ci-preprocessor.yml

name: Preprocessor CI

on:
  workflow_dispatch:
    branches:
      - '*'
  push:
    branches:
      - '*'
    paths:
      - '.github/workflows/ci-preprocessor.yml'
      - 'preprocessor/**'

# cancel current build on push from the same PR, branch or tag (https://stackoverflow.com/a/72408109/1063501)
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  BCFTOOLS_VERSION: '1.20'
  HTSLIB_VERSION: '1.20'
  REFERENCE_FASTA_ZENODO_ID: 7288118
  TOOLS_DIR: /home/runner/work/PharmCAT/PharmCAT/tools

jobs:
  build:
    name: Build project
    runs-on: ubuntu-latest

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Cache bcftools
        id: cache-bcftools
        uses: actions/cache@v4
        with:
          path: ${{ env.TOOLS_DIR }}/bcftools
          key: bcftools-${{ env.BCFTOOLS_VERSION }}

      - name: Install bcftools
        if: steps.cache-bcftools.outputs.cache-hit != 'true'
        run: |
          wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
          tar -xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2
          cd bcftools-${BCFTOOLS_VERSION}
          ./configure --prefix ${TOOLS_DIR}/bcftools
          make
          make install

      - name: Cache htslib
        id: cache-htslib
        uses: actions/cache@v4
        with:
          path: ${{ env.TOOLS_DIR }}/htslib
          key: htslib-${{ env.HTSLIB_VERSION }}

      - name: Install htslib
        if: steps.cache-htslib.outputs.cache-hit != 'true'
        run: |
          wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
          tar -xjf htslib-${HTSLIB_VERSION}.tar.bz2
          cd htslib-${HTSLIB_VERSION}
          ./configure --prefix ${TOOLS_DIR}/htslib
          make
          make install

      - name: Add tools to path
        run: echo "${TOOLS_DIR}/bcftools/bin:${TOOLS_DIR}/htslib/bin" >> $GITHUB_PATH

      # need JDK present for tests
      - name: Set up JDK
        uses: actions/setup-java@v4
        with:
          distribution: 'temurin'
          java-version: '17'

      - name: Set up python
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'
          cache: 'pip'

      - name: Install python dependencies
        run: pip3 install -r preprocessor/requirements.txt

      - name: Install pytest
        run: pip3 install pytest pytest-cov pytest-github-actions-annotate-failures

      - name: Cache reference FASTA
        id: cache-ref-fasta
        uses: actions/cache@v4
        with:
          path: |
            reference.fna.bgz
            reference.fna.bgz.fai
            reference.fna.bgz.gzi
          key: ref-fasta-${{ env.REFERENCE_FASTA_ZENODO_ID }}

      - name: Download reference FASTA
        if: steps.cache-ref-fasta.outputs.cache-hit != 'true'
        run: |
          wget https://zenodo.org/record/${REFERENCE_FASTA_ZENODO_ID}/files/GRCh38_reference_fasta.tar
          tar -xf GRCh38_reference_fasta.tar
          rm -f GRCh38_reference_fasta.tar

      # wait a bit on a release commit to give release action time to upload the resources necessary for test
      - name: Sleep for 60 seconds
        run: sleep 60s
        shell: bash
        if: ${{ startsWith(github.event.head_commit.message, 'chore(release)') }}

      - name: Run preprocessor tests
        run: python3 -m pytest --cov-config=../.coveragerc --cov-report=xml --cov=preprocessor
        working-directory: preprocessor

      - name: Codecov
        uses: codecov/codecov-action@v3
        with:
          files: preprocessor/coverage-python.xml
          flags: Preprocessor

      - name: Send Slack notification on failure
        if: failure()
        uses: slackapi/slack-github-action@v1
        with:
          channel-id: 'dev'
          payload: |
            {
              "attachments": [{
                "color": "#ff0000",
                "blocks": [
                  {
                    "type": "section",
                    "text": {
                      "type": "mrkdwn",
                      "text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
                    }
                  },
                  {
                    "type": "section",
                    "text": {
                      "type": "mrkdwn",
                      "text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
                    }
                  },
                  {
                    "type": "context",
                    "elements": [
                      {
                        "type": "mrkdwn",
                        "text": "Last commit:\n${{ github.event.head_commit.message }}"
                      }
                    ]
                  }
                ]
            }]
            }
        env:
          SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}