Add the polishing changes from #435 in their own PR (#442)

* Add the polishing changes

* No manage-gha

* No login needed

* Make it simpler for commits and pushes

.github/workflows/check-quizzes.yml

@@ -1,16 +1,15 @@
-
 # Candace Savonen Jan 2022
 
 name: Check Leanpub Quizzes
 
+#---TRIGGER-START---#
 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 #########
+ pull_request:
+ branches: [ main, staging ]
+ paths:
+ - 'quizzes/*'
+#---TRIGGER-END----#
 
 jobs:
  check-quizzes:

.github/workflows/delete-preview.yml

@@ -2,12 +2,14 @@
 
 name: Delete Preview
 
+#---TRIGGER-START---#
 on:
  pull_request:
  types: [closed]
+#---TRIGGER-END---#
 
 jobs:
- build-all:
+ delete-preview:
  runs-on: ubuntu-latest
  steps:
 

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

@@ -1,41 +1,33 @@
-# This code was originally written by Josh Shapiro
-# for the Childhood Cancer Data Lab, an initiative of Alexs Lemonade Stand Foundation.
-# https://github.com/AlexsLemonade/refinebio-examples/blob/33cdeff66d57f9fe8ee4fcb5156aea4ac2dce07f/.github/workflows/style-and-sp-check.yml#L1
+# Candace Savonen Apr 2021
 
-# Adapted for this jhudsl repository by Candace Savonen Apr 2021
+name: Build of Docker
 
-name: Test build of Dockerfile
 
-# Controls when the action will run. Triggers the workflow for a pull request for
-# master
+#---TRIGGER-START---#
 on:
  release:
  types:
  - created
  pull_request:
- branches:
- - 'main'
+ branches: [ main, staging ]
  paths: [ docker/Dockerfile, docker/github_package_list.tsv ]
  workflow_dispatch:
  inputs:
  dockerhubpush:
  description: 'Push to Dockerhub?'
  required: true
  default: 'false'
+#---TRIGGER-END----#
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
- # This workflow contains a single job called "build"
- build:
- # The type of runner that the job will run on
+ build-docker:
  runs-on: ubuntu-latest
 
- # Steps represent a sequence of tasks that will be executed as part of the job
  steps:
  - name: checkout repo
  uses: actions/checkout@v2
 
- - name: login as jhudsl-robot
+ - name: Login as jhudsl-robot
  run: |
  git config --local user.email "itcrtrainingnetwork@gmail.com"
  git config --local user.name "jhudsl-robot"

.github/workflows/release-notes.yml

@@ -2,10 +2,12 @@
 
 name: Release note PR comment
 
+#---TRIGGER-START---#
 on:
  pull_request:
- branches: [ main ]
+ branches: [ main, staging ]
  types: [ opened ]
+#---TRIGGER-END----#
 
 jobs:
  pr-comment:

.github/workflows/render-bookdown.yml

@@ -1,72 +1,36 @@
 
-# This code was originally written by Josh Shapiro and Candace Savonen
-# for the Childhood Cancer Data Lab, an initiative of Alexs Lemonade Stand Foundation.
-# https://github.com/AlexsLemonade/refinebio-examples/blob/33cdeff66d57f9fe8ee4fcb5156aea4ac2dce07f/.github/workflows/style-and-sp-check.yml#L1
+# Candace Savonen Apr 2021
 
-# Adapted for this jhudsl repository by Candace Savonen Apr 2021
+name: Render Bookdown
 
-name: Render Bookdown and Coursera
-
-# Controls when the action will run. Triggers the workflow on push
-# events only for the master branch
+#---TRIGGER-START---#
 on:
  workflow_dispatch:
  push:
- branches: [ main ]
+ branches: [ main, staging ]
  paths:
  - '**.Rmd'
- - docker/*
  - assets/*
+#---TRIGGER-END----#
+
 jobs:
- # This workflow contains a single job called "build-all"
- render-main:
+ render-bookdown:
  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
  - name: checkout
  uses: actions/checkout@v2
  with:
- # get the full repo
  fetch-depth: 0
- # use github PAT
  token: ${{ secrets.GH_PAT }}
 
