Update Staging branch with what's in main

.github/automatic-issues/git-secrets.md

@@ -7,19 +7,9 @@ It's important that these are set up and named exactly what they are below in or
 
 To set up these repository secrets, on your repository's main Github page, go to `Settings` and scroll down to see `Secrets` on the left side menu bar.
 
-For each new secret, click the `New repository secret` button and set each as follows, clicking `Add secret` as you fill each in appropriately:  
-
-- [ ] Set `DOCKERHUB_USERNAME`  
-`Name`: `DOCKERHUB_USERNAME`
-`value`: put your login username for https://hub.docker.com/
-
-- [ ] Set `DOCKERHUB_TOKEN`  
-`Name`:`DOCKERHUB_TOKEN`
-`value`: put a access token for Dockerhub which you can create this by following [these instructions](https://docs.docker.com/docker-hub/access-tokens/#create-an-access-token).
-
-- [ ] Set `GIT_TOKEN`
-`Name`:  `GIT_TOKEN`
-`value`: A personal access token [following these instructions](https://docs.github.com/en/github/authenticating-to-github/creating-a-personal-access-token#creating-a-token).
+- [ ] Set `GH_PAT`
+`Name`:  `GH_PAT`
+`value`: A personal access token [following these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token).
 Underneath `Select scopes`, check both `repo` and `workflow`.
 Then copy the PAT and save as the value.
 

.github/automatic-issues/images-checklist.md

@@ -12,14 +12,14 @@ See [Setting Up Images and Graphics](https://github.com/jhudsl/OTTR_Template/wik
 - [ ] The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies.
 You can check this using [Color Oracle](https://colororacle.org/).
 
-- [ ] Every image is [inserted into the text](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text) using one of these options: `leanbuild::include_slide()`, `knitr::include_image()`, or this format: `<img src="blah.png" alt="SOMETHING">`.
+- [ ] Every image is [inserted into the text](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text) using one of these options: `ottr::include_slide()`, `knitr::include_image()`, or this format: `<img src="blah.png" alt="SOMETHING">`.
 
 - [ ] Every image has [alternative text added to it](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-images-and-graphics#adding-images-and-graphics-in-text).
 
 - [ ] The beginning of each Rmd contains this chunk so the images are saved in the correct spot:
 
 `````
 ```{r, include = FALSE}
-leanbuild::set_knitr_image_path()
+ottr::set_knitr_image_path()
 ```
 `````

.github/automatic-issues/set-repo-settings.md

@@ -1,19 +1,23 @@
 
-For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings).
-
-### Needed settings:
+For more information on these settings see instructions in the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course).
 
+- [ ] This course repository is set to `public`.
 - [ ] [Add the `jhudsl-robot` as a collaborator to your repository.](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings#add-jhudsl-robot-as-a-collaborator).
+- [ ] [GH_PAT has been set up as a GitHub secret](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token)
 
-#### Turn on GitHub pages
-- [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`.  
-- [ ] Check `Enforce HTTPS`.
+- [ ] GitHub pages is turned on
+  - [ ] Go to `Settings` > `Pages`. Underneath `Source`, choose `main` for the branch and select the `docs` folder. Then click `Save`.  
+  - [ ] Check `Enforce HTTPS`.
 
-#### Set protections for main branch
-\* Don't set these settings right away! Wait a few minutes after starting your repository.
+- [ ] [Github secret `GH_PAT` has been set](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#6-set-up-your-github-personal-access-token)
+  `Name`:  `GH_PAT`
+  `value`: A personal access token [following these instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-token).
+  Underneath `Select scopes`, check both `repo` and `workflow`.
+  Then copy the PAT and save as the value.
 
-- [ ] `main` branch has been set up:
-  - [ ] `Require pull request reviews before merging` box is checked.
-  - [ ] `Require status checks to pass before merging` box is checked.
-    - [ ] Underneath that `Require branches to be up to date before merging` box is checked.
-- [ ] Click `Save` at the bottom of the page!
+- [ ] [Set branch protections settings](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#9-set-up-branch-rules)
+  - [ ] `main` branch has been set up:
+    - [ ] `Require pull request reviews before merging` box is checked.
+    - [ ] `Require status checks to pass before merging` box is checked.
+      - [ ] Underneath that `Require branches to be up to date before merging` box is checked.
+  - [ ] Click `Save` at the bottom of the page!

