up #2056
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| --- | |
| name: External Use | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - dev | |
| pull_request: | |
| branches: | |
| - main | |
| - dev | |
| workflow_dispatch: null | |
| permissions: read-all | |
| jobs: | |
| tima-test: | |
| name: tima-${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - macos-latest | |
| - windows-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Get number of CPU cores | |
| uses: SimenB/github-actions-cpu-cores@v2 | |
| id: cpu-cores | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| Ncpus: ${{ steps.cpu-cores.outputs.count }} | |
| - name: Install dependencies (Linux) | |
| if: matrix.os == 'ubuntu-latest' | |
| run: > | |
| sudo apt-get update && sudo apt-get install -y --no-install-recommends | |
| libarchive-dev libcurl4-openssl-dev libfribidi-dev libharfbuzz-dev \ | |
| && sudo apt-get clean \ | |
| && sudo rm -rf /var/lib/apt/lists/* | |
| - name: Install (Linux) | |
| if: matrix.os == 'ubuntu-latest' | |
| run: > | |
| install.packages("tima", repos = | |
| c("https://taxonomicallyinformedannotation.r-universe.dev", | |
| "https://bioc.r-universe.dev", "https://cloud.r-project.org"), type = | |
| "source") | |
| tima::install_tima() | |
| shell: Rscript {0} | |
| - name: Install (MacOS and Windows) | |
| if: matrix.os != 'ubuntu-latest' | |
| run: > | |
| install.packages("tima", repos = | |
| c("https://taxonomicallyinformedannotation.r-universe.dev", | |
| "https://bioc.r-universe.dev", "https://cloud.r-project.org"), type = | |
| "binary") | |
| tima::install_tima() | |
| shell: Rscript {0} | |
| - name: Get example files | |
| run: | | |
| tima::get_example_files() | |
| shell: Rscript {0} | |
| - name: Run pipeline | |
| run: | | |
| tima::run_tima() | |
| # Check if targets works correctly | |
| tima::run_tima() | |
| shell: Rscript {0} |