update to R 4.4.0 #818
Workflow file for this run
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| name: Validate pull request | |
| on: | |
| pull_request: | |
| types: [ opened, reopened, edited ] | |
| jobs: | |
| # BEWARE: GitHub uses Microsoft-style line endings (CRLF) | |
| # instead of Unix-style (LF) interally for things like PR text. | |
| # | |
| # You MUST check for `\r\n` as the line separator instead of `\n` | |
| # in this workflow. | |
| lint-pr-body: | |
| name: Lint pull request body | |
| runs-on: ubuntu-20.04 | |
| concurrency: | |
| group: ${{ github.head_ref }} | |
| cancel-in-progress: true | |
| outputs: | |
| is-staging-na: ${{ steps.extract-staging.outputs.is-staging-na }} | |
| sandbox: ${{ steps.extract-staging.outputs.sandbox }} | |
| is-e2e-box-checked: ${{ steps.check-e2e-checkbox.outcome }} | |
| steps: | |
| - id: install | |
| name: Install requirements | |
| run: |- | |
| sudo apt-get update -y | |
| sudo apt-get install -y pcregrep | |
| - id: extract-staging | |
| name: Check staging URL | |
| run: |- | |
| REGEX="#### Link to staging deployment URL \(or set N\/A\)\s?\r\n(https:\/\/ui-(.+)\.scp-staging\.biomage\.net|https:\/\/ui-(.+)\.staging\.single-cell-platform\.net|N\/A)" | |
| echo "REGEX to test against:" | |
| echo $REGEX | |
| echo "Now looking at regex result:" | |
| URL=$(pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| IS_STAGING_NA='false' | |
| if [ $URL = 'N/A' ]; then | |
| IS_STAGING_NA='true' | |
| fi | |
| echo "Is staging N/A?" | |
| echo $IS_STAGING_NA | |
| echo "is-staging-na=$IS_STAGING_NA" >> $GITHUB_OUTPUT | |
| echo "Full URL:" | |
| echo $URL | |
| echo "url=$URL" >> $GITHUB_OUTPUT | |
| SANDBOX=$(pcregrep -o2 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| echo "Extracted sandbox:" | |
| echo $SANDBOX | |
| echo "sandbox=$SANDBOX" >> $GITHUB_OUTPUT | |
| - id: reach-staging | |
| if: steps.extract-staging.outputs.url != 'N/A' | |
| name: Attempt to reach staging environments | |
| uses: nick-fields/retry@v2 | |
| with: | |
| timeout_seconds: 30 | |
| max_attempts: 5 | |
| retry_on: error | |
| command: curl -f ${{ steps.extract-staging.outputs.url }} | |
| # Add jitter to break up correlated events. | |
| on_retry_command: sleep $[($RANDOM % 10) + 5]s | |
| - id: check-e2e-checkbox | |
| name: Check if E2E testing is checked | |
| continue-on-error: true | |
| run: |- | |
| REGEX="\[[Xx]\] Started end-to-end tests on the latest commit\." | |
| pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| run-integration-tests: | |
| name: Run integration tests | |
| runs-on: ubuntu-20.04 | |
| needs: lint-pr-body | |
| concurrency: | |
| group: ${{ github.sha }} | |
| steps: | |
| - id: check-e2e-run | |
| name: Check if E2E should run | |
| run: |- | |
| SHOULD_RUN_E2E='true' | |
| SHOULD_CANCEL_E2E='false' | |
| echo "Should E2E cancel?" | |
| if [ "${{ needs.lint-pr-body.outputs.is-staging-na}}" = "false" ] && [ "${{ needs.lint-pr-body.outputs.is-e2e-box-checked }}" != "success" ]; then | |
| SHOULD_CANCEL_E2E='true' | |
| fi | |
| echo $SHOULD_CANCEL_E2E | |
| echo "Should E2E be run?" | |
| if [ "${{ needs.lint-pr-body.outputs.is-staging-na}}" = 'true' ]; then | |
| SHOULD_RUN_E2E='false' | |
| fi | |
| echo $SHOULD_RUN_E2E | |
| echo "should-e2e-cancel=$SHOULD_CANCEL_E2E" >> $GITHUB_OUTPUT | |
