run-tests.yaml

on:
  push:
    branches:
      - master
  pull_request:

name: Run unit tests

jobs:
  create_mock:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Cache RDS files
        id: cache-mock
        uses: actions/cache@v4
        with:
          path: tests/mock-files
          key: mock-${{ hashFiles('tests/mock.R') }}

      - name: Set directories
        if: steps.cache-mock.outputs.cache-hit != 'true'
        run: |
          echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV

      - name: Restore the package directory
        if: steps.cache-mock.outputs.cache-hit != 'true'
        uses: actions/cache@v4
        with:
          path: ${{ env.R_PKG_DIR }}
          key: check-packages

      - name: Clone the wobbegong R package
        if: steps.cache-mock.outputs.cache-hit != 'true'
        run: git clone https://github.com/kanaverse/wobbegong-R rpkg

      - name: Install dependencies
        if: steps.cache-mock.outputs.cache-hit != 'true'
        shell: Rscript {0}
        run: |
          stuff <- read.dcf("rpkg/DESCRIPTION")
          stuff <- stuff[,intersect(colnames(stuff), c("Imports", "LinkingTo", "Suggests", "Depends"))]
          deps <- sub(" .*", "", unlist(strsplit(stuff, ",\\s*"), use.names=FALSE))
          BiocManager::install(deps)

      - name: Install the R package
        if: steps.cache-mock.outputs.cache-hit != 'true'
        run: R CMD INSTALL rpkg

      - name: Build the mock files
        if: steps.cache-mock.outputs.cache-hit != 'true'
        run: |
          cd tests
          R -f mock.R

  test:
    runs-on: ubuntu-latest
    needs: [ create_mock ]

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Set up Node
        uses: actions/setup-node@v4
        with:
          node-version: 22

      - name: Cache Modules
        uses: actions/cache@v4
        with:
          path: '**/node_modules'
          key: npm-${{ hashFiles('package.json') }}

      - name: Update NPM packages
        run: npm i --include=dev

      - name: Cache mock files
        uses: actions/cache@v4
        with:
          path: tests/mock-files
          key: mock-${{ hashFiles('tests/mock.R') }}

      - name: Run tests
        run: npm run test