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rcannoodrcannood
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Merge remote-tracking branch 'origin/main' into switch_to_arrays
2 parents f9aaf74 + 1283c10 commit 0e2635a

93 files changed

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‎.github/workflows/ns_test.yml‎

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@@ -7,10 +7,10 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Set up java
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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distribution: temurin
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java-version: '11'

‎.github/workflows/prep_release.yml‎

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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: Set up JDK 17
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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java-version: '17'
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distribution: 'temurin'
@@ -39,11 +39,13 @@ jobs:
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id: get_version
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run: |
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viash_version=$(bin/viash --version | cut -d ' ' -f 2)
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viash_minor_version=$(echo $viash_version | cut -d. -f1,2)
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echo "Detected Viash version: $viash_version"
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echo "Detected Viash minor version: $viash_minor_version"
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echo "viash_version=$viash_version" >> "$GITHUB_OUTPUT"
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# fetch relevant changelog section
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changelog_section=$(awk "/# Viash ${viash_version}.*/{flag=1;next}/^# /{flag=0}flag" CHANGELOG.md)
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changelog_section=$(awk "/# Viash ${viash_version}.*/{flag=1;print;next}/^# /{flag=0}flag" CHANGELOGS/CHANGELOG_${viash_minor_version}.md)
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echo "changelog_section<<GITHUB_EOF" >> "$GITHUB_OUTPUT"
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echo "$changelog_section" >> "$GITHUB_OUTPUT"

‎.github/workflows/sbt_test.yml‎

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@@ -19,7 +19,7 @@ jobs:
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- { ver: '21', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- uses: viash-io/viash-actions/project/update-docker-engine@v6
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if: runner.os == 'Linux'
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testthat
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- name: Set up java
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uses: actions/setup-java@v4
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uses: actions/setup-java@v5
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with:
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distribution: temurin
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java-version: ${{ matrix.java.ver }}
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fi
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- name: Set up Python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: '3.x'
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‎.github/workflows/weekly_branch_tests.yml‎

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name: Weekly Branch Tests
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on:
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schedule:
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# Run every Sunday at 02:30 UTC (30 minutes after download test)
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- cron: '30 2 * * 0'
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workflow_dispatch: # Allow manual triggering
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jobs:
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weekly-test:
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runs-on: ${{ matrix.config.os }}
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if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/develop'
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strategy:
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fail-fast: false
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matrix:
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config:
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- { name: 'ubuntu_latest', os: ubuntu-latest }
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- { name: 'macos_latest', os: macos-latest }
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java:
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- { ver: '11', run_nextflow: true, run_coverage: false, nxf_ver: "22.04.5" }
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- { ver: '17', run_nextflow: true, run_coverage: true, nxf_ver: latest }
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- { ver: '21', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
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branch:
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- main
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- develop_0_9
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steps:
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- name: Checkout ${{ matrix.branch }} branch
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uses: actions/checkout@v5
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with:
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ref: ${{ matrix.branch }}
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- uses: viash-io/viash-actions/project/update-docker-engine@v6
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if: runner.os == 'Linux'
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Set up R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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packages: |
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processx
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testthat
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- name: Set up java
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uses: actions/setup-java@v5
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with:
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distribution: temurin
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java-version: ${{ matrix.java.ver }}
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- name: Set up sbt
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uses: sbt/setup-sbt@v1
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- name: Set up Scala
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run: |
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if [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
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brew install scala
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else
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sudo apt-get update
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sudo apt-get install -y scala
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fi
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.x'
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- name: Set up Nextflow
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if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
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uses: nf-core/setup-nextflow@v2
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with:
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version: ${{ matrix.java.nxf_ver }}
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- name: Run tests
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run: |
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if [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_coverage }}" == "true" ]]; then
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# only run coverage on main runner
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sbt clean coverage test coverageReport
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elif [[ "${{ matrix.config.name }}" =~ ^ubuntu.*$ ]] && [[ "${{ matrix.java.run_nextflow }}" == "false" ]]; then
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sbt 'testOnly -- -l io.viash.NextflowTest'
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elif [[ "${{ matrix.config.os }}" =~ ^macos.*$ ]]; then
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# macOS on github actions does not have Docker, so skip those
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sbt 'testOnly -- -l io.viash.DockerTest -l io.viash.NextflowTest'
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else
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sbt test
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fi
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- name: Upload coverage on success
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if: ${{ matrix.java.run_coverage }}
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run: bash <(curl -s https://codecov.io/bash)
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- name: Upload check results on fail
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ matrix.config.name }}_${{ matrix.branch }}_${{ matrix.java.ver }}_results
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path: check
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- name: Notify on failure
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if: failure()
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run: |
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curl -X POST \
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-H 'Content-Type: application/json' \
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-d '{
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"text": "🚨 *Weekly Tests Failed*\n\n• **Branch**: ${{ matrix.branch }}\n• **OS**: ${{ matrix.config.name }}\n• **Java**: ${{ matrix.java.ver }}\n• **Repository**: ${{ github.repository }}\n• **Run**: <${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}|View Logs>"
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}' \
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"${{ secrets.GOOGLE_CHAT_WEBHOOK_URL }}"

‎.github/workflows/weekly_download_test.yml‎

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name: Weekly Download Test
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on:
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schedule:
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# Run every Sunday at 02:00 UTC
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- cron: '0 2 * * 0'
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workflow_dispatch: # Allow manual triggering
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jobs:
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download-install-test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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steps:
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- name: Test viash download and installation
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run: |
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echo "Testing viash download from https://dl.viash.io"
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# Download viash
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curl -fsSL https://dl.viash.io | bash
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# Verify installation
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if [ -f "./viash" ]; then
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echo "✅ viash binary exists locally"
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./viash --version
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echo "✅ viash version check successful"
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else
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echo "❌ viash binary not found in local directory after installation"
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exit 1
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fi
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# Test basic functionality
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echo "Testing basic viash functionality..."
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./viash --help > /dev/null
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echo "✅ viash help command works"
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- name: Notify download test failure
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if: failure()
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run: |
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curl -X POST \
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-H 'Content-Type: application/json' \
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-d '{
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"text": "🚨 *Viash Download Test Failed*\n\n• **OS**: ${{ matrix.os }}\n• **Issue**: Failed to download/install viash from https://dl.viash.io\n• **Repository**: ${{ github.repository }}\n• **Run**: <${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}|View Logs>"
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}' \
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"${{ secrets.GOOGLE_CHAT_WEBHOOK_URL }}"

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