named as such in the
# root directory
@@ -153,7 +163,7 @@ jobs:
mv _bookdown.yml _output.yml student-guide
mv tmp1/_bookdown.yml tmp1/_output.yml .
rm -r tmp1
-
+
# Run TOC-less version
# Rendered content for Leanpub and Coursera is very similar.
# This job creates a shared scaffold for both.
@@ -170,6 +180,9 @@ jobs:
echo Toc-less status ${{steps.tocless.outcome}}
exit 1
+ - name: Website preview for download
+ run: zip website-preview.zip docs/* -r
+
# Commit the rendered bookdown files
- name: Commit rendered bookdown files to preview branch
id: commit
@@ -179,7 +192,7 @@ jobs:
echo "changes=$changes" >> $GITHUB_OUTPUT
git add . --force
git commit -m 'Render preview' || echo "No changes to commit"
- git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+ git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
git push --force || echo "No changes to commit"
shell: bash
@@ -197,7 +210,8 @@ jobs:
course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
- student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
+ student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx") zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+ echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
@@ -213,11 +227,13 @@ jobs:
issue-number: ${{ github.event.pull_request.number }}
body: |
Re-rendered previews from the latest commit:
- - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
- - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
- - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
+ - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
+ - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
+ - Download the [.docx file](${{ steps.build-components.outputs.docx_link }})
- _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+ \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
+
+ _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
edit-mode: replace
- name: Comment if no changes
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 4ebcbdc..8bb8ecb 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -10,6 +10,7 @@ on:
paths:
- '**.Rmd'
- assets/*
+ - quizzes/*
jobs:
@@ -18,7 +19,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
# Use the yaml-env-action action.
- name: Load environment from YAML
@@ -29,6 +30,7 @@ jobs:
toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}"
toggle_coursera: "${{ env.RENDER_COURSERA }}"
toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
+ make_book_txt: "${{ env.MAKE_BOOK_TXT }}"
rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
@@ -42,21 +44,26 @@ jobs:
steps:
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
token: ${{ secrets.GH_PAT }}
- - name: Login as jhudsl-robot
+ - name: Login as github actions bot
run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ 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'
# We want a fresh run of the renders each time
- name: Delete old docs/*
run: rm -rf docs/*
+ # Make sure the link for AnVIL feedback is prepopulated for the specific course
+ - name: Set up feedback link
+ id: feedback
+ run: bash scripts/AnVIL_Feedback_Script.sh
+
# Run bookdown rendering
- name: Run bookdown render
id: bookdown
@@ -93,14 +100,15 @@ jobs:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+ git fetch origin
git add --force docs/*
git commit -m 'Render bookdown' || echo "No changes to commit"
git pull --allow-unrelated-histories --strategy-option=ours
- git push origin main || echo "No changes to push"
+ git push -u origin main || echo "No changes to push"
render-tocless:
name: Render TOC-less version for Leanpub or Coursera
- needs: [yaml-check]
+ needs: [yaml-check, render-bookdown]
runs-on: ubuntu-latest
container:
image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -108,16 +116,16 @@ jobs:
steps:
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
token: ${{ secrets.GH_PAT }}
- - name: Login as jhudsl-robot
+ - name: Login as github-actions bot
run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ 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'
# Rendered content for Leanpub and Coursera is very similar.
# This job creates a shared scaffold for both.
@@ -131,10 +139,11 @@ jobs:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+ git fetch origin
git add --force docs/no_toc*
git commit -m 'Render toc-less' || echo "No changes to commit"
- git pull --allow-unrelated-histories --strategy-option=ours
- git push origin main || echo "No changes to push"
+ git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+ git push -u origin main || echo "No changes to push"
render-leanpub:
name: Finish Leanpub prep
@@ -146,16 +155,16 @@ jobs:
steps:
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
token: ${{ secrets.GH_PAT }}
- - name: Login as jhudsl-robot
+ - name: Login as github actions bot
run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ git config --global --add safe.directory $GITHUB_WORKSPACE
+ git config --global user.name 'github-actions[bot]'
+ git config --global user.email 'github-actions[bot]@users.noreply.github.com'
# Create screenshots
- name: Run the screenshot creation
@@ -164,31 +173,41 @@ jobs:
rm -rf resources/chapt_screen_images
# Make new screenshots
- chapt_urls=$(Rscript --vanilla scripts/make_screenshots.R \
+ curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
+ chapt_urls=$(Rscript --vanilla make_screenshots.R \
--git_pat ${{ secrets.GH_PAT }} \
--repo $GITHUB_REPOSITORY \
--output_dir resources/chapt_screen_images)
# We want a fresh run of the renders each time
- - name: Delete old manuscript/
- run: rm -rf manuscript/
+ - name: Delete manuscript/
+ env:
+ GH_PAT: ${{ secrets.GH_PAT }}
+ run: |
+ rm -rf manuscript/
+ git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+ git fetch origin
+ git add .
