'Add release automation and coverage' (#289)

.Rbuildignore

@@ -35,3 +35,4 @@
 ^TODO\.md$
 ^staged_dependencies\.yaml$
 ^\.gitlab-ci\.yml$
+coverage.*

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

@@ -2,6 +2,8 @@ name: R CMD Check
 
 on:
   push:
+    tags:
+      - "v*"
     branches:
       - main
       - pre-release
@@ -116,10 +118,16 @@ jobs:
           if (file.exists("staged_dependencies.yaml")) {
             cat("\nInstall Staged Dependencies\n\n\n")
             if (!require("staged.dependencies")) {
-              remotes::install_github("openpharma/staged.dependencies", ref = "v0.2.1", Ncpus = ncores, upgrade = "never")
+              remotes::install_github("openpharma/staged.dependencies", ref = "97tags@main", Ncpus = ncores, upgrade = "never")
+            }
+            cat("\nCalculating Staged Dependency Table for ref: ${{ github.ref }} ...\n\n")
+            ref = "${{ github.ref }}"
+            if (startsWith(ref, "refs/tags")){
+              x <- staged.dependencies::dependency_table(ref=ref)
+            }
+            else {
+              x <- staged.dependencies::dependency_table()
             }
-            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)
@@ -175,3 +183,43 @@ jobs:
       - name: Install R package
         run: R CMD INSTALL ${{ env.PKGBUILD }}
         shell: bash
+
+      - name: Upload package
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: actions/upload-artifact@v2
+        with:
+          path: ${{ env.PKGBUILD }}
+          name: ${{ env.PKGBUILD }}
+
+  upload-release-assets:
+    name: Upload build tar.gz
+    needs: build-install-check
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Wait for release to succeed
+        timeout-minutes: 2
+        uses: lewagon/[email protected]
+        with:
+          ref: "${{ github.ref }}"
+          check-name: 'Release'
+          repo-token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          wait-interval: 10
+      - name: Set env
+        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV
+      - name: Get package name
+        run: echo "PKGBUILD=${{ github.event.repository.name }}_${{ env.RELEASE_VERSION }}.tar.gz" >> $GITHUB_ENV
+      - name: Download artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: "${{ env.PKGBUILD }}"
+      - name: Upload binaries to release
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          file: "${{ env.PKGBUILD }}"
+          asset_name: "${{ env.PKGBUILD }}"
+          tag: "${{ github.ref }}"
+          overwrite: false

.github/workflows/links.yml

@@ -18,7 +18,16 @@ jobs:
       - name: Check URLs in docs
         uses: lycheeverse/lychee-action@v1
         with:
-          args: --exclude-private --exclude "https://github.com.*.git|https://insightsengineering.github.io.*" --verbose --no-progress **/*.md **/*.html **/*.Rmd **/*.yaml **/*.yml
+          args: >-
+            --exclude-private
+            --exclude "https://github.com.*.git|https://insightsengineering.github.io.*|lewagon.*|knightdave.*"
+            --verbose
+            --no-progress
+            **/*.md
+            **/*.html
+            **/*.Rmd
+            **/*.yaml
+            **/*.yml
         env:
           GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
 

.github/workflows/pkgdown.yml

@@ -2,6 +2,8 @@ name: Pkgdown Docs
 
 on:
   push:
+    tags:
+      - "v*"
     branches:
       - main
   pull_request:
@@ -104,10 +106,16 @@ jobs:
           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")
+              remotes::install_github("openpharma/staged.dependencies", ref = "97tags@main", Ncpus = ncores, upgrade = "never")
+            }
+            cat("\nCalculating Staged Dependency Table for ref: ${{ github.ref }} ...\n\n")
+            ref = "${{ github.ref }}"
+            if (startsWith(ref, "refs/tags")){
+              x <- staged.dependencies::dependency_table(ref=ref)
+            }
+            else {
+              x <- staged.dependencies::dependency_table()
             }
-            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)
@@ -140,12 +148,19 @@ jobs:
           }
         shell: Rscript {0}
 
