fix(preprocessor): add back --missing-to-ref #125
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| 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 }} |