-###### If you will be making changes to the Docker image to make specific to the
-###### course, then highlight this chunk and uncomment it. #####################
-###### Recommend using short cut -- Command and / works for some editors.#######
-###### START OF DOCKER UPDATE CHUNK
- # # Login to Dockerhub
- # - name: Login to DockerHub
- # uses: docker/login-action@v1
- # with:
- # username: ${{ secrets.DOCKERHUB_USERNAME }}
- # password: ${{ secrets.DOCKERHUB_TOKEN }}
- #
- # # Set up Docker build
- # - name: Set up Docker Build
- # uses: docker/setup-buildx-action@v1
- #
- # - name: Get Token
- # run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt
- #
- # # Build docker image
- # - name: Build Docker image
- # uses: docker/build-push-action@v2
- # with:
- # push: false
- # load: true
- # context: docker
- # file: docker/Dockerfile
- # tags: jhudsl/course_template
- #
- # # Push the Docker image
- # - name: Push Docker image
- # run: docker push jhudsl/course_template
-
-###### END OF DOCKER UPDATE CHUNK ##############################################
-
+ - name: Login as jhudsl-robot
+ run: |
+ git config --local user.email "itcrtrainingnetwork@gmail.com"
+ git config --local user.name "jhudsl-robot"
+ 
  # We want a fresh run of the renders each time
  - name: Delete old docs/*
  run: rm -r docs/*
@@ -75,33 +39,15 @@ jobs:
  - name: Run bookdown render
  id: bookdown
  run: |
- docker run \
- --mount type=bind,target=/home/rstudio,source=$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: |
- 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 ########################################
-
  # 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
- if: steps.bookdown.outcome != 'success' || steps.coursera.outcome != 'success'
+ - name: Check on render step
+ if: steps.bookdown.outcome != 'success'
  run: |
  echo Bookdown status ${{steps.bookdown.outcome}}
- echo Coursera status ${{steps.coursera.outcome}}
  exit 1
 
  # Commit the rendered bookdown files

.github/workflows/render-coursera.yml

@@ -0,0 +1,54 @@
+
+# Candace Savonen Apr 2021
+
+name: Render Coursera
+
+#---TRIGGER-START---#
+on:
+ workflow_dispatch:
+ workflow_run:
+ workflows: [ "Render Bookdown" ]
+ branches: [ main, staging ]
+ types:
+ - completed
+#---TRIGGER-END----#
+
+jobs:
+ render-coursera:
+ runs-on: ubuntu-latest
+ container:
+ image: jhudsl/course_template
+
+ steps:
+ - name: checkout
+ uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+ token: ${{ secrets.GH_PAT }}
+
+ - name: Login as jhudsl-robot
+ run: |
+ git config --local user.email "itcrtrainingnetwork@gmail.com"
+ git config --local user.name "jhudsl-robot"
+ 
+ # Run Coursera version
+ - name: Run Coursera version of render
+ id: coursera
+ run: Rscript -e "ottr::render_coursera(convert_quizzes = TRUE)"
+
+ # 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
+ if: steps.coursera.outcome != 'success'
+ run: |
+ echo Coursera status ${{steps.coursera.outcome}}
+ exit 1
+
+ # Commit the rendered bookdown files
+ - name: Commit rendered Coursera files
+ run: |
+ git config --local user.email "actions@github.com"
+ git config --local user.name "GitHub Actions"
+ git add --force docs/coursera/*
+ git commit -m 'Render Coursera' || echo "No changes to commit"
+ git push origin main || echo "No changes to push"

.github/workflows/render-leanpub.yml

@@ -1,59 +1,54 @@
 
 # Jan 2022 Candace Savonen
 
-name: Render and publish Leanpub
+name: Render Leanpub
 
+#---TRIGGER-START---#
 on:
  workflow_dispatch:
-### UNCOMMENT THIS SECTION IF YOU WISH PREPARE YOUR COURSE FOR LEANPUB AUTOMATICALLY
- # workflows: [ "Render Bookdown and Coursera" ]
- # branches: [ main ]
- # types:
- # - completed
- # paths:
- # - '**.Rmd'
- # - docker/*
- # - assets/*
- # - quizzes/*
-######### END OF SECTION #########
+ workflow_run:
+ workflows: [ "Render Coursera" ]
+ branches: [ main, staging ]
+ types:
+ - completed
+#---TRIGGER-END----#
 
 jobs:
- # This workflow contains a single job called "build-all"
- render-main:
+ render-leanpub:
  runs-on: ubuntu-latest
  container:
  image: jhudsl/ottr
 
- # 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
  - name: checkout
  uses: actions/checkout@v2
  with:
- # get the full repo
  fetch-depth: 0
- # use github PAT
  token: ${{ secrets.GH_PAT }}
 
- # Run leanpub rendering
+ - name: Login as jhudsl-robot
+ run: |
+ git config --local user.email "itcrtrainingnetwork@gmail.com"
+ git config --local user.name "jhudsl-robot"
+ 
+ # Create screenshots
  - name: Run the screenshot creation
  run: |
  chapt_urls=$(Rscript --vanilla scripts/make_screenshots.R \
  --git_pat ${{ secrets.GH_PAT }} \
  --repo $GITHUB_REPOSITORY)
 
+ # We want a fresh run of the renders each time
+ - name: Delete old manuscript/
+ run: rm -rf manuscript/
+
  # Run Leanpub rendering
  - name: Run ottr::bookdown_to_embed_leanpub
  run: |
- rm -rf manuscript
  Rscript -e "ottr::bookdown_to_embed_leanpub( \
  chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
  make_book_txt = TRUE)"
 
- # Convert quizzes to Coursera format
- - name: Convert quizzes to coursera
- run: Rscript -e "ottr::render_coursera(convert_quizzes = TRUE)"
-
  # Commit the rendered leanpub files
  - name: Commit rendered leanpub files
  run: |