Add workflow: germline-gpu #37
Workflow file for this run
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| name: "yevis-test-pr" | ||
| on: | ||
| pull_request_target: | ||
| branches: | ||
| - main | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| issue_comment: | ||
| types: | ||
| - created | ||
| # https://docs.github.com/ja/actions/security-guides/automatic-token-authentication#permissions-for-the-github_token | ||
| permissions: | ||
| pull-requests: write | ||
| actions: read | ||
| jobs: | ||
| test: | ||
| runs-on: ubuntu-20.04 | ||
| if: > | ||
| (github.event_name == 'issue_comment' && | ||
| contains(github.event.comment.html_url, '/pull/') && | ||
| startsWith(github.event.comment.body, '/re-run') && | ||
| !contains(github.event.issue.labels.*.name, 'nig-gpu')) || | ||
| (github.event_name == 'pull_request_target' && | ||
| !contains(github.event.pull_request.labels.*.name, 'nig-gpu')) | ||
| steps: | ||
| - name: "Set environment variables" | ||
| id: set-env | ||
| run: | | ||
| if [[ "${{ github.event_name }}" == "issue_comment" ]]; then | ||
| echo "PR_URL=${{ github.event.issue.html_url }}" >> $GITHUB_ENV | ||
| echo "PR_NUM=${{ github.event.issue.number }}" >> $GITHUB_ENV | ||
| elif [[ "${{ github.event_name }}" == "pull_request_target" ]]; then | ||
| echo "PR_URL=${{ github.event.pull_request.html_url }}" >> $GITHUB_ENV | ||
| echo "PR_NUM=${{ github.event.pull_request.number }}" >> $GITHUB_ENV | ||
| fi | ||
| - name: "Download yevis binary from artifact" | ||
| id: download-binary-artifact | ||
| run: | | ||
| RUN_ID=`gh run --repo sapporo-wes/yevis-cli list --workflow build_binary --json databaseId --jq .[0].databaseId` | ||
| gh run --repo sapporo-wes/yevis-cli download ${RUN_ID} -n yevis | ||
| chmod +x yevis | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| continue-on-error: true | ||
| - name: "Download yevis binary from release" | ||
| if: ${{ steps.download-binary-artifact.outcome != 'success' }} | ||
| run: | | ||
| curl -fsSL -O https://github.com/sapporo-wes/yevis-cli/releases/latest/download/yevis | ||
| chmod +x ./yevis | ||
| - name: "Run tests" | ||
| id: test | ||
| run: | | ||
|
Check failure on line 60 in .github/workflows/yevis-test-pr.yml
|
||
| mkdir -p ./test-logs ./test-results | ||
| SAPPORO_RUN_DIR=${GITHUB_WORKSPACE}/test-results \ | ||
| ./yevis test \ | ||
| --verbose \ | ||
| --fetch-ro-crate \ | ||
| --from-pr ${{ PR_URL }} \ | ||
| 2>&1 | tee ./test-logs/yevis-log.txt | ||
| exit ${PIPESTATUS[0]} | ||
| continue-on-error: true | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: "List test results" | ||
| run: sudo ls -lR ./test-results > ./test-logs/test-results-list.txt | ||
| - name: "Upload test logs" | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: yevis-test-logs | ||
| path: test-logs/* | ||
| if-no-files-found: ignore | ||
| - name: "Comment to the pull request" | ||
| run: | | ||
| if [[ "${{ steps.test.outcome }}" == "success" ]]; then | ||
| gh pr --repo ${{ github.repository }} edit ${{ PR_NUM }} --remove-label invalid | ||
| else | ||
| gh pr --repo ${{ github.repository }} edit ${{ PR_NUM }} --add-label invalid | ||
| fi | ||
| COMMENT=$(cat <<EOF | ||
| ## Test results | ||
| - Test status: ${{ steps.test.outcome }} | ||
| - Test URL: https://github.com/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID} | ||
| - Test logs artifact: yevis-test-logs | ||
| EOF | ||
| ) | ||
| gh pr --repo ${{ github.repository }} comment ${{ PR_NUM }} --body "${COMMENT}" | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: "Check test status" | ||
| if: steps.test.outcome != 'success' | ||
| run: exit 1 | ||
