Initial commit #6
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| --- | |
| name: Test and QC 🧪 | |
| on: | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| concurrency: | |
| group: test-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| TEMPLATE_REF: main | |
| TEMPLATE_REPO: boehringer-ingelheim/dv.templates | |
| jobs: | |
| test: | |
| name: ${{ vars.CI_IMAGE }} | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{ vars.CI_IMAGE }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout project ⬇️ | |
| uses: actions/checkout@v4 | |
| - name: Checkout templates repo ⬇️ | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{env.TEMPLATE_REF}} | |
| repository: ${{env.TEMPLATE_REPO}} | |
| sparse-checkout: | | |
| scripts/ | |
| inst/validation | |
| path: templates | |
| - name: Overwrite quality control scripts with dv.templates ones 🧹 | |
| shell: bash | |
| run: | | |
| TEMPLATE_DIR="templates/inst/validation" | |
| REPO_DIR="inst/validation" | |
| if test ! -d "${REPO_DIR}"; then | |
| echo "### Quality Control documentation is not present" | |
| echo "### Include quality control documentation or skip it by creating following file 'inst/validation/skip_qc'" | |
| exit 1 | |
| fi | |
| if test -f "${REPO_DIR}/skip_qc"; then | |
| echo "skip_qc file found skipping qc documentation" | |
| exit 0 | |
| fi | |
| # Conserve specs.R file | |
| cp "${REPO_DIR}/specs.R" "${TEMPLATE_DIR}/specs.R" | |
| set +e # Disable immediate exit in conflicting parts on error for diff command | |
| DIFF_OUTPUT=$(diff -qr "${TEMPLATE_DIR}" "${REPO_DIR}") | |
| set -e # Enable immediate exit on error after diff command | |
| echo "# Quality control files" | tee -a "${GITHUB_STEP_SUMMARY}" | |
| if [ -n "${DIFF_OUTPUT}" ]; then | |
| echo "Warning: The contents of the directories are different!" | tee -a "${GITHUB_STEP_SUMMARY}" | |
| echo "Modified files:" | tee -a "${GITHUB_STEP_SUMMARY}" | |
| echo "$DIFF_OUTPUT" | tee -a "${GITHUB_STEP_SUMMARY}" | |
| else | |
| echo "The directories are identical." | tee -a "${GITHUB_STEP_SUMMARY}" | |
| fi | |
| rm -rf "${REPO_DIR}" | |
| mv "${TEMPLATE_DIR}" "${REPO_DIR}" | |
| - name: Install package dependencies 📄 | |
| uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main | |
| - name: Test and QC2 🧪 | |
| run: Rscript templates/scripts/test_qc_pkg.R | |
| - name: Archive snap results ⬆️ | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: snap_results | |
| path: tests/testthat/_snaps | |