lintr.yml

on:
  workflow_dispatch:
  workflow_call:
    inputs:
      r-version:
        description: 'The version of R to use'
        default: '4.1'
        required: false
        type: string
      lint-all-files:
        description: 'Lint all files every time'
        default: 'false'
        required: false
        type: string
  push:
    branches:
      - main
      - devel
      - pre-release
      - patch
  pull_request:
    branches:
      - main
      - devel
      - pre-release
      - patch

name: Lint

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

jobs:
  get_r_version:
    name: Get R version
    runs-on: ubuntu-latest
    if: >
      !contains(github.event.commits[0].message, '[skip lint]')
    outputs:
      r-version: ${{ steps.normalizer.outputs.R_VERSION }}
    steps:
      - name: Normalize inputs
        id: normalizer
        run: |
          R_VERSION="${{ inputs.r-version }}"
          if [ "$R_VERSION" == "" ]
          then {
            R_VERSION="4.1"
          }
          fi
          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
        shell: bash
  lint:
    name: Lint
    runs-on: ubuntu-latest
    container:
      image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest"
    if: >
      !contains(github.event.commits[0].message, '[skip lint]')
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    needs: get_r_version
    steps:
      ##################### BEGIN boilerplate steps #####################
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v5.4

      - name: Checkout repo (PR) 🛎
        uses: actions/checkout@v3
        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@v3
        if: github.event_name != 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}

      - name: Normalize inputs
        id: normalizer
        run: |
          R_VERSION="${{ inputs.r-version }}"
          if [ "$R_VERSION" == "" ]
          then {
            R_VERSION="4.1"
          }
          fi
          echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
        shell: bash

      - name: Restore cache
        uses: actions/cache@v3
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        with:
          run-system-dependencies: false
          renv-restore: false
          enable-check: false
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      ##################### END boilerplate steps #####################

      - name: Changed files
        id: files
        uses: Ana06/get-changed-files@v2.2.0
        with:
          format: 'json'
          filter: '*'

      - name: Lint
        run: |
          exclusions_list <- NULL
          if (!identical("${{ inputs.lint-all-files }}", "true")) {
            changed_files <- jsonlite::fromJSON('${{ steps.files.outputs.added_modified }}')
            all_files <- list.files(recursive = TRUE)
            exclusions_list <- if (any(changed_files %in% c(".lintr", "renv.lock"))) {
              as.list(setdiff(all_files, changed_files))
            } else {
              NULL
            }
          }
          lints <- lintr::lint_package(exclusions = exclusions_list)
          saveRDS(lints, file = "lints.rds")
        shell: Rscript {0}

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