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Merge pull request #151 from pharmaverse/chore/customize-workflows
Chore: customize github workflows to correctly install system dependencies
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,149 @@ | ||
| # Source: | ||
| # https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/lintr.yml | ||
| # Modified to install system dependencies. | ||
|
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||
| name: Lint | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| r-version: | ||
| description: "The version of R to use" | ||
| default: "release" | ||
| required: false | ||
| type: choice | ||
| options: | ||
| - devel | ||
| - latest | ||
| lint-all-files: | ||
| description: "Lint all files every time" | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
| latest-lintr: | ||
| description: "Latest lintr CRAN release" | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
| install-package: | ||
| description: "Install package locally." | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
| workflow_call: | ||
| inputs: | ||
| r-version: | ||
| description: "The version of R to use" | ||
| default: "release" | ||
| required: false | ||
| type: string | ||
| lint-all-files: | ||
| description: "Lint all files every time" | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
| latest-lintr: | ||
| description: "Latest lintr CRAN release" | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
| install-package: | ||
| description: "Install package locally." | ||
| default: "false" | ||
| required: false | ||
| type: string | ||
|
|
||
| concurrency: | ||
| group: lint-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| lint: | ||
| name: Lint | ||
| runs-on: ubuntu-latest | ||
| container: | ||
| image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest" | ||
| if: > | ||
| !contains(github.event.commits[0].message, '[skip lint]') | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| ##################### BEGIN boilerplate steps ##################### | ||
| - name: Get branch names | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v8 | ||
|
|
||
| - name: Checkout repo (PR) 🛎 | ||
| uses: actions/[email protected] | ||
| if: github.event_name == 'pull_request' | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| repository: ${{ github.event.pull_request.head.repo.full_name }} | ||
|
|
||
| - name: Checkout repository | ||
| uses: actions/[email protected] | ||
| if: github.event_name != 'pull_request' | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
|
|
||
| - name: Restore cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.staged.dependencies | ||
| key: staged-deps | ||
|
|
||
| - name: Run Staged dependencies | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: true | ||
| renv-restore: false | ||
| enable-check: false | ||
| direction: upstream | ||
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| - name: Install latest release of lintr | ||
| run: | | ||
| install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/") | ||
| shell: Rscript {0} | ||
| if: ${{ inputs.latest-lintr == 'true' }} | ||
|
|
||
| - name: Install package | ||
| run: renv::install(".", dependencies = "no-deps") | ||
| shell: Rscript {0} | ||
| if: ${{ inputs.install-package == 'true' }} | ||
| ##################### END boilerplate steps ##################### | ||
|
|
||
| - name: Changed files | ||
| id: files | ||
| uses: Ana06/[email protected] | ||
| with: | ||
| format: "json" | ||
| filter: "*" | ||
|
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||
| - name: Lint | ||
| run: | | ||
| exclusions_list <- NULL | ||
| if (!identical("${{ inputs.lint-all-files }}", "true")) { | ||
| changed_files <- jsonlite::fromJSON('${{ steps.files.outputs.added_modified }}') | ||
| all_files <- list.files(recursive = TRUE) | ||
| exclusions_list <- if (any(changed_files %in% c(".lintr", "renv.lock"))) { | ||
| as.list(setdiff(all_files, changed_files)) | ||
| } else { | ||
| NULL | ||
| } | ||
| } | ||
| lints <- lintr::lint_package(exclusions = exclusions_list) | ||
| saveRDS(lints, file = "lints.rds") | ||
| shell: Rscript {0} | ||
|
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||
| - name: Error if lints are detected | ||
| run: | | ||
| lints <- readRDS("lints.rds") | ||
| if (length(lints) > 0L) { | ||
| print(lints) | ||
| stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE) | ||
| } | ||
| shell: Rscript {0} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| # Source: | ||
| # https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/man-pages.yml | ||
| # Modified to install system dependencies. | ||
|
|
||
| name: Man Pages | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| r-version: | ||
| description: "The version of R to use" | ||
| default: "release" | ||
| required: false | ||
| type: choice | ||
| options: | ||
| - devel | ||
| - latest | ||
| workflow_call: | ||
| inputs: | ||
| r-version: | ||
| description: "The version of R to use" | ||
| default: "release" | ||
| required: false | ||
| type: string | ||
|
|
||
| concurrency: | ||
| group: roxygen-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
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||
| jobs: | ||
| lint: | ||
| name: Roxygen | ||
| runs-on: ubuntu-latest | ||
| container: | ||
| image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest" | ||
| if: > | ||
| !contains(github.event.commits[0].message, '[skip lint]') | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| steps: | ||
| ##################### BEGIN boilerplate steps ##################### | ||
| - name: Get branch names | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v8 | ||
|
|
||
| - name: Checkout repo (PR) 🛎 | ||
| uses: actions/[email protected] | ||
| if: github.event_name == 'pull_request' | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| repository: ${{ github.event.pull_request.head.repo.full_name }} | ||
|
|
||
| - name: Checkout repository | ||
| uses: actions/[email protected] | ||
| if: github.event_name != 'pull_request' | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
|
|
||
| - name: Restore cache | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: | | ||
| ~/.staged.dependencies | ||
| key: staged-deps | ||
|
|
||
| - name: Run Staged dependencies | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: true | ||
| renv-restore: false | ||
| enable-check: false | ||
| direction: upstream | ||
| git-ref: ${{ steps.branch-name.outputs.current_branch }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| - name: Install dependencies from DESCRIPTION | ||
| run: | | ||
| remotes::install_local(force = TRUE, dependencies = TRUE) | ||
| shell: Rscript {0} | ||
| env: | ||
| R_REMOTES_STANDALONE: "true" | ||
|
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||
| ##################### END boilerplate steps ##################### | ||
|
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||
| - name: Generate man pages | ||
| run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) | ||
| shell: Rscript {0} | ||
|
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||
| - name: Set-up safe dir | ||
| run: git config --global --add safe.directory "${GITHUB_WORKSPACE}" | ||
| shell: bash | ||
|
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||
| - name: Roxygen check | ||
| if: "!startsWith(github.event.comment.body, '/roxygenize')" | ||
| run: | | ||
| git status -s | ||
| if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]] | ||
| then { | ||
| ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')" | ||
| echo "🙈 Manuals are not up-to-date with roxygen comments!" | ||
| echo "🔀 The following differences were noted:" | ||
| git diff man/* DESCRIPTION | ||
| echo -e "\n💻 Please rerun the following command on your workstation and push your changes" | ||
| echo "--------------------------------------------------------------------" | ||
| echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))" | ||
| echo "--------------------------------------------------------------------" | ||
| echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION" | ||
| echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version" | ||
| exit 1 | ||
| } else { | ||
| echo "💚 Manuals are up-to-date with roxygen comments" | ||
| } | ||
| fi | ||
| shell: bash |
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