Initial commit

.github/switch_sync_repo.R

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+#!/usr/bin/env Rscript
+
+# This script switches the repo entry for the yaml file to whatever is specified
+# Written by Candace Savonen Jan 2022
+
+if (!("optparse" %in% installed.packages())){
+  install.packages("optparse")
+}
+
+library(optparse)
+
+option_list <- list(
+  optparse::make_option(
+    c("--repo"),
+    type = "character",
+    default = "jhudsl/OTTR_Template_Test",
+    help = "GitHub repository name, e.g. jhudsl/OTTR_Template_Test",
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Get test sync yaml path
+sync_file_path <- file.path(root_dir, ".github", "test-sync.yml")
+
+yaml_contents <- yaml::yaml.load_file(sync_file_path)
+
+# Only keep first grouping
+yaml_contents$group <- yaml_contents$group[[1]]
+
+# Switch out repo
+yaml_contents$group$repos <- opt$repo
+
+yaml::write_yaml(yaml_contents, sync_file_path)

.github/sync.yml

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+# Candace Savonen Aug 2021
+# For info on how to update this file see: https://github.com/marketplace/actions/repo-file-sync-action#%EF%B8%8F-sync-configuration
+
+group:
+  - files:
+      - source: .github/workflows/
+        dest: .github/workflows/
+        deleteOrphaned: true
+        exclude: |
+          send-updates.yml
+          test-send-updates.yml
+          starting-course.yml
+          release-notes.yml
+      - source: .github/workflows/delete-preview.yml
+        dest: .github/workflows/delete-preview.yml
+      - source: .github/workflows/render-site.yml
+        dest: .github/workflows/render-site.yml
+      - source: .github/workflows/pull_request.yml
+        dest: .github/workflows/pull_request.yml
+      - source: config_automation.yml
+        dest: config_automation.yml
+  # Repositories to receive changes
+    repos: |
+      jhudsl/ottrproject.org
+      jhudsl/Baltimore_Community_Course
+      maculatus/test-ottr-website
+      dr-sayyadhury/OTTR_Template_Website_repo
+      whalera1901/Current-projects
+      GenetcXBiotech1/Dr.Fierst_lab
+      buriedsand/glbio-personal-website
+      PurplFeesh/test-ottr-site
+      jcha40/ottr_test_site
+      jhudsl/ITN_computing_resources
+      fhdsl/ITN_course_search
+      cansavvy/cansavvy_website
+      fhdsl/metricminer-dashboard
+      fhdsl/Intermediate_R
+      fhdsl/AnVIL_Poll_2024
+###ADD NEW REPO HERE following the format above#
+
+### These are custom groups for syncing -- not all files needs to be synced # will update later
+  # - files:
+  #   - source: config_automation.yml
+  #     dest: config_automation.yml
+  #   - source: .github/workflows/pull-request.yml
+  #     dest: .github/workflows/pull-request.yml
+  #   - source: scripts/spell-check.R
+  #     dest: scripts/spell-check.R
+  #   repos: |
+  #     jhudsl/Baltimore_Community_Course

.github/workflows/delete-preview.yml

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+# Candace Savonen Apr 2021
+
+name: Delete Preview
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  delete-preview:
+    runs-on: ubuntu-latest
+    steps:
+
+      # This is because if a PR is closed before a render finishes it won't find it.
+      - name: Sleep for 5 minutes
+        run: sleep 300s
+        shell: bash
+
+      # Check out current repository
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Delete the branch!
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"

.github/workflows/docker-test.yml

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+
+# Candace Savonen Apr 2022
+
+name: Build Docker Image
+
+on:
+  workflow_dispatch:
+    inputs:
+      directory:
+        required: true
+        type: string
+      tag:
+        required: true
+        type: string
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: false
+        default: 'false'
+        type: string
+    secrets:
+      GH_PAT:
+        required: true
+      DOCKERHUB_USERNAME:
+        required: false
+      DOCKERHUB_TOKEN:
+        required: false
+
+jobs:
+
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+      - name: Verify Dockerfiles changed?
+        uses: tj-actions/[email protected]
+        id: verify-changed-files
+        with:
+          files: |
+             ${{ inputs.directory }}/Dockerfile
+             ${{ inputs.directory }}/github_package_list.tsv
+
+      - name: Login as jhudsl-robot
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "jhudsl-robot"
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Set up Docker Build
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: false
+          load: true
+          context: ${{ inputs.directory }}
+          file: ${{ inputs.directory }}/Dockerfile
+          tags: ${{ inputs.tag }}
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        run: docker push ${{ inputs.tag }}

.github/workflows/pull_request.yml

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+# Candace Savonen Dec 2021
+# Updated April 2023
+name: Pull Request
+
+on:
+  pull_request:
+    branches: [ main, staging ]
+
+jobs:
+
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        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.
+
+      # Delete the branch if this has been run before
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
+
+      # Make the branch fresh
+      - name: Make the branch fresh
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          echo branch doesnt exist
+          git checkout -b $branch_name || echo branch exists
+          git push --set-upstream origin $branch_name
+        shell: bash
+
+    outputs:
+      public_repository: "${{ steps.public_repository.outputs.public }}"
+      toggle_spell_check: "${{ env.SPELL_CHECK }}"
+      toggle_url_check: "${{ env.URL_CHECKER }}"
+      toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
+
+########################## Make the error reports ##############################
+  spell-check:
+    name: Check spelling
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: spelling
+      error_min: 3
+      gh_pat: secrets.GH_PAT
+
+  url-check:
+    name: Check URLs
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT
+
+  render-preview:
+    name: Render preview
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    container:
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
+    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Set up git checkout
+      - name: Set up git checkout
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git fetch --all
+          git checkout $branch_name
+          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
+        shell: bash
+
+      # We want a fresh run of the renders each time - so first delete old html files
+      - name: Delete old *.html
+        run: Rscript -e "rmarkdown::clean_site(preview = FALSE)"
+
+       # Now we want to render all the html files from the Rmd files
+      - name: Run render html
+        id: site
+        run: Rscript -e "rmarkdown::render_site()"
+
+      # 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.site.outcome != 'success'
+        run: |
+          echo site status ${{steps.site.outcome}}
+          exit 1
+
+      - name: Website preview for download
+        run: zip website-preview.zip docs/* -r
+
+      # Commit the rendered website files
+      - name: Commit rendered website files to preview branch
+        id: commit
+        run: |
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git diff origin/main -- '*.html' >/dev/null && changes=true || changes=false
+          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 push --force || echo "No changes to commit"
+        shell: bash
+
+      - name: Find Comment
+        uses: peter-evans/find-comment@v1
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: latest commit
+
+      - name: Build components of the comment
+        id: build-components
+        run: |
+          course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
+          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
+          docs_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          echo "zip_link=$docs_link" >> $GITHUB_OUTPUT
+          echo "website_link=$website_link" >> $GITHUB_OUTPUT
+          echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+          echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
+          echo ${{steps.commit.outputs.changes}}
+
+      - name: Create or update comment
+        if: steps.commit.outputs.changes == 'true'
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            :eyes: Quick [preview of website here](${{ steps.build-components.outputs.website_link }}) \*
+            :microscope: Comprehensive [download of the website here](${{ steps.build-components.outputs.zip_link }})
+
+            \* 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: No comment if no changes
+        if: steps.commit.outputs.changes == 'false'
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            The latest commit did not produce rendering changes.
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace