Merge branch 'main' into add-debug-to-rBinaryPath-search

.github/actions/docker/action.yml

@@ -28,16 +28,9 @@ runs:
   using: "composite"
   steps:
     - shell: bash
-      run: echo "BASE_NM=ghcr.io/${{ inputs.org }}/${{ inputs.name }}" >> $GITHUB_ENV
-
-    - name: Create DockerFile
-      shell: bash
       run: |
-        cat << 'EOF' >> Dockerfile
-        FROM ubuntu:22.04
-        COPY ["${{ inputs.source }}", "quarto-linux-amd64.deb"]
-        RUN dpkg -i quarto-linux-amd64.deb && rm quarto-linux-amd64.deb
-        EOF
+        echo "BASE_NM=ghcr.io/${{ inputs.org }}/${{ inputs.name }}" >> $GITHUB_ENV
+        echo "FULL_NM=ghcr.io/${{ inputs.org }}/${{ inputs.name }}-full" >> $GITHUB_ENV
 
     - if: ${{ inputs.daily == 'false' }}
       shell: bash
@@ -47,9 +40,38 @@ runs:
       shell: bash
       run: echo "DAILY_TAG=-t ${{ env.BASE_NM }}:daily" >> $GITHUB_ENV
 
-    - name: Push image
+    - name: Create Base DockerFile
+      shell: bash
+      run: |
+        cat << 'EOF' >> Dockerfile
+        FROM ubuntu:22.04
+        COPY ["${{ inputs.source }}", "quarto-linux-amd64.deb"]
+        RUN dpkg -i quarto-linux-amd64.deb && rm quarto-linux-amd64.deb
+        EOF
+
+    - name: Push Base Image
       shell: bash
       run: |
         echo ${{ inputs.token }} | docker login https://ghcr.io -u ${{ inputs.username }} --password-stdin
         docker build -t ${{ env.BASE_NM }}:${{ inputs.version }} ${{ env.LATEST_TAG }} ${{ env.DAILY_TAG }} .
         docker push ${{ env.BASE_NM }} --all-tags
+
+    - name: Create Full DockerFile
+      shell: bash
+      run: |
+        rm -rf Dockerfile
+        cat << 'EOF' >> Dockerfile
+        FROM rstudio/r-base:4.3-focal
+        ENV DEBIAN_FRONTEND=noninteractive
+        COPY ["${{ inputs.source }}", "quarto-linux-amd64.deb"]
+        RUN dpkg -i quarto-linux-amd64.deb && rm quarto-linux-amd64.deb
+        RUN quarto install tinytex --no-prompt
+        EOF
+    
+    - name: Push Full Image
+      shell: bash
+      run: |
+        echo ${{ inputs.token }} | docker login https://ghcr.io -u ${{ inputs.username }} --password-stdin
+        docker build -t ${{ env.FULL_NM }}:${{ inputs.version }} ${{ env.LATEST_TAG }} ${{ env.DAILY_TAG }} .
+        docker push ${{ env.FULL_NM }} --all-tags
+        

.github/workflows/create-release.yml

@@ -171,7 +171,7 @@ jobs:
           curl -L https://anaconda.org/conda-forge/deno/${DENO:1}/download/linux-64/deno-${DENO:1}-he8a937b_0.conda --output deno.conda
           unzip deno.conda
           tar --use-compress-program=unzstd -xvf pkg-deno-${DENO:1}-he8a937b_0.tar.zst
-          cp bin/deno package/pkg-working/bin/tools/deno-x86_64-unknown-linux-gnu/deno
+          cp bin/deno package/pkg-working/bin/tools/x86_64/deno
 
       - name: Make Tarball
         run: |
@@ -432,6 +432,11 @@ jobs:
     steps:
       - name: Download Artifacts
         uses: actions/download-artifact@v3
+
+      - name: Rename news
+        run: |
+          ls -la ./News
+          mv ./News/changelog-${{needs.configure.outputs.version_base}}.md ./News/changelog.md
 
       - name: Generate Checksums
         id: generate_checksum
@@ -499,7 +504,7 @@ jobs:
             ./Windows Zip/quarto-${{needs.configure.outputs.version}}-win.zip
             ./Mac Installer/quarto-${{needs.configure.outputs.version}}-macos.pkg
             ./Mac Zip/quarto-${{needs.configure.outputs.version}}-macos.tar.gz
-            ./News/changelog-${{needs.configure.outputs.version_base}}.md
+            ./News/changelog.md
             quarto-${{needs.configure.outputs.version}}-checksums.txt
 
   docker-push:

.github/workflows/test-smokes-parallel.yml

@@ -3,11 +3,61 @@
 name: Parallel Smokes Tests
 on:
   workflow_dispatch:
+    inputs:
+      nBuckets:
+        description: "Number of buckets to split tests into"
+        required: true
+        default: 10
+        type: number
+  pull_request:
+    branches: [main]
+  push:
+    # only trigger on branches, not on tags
+    branches: [main]
 
 jobs:
-  do-nothing:
+  jobs-matrix:
     runs-on: ubuntu-latest
+    outputs:
+      BUCKETS: ${{ steps.tests-buckets.outputs.BUCKETS }}
     steps:
-      - name: Placeholder
+      - name: Checkout Repo
+        uses: actions/checkout@v3
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: pre-release
+
+      - name: Create Job for tests
+        id: tests-buckets
+        run: |
+          echo "BUCKETS=$(./run-parallel-tests.sh -n=${{ inputs.nBuckets || 20 }} --json-for-ci --timing-file=timing-for-ci.txt | jq -rc 'def lpad(n): tostring | if (n > length) then ((n - length) * "0") + . else . end; to_entries | map(.key |= tostring)| map({ num: .key| tonumber | (. + 1) | lpad(2), files: .value | tojson }) | {buckets: .}')" >> "$GITHUB_OUTPUT"
+        working-directory: tests
+      - name: Read buckets
+        run: |
+          echo ${{ steps.tests-buckets.outputs.BUCKETS }}
+
+  check-matrix:
+    runs-on: ubuntu-latest
+    needs: jobs-matrix
+    steps:
+      - name: Install json2yaml
+        run: |
+          sudo npm install -g json2yaml
+
+      - name: Check matrix definition
         run: |
-          echo "This is a dummy workflow to be able to run the real one leaving on a branch for now."
+          matrix='${{ needs.jobs-matrix.outputs.BUCKETS }}'
+          echo $matrix
+          echo $matrix | jq .
+          echo $matrix | json2yaml
+  run-smoke-tests:
+    needs: jobs-matrix
+    name: Running Tests buckets ${{ matrix.buckets.num }}
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJSON(needs.jobs-matrix.outputs.BUCKETS) }}
+    uses: ./.github/workflows/test-smokes.yml
+    with:
+      buckets: ${{ matrix.buckets.files }}

.github/workflows/test-smokes.yml

@@ -2,29 +2,51 @@
 # A failure indicates some signficant portion of functionality is likely to be broken.
 name: Smoke Tests
 on:
+  workflow_call:
+    inputs:
+      buckets:
+        description: "JSON string for buckets of tests to run in loop. Array of grouped tests."
+        required: true
+        type: string
+      time-test:
+        description: "Should we run tests to produce test file"
+        required: false
+        type: boolean
+        default: false
   workflow_dispatch:
-  pull_request:
-    branches: [main]
-  push:
-    # only trigger on branches, not on tags
-    branches: [main]
+    inputs:
+      buckets:
+        description: "JSON string for buckets of tests to run in loop. Array of grouped tests."
+        required: false
+        type: string
+        default: ""
+      time-test:
+        description: "Should we run tests to produce test file"
+        required: false
+        type: boolean
+        default: false
   schedule:
     - cron: "0 6 * * *"
 
 jobs:
   run-smokes:
+    name: Run smoke (${{ matrix.os }})${{ matrix.time-test && ' with timed file' || ''}}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
+        time-test:
+          - ${{ inputs.time-test }}
+        exclude:
+          # only run timed tests on Linux
+          - os: windows-latest
+            time-test: true
     runs-on: ${{ matrix.os }}
-
+    env:
+      QUARTO_TESTS_FORCE_NO_PIPENV: true
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v3
-        with:
-          # checkout full tree
-          fetch-depth: 0
 
       - name: Fix temp dir to use runner one (windows)
         if: runner.os == 'Windows'
@@ -54,7 +76,7 @@ jobs:
         if: ${{ runner.os != 'Windows' || github.event_name == 'schedule' }}
         run: npx playwright install --with-deps
         working-directory: ./tests/integration/playwright
-        
+
       - name: Install MECA validator
         if: ${{ runner.os != 'Windows' }}
         run: npm install -g meca
@@ -90,8 +112,9 @@ jobs:
           if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')
           renv::restore()
           # Install dev versions for our testing 
-          renv::install("yihui/knitr")
-          renv::install("rstudio/rmarkdown")
+          # Use r-universe to avoid github api calls
+          try(renv::install('knitr', repos = c('https://yihui.r-universe.dev')))
+          try(renv::install('rmarkdown', repos = c('https://rstudio.r-universe.dev')))
         shell: Rscript {0}
         env:
           RENV_CONFIG_REPOS_OVERRIDE: https://packagemanager.rstudio.com/cran/latest
@@ -135,40 +158,95 @@ jobs:
         run: |
           julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.build(\"IJulia\"); Pkg.precompile()"
 
