Add release workflow. (#4)

* Updates to workflow and add pkgdown

* Fixed documentation and typo in readme

* Draft of release pipeline and renaming of check to seperate main and supporting workflows

* Increment version number to 0.1.0

* updated NEWS.md

.Rbuildignore

@@ -16,4 +16,9 @@ setImgSrc.js
 ^docs$
 ^pkgdown$
 ^README\.Rmd$
+^README\.html$	
 ^LICENSE\.md$
+^\.pre-commit-config\.yaml
+\.githooks
+\.github
+RELEASE_BODY\.txt

.github/workflows/Check.yaml → .github/workflows/Check-package.yaml

@@ -19,7 +19,7 @@ jobs:
     name: License Check 🃏
     uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
 
-  check-reuse:
+  check:
     name: RMD check 📦
     uses: ./.github/workflows/R-CMD-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/Release-package.yaml

@@ -0,0 +1,20 @@
+  on:
+    push:
+      branches: main
+    pull_request:
+      branches: main
+    workflow_dispatch:
+
+  name: release
+
+  jobs:
+    build:
+      name: RMD Build and check
+      uses: ./.github/workflows/R-CMD-check.yaml
+    docs:
+      name: Build and Deploy Docs
+      uses: ./.github/workflows/pkgdown.yaml
+    release:
+      name: Release
+      if: github.event_name == 'push'
+      uses: ./.github/workflows/release.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/fast-forward-js-action@2.1
-          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/fast-forward-js-action@2.1
+        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 +1,88 @@
+# 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:
+    workflow_call:
+
+  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: ${{ secrets.GITHUB_TOKEN }}
+      steps:
+        - uses: actions/checkout@v4
+
+        - uses: r-lib/actions/setup-pandoc@v2
+
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            use-public-rspm: true
+
+        - uses: r-lib/actions/setup-r-dependencies@v2
+          with:
+            extra-packages: any::pkgdown, local::.
+            needs: website
+
+        - name: Build site
+          run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+          shell: Rscript {0}
+
+        # If not pull request a brand new webpage is deployed
+
+        - name: Deploy to GitHub pages 🚀
+          if: github.event_name != 'pull_request'
+          uses: JamesIves/github-pages-deploy-action@v4.5.0
+          with:
+            clean: false
+            branch: gh-pages
+            folder: docs
+
+        # If pull request the webpage is deployed inside a dev/"PR number" folder for review
+
+        - name: Add pkgdown PR Comment
+          uses: marocchino/sticky-pull-request-comment@v2
+          if: github.event_name == 'pull_request'
+          with:
+            recreate: true
+            header: pkgdown
+            message: |
+              # Github pages
+              Review the pkgdown webpage for the PR [here](https://${{ 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 "actions-robot@novonordisk.com"
+            git config --global user.name "Actions Robot From Github Actions"
+            git add .
+            git commit -m "Update gh pages from the PR"
+            git push

.github/workflows/release.yaml

@@ -0,0 +1,81 @@
+---
+    name: Release 🚀
+
+    on:
+      workflow_call:
+        inputs:
+          create-dev-releases:
+            description: 'Create dev releases'
+            required: false
+            default: false
+            type: boolean
+          is-pre-release:
+              description: 'Mark as pre-release'
+              required: false
+              default: true
+              type: boolean
+      workflow_dispatch:
+
+    concurrency:
+      group: release-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+
+    jobs:
+      release:
+        name: Release 🚀
+        runs-on: ubuntu-latest
+        permissions:
+          contents: write
+        steps:
+          - name: Setup token 🔑
+            id: github-token
+            run: |
+              if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
+                echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
+                echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
+              else
+                echo "Using REPO_GITHUB_TOKEN."
+                echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
+              fi
+            shell: bash
+
+          - name: Checkout repo 🛎
+            uses: actions/checkout@v4
+
+          - name: Get branch names 🌿
+            id: branch-name
+            uses: tj-actions/branch-names@v7
+
+          - name: Check if running with dev tag 🏷️
+            id: dev-tag
+            run: |
+              echo "Current tag: ${{ steps.branch-name.outputs.tag }}"
+              current_tag="${{ steps.branch-name.outputs.tag }}"
+              if [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)(-[0-9]+)$")" != "" ]; then
+                echo "Running for rc-tag."
+                echo "is-dev-tag=true" >> $GITHUB_OUTPUT
+              else
+                echo "is-dev-tag=false" >> $GITHUB_OUTPUT
+              fi
+            shell: bash
+
+          - name: Generate Changelog 📜
+            run: |
+              RELEASE_VERSION=$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)
+              REPOSITORY_NAME="${{ github.event.repository.name }}"
+              (awk "/^#+.*${REPOSITORY_NAME//./\.}.*${RELEASE_VERSION//./\.}$/{flag=1;next}/^#+.*${REPOSITORY_NAME//./\.}.*/{flag=0}flag" NEWS.md | grep -v "^$" || echo "* ${RELEASE_VERSION}") > RELEASE_BODY.txt
+    
+          - name: Create release 🌟
+            if: >-
+              steps.dev-tag.outputs.is-rc-tag == 'false' ||
+                inputs.create-dev-releases == true
+            # https://github.com/softprops/action-gh-release/pull/406#issuecomment-1934635958
+            uses: softprops/action-gh-release@4634c16e79c963813287e889244c50009e7f0981
+            with:
+              body_path: RELEASE_BODY.txt
+              token: ${{ steps.github-token.outputs.token }}
+              generate_release_notes: true
+              files: |
+                LICENSE
+                LICENSE.md
+              prerelease: inputs.pre-release

.gitignore

@@ -3,3 +3,6 @@ docs
 inst/doc
 .Rhistory
 **/debug
+**/*.html
+README.html
+RELEASE_BODY.txt

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: chefStats
 Title: Provide methods for different statistics
-Version: 0.0.0.9001
+Version: 0.1.0
 Authors@R:
     c(person(given = "MEWP (Matthew Phelps)",
              role = "aut",
@@ -48,3 +48,4 @@ Remotes:
     hta-pharma/chef
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Config/testthat/parallel: true

NEWS.md

@@ -0,0 +1,4 @@
+# chefStats 0.1.0
+- Initial release of chefstats
+- Contains an initial selection of statistical functions for use in the {ramnog} ecosystem.
+

README.Rmd

@@ -24,7 +24,7 @@ This project supports two styles of githooks.
 
 1.  The first style is to use the githooks provided in the `.githooks` directory. To use these hooks, run the following command in the root of the project:
   - These hooks are very simple just blocking the commit to protected branches.
-``
+```
 git config --local core.hooksPath .githooks/
 ```