.github/automatic-issues/templates-to-edit.md

@@ -1,21 +1,8 @@
 
-[Follow the Wiki instructions here](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-files#setting-up-the-repository) for details on how to complete the items in this issue.
+[Follow the Wiki instructions here](https://github.com/jhudsl/OTTR_Template/wiki/Start-editing-your-course) for details on how to complete the items in this issue.
 
 The following files need to be edited to get this new course started!
 
-### Picking a style
-
-See more [about customizing style on this page in the guide](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style).
-By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.
-
-#### Using a style set
-
-[Read more about the style sets here](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style#using-a-style-set).
-
-- [ ] On a new branch, copy the `style-sets/<set-name>/index.Rmd` and `style-sets/<set-name>/_output.yml` to the top of the repository to overwrite the default `index.Rmd` and `_output.yml`.
-- [ ] Copy over all the files in the `style-sets/<set-name>/copy-to-assets` to the `assets` folder in the top of the repository.
-- [ ] [Create a pull request](https://github.com/jhudsl/OTTR_Template/wiki/About-pull-request-review) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
-
 ### Files that need edited upon creating a new course.
 
 - [ ] `README.md` - Fill in all the `{ }`.
@@ -28,6 +15,20 @@ By default this course template will use the jhudsl data science lab style. Howe
 - [ ] `_bookdown.yml` - The list of Rmd files that need to be rendered needs to be updated. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-with-Bookdown).
 - [ ] `book.bib` - any citations need to be added. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Citations).
 
+
+### Picking a style
+
+See more [about customizing style on this page in the guide](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style).
+By default this course template will use the jhudsl data science lab style. However, you can customize and switch this to another style set.
+
+#### Using a style set
+
+[Read more about the style sets here](https://github.com/jhudsl/OTTR_Template/wiki/Change-Title-&-Customize-style#using-a-style-set).
+
+- [ ] On a new branch, copy the `style-sets/<set-name>/index.Rmd` and `style-sets/<set-name>/_output.yml` to the top of the repository to overwrite the default `index.Rmd` and `_output.yml`.
+- [ ] Copy over all the files in the `style-sets/<set-name>/copy-to-assets` to the `assets` folder in the top of the repository.
+- [ ] [Create a pull request](https://github.com/jhudsl/OTTR_Template/wiki/Start-editing-your-course#getting-started-with-the-github-workflow) with these changes, and double check the rendered preview to make sure that the style is what you are looking for.
+
 ### Files that need to be edited upon adding new packages that the book's code uses:
 
 - `docker/Dockerfile` needs to have the new package added so it will be installed. See [instructions](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image).

.github/automatic-issues/update-enrollment.md

@@ -4,6 +4,6 @@ We are working on adding more features and smoothing out bugs as we go.
 
 If you want to receive updates from the original template to your course template, you will need to enroll this repository to the template updates by adding it to the `sync.yml` file.
 
-- [ ] [Follow these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Receiving-template-updates#how-to-enroll-a-repository-to-receive-template-updates) to enroll your course repository to receive these updates.
+- [ ] [Follow these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#10-enroll-your-repository-for-ottr-updates) to enroll your course repository to receive these updates.
 
-- [ ] [Ensure that you have followed these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Setting-up-your-repository-settings#add-jhudsl-robot-as-a-collaborator) to add the `jhudsl-robot` as a collaborator to your repository.
+- [ ] [Ensure that you have followed these instructions](https://github.com/jhudsl/OTTR_Template/wiki/Start-a-new-course#5-add-jhudsl-robot-as-a-collaborator) to add the `jhudsl-robot` as a collaborator to your repository.