+ git commit -m 'Delete manuscript folder' || echo "No changes to commit"
+ git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+ git push -u origin main || echo "No changes to push"
- name: Run ottrpal::bookdown_to_embed_leanpub
- if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+ if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
run: |
Rscript -e "ottrpal::bookdown_to_embed_leanpub(
render = FALSE, \
chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
- make_book_txt = TRUE, \
+ make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \
quiz_dir = NULL)"
- name: Run ottrpal::bookdown_to_embed_leanpub
- if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+ if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
run: |
Rscript -e "ottrpal::bookdown_to_embed_leanpub(
render = FALSE, \
chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
- make_book_txt = TRUE)"
+ make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'))"
# Commit the rendered Leanpub files
- name: Commit rendered Leanpub files
@@ -196,13 +215,12 @@ jobs:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
mkdir -p manuscript
- git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
git add --force manuscript/*
git add --force resources/*
git add --force docs/*
git commit -m 'Render Leanpub' || echo "No changes to commit"
git pull --allow-unrelated-histories --strategy-option=ours
- git push origin main || echo "No changes to push"
+ git push --force --set-upstream origin main || echo "No changes to push"
render-coursera:
name: Finish Coursera prep
@@ -214,16 +232,16 @@ jobs:
steps:
- name: checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
fetch-depth: 0
token: ${{ secrets.GH_PAT }}
- - name: Login as jhudsl-robot
+ - name: Login as github action
run: |
- git config --system --add safe.directory "$GITHUB_WORKSPACE"
- git config --local user.email "itcrtrainingnetwork@gmail.com"
- git config --local user.name "jhudsl-robot"
+ 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'
# Run Coursera version
- name: Convert Leanpub quizzes to Coursera
@@ -232,14 +250,19 @@ jobs:
run: Rscript -e "ottrpal::convert_coursera_quizzes()"
# Commit the rendered bookdown files
+ # Only commit coursera quizzes if the directory is present
- name: Commit rendered Coursera files
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+ git fetch origin
+ if [ -d 'coursera_quizzes' ]; then
+ git add --force coursera_quizzes/*
+ fi
git add --force manuscript/*
git add --force resources/*
git add --force docs/*
git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
- git pull --allow-unrelated-histories --strategy-option=ours
- git push origin main || echo "No changes to push"
+ git pull --rebase --allow-unrelated-histories --strategy-option=ours
+ git push -u origin main || echo "No changes to push"
diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml
index 3c3577e..dae4141 100644
--- a/.github/workflows/transfer-rendered-files.yml
+++ b/.github/workflows/transfer-rendered-files.yml
@@ -21,7 +21,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
# Use the yaml-env-action action.
- name: Load environment from YAML
@@ -42,21 +42,23 @@ jobs:
if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
steps:
+ - name: Checkout from Bookdown Repo
+ uses: actions/checkout@v4
+ with:
+ path: bookdown
+ token: ${{ secrets.GH_PAT }}
+
- name: Run git repo check
id: git_repo_check
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
- sudo apt-get install subversion
-
# What's the Quizzes repository's name?
QUIZ_REPO=$(echo ${GITHUB_REPOSITORY} | sed "s/_Bookdown/ /g" | sed "s/_Template/ /g" | awk '{print $1"_Quizzes"}')
echo $QUIZ_REPO
- # Get repo check script
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/scripts/git_repo_check.R git_repo_check.R
-
# Run repo check script
+ curl -o git_repo_check.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/git_repo_check.R
results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
echo $QUIZ_REPO exists: $results
@@ -65,8 +67,9 @@ jobs:
- name: Checkout code from Leanpub repo
if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
with:
+ path: quizzes
repository: ${{ steps.git_repo_check.outputs.leanpub_repo }}
token: ${{ secrets.GH_PAT }}
@@ -76,17 +79,19 @@ jobs:
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
- # Copy over images folder
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/resources/chapt_screen_images resources/chapt_screen_images
+ # Copy over images folder (from bookdown to quizzes repo)
+ mkdir -p quizzes/resources/chapt_screen_images
+ cp bookdown/resources/chapt_screen_images/* quizzes/resources/chapt_screen_images
- # Copy over _bookdown.yml
- svn export --force https://github.com/${GITHUB_REPOSITORY}.git/branches/${GITHUB_REF#refs/heads/}/_bookdown.yml _bookdown.yml
+ # Copy over _bookdown.yml (from bookdown to quizzes repo)
+ cp bookdown/_bookdown.yml quizzes/_bookdown.yml
- name: Create PR with resources files
if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
uses: peter-evans/create-pull-request@v3
id: cpr
with:
+ path: quizzes # Must create the PR in the Quizzes Repo
token: ${{ secrets.GH_PAT }}
