docker-image.yml

name: Docker Image CI

on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master" ]

jobs:

  R-CMD-check:
    runs-on: ubuntu-latest
    container:
      image: rocker/verse:latest
    strategy:
       matrix:
          TEST_DATA: [
              "inst/extdata/ExampleDb.tsv",
              "test_repertoires/airr-covid-19.tsv",
              "test_repertoires/PRJNA381394_12.tsv"
          ]
          FORMAT: [
              "html",
              "pdf"
          ]
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install dependencies
        run: |
          if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
          BiocManager::install(c("Biostrings", "GenomicAlignments", "IRanges"))
          install.packages(c("airr", "alakazam", "ape", "ggpubr", "kableExtra", "markdown", "optparse", "tigger"))
        shell: Rscript {0}

      - name: Document
        run: |
          devtools::document()
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_: false
        run: |
          options(crayon.enabled=TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), error_on="warning", check_dir="check")
        shell: Rscript {0}

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash
        
      - name: Install repcred
        run: |
          devtools::install(".")
        shell: Rscript {0}        
        
      - name: Run tests matrix
        run: |
           inst/repcred.R -r ${{ matrix.TEST_DATA }} -o outdir -d TRUE -f ${{ matrix.FORMAT }}

      - name: Create artifact name
        run: |
          test_name="${{ matrix.FORMAT }}_${{ matrix.TEST_DATA }}"
          artifact_name=$(echo -n "$test_name" | sed -e 's/\//_/g' | sed -e 's/.tsv$//g' )
          echo "ARTIFACT_NAME=$artifact_name" >> $GITHUB_ENV
           
      - name: Archive results
        uses: actions/upload-artifact@v4
        with:
          name: "repcred-report_${{ env.ARTIFACT_NAME }}"
          path: |
            outdir/results
          
  build-container:

    runs-on: ubuntu-latest
    needs: R-CMD-check

    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Set up QEMU
        uses: docker/setup-qemu-action@v2      
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2
      - name: Login to Docker Hub
        uses: docker/login-action@v2
        with:
          username: ${{ secrets.DOCKER_HUB_USERNAME }}
          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
      - name: Build and push to Docker
        uses: docker/build-push-action@v4
        with:
          context: ./docker
          file: ./docker/Dockerfile
          push: true
          no-cache: true
          tags: airrc/rep-cred:latest
          
  test-container:

    runs-on: ubuntu-latest
    needs: build-container
    
    container:
      image: airrc/rep-cred:latest
    
    strategy:
       matrix:
          TEST_DATA: [
              "test_repertoires/airr-covid-19.tsv",
              "test_repertoires/1434_exp_RLQ_pos_beta.tsv"
          ]
          FORMAT: [
              "html",
              "pdf"
          ]
    
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        
      - name: Run repcred command
        run: |
           repcred -r ${{ matrix.TEST_DATA }} -o outdir -d TRUE -f ${{ matrix.FORMAT }}