-      - name: Smoke Test Commits
-        if: github.event.before != ''
+      - name: Setup timing file for timed test
+        if: ${{ matrix.time-test == true }}
+        run: |
+          echo "QUARTO_TEST_TIMING=timing-for-ci.txt" >> "$GITHUB_ENV"
+
+      - name: Run all Smoke Tests Windows
+        if: ${{ runner.os == 'Windows' && format('{0}', inputs.buckets) == '' && matrix.time-test == false }}
         env:
           # Useful as TinyTeX latest release is checked in run-test.sh
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          git checkout ${{ github.sha}}
-          pushd tests
-          case $RUNNER_OS in
-            "Windows")
-              pwsh -F ./run-tests.ps1
-              ;;
-            *)
-              ./run-tests.sh
-              ;;
-          esac
-          popd
+        run: ./run-tests.ps1
+        working-directory: tests
+        shell: pwsh
+
+      - name: Run all Smoke Tests Linux
+        if: ${{ runner.os != 'Windows' && format('{0}', inputs.buckets) == '' }}
+        env:
+          # Useful as TinyTeX latest release is checked in run-test.sh
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: ./run-tests.sh
+        working-directory: tests
         shell: bash
 
-      - name: Smoke Test Head
+      - name: Run Smoke Tests as a bucket on Linux
+        if: ${{ runner.os != 'Windows' && format('{0}', inputs.buckets) != '' }}
         env:
           # Useful as TinyTeX latest release is checked in run-test.sh
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: github.event.before == ''
         run: |
-          case $RUNNER_OS in
-            "Windows")
-              ../package/dist/bin/quarto.cmd render docs/test.qmd --to pdf
-              pwsh -F ./run-tests.ps1
-              ;;
-            *)
-              quarto render docs/test.qmd --to pdf
-              ./run-tests.sh
-              ;;
-          esac
+          haserror=0
+          readarray -t my_array < <(echo '${{ inputs.buckets }}' | jq -rc '.[]')
+          for file in "${my_array[@]}"; do 
+            echo ">>> ./run-tests.sh ${file}"
+            ./run-tests.sh $file
+            status=$?
+            [ $status -eq 0 ] && echo ">>> No error in this test file" || haserror=1
+          done
+          [ $haserror -eq 0 ] && echo ">>> All tests passed" || exit 1
         working-directory: tests
         shell: bash
+
+      - name: Run Smoke Tests as a bucket on Windows
+        if: ${{ runner.os == 'Windows' && format('{0}', inputs.buckets) != '' }}
+        env:
+          # Useful as TinyTeX latest release is checked in run-test.sh
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          $haserror=$false
+          foreach ($file in ('${{ inputs.buckets }}' | ConvertFrom-Json)) {
+            Write-Host ">>> ./run-tests.ps1 ${file}"
+            ./run-tests.ps1 $file
+            $status=$LASTEXITCODE
+            if ($status -eq 1) {
+              Write-Host ">>> Error found in test file"
+              $haserror=$true
+            } else {
+              Write-Host ">>> No error in this test file"
+            }
+          }
+          if ($haserror) {
+            Exit 1
+          } else {
+            Write-Host ">>> All tests have passed"
+          }
+        working-directory: tests
+        shell: pwsh
+
+      - name: Create Pull Request for new tests timing
+        if: matrix.time-test
+        id: cpr
+        uses: peter-evans/create-pull-request@v5
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          add-paths: tests/timing-for-ci.txt
+          commit-message: |
+            timing for new tests [auto PR]
+          branch: updates/timing-for-ci
+          delete-branch: true
+          assignees: cderv
+          reviewers: cderv
+          title: |
+            [CI] Update timing file
+          body: |
+            This PR was created automatically with new timing test file for our parallel smoke tests. 
+            Please review and merge to trigger a new build of the website.
+
+      - name: Check auto PR outputs
+        if: steps.cpr.outcome == 'success'
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"
+          echo "Pull Request Action Performed - ${{ steps.cpr.outputs.pull-request-operation }}"

.github/workflows/update-test-timing.yml

@@ -0,0 +1,16 @@
+# Upate the timing test file required for parallel test
+on:
+  workflow_dispatch:
+  schedule:
+    # run weekly on Monday
+    - cron: "13 3 * * 1"
+
+name: Update timing test file
+
+jobs:
+  run-timed-tests:
+    name: Running Tests to produce timed file
+    uses: ./.github/workflows/test-smokes.yml
+    with:
+      buckets: ""
+      time-test: true

configuration

@@ -8,18 +8,18 @@
 # deno_dom should match release at https://github.com/b-fuze/deno-dom/releases
 
 # Binary dependencies
-export DENO=v1.33.2
+export DENO=v1.33.4
 export DENO_DOM=v0.1.35-alpha-artifacts
-export PANDOC=3.1.5
+export PANDOC=3.1.2
 export DARTSASS=1.55.0
-export ESBUILD=0.15.6
-export TYPST=0.6.0
+export ESBUILD=0.18.15
+export TYPST=0.7.0
 
 # Bootstrap dependencies from bslib
 # (use commit hash from bslib repo)
-export BOOTSTRAP=8dc31b40bd9b387c4a3c36ac1f63bb853037cba6
+export BOOTSTRAP=ff3e498179a066043ceb8f2cb3188f10d0d6ebc4
 export BOOTSTRAP_FONT=1.10.5
-export BOOTSWATCH=5.2.3
+export BOOTSWATCH=5.3.1
 
 # javascript HTML dependencies
 export ANCHOR_JS=5.0.0