create github workflows to check pkg and build site

.github/workflows/R-CMD-CHECK.yaml

@@ -0,0 +1,43 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: rcmdcheck
+
+jobs:
+  rcmdcheck:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: rcmdcheck-${{ github.event_name != 'pull_request' }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Run R-CMD-CHECK
+        if: github.event_name != 'pull_request'
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran", "--no-tests", "--no-examples")'
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          DISPLAY: 99.0

.github/workflows/document.yaml

@@ -0,0 +1,56 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+    paths: 
+      - '.github/workflows/document.yaml'
+      - 'R/**'
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: document-${{ github.event_name != 'pull_request' }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_DOCS }}
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin master || echo "No changes to commit"        
+        

.github/workflows/pkgdown.yaml

@@ -0,0 +1,63 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+    paths: 
+      - '.github/workflows/pkgdown.yaml'
+      - 'vignettes/**'
+      - 'man/**.Rd'
+      - 'README.md'
+      - 'DESCRIPTION'
+      - 'LICENSE'      
+      - 'NEWS.md'
+      - '_pkgdown.yml'
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          token: ${{ secrets.GH_DOCS }}
+          branch: gh-pages
+          folder: .
+          clean: false

.github/workflows/render-news-rmd.yml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+    paths: 
+      - '.github/workflows/render-news-rmd.yaml'
+      - 'NEWS.Rmd'
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: render-news-rmd
+
+jobs:
+  render-news-rmd:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: news-${{ github.event_name != 'pull_request' }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_DOCS }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+          needs: render
+
+      - name: Render NEWS
+        run: Rscript -e 'rmarkdown::render("NEWS.Rmd", output_format="md_document")'
+
+      - name: Commit rendered NEWS
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add NEWS.md
+          git commit -m "Re-build NEWS.md" || echo "No changes to commit"
+          git push origin master || echo "No changes to commit"
+          

.github/workflows/render-readme-rmd.yml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: master
+    paths: 
+      - '.github/workflows/render-readme-rmd.yaml'
+      - 'README.Rmd'
+  pull_request:
+    branches: master
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: render-readme-rmd
+
+jobs:
+  render-readme-rmd:
+    runs-on: ubuntu-latest
+    