check.yaml

---
name: Check 🛠

on:
  workflow_dispatch:
  pull_request:
    types:
      - opened
      - synchronize
      - reopened
      - ready_for_review
    branches:
      - main
  push:
    branches:
      - main

jobs:
  audit:
    name: Audit Dependencies 🕵️‍♂️
    uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
  r-cmd:
    name: R CMD Check 🧬
    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
    secrets:
      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    with:
      enable-staged-dependencies-check: false
  coverage:
    if: github.event_name == 'pull_request'
    name: Coverage 📔 
    uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
    secrets:
      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  roxygen:
    name: Roxygen 🅾
    uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main
    secrets:
      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  gitleaks:
    name: gitleaks 💧
    uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
  links:
    if: github.event_name == 'pull_request'
    name: Check URLs 🌐
    uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
  version:
    name: Version Check 🏁
    uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main
  e2e-test:
    runs-on: ubuntu-latest
    container:
      image: ${{ matrix.config.image }}:${{ matrix.config.tag }}
    name: E2E Test on ${{ matrix.config.image }}:${{ matrix.config.tag }}
    if: >
      !contains(github.event.commits[0].message, '[skip e2e tests]')
        && github.event.pull_request.draft == false
    strategy:
      fail-fast: false
      matrix:
        config:
          - {image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15, tag: latest}
    steps:
      - name: Install package
        run: >
          remotes::install_github(
            "${{ github.repository }}",
            ref = "${{ github.sha }}",
            auth_token = "${{ github.token }}"
          )
        shell: Rscript {0}
      - name: Execute E2E Test
        run: |
          library(staged.dependencies)
          print("Creating dependency table")
          x <- dependency_table("openpharma/stageddeps.food", "repo@host", ref = "fixgarden@main")
          print(x)
          print("Checking consistent yamls")
          check_yamls_consistent(x)
          print("Install upstream deps")
          install_deps(x)
          print("Checking downstream")
          check_downstream(x, check_args = "--no-manual")
          print("Build, check, install")
          build_check_install(x, packages_to_process = "stageddeps.house", rcmd_args = list(check = "--no-manual"))
          print("Get all external dependencies")
          deps <- get_all_external_dependencies(x)
          print(deps)
        shell: Rscript {0}