| echo "should-e2e-run=$SHOULD_RUN_E2E" >> $GITHUB_OUTPUT | |
| - id: cancel | |
| name: Cancel if staging is not N/A and box is not checked | |
| if: steps.check-e2e-run.outputs.should-e2e-cancel == 'true' | |
| uses: andymckay/[email protected] | |
| - id: install | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Install requirements | |
| run: |- | |
| sudo apt-get update -y | |
| sudo apt-get install -y pcregrep | |
| - id: extract-commit-details | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Get details of last commit | |
| run: |- | |
| echo "SHA of latest GitHub branch commit:" | |
| echo ${{ github.event.pull_request.head.sha }} | |
| echo "github_sha=${{ github.event.pull_request.head.sha }}" >> $GITHUB_OUTPUT | |
| REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}') | |
| echo "Repo name:" | |
| echo $REPO_NAME | |
| echo "repo_name=$REPO_NAME" >> $GITHUB_OUTPUT | |
| - id: extract-integration-test-ref | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Get integration test ref | |
| run: |- | |
| REGEX="#### Integration test branch\s?\r\n(.+)\s?\r\n" | |
| echo "REGEX to test against:" | |
| echo $REGEX | |
| echo "Now looking at regex result:" | |
| INTEGRATION_TEST_REF=$(pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| echo "Ref given is $INTEGRATION_TEST_REF, setting it as is." | |
| echo "ref=$INTEGRATION_TEST_REF" >> $GITHUB_OUTPUT | |
| - id: run-integration-test | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Run integration tests | |
| uses: aurelien-baudet/workflow-dispatch@v2 | |
| with: | |
| workflow: Run end-to-end tests | |
| repo: ${{ github.repository_owner }}/testing | |
| token: ${{ secrets.API_TOKEN_GITHUB }} | |
| ref: ${{ steps.extract-integration-test-ref.outputs.ref }} | |
| inputs: '{ "environment": "staging", "ref": "${{ steps.extract-integration-test-ref.outputs.ref }}", "sandboxId": "${{needs.lint-pr-body.outputs.sandbox}}", "image_sha" : "${{ steps.extract-commit-details.outputs.github_sha }}", "namespace": "${{steps.extract-commit-details.outputs.repo_name}}-${{needs.lint-pr-body.outputs.sandbox}}" }' | |
| - id: get-pr-body | |
| if: failure() | |
| name: Get the current PR body | |
| uses: jwalton/gh-find-current-pr@v1 | |
| with: | |
| state: open | |
| - id: create-unchecked-pr-body | |
| if: failure() | |
| name: Create unchecked PR body | |
| run: |- | |
| UNCHECKED_BODY=$(sed 's/- \[[Xx]\] Started end-to-end tests on the latest commit\./- \[ \] Started end-to-end tests on the latest commit\./' <<\EOF | |
| ${{ steps.get-pr-body.outputs.body }} | |
| EOF | |
| ) | |
| echo "Unchecked PR body" | |
| echo $UNCHECKED_BODY | |
| # This sets multiline strings into the output variable | |
| # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string | |
| echo "body<<EOF" >> "$GITHUB_OUTPUT" | |
| echo "$UNCHECKED_BODY" >> "$GITHUB_OUTPUT" | |
| echo "EOF" >> "$GITHUB_OUTPUT" | |
| - id: uncheck-integration-checkbox | |
| if: failure() | |
| name: Uncheck the integration checkbox | |
| uses: tzkhan/pr-update-action@v2 | |
| with: | |
| repo-token: "${{ secrets.API_TOKEN_GITHUB }}" | |
| head-branch-regex: '${{ github.head_ref }}' | |
| lowercase-branch: false | |
| body-template: "${{ steps.create-unchecked-pr-body.outputs.body }}" | |
| body-update-action: 'replace' |