Add AI Copilot module #667
Workflow file for this run
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| name: Playbase unittest | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| permissions: | |
| contents: write | |
| env: | |
| DOCKER_TAG: bigomics/omicsplayground:devel | |
| jobs: | |
| unittest: | |
| # runs-on: ubuntu-latest | |
| runs-on: self-hosted | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.head_ref || github.ref }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - | |
| name: Update DESCRIPTION imports | |
| run: | | |
| docker run --rm -v "$PWD":/playbase -w /playbase rocker/tidyverse:4.3 \ | |
| Rscript -e "install.packages('renv', repos='https://cloud.r-project.org'); source('dev/write_description.R')" | |
| - | |
| name: Commit updated DESCRIPTION | |
| run: | | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| git add DESCRIPTION | |
| git diff --staged --quiet || git commit -m "chore: update DESCRIPTION imports [skip ci]" | |
| git push | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| # - | |
| # name: Setup upterm session | |
| # uses: lhotari/action-upterm@v1 | |
| # with: | |
| # ## limits ssh access and adds the ssh public key for the user which triggered the workflow | |
| # limit-access-to-actor: true | |
| # ## limits ssh access and adds the ssh public keys of the listed GitHub users | |
| # limit-access-to-users: mauromiguelm | |
| # wait-timeout-minutes: 120 | |
| - | |
| name: Build OPG docker | |
| id: build-opg-docker | |
| run: | | |
| docker build --build-arg DOCKER_TAG=$DOCKER_TAG -t $DOCKER_TAG -f ./.github/workflows/unittest/Dockerfile . | |
| # - | |
| # name: Setup upterm session | |
| # uses: lhotari/action-upterm@v1 | |
| # with: | |
| # ## limits ssh access and adds the ssh public key for the user which triggered the workflow | |
| # limit-access-to-actor: true | |
| # ## limits ssh access and adds the ssh public keys of the listed GitHub users | |
| # limit-access-to-users: mauromiguelm | |
| # wait-timeout-minutes: 120 | |
| - | |
| name: Unittest docker | |
| id: test-snapshot | |
| run: | | |
| docker run --name run_tests -e CI=true $DOCKER_TAG | |
| docker cp run_tests:/test_result.txt . | |
| - | |
| name: Check workflow result | |
| id: check-workflow-result | |
| run: | | |
| if [[ "${{ steps.test-snapshot.outputs.workflow_result }}" == "false" ]]; then | |
| echo "Workflow failed." | |
| exit 1 | |
| fi | |
| - | |
| name: Upload error log | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: test-error-log | |
| path: ./test_result.txt | |
| if-no-files-found: ignore |