Updates to workflow and add pkgdown

.github/workflows/Check.yaml

@@ -37,11 +37,10 @@ jobs:
     name: Version Bump 🤜🤛
     if: github.event_name == 'push' && github.ref != 'refs/heads/main'
     uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
+    with: 
+      disable-precommit-autoupdate: true
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  # roxygen:
-  #   name: Roxygen 📦
-  #   uses: ./.github/workflows/Roxygen.yaml
 
 

.github/workflows/Test.yaml

@@ -5,9 +5,9 @@ on:
 
 name: test-coverage
 
-# concurrency:
-#   group: roxygen-${{ github.event.pull_request.number || github.ref }}
-#   cancel-in-progress: true
+permissions:
+  contents: read
+  pull-requests: write
 
 jobs:
   test-coverage:
@@ -24,23 +24,27 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: |
+            any::covr
+            any::xml2
+            any::dplyr
+            any::knitr
           needs: coverage
 
       - name: Test coverage
         run: |
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
@@ -49,3 +53,41 @@ jobs:
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
+
+      - name: Create Coverage Report for comment
+        run: |
+          covr::package_coverage() |>
+            covr::to_cobertura(filename = "cobertura.xml")
+
+          xml <- xml2::read_xml("cobertura.xml")
+
+          pkg_cov <- xml |>
+            xml2::xml_find_first("packages/package") |>
+            xml2::xml_attrs() |>
+            dplyr::bind_rows()
+
+          fnc_cov <- xml |>
+            xml2::xml_find_first("packages/package") |>
+            xml2::xml_find_all("classes/class") |>
+            xml2::xml_attrs() |>
+            lapply(dplyr::bind_rows)
+
+          res <- list(pkg_cov, fnc_cov) |>
+            dplyr::bind_rows() |>
+            dplyr::transmute(
+              Name = dplyr::coalesce(filename, name),
+              `Coverage (%)` = round(as.numeric(`line-rate`)*100, digits = 2)
+            ) |>
+            knitr::kable()
+
+          c("# Code coverage", res) |>
+            writeLines(con = "coverage.md")
+        shell: Rscript {0}
+
+      - name: Add Coverage PR Comment
+        uses: marocchino/sticky-pull-request-comment@v2
+        if: github.event_name == 'pull_request'
+        with:
+          recreate: true
+          header: coverage
+          path: coverage.md

.github/workflows/fast-forward.yaml

@@ -1,22 +1,22 @@
-  name: Fast Forward PR
-  on: 
-    issue_comment:
-        types: [created]
-  
-  jobs:
-    fast_forward_job:
-      name: Fast Forward
-      if: github.event.issue.pull_request != '' && contains(github.event.comment.body, '/fast-forward')   
-      runs-on: ubuntu-latest
-      steps:
-        # To use this repository's private action, you must check out the repository
-        - name: Checkout
-          uses: actions/checkout@v2
-        # Basic use case example
-        - name: Fast Forward PR
-          id: ff-action
-          uses:  endre-spotlab/[email protected]
-          with:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-            success_message: 'Success! Fast forwarded ***target_base*** to ***source_head***! ```git checkout target_base && git merge source_head --ff-only``` '
-            failure_message: 'Failed! Cannot do fast forward! - try merging the target back into source first.'
+name: Fast Forward PR
+on: 
+  issue_comment:
+      types: [created]
+
+jobs:
+  fast_forward_job:
+    name: Fast Forward
+    if: github.event.issue.pull_request != '' && contains(github.event.comment.body, '/fast-forward')   
+    runs-on: ubuntu-latest
+    steps:
+      # To use this repository's private action, you must check out the repository
+      - name: Checkout
+        uses: actions/checkout@v2
+      # Basic use case example
+      - name: Fast Forward PR
+        id: ff-action
+        uses:  endre-spotlab/[email protected]
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          success_message: 'Success! Fast forwarded ***target_base*** to ***source_head***! ```git checkout target_base && git merge source_head --ff-only``` '
+          failure_message: 'Failed! Cannot do fast forward! - try merging the target back into source first.'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,87 @@
+# Workflow adjusted from usethis::use_pkgdown_github_pages() to also publish pages from PRs in a subfolder
+
+  on:
+    push:
+      branches: [main, master]
+    pull_request:
+      branches: [main, master]
+    release:
+      types: [published]
+    workflow_dispatch:
+
+  permissions:
+    contents: write
+    pull-requests: write
+
+  name: pkgdown
+
+  jobs:
+    pkgdown:
+      runs-on: ubuntu-latest
+      # Only restrict concurrency for non-PR jobs
+      concurrency:
+        group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      steps:
+        - uses: actions/checkout@v4
+
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::pkgdown, local::.
+            needs: website
+
+        - name: Build site
+          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          shell: Rscript {0}
+
+        # If not pull request a brand new webpage is deployed
+
+        - name: Deploy to GitHub pages 🚀
+          if: github.event_name != 'pull_request'
+          uses: JamesIves/[email protected]
+          with:
+            clean: false
+            branch: gh-pages
+            folder: docs
+
+        # If pull request the webpage is deployed inside a dev/"PR number" folder for review
+
+        - name: Add pkgdown PR Comment
+          uses: marocchino/sticky-pull-request-comment@v2
+          if: github.event_name == 'pull_request'
+          with:
+            recreate: true
+            header: pkgdown
+            message: |
+              # Github pages
+              Review the pkgdown webpage for the PR [here](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/dev/${{ github.event.pull_request.number }})
+  
+        - name: Copy page to temp folder
+          if: github.event_name == 'pull_request'
+          run: |
+            mkdir -p /home/runner/work/dev
+            cp -r ./docs/* /home/runner/work/dev
+  
+        - name: Check out gh-pages branch
+          if: github.event_name == 'pull_request'
+          uses: actions/checkout@v4
+          with:
+            ref: gh-pages
+
+        - name: Copy and push to gh-pages
+          if: github.event_name == 'pull_request'
+          run: |
+            mkdir -p dev/${{ github.event.pull_request.number }}
+            cp -r /home/runner/work/dev/* ./dev/${{ github.event.pull_request.number }}
+            git config --global user.email "[email protected]"
+            git config --global user.name "Actions Robot From Github Actions"
+            git add .
+            git commit -m "Update gh pages from the PR"
+            git push

DESCRIPTION

@@ -48,3 +48,4 @@ Remotes:
     hta-pharma/chef
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Config/testthat/parallel: true