Check branch develop on push by brgew #126
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # | |
| # Check Monocle3 repository on push event. | |
| # | |
| # There is information on Docker container security at | |
| # URL: https://docs.docker.com/engine/security/ | |
| # URL: https://cheatsheetseries.owasp.org/cheatsheets/Docker_Security_Cheat_Sheet.html | |
| # Note: I don't see how one can specify the 'user' for the | |
| # Actions runs so I don't see the value of creating | |
| # a non-root user when the container is built. | |
| # There is information on Github Actions security at | |
| # URL: https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions | |
| # URL: https://blog.gitguardian.com/github-actions-security-cheat-sheet/ | |
| # This Github Actions page notes: | |
| # o Using CODEOWNERS to monitor changes: specifically changes to.github/workflows/* | |
| # o Preventing GitHub Actions from creating or approving pull requests | |
| # Security notes: | |
| # o secure the docker container against meddling | |
| # o secure the monocle3 repository against meddling | |
| # | |
| name: Monocle3 check on push | |
| run-name: Check branch ${{ github.ref_name }} on push by ${{ github.actor }} | |
| on: [push] | |
| jobs: | |
| monocle3_check_on_push: | |
| # Notes: ubuntu. | |
| # o use Ubuntu - there are messages on line about needing to use Ubuntu | |
| # for use with Github Actions. | |
| # o use a Docker container that has the Monocle3 dependencies installed. | |
| # see 'github.com:cole-trapnell-lab/monocle3/src/docker/NOTES' and | |
| # 'github.com:cole-trapnell-lab/Docker//monocle3_depend/NOTES'. | |
| # o Github Actions has a limited variety of Linux runners. See | |
| # URL: https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| runs-on: ubuntu-latest | |
| # One can add fine-grain-control over GITHUB_TOKEN permissions but | |
| # I have not found authoratative descriptions of the permissions | |
| # targets. www pages have some information | |
| # URL: https://github.blog/changelog/2021-04-20-github-actions-control-permissions-for-github_token/ | |
| # URL: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#permissions | |
| # permissions: | |
| # actions: read|write|none | |
| # checks: read|write|none | |
| # contents: read|write|none | |
| # deployments: read|write|none | |
| # id-token: read|write|none | |
| # issues: read|write|none | |
| # discussions: read|write|none | |
| # packages: read|write|none | |
| # pages: read|write|none | |
| # pull-requests: read|write|none | |
| # repository-projects: read|write|none | |
| # security-events: read|write|none | |
| # statuses: read|write|none | |
| container: | |
| # Note: | |
| # in order for the GITHUB_TOKEN to work as a credential one must | |
| # allow the Monocle3 repository to access the container 'package'. | |
| # Navigate to the Packages tab -> <repository> tab -> Package settings -> | |
| # Manage Actions access: click on Add Repository; give repository name | |
| # | |
| # The following Docker image was pushed initially to the Docker container | |
| # but we use now the Github container registry. The following image and | |
| # credential lines are here for documentation, if require in the future. | |
| # image: docker.io/brgew/monocle3_depend:v1.4.0 | |
| # | |
| # The following three (commented out) lines give credentials for a docker | |
| # image stored at the Docker container registry. | |
| # credentials: | |
| # username: brgew | |
| # password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN_READ }} | |
| # | |
| # The following Docker image was pushed to the Github container registry, | |
| # which is found at the Github Packages tab. | |
| # image: ghcr.io/cole-trapnell-lab/monocle3_depend.v1.3.0_20221103:v1 # old and replaced | |
| image: ghcr.io/cole-trapnell-lab/monocle3_depend:v1.4.0_1 | |
| # | |
| # | |
| # The following three uncommented lines give credentials for a Github | |
| # container registry. There is information about github.ACTOR at | |
| # URL: https://docs.github.com/en/actions/learn-github-actions/contexts | |
| # where there is the statement | |
| # github.actor string The username of the user that triggered the | |
| # initial workflow run. If the workflow run is | |
| # a re-run, this value may differ from | |
| # github.triggering_actor. Any workflow re-runs | |
| # will use the privileges of github.actor, even | |
| # if the actor initiating the re-run | |
| # (github.triggering_actor) has different | |
| # privileges. | |
| credentials: | |
| username: ${{ github.ACTOR }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| # TRAVIS: the testthat scripts check for the TRAVIS environment variable | |
| # in order to choose the correct set of target values and to avoid | |
| # running interactive code. For convenience, I keep the name TRAVIS after | |
| # switching to Github Actions CI. | |
| # _R_CHECK_TESTS_NLINES_: instruct the devtools::test scripts to output all | |
| # error lines rather than the last 13. See | |
| # https://yihui.org/en/2017/12/last-13-lines-of-output/ | |
| env: | |
| TRAVIS: true | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| # Get current repository contents. | |
| - uses: actions/checkout@v3 | |
| # Run tests. | |
| # Notes: | |
| # o the RCMD check command appears to not output the regression tests | |
| # output unless an error occurs, in which case, the output of all | |
| # regressions tests is output. | |
| - name: Run R CMD build and R CMD check | |
| run: | | |
| R CMD build . | |
| R CMD check monocle3*tar.gz | |
| shell: bash | |