copied over from Roche/respectables (#43)

* copied over from Roche/respectables

* Use R 4.1.0 for pkgdown

* Add staged.deps install logic

* Update working dir

Co-authored-by: Adrian Waddell <[email protected]>
Co-authored-by: Dinakar <[email protected]>

.github/workflows/build-check-install.yaml

@@ -111,7 +111,6 @@ jobs:
           } else {
             remotes::install_deps(dependencies = TRUE, upgrade = "never", Ncpus = ncores)
           }
-
           if (file.exists("staged_dependencies.yaml")) {
             cat("\nInstall Staged Dependencies\n\n\n")
             if (!require("staged.dependencies")) {

.github/workflows/pkgdown.yaml

@@ -0,0 +1,134 @@
+name: Pkgdown Docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pkgdown:
+    name: Generate
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/insightsengineering/rstudio_4.1.0_bioc_3.13:latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Gather info from PR
+        uses: actions/github-script@v4
+        id: get-pr
+        if: github.event_name == 'pull_request'
+        with:
+          script: |
+            const request = {
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              pull_number: context.issue.number
+            }
+            core.info(`Getting PR #${request.pull_number} from ${request.owner}/${request.repo}`)
+            try {
+              const result = await github.pulls.get(request)
+              return result.data
+            } catch (err) {
+              core.setFailed(`Request failed with error ${err}`)
+            }
+
+      - name: Install remotes R package if needed
+        run: |
+           options(repos = c(CRAN = "https://cloud.r-project.org/"))
+           ncores <- parallel::detectCores(all.tests = FALSE, logical = TRUE)
+           cat(paste("\n\nnumber of cores detected:", ncores, "\n\n"))
+           if (!require("remotes")) install.packages("remotes", upgrade = "never", Ncpus = ncores)
+        shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }} # or ${{ secrets.GITHUB_TOKEN }}
+
+
+      - name: Checkout repo during PR
+        uses: actions/checkout@v2
+        if: github.event_name == 'pull_request'
+        with:
+          repository: ${{ fromJSON(steps.get-pr.outputs.result).head.repo.full_name }}
+          ref: ${{ fromJSON(steps.get-pr.outputs.result).head.ref }}
+          path: ${{ github.event.repository.name }}
+
+      - name: Checkout repo from push
+        uses: actions/checkout@v2
+        if: github.event_name == 'push'
+        with:
+          path: ${{ github.event.repository.name }}
+
+      - name: Install system dependencies for R package
+        run: |
+          ubuntu_info <- read.csv("/etc/os-release", sep = "=", header = FALSE)
+          v_ubuntu_info <- setNames(ubuntu_info$V2, ubuntu_info$V1)
+          if (v_ubuntu_info[['NAME']] != "Ubuntu") stop("only works on ubuntu")
+          ubuntu_version <- v_ubuntu_info[['VERSION_ID']]
+
+          sys_deps_for_pkg <- remotes::system_requirements("ubuntu", ubuntu_version, path = "${{ github.event.repository.name }}")
+
+          sys_pgks <- gsub("^apt-get install -y ", "", sys_deps_for_pkg)
+
+          has_pkgs <- vapply(sys_pgks, function(pkg) system2("dpkg", c("-l", pkg), stdout = NULL, stderr = NULL) == 0,  logical(1))
+
+          if (any(!has_pkgs)) {
+            system2("apt-get", "update")
+            system2("apt-get", c("install", "-y", sys_pgks[!has_pkgs]))
+          }
+        shell: Rscript {0}
+
+      - name: Install R package dependencies
+        run: |
+          setwd("${{ github.event.repository.name }}")
+          options(repos = c(CRAN = "https://cloud.r-project.org/"))
+          ncores <- parallel::detectCores(all.tests = FALSE, logical = TRUE)
+          cat(paste("\n\nnumber of cores detected:", ncores, "\n\n"))
+          if (file.exists("renv.lock")) {
+            renv::restore()
+          } else {
+            remotes::install_deps(dependencies = TRUE, upgrade = "never", Ncpus = ncores)
+          }
+          if (file.exists("staged_dependencies.yaml")) {
+            cat("\nInstall Staged Dependencies\n\n\n")
+            if (!require("staged.dependencies")) {
+              remotes::install_github("openpharma/staged.dependencies", ref = "v0.2", Ncpus = ncores, upgrade = "never")
+            }
+            cat("\nCalculating Staged Dependency Table...\n\n")
+            x <- staged.dependencies::dependency_table()
+            print(x, width = 120)
+            cat("\n\n")
+            staged.dependencies::install_deps(dep_structure = x, install_project = FALSE, verbose = TRUE)
+          }
+        shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
+
+      - name: Install R package
+        run: R CMD INSTALL ${{ github.event.repository.name }}
+        shell: bash
+
+      - name: Build docs
+        run: |
+          options(repos = c(CRAN = "https://cloud.r-project.org/"))
+          "pkgdown" %in% installed.packages() || install.packages("pkgdown", upgrade = "never")
+          pkgdown::build_site("${{ github.event.repository.name }}", devel = TRUE)
+        shell: Rscript {0}
+
+      - name: Upload docs for review
+        if: github.ref != 'refs/heads/main' # Only during PR
+        uses: actions/upload-artifact@v2
+        with:
+          name: docs
+          path: ${{ github.event.repository.name }}/docs/
+
+      - name: Publish docs
+        if: github.ref == 'refs/heads/main' # Only after merge or push to master
+        run: |
+          cd ${{ github.event.repository.name }}
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'