fix #1325
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| name: External Use | |
| on: | |
| push: | |
| branches: | |
| - "main" | |
| - "dev" | |
| pull_request: | |
| branches: | |
| - "main" | |
| - "dev" | |
| workflow_dispatch: | |
| 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@v4 | |
| - 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 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() | |
| 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() | |
| shell: Rscript {0} | |
| - name: Get example files | |
| run: | | |
| tima::get_example_files() | |
| shell: Rscript {0} | |
| - name: Run pipeline | |
| run: | | |
| tima::tima_full() | |
| # Check if targets works correctly | |
| tima::tima_full() | |
| shell: Rscript {0} |