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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| At least one of the Docker images that is part of the [Build all Docker images](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/docker_all-modules.yml) workflow has failed. | ||
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| Check the latest output from the workflow at the following link to see which module failed. | ||
| https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/docker_all-modules.yml | ||
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| Then assign an OpenScPCA admin to this issue and add to this issue a list of the modules with failing docker builds. | ||
| Alternatively, file a new issue for each failing Docker image. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| At least one of the modules that is part of the [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/all_modules.yml) workflow has failed. | ||
| At least one of the modules that is part of the [Run all analysis modules](https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/run_all-modules.yml) workflow has failed. | ||
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| Check the latest output from the workflow at the following link to see which module failed. | ||
| https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/all_modules.yml | ||
| https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/workflows/run_all-modules.yml | ||
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| Then assign an OpenScPCA admin to this issue and add to this issue a list of the failing modules. | ||
| Alternatively, file a new issue for each failing module. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| name: Build and push a Docker image for a module | ||
| # This action is meant to be called by other actions, | ||
| # namely the `build-docker-modules` job in `docker_all-modules.yml` and | ||
| # the `build-push` job in `docker_{module}.yml` for each analysis module. | ||
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| on: | ||
| workflow_call: | ||
| inputs: | ||
| module: | ||
| required: true | ||
| type: string | ||
| push-ecr: | ||
| description: "Push to AWS ECR" | ||
| type: boolean | ||
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| permissions: | ||
| id-token: write | ||
| contents: read | ||
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| jobs: | ||
| build-push: | ||
| name: Build and Push Docker Image | ||
| if: inputs.push-ecr && github.repository_owner == 'AlexsLemonade' | ||
| environment: prod | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v4 | ||
| with: | ||
| role-to-assume: arn:aws:iam::992382809252:role/GithubOpenId | ||
| role-session-name: githubActionSession | ||
| aws-region: us-east-1 | ||
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| - name: Log in to Amazon ECR | ||
| id: login-ecr | ||
| uses: aws-actions/amazon-ecr-login@v2 | ||
| with: | ||
| registry-type: public | ||
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| - name: Create ECR repository if needed | ||
| id: create-ecr | ||
| run: | | ||
| aws ecr-public describe-repositories --repository-names ${{ inputs.module }} \ | ||
| || aws ecr-public create-repository --repository-name ${{ inputs.module }} | ||
| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v3 | ||
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| - name: Docker metadata | ||
| id: meta | ||
| uses: docker/metadata-action@v5 | ||
| with: | ||
| images: public.ecr.aws/openscpca/${{ inputs.module }} | ||
| # tag with 'latest' for main branch pushes, semantic version for releases/tags | ||
| tags: | | ||
| type=raw,value=latest,enable={{is_default_branch}} | ||
| type=semver,pattern={{raw}} | ||
| - name: Build and push image | ||
| uses: docker/build-push-action@v5 | ||
| with: | ||
| push: true | ||
| context: "{{defaultContext}}:analyses/${{ inputs.module }}" | ||
| tags: ${{ steps.meta.outputs.tags }} | ||
| labels: ${{ steps.meta.outputs.labels }} | ||
| cache-from: type=gha |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| name: Code styling | ||
| on: | ||
| #pull_request: | ||
| # branches: | ||
| # - main | ||
| workflow_dispatch: | ||
| # schedule: | ||
| # - cron: "0 0 15 1/3 *" # 15th of every 3rd month, for now | ||
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| concurrency: | ||
| # only one run per branch at a time | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
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| jobs: | ||
| style-code: | ||
| runs-on: ubuntu-latest | ||
| name: Perform code styling | ||
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| steps: | ||
| - name: Checkout repo | ||
| uses: actions/checkout@v4 | ||
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| ## First, style the R code ## | ||
| - name: Install R | ||
| uses: r-lib/actions/setup-r@v2 | ||
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| - name: Install R dependencies | ||
| run: install.packages(c("styler", "knitr", "roxygen2"), repos = "https://p3m.dev/cran/__linux__/jammy/latest") | ||
| shell: Rscript --no-init-file {0} | ||
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| - name: Style analysis modules R code | ||
| run: | | ||
| list.files( | ||
| "analyses", | ||
| recursive = TRUE, | ||
| full.names = TRUE, | ||
| pattern = "\\.(r|rmd)$", ignore.case = TRUE | ||
| ) |> | ||
| # do not style renv/activate.R | ||
| purrr::discard(\(x) grepl("renv/activate.R", x)) |> | ||
| # perform styling | ||
| styler::style_file() | ||
| shell: Rscript --no-init-file {0} | ||
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| ## Second, style the python code ## | ||
| - name: Format python files | ||
| uses: chartboost/ruff-action@v1 | ||
| with: | ||
| args: format analyses/ | ||
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| - name: Create PR with styled code | ||
| uses: peter-evans/create-pull-request@v6 # defaults to ${GITHUB_TOKEN} token | ||
| with: | ||
| commit-message: Styled code | ||
| signoff: false | ||
| branch: style-analysis-modules | ||
| base: main | ||
| delete-branch: true | ||
| title: "GHA: Automated analysis module code styling" | ||
| body: | | ||
| ### Description: | ||
| This PR was auto-generated by GitHub Actions to style all R (scripts and notebooks) and Python (scripts only) code in `analyses`. | ||
| ### Instruction for reviewers: | ||
| Make sure that all code changes are acceptable. | ||
| labels: | | ||
| OpenScPCA admin | ||
| code styling |
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