+      - name: Create artifacts
+        run: |
+          pushd ${{ github.event.repository.name }}/docs/
+          zip -r9 $OLDPWD/pkgdown.zip *
+          popd
+        shell: bash
+
       - name: Upload docs for review
         if: github.ref != 'refs/heads/main'
         uses: actions/upload-artifact@v2
         with:
-          name: docs
-          path: ${{ github.event.repository.name }}/docs/
+          name: pkgdown.zip
+          path: pkgdown.zip
 
       - name: Publish docs
         if: github.ref == 'refs/heads/main' # Only after merge or push to main
@@ -154,3 +169,32 @@ jobs:
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
           Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+
+  upload-release-assets:
+    name: Upload documentation assets
+    needs: pkgdown
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Wait for release to succeed
+        timeout-minutes: 2
+        uses: lewagon/[email protected]
+        with:
+          ref: "${{ github.ref }}"
+          check-name: 'Release'
+          repo-token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          wait-interval: 10
+      - name: Download artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: pkgdown.zip
+      - name: Upload binaries to release
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          file: pkgdown.zip
+          asset_name: pkgdown.zip
+          tag: ${{ github.ref }}
+          overwrite: false

.github/workflows/release.yaml

@@ -0,0 +1,23 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set env
+        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV
+      - name: Generate Changelog
+        run: (awk "/^#.*${{ env.RELEASE_VERSION }}$/{flag=1;next}/^#.*/{flag=0}flag" NEWS.md |grep -v "^$" || echo "* ${{ env.RELEASE_VERSION }}") > RELEASE_BODY.txt
+      - name: Release
+        uses: softprops/action-gh-release@v1
+        with:
+          body_path: RELEASE_BODY.txt
+          token: ${{ secrets.REPO_GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,184 @@
+name: Coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+      - pre-release
+
+jobs:
+  test-coverage:
+    name: Coverage
+    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 = "v0.2.1", 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: Install covr
+        run: if (!require("covr")) install.packages("covr", repos="http://cran.rstudio.com/", upgrade = "never")
+        shell: Rscript {0}
+
+      - name: Run coverage
+        run: |
+          tryCatch(
+            expr = {
+                x <- covr::package_coverage()
+                print(x)
+                covr::to_cobertura(x, filename = "coverage.xml")
+                p <- covr::percent_coverage(x)
+                cat(p, file = "coverage.txt", sep = "")
+                covr::report(
+                    x,
+                    file = "coverage-report.html",
+                    browse = FALSE
+                )
+            },
+            error = function(e) {
+                message("Errors generated during coverage analysis:")
+                print(e)
+            },
+            warning = function(w) {
+                message("Warnings generated during coverage analysis:")
+                print(w)
+            }
+          )
+        shell: Rscript {0}
+
+      - name: Check whether coverage reports exists
+        id: check_coverage_reports
+        uses: andstor/file-existence-action@v1
+        with:
+          files: "coverage.xml, coverage.txt, coverage-report.html"
+
+      - name: cobertura-report
+        if: steps.check_coverage_reports.outputs.files_exists == 'true'
+        uses: 5monkeys/cobertura-action@v9
+        with:
+          path: coverage.xml
+          repo_token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          minimum_coverage: 80
+          fail_below_threshold: false
+          skip_covered: true
+
+      - name: Set env
+        if: steps.check_coverage_reports.outputs.files_exists == 'true'
+        run: echo "OVERALL_COVERAGE=$(cat coverage.txt)" >> $GITHUB_ENV
+
+      - name: Badge for coverage
+        if: steps.check_coverage_reports.outputs.files_exists == 'true'
+        uses: knightdave/[email protected]
+        with:
+          file: coverage.svg
+          value: ${{ env.OVERALL_COVERAGE }}
+          anybadge_args: coverage
+
+      - name: Upload badge
+        if: steps.check_coverage_reports.outputs.files_exists == 'true'
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage
+          path: coverage.svg
+
+      - name: Upload report
+        if: steps.check_coverage_reports.outputs.files_exists == 'true'
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: "coverage-report.html"

.gitignore

@@ -26,3 +26,4 @@ tmp.*
 vignettes/*.html
 vignettes/*.md
 vignettes/*.R
+coverage.*