commit-message: Copy files from Bookdown repository
signoff: false
diff --git a/_output.yml b/_output.yml
index 37feea5..2bbb202 100644
--- a/_output.yml
+++ b/_output.yml
@@ -2,7 +2,6 @@ bookdown::gitbook:
# When using multiple css files, the default file path will be the first one #
css: [assets/style.css, assets/GDSCN_style/gdscn.css]
includes:
- in_header: GA_Script.html
before_body: assets/GDSCN_style/big-image_gdscn.html
after_body: assets/GDSCN_style/footer.html
highlight: tango
@@ -16,5 +15,6 @@ bookdown::gitbook:
The Johns Hopkins Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
-
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/assets/AnVIL_style/logo-anvil-img.png b/assets/AnVIL_style/logo-anvil-img.png
new file mode 100644
index 0000000..b5e3c39
Binary files /dev/null and b/assets/AnVIL_style/logo-anvil-img.png differ
diff --git a/assets/box_images/under_construction.png b/assets/box_images/under_construction.png
new file mode 100644
index 0000000..a67bd5c
Binary files /dev/null and b/assets/box_images/under_construction.png differ
diff --git a/assets/style.css b/assets/style.css
index 21ed0c6..748acad 100755
--- a/assets/style.css
+++ b/assets/style.css
@@ -250,7 +250,7 @@ li.appendix span, li.part span { /* for TOC part names */
/* Sidebar formating --------------------------------------------*/
/* from r-pkgs.org*/
-div.notice, div.warning, div.github, div.dictionary, div.reflection {
+div.notice, div.warning, div.github, div.dictionary, div.reflection, div.wip {
padding: 1em;
margin: 1em 0;
padding-left: 100px;
@@ -304,6 +304,14 @@ div.reflection{
background-image: url("../assets/box_images/thinking_face.png");
}
+div.wip{
+ border: 4px #000000;
+ border-style: solid;
+ background-size: 70px;
+ background-position: 15px center;
+ background-color: #f4d03f;
+ background-image: url("../assets/box_images/under_construction.png");
+}
/* .book .book-body .page-wrapper .page-inner section.normal is needed
to override the styles produced by gitbook, which are ridiculously
diff --git a/scripts/AnVIL_Feedback_Script.sh b/scripts/AnVIL_Feedback_Script.sh
new file mode 100644
index 0000000..5269b76
--- /dev/null
+++ b/scripts/AnVIL_Feedback_Script.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Extract the title from the YAML front matter of index.Rmd
+title=$(awk '/^title:/{gsub(/^title: /,""); print}' "index.Rmd" | grep -v '^$')
+
+# Remove the outside quotation marks
+title=$(sed -e 's/^"//' -e 's/"$//' <<< "$title")
+
+# Replace spaces with '+'
+title=${title// /+}
+
+# Base url for the AnVIL Google Form
+url_base="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805="
+
+# Replace the url inside _output.yml
+perl -i -pe 's|https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform\?usp=pp_url&entry\.1565230805=.*"> Click|'${url_base}${title}'"> Click|g' _output.yml
+
+# Print for Github actions
+echo "The feedback link is: ${url_base}${title}"
\ No newline at end of file
diff --git a/style-sets/AnVIL/_output.yml b/style-sets/AnVIL/_output.yml
index 9b76c2c..7d6b017 100644
--- a/style-sets/AnVIL/_output.yml
+++ b/style-sets/AnVIL/_output.yml
@@ -2,6 +2,7 @@ bookdown::gitbook:
# 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
after_body: assets/AnVIL_style/footer.html
highlight: tango
@@ -15,4 +16,6 @@ bookdown::gitbook:
The Fred Hutch Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/AnVIL_FH/_output.yml b/style-sets/AnVIL_FH/_output.yml
index 9b76c2c..7cba311 100644
--- a/style-sets/AnVIL_FH/_output.yml
+++ b/style-sets/AnVIL_FH/_output.yml
@@ -15,4 +15,6 @@ bookdown::gitbook:
The Fred Hutch Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/AnVIL_JHU/_output.yml b/style-sets/AnVIL_JHU/_output.yml
index ba187ea..a3a7145 100644
--- a/style-sets/AnVIL_JHU/_output.yml
+++ b/style-sets/AnVIL_JHU/_output.yml
@@ -15,5 +15,6 @@ bookdown::gitbook:
The Johns Hopkins Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
-
\ No newline at end of file
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/GDSCN/_output.yml b/style-sets/GDSCN/_output.yml
index 338cd83..4156fd7 100644
--- a/style-sets/GDSCN/_output.yml
+++ b/style-sets/GDSCN/_output.yml
@@ -15,5 +15,6 @@ bookdown::gitbook:
The Fred Hutch Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
-
\ No newline at end of file
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/GDSCN_JHU/_output.yml b/style-sets/GDSCN_JHU/_output.yml
index cb0d27f..2bbb202 100644
--- a/style-sets/GDSCN_JHU/_output.yml
+++ b/style-sets/GDSCN_JHU/_output.yml
@@ -15,5 +15,6 @@ bookdown::gitbook:
The Johns Hopkins Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
-
-
\ No newline at end of file
+
+
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
\ No newline at end of file
diff --git a/style-sets/fhdasl/_output.yml b/style-sets/fhdasl/_output.yml
index d00716f..0a86496 100644
--- a/style-sets/fhdasl/_output.yml
+++ b/style-sets/fhdasl/_output.yml
@@ -11,7 +11,8 @@ bookdown::gitbook:
before: |
after: |
- This content was published with bookdown by:
+ This content was published with bookdown using
+ The OTTR Template by:
The Fred Hutch Data Science Lab
Style adapted from: rstudio4edu-book (CC-BY 2.0)
