fix: update SIDISH document #131
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| # See https://github.com/r-lib/actions/tree/master/examples#readme for | |
| # additional example workflows available for the R community. | |
| # ======================================================== # | |
| # Determines when the action is triggered # | |
| # ======================================================== # | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| # 添加手动触发器 | |
| workflow_dispatch: | |
| inputs: | |
| os_selection: | |
| description: "Operating system to test" | |
| required: false | |
| type: choice | |
| options: | |
| - "all" | |
| - "ubuntu-latest" | |
| - "windows-latest" | |
| - "macOS-latest" | |
| default: "all" | |
| r_version: | |
| description: "R version to test" | |
| required: false | |
| type: choice | |
| options: | |
| - "release" | |
| - "devel" | |
| - "oldrel-1" | |
| default: "release" | |
| run_examples: | |
| description: "Run package examples" | |
| required: false | |
| type: boolean | |
| default: true | |
| run_tests: | |
| description: "Run package tests" | |
| required: false | |
| type: boolean | |
| default: true | |
| name: R-CMD-check | |
| # ======================================================== # | |
| # Determine actions to take # | |
| # ======================================================== # | |
| jobs: | |
| # 动态配置矩阵 | |
| setup-matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: Set up test matrix | |
| id: set-matrix | |
| run: | | |
| if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then | |
| OS="${{ inputs.os_selection }}" | |
| R_VERSION="${{ inputs.r_version }}" | |
| if [ "$OS" = "all" ]; then | |
| echo 'matrix={"os":["ubuntu-latest","windows-latest","macOS-latest"],"r":["'"$R_VERSION"'"]}' >> $GITHUB_OUTPUT | |
| else | |
| echo 'matrix={"os":["'"$OS"'"],"r":["'"$R_VERSION"'"]}' >> $GITHUB_OUTPUT | |
| fi | |
| else | |
| # 默认配置（push/PR 触发） | |
| echo 'matrix={"os":["ubuntu-latest","windows-latest","macOS-latest"],"r":["release"]}' >> $GITHUB_OUTPUT | |
| fi | |
| R-CMD-check: | |
| needs: setup-matrix | |
| runs-on: ${{ matrix.os }} | |
| name: ${{ matrix.os }} (R ${{ matrix.r }}) | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.setup-matrix.outputs.matrix) }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - name: Display trigger information | |
| run: | | |
| echo "Triggered by: ${{ github.event_name }}" | |
| if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then | |
| echo "OS selection: ${{ inputs.os_selection }}" | |
| echo "R version: ${{ inputs.r_version }}" | |
| echo "Run examples: ${{ inputs.run_examples }}" | |
| echo "Run tests: ${{ inputs.run_tests }}" | |
| fi | |
| - name: Checking out the repository | |
| uses: actions/checkout@v4 | |
| - name: Setting up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setting up R ${{ matrix.r }} on ${{ matrix.os }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r }} | |
| use-public-rspm: true | |
| - name: Installing R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::remotes | |
| github::Exceret/ScPP | |
| github::ShixiangWang/IDConverter | |
| github::Exceret/scAB | |
| github::Exceret/Scissor | |
| github::Exceret/scPAS | |
| github::Exceret/SigBridgeRUtils | |
| github::Exceret/DEGAS | |
| github::Exceret/PIPET | |
| github::Exceret/LPSGL | |
| dependencies: '"all"' | |
| needs: check | |
| - name: Running R CMD check | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' | |
| args: 'c("--no-manual", "--as-cran")' | |
| error-on: '"warning"' |