ci.yml

name: CI

on:
  push:
    branches:
      - main
      - dev
    paths-ignore:
      - "**/meta.yml"
  pull_request:
    branches:
      - main
    paths-ignore:
      - "**/meta.yml"
  workflow_dispatch:

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  NXF_ANSI_LOG: false
  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
  NXF_VER: "25.04.8"
  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
  NFT_VER: "0.9.3"

jobs:
  prettier:
    runs-on: ubuntu-latest
    steps:
      - name: Check out code
        uses: actions/checkout@v4

      - name: Setup Node
        uses: actions/setup-node@v4
        with:
          node-version: "20"

      - name: Install Prettier
        run: npm install -g prettier

      - name: Run Prettier check
        run: prettier --check .

  editorconfig:
    runs-on: ubuntu-latest
    steps:
      - name: Check out code
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install editorconfig-checker
        run: pip install editorconfig-checker

      - name: Run editorconfig-checker
        run: ec

  detect-changed-modules:
    name: Detect changed modules
    runs-on: ubuntu-latest
    outputs:
      modules: ${{ steps.components.outputs.modules }}
      test_files: ${{ steps.list.outputs.test_files }}
    steps:
      - name: Check out code
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Detect changed test files
        id: list
        run: |
          # Get base commit for comparison
          if [ "${{ github.event_name }}" == "pull_request" ]; then
              BASE_SHA="${{ github.event.pull_request.base.sha }}"
          else
              BASE_SHA="HEAD~1"
          fi

          echo "Comparing against: $BASE_SHA"

          # Get changed files
          CHANGED_FILES=$(git diff --name-only $BASE_SHA...HEAD || git diff --name-only HEAD~1 HEAD)

          echo "Changed files:"
          echo "$CHANGED_FILES"

          # Extract test files for changed modules
          TEST_FILES=()

          while IFS= read -r file; do
              # Walk up from the changed file to the nearest module (the closest
              # ancestor dir with tests/main.nf.test). This handles both flat
              # modules (modules/org/tool/) and subtool modules
              # (modules/org/tool/subtool/), e.g. bigbio/qpx/diann.
              if [[ "$file" == modules/* ]]; then
                  dir=$(dirname "$file")
                  while [[ "$dir" == modules/* && "$dir" != "modules" ]]; do
                      test_file="${dir}/tests/main.nf.test"
                      if [ -f "$test_file" ]; then
                          if [[ ! " ${TEST_FILES[@]} " =~ " ${test_file} " ]]; then
                              TEST_FILES+=("$test_file")
                          fi
                          break
                      fi
                      dir=$(dirname "$dir")
                  done
              fi
          done <<< "$CHANGED_FILES"

          # Convert to JSON array
          if [ ${#TEST_FILES[@]} -eq 0 ]; then
              echo 'test_files=[]' >> $GITHUB_OUTPUT
              echo "No changed modules with tests found."
          else
              TEST_FILES_JSON=$(printf '%s\n' "${TEST_FILES[@]}" | jq -R . | jq -s .)
              {
                  echo "test_files<<EOF"
                  echo "$TEST_FILES_JSON"
                  echo "EOF"
              } >> $GITHUB_OUTPUT
              echo "Changed test files:"
              printf '%s\n' "${TEST_FILES[@]}"
          fi

      - name: Extract module names
        id: components
        run: |
          TEST_FILES='${{ steps.list.outputs.test_files }}'
          if [ "$TEST_FILES" == "[]" ]; then
              echo 'modules=[]' >> $GITHUB_OUTPUT
          else
              # Extract module paths from test file paths
              # modules/bigbio/thermorawfileparser/tests/main.nf.test -> bigbio/thermorawfileparser
              MODULES=$(echo "$TEST_FILES" | jq -c 'map(gsub("modules/"; "") | gsub("/tests/main.nf.test"; ""))')
              {
                  echo "modules<<EOF"
                  echo "$MODULES"
                  echo "EOF"
              } >> $GITHUB_OUTPUT
          fi

  test-modules:
    name: "${{ matrix.profile }} | ${{ matrix.module }}"
    needs: [detect-changed-modules]
    if: needs.detect-changed-modules.outputs.modules != '[]'
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        module: ${{ fromJson(needs.detect-changed-modules.outputs.modules) }}
        profile: [docker]
    steps:
      - name: Check out code
        uses: actions/checkout@v4

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: ${{ env.NXF_VER }}

      - name: Install nf-test
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s ${{ env.NFT_VER }}
          sudo mv nf-test /usr/local/bin/

      - name: Download onsite test data directory
        if: matrix.module == 'bigbio/onsite'
        run: |
          DIR="tests/data/onsite/Phospho_redissolve_final_01_clean_perc.idparquet"
          mkdir -p "$DIR"
          BASE_URL="https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/Phospho_redissolve_final_01_clean_perc.idparquet"
          for f in psms.parquet proteins.parquet protein_groups.parquet search_params.parquet; do
            echo "Downloading $f ..."
            curl -sL -o "$DIR/$f" "$BASE_URL/$f"
          done
          ls -lh "$DIR"

      - name: Run nf-test for ${{ matrix.module }}
        env:
          PROFILE: ${{ matrix.profile }}
          ONSITE_IDPARQUET_PATH: ${{ github.workspace }}/tests/data/onsite/Phospho_redissolve_final_01_clean_perc.idparquet
        run: |
          MODULE_PATH="${{ matrix.module }}"
          TEST_FILE="modules/${MODULE_PATH}/tests/main.nf.test"

          echo "Testing module: ${MODULE_PATH}"
          echo "Test file: ${TEST_FILE}"
          echo "Profile: ${{ matrix.profile }}"

          if [ ! -f "${TEST_FILE}" ]; then
              echo "Error: Test file ${TEST_FILE} not found"
              exit 1
          fi

          # Run nf-test with profile (without TAP output to avoid path issues)
          nf-test test \
              --profile ${{ matrix.profile }} \
              ${TEST_FILE}

      - name: Sanitize module name for artifact
        if: always()
        id: sanitize
        run: |
          # Replace / with - to make valid artifact name
          SANITIZED=$(echo "${{ matrix.module }}" | tr '/' '-')
          echo "name=test-results-${{ matrix.profile }}-${SANITIZED}" >> $GITHUB_OUTPUT

      - name: Upload test results
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: ${{ steps.sanitize.outputs.name }}
          path: test_results/${{ matrix.module }}/
          retention-days: 7

  confirm-pass-tests:
    name: Check test results
    runs-on: ubuntu-latest
    needs: [test-modules]
    if: always()
    steps:
      - name: One or more tests failed
        if: ${{ contains(needs.*.result, 'failure') }}
        run: exit 1

      - name: One or more tests cancelled
        if: ${{ contains(needs.*.result, 'cancelled') }}
        run: exit 1

      - name: All tests ok
        if: ${{ !contains(needs.*.result, 'failure') && !contains(needs.*.result, 'cancelled') }}
        run: exit 0