.github/sync.yml

@@ -22,12 +22,15 @@ group:
     jhudsl/GDSCN_Book_SARS_Galaxy_on_AnVIL
     abyzovlab/CNVpytor_course
     opencasestudies/OCS_Guide
+    tmm211/dsp-terra-mooc-test2
 ###ADD NEW REPO HERE following the format above#
   files:
     - source: .github/workflows/render-bookdown.yml
       dest: .github/workflows/render-bookdown.yml
     - source: .github/workflows/render-preview.yml
       dest: .github/workflows/render-preview.yml
+    - source: .github/workflows/render-leanpub.yml
+      dest: .github/workflows/render-leanpub.yml
     - source: .github/workflows/docker-build-test.yml
       dest: .github/workflows/docker-build-test.yml
     - source: .github/workflows/transfer-rendered-files.yml
@@ -44,6 +47,8 @@ group:
       dest: .github/ISSUE_TEMPLATE/course-problem-report.md
     - source: .github/ISSUE_TEMPLATE/course-content-add.md
       dest: .github/ISSUE_TEMPLATE/course-content-add.md
+    - source: scripts/make_screenshots.R
+      dest: scripts/make_screenshots.R
     - source: scripts/spell-check.R
       dest: scripts/spell-check.R
     - source: scripts/get_spell_errors.R
@@ -55,6 +60,15 @@ group:
     - source: style-sets
       dest: style-sets
 
+  repos: |
+    jhudsl/OTTR_Template_Website
+  - source: .github/workflows/style-and-sp-check.yml
+    dest: .github/workflows/style-and-sp-check.yml
+  - source: .github/workflows/url-checker.yml
+    dest: .github/workflows/url-checker.yml
+  - source: scripts/spell-check.R
+    dest: scripts/spell-check.R
+
 ###### TO ADD NEW REPOSITORY USE THIS FORMAT; Feel free to add/drop files that
 # you specifically would like synced (or not).
 #

.github/workflows/check-quizzes.yml

@@ -0,0 +1,117 @@
+
+# Candace Savonen Jan 2022
+
+name: Check Leanpub Quizzes
+
+on:
+  workflow_dispatch:
+### UNCOMMENT THIS SECTION IF YOU WISH PREPARE YOUR COURSE QUIZZES FOR LEANPUB AUTOMATICALLY
+#  pull_request:
+#    branches: [ main, staging]
+#    paths:
+#      - 'quizzes/*'
+######### END OF SECTION #########
+
+jobs:
+  check-quizzes:
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/course_template
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Configure git
+        run: |
+          git config --local user.email "itcrtrainingnetwork@gmail.com"
+          git config --local user.name "jhudsl-robot"
+
+          branch_name='check-${{ github.event.pull_request.number }}'
+          exists=$(git ls-remote https://${{ secrets.GH_PAT }}@github.com/$GITHUB_REPOSITORY $branch_name | wc -l | xargs)
+          if [[ $exists == 0 ]];then
+            echo branch doesnt exist
+            git checkout -b $branch_name
+            git push --set-upstream origin $branch_name
+          else
+            echo branch does exist
+            git fetch --all
+            git checkout $branch_name
+            git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }}
+          fi
+        shell: bash
+
+      - name: Run quiz check
+        id: quiz_check_run
+        run: |
+          Rscript -e "ottr::check_quizzes(quiz_dir = 'quizzes', write_report = TRUE, verbose = TRUE)"
+          results=0
+          if -f "question_error_report.tsv"; then
+            results=$(wc -l < question_error_report.tsv >/dev/null)
+          fi
+          echo ::set-output name=quiz_chk_results::$results
+
+      - name: Commit quiz check errors
+        run: |
+          branch_name='check-${{ github.event.pull_request.number }}'
+          git diff --name-only origin/main -- question_error_report.tsv >/dev/null && changes=true || changes=false
+          echo $changes
+          if $changes == true; then
+            git diff --name-only origin/$branch_name question_error_report.tsv >/dev/null && changes=true || changes=false
+            echo $changes
+            if $changes == true; then
+              git add --force question_error_report.tsv
+              git diff-index --quiet HEAD || git commit -m 'Add question error report file'
+              git pull --set-upstream origin $branch_name --allow-unrelated-histories
+              git push origin $branch_name
+            fi
+          fi
+
+      - name: Build components of the quiz check comment
+        id: build-components
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          branch_name='check-${{ github.event.pull_request.number }}'
+          quiz_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/question_error_report.tsv
+          echo ::set-output name=time::$(date +'%Y-%m-%d')
+          echo ::set-output name=commit_id::$GITHUB_SHA
+          echo ::set-output name=quiz_error_url::$quiz_error_url
+
+      # Handle the commenting
+      - name: Find Comment
+        uses: peter-evans/find-comment@v1
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: quiz errors
+
+      - name: Quiz errors!
+        if: ${{ steps.quiz_check_run.outputs.quiz_chk_results >= 2 }}
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            :warning: There are quiz errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Publishing-on-Leanpub#setting-up-quizzes).
+            [Download the errors here.](${{ steps.build-components.outputs.quiz_error_url }})
+            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+      - name: Check quiz check results - fail if too many errors
+        if: ${{ steps.quiz_check_run.outputs.quiz_chk_results >= 2 }}
+        run: exit 1
+
+      - name: No quiz errors
+        if: ${{ steps.quiz_check_run.outputs.quiz_chk_results < 2 }}
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            No quiz errors detected! :tada:
+            _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace

.github/workflows/delete-preview.yml

@@ -22,15 +22,3 @@ jobs:
         with:
           github_token: ${{ secrets.GH_PAT }}
           branches: preview-${{ github.event.pull_request.number }}
-
-      - name: Delete gist
-        id: gist
-        run: |
-          echo ${{ secrets.GH_PAT }} > docker/git_token.txt
-          gist_key=${GITHUB_REPOSITORY}_spell_check_${{ github.event.pull_request.number }}
-          gist_url=$(Rscript --vanilla scripts/get_the_gist.R \
-            --git_pat docker/git_token.txt \
-            --gist_key $gist_key \
-            --file resources/spell_check_results.tsv \
-            --delete)
-          rm docker/git_token.txt

.github/workflows/docker-build-test.yml

@@ -44,14 +44,15 @@ jobs:
         if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }}
         run: |
           echo This was tested on OTTR_Template no need to re-run
-          exit 1
 
       # Set up Docker build
       - name: Set up Docker Buildx
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         uses: docker/setup-buildx-action@v1
 
       # Setup layer cache
       - name: Cache Docker layers
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         uses: actions/cache@v2
         with:
           path: /tmp/.buildx-cache
@@ -61,13 +62,16 @@ jobs:
 
       # Set up Docker build
       - name: Set up Docker Build
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         uses: docker/setup-buildx-action@v1
 
       - name: Get token
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt
 
       # Build docker image
       - name: Build Docker image
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         uses: docker/build-push-action@v2
         with:
           push: false
@@ -90,6 +94,7 @@ jobs:
         run: docker push jhudsl/course_template
 
       - name: Get the version
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
         id: get_version
         run: |
           echo ::set-output name=version::$(echo $GITHUB_REF | cut -d / -f 3)
@@ -99,4 +104,4 @@ jobs:
         if: ${{ github.event_name == 'release' }}
         run: |
           docker tag jhudsl/course_template:latest jhudsl/course_template:${{ steps.get_version.outputs.version }}
-          docker push jhudsl/course_template:1.0
+          docker push jhudsl/course_template:${{ steps.get_version.outputs.version }}

.github/workflows/render-bookdown.yml

@@ -21,8 +21,7 @@ jobs:
   # This workflow contains a single job called "build-all"
   render-main:
     runs-on: ubuntu-latest
-    container:
-      image: jhudsl/course_template
+
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
@@ -75,13 +74,24 @@ jobs:
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+        run: |
+          docker run \
+          --mount type=bind,target=/home/rstudio,source=$PWD \
+          --user "$(id -u):$(id -g)" \
+          jhudsl/course_template \
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
+          file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
 
 ##### If you do not wish to host your course on Coursera, you can delete this section #####
       # Run Coursera version
       - name: Run Coursera version of render
         id: coursera
-        run: Rscript -e "leanbuild::render_coursera()"
+        run: |
+          docker run \
+          --mount type=bind,target=/home/rstudio,source=$PWD \
+          --user "$(id -u):$(id -g)" \
+          jhudsl/course_template \
+          Rscript -e "ottr::render_coursera()"
 
 ##### End of Coursera rendering section ########################################