main.yml

# Source: https://github.com/pharmaverse/admiralci
# Stripped down version of admiralci checks. Good for
# the developement process. When package is ready to
# be published, revisit and add release-related
# workflows.
name: admiral CI/CD Wortkflows

on:
  workflow_dispatch:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

concurrency:
  group: admiral-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  R_VERSION: "release"

jobs:
  get_r_version:
    name: Get R version
    runs-on: ubuntu-latest
    outputs:
      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
    steps:
      - name: Get R Version for Downstream Container Jobs
        id: get_r_version
        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
        shell: bash

  spellcheck:
    name: Spelling
    runs-on: ubuntu-latest
    needs: get_r_version
    container:
      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
    steps:
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v8

      - name: Checkout repo
        uses: actions/checkout@v4.2.2
        if: github.event_name == 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          repository: ${{ github.event.pull_request.head.repo.full_name }}

      - name: Checkout repository
        uses: actions/checkout@v4.2.2
        if: github.event_name != 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}

      - name: Restore cache
        uses: actions/cache@v4
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        with:
          run-system-dependencies: true
          renv-restore: false
          enable-check: false
          direction: upstream
          git-ref: ${{ steps.branch-name.outputs.current_branch }}

      - name: Run Spellcheck
        uses: insightsengineering/r-spellcheck-action@v3

  lint:
    name: Lint
    runs-on: ubuntu-latest
    needs: get_r_version
    container:
      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
    steps:
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v8

      - name: Checkout repo
        uses: actions/checkout@v4.2.2
        if: github.event_name == 'pull_request'
        with:
            ref: ${{ steps.branch-name.outputs.head_ref_branch }}
            repository: ${{ github.event.pull_request.head.repo.full_name }}

      - name: Checkout repository
        uses: actions/checkout@v4.2.2
        if: github.event_name != 'pull_request'
        with:
            ref: ${{ steps.branch-name.outputs.head_ref_branch }}

      - name: Restore cache
        uses: actions/cache@v4
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        with:
            run-system-dependencies: true
            renv-restore: false
            enable-check: false
            direction: upstream
            git-ref: ${{ steps.branch-name.outputs.current_branch }}
        env:
            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Install latest release of lintr
        run: |
            install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
        shell: Rscript {0}

      - name: Lint
        run: |
          lints <- lintr::lint_package()
          if (length(lints) > 0L) {
              print(lints)
              stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
          }
        shell: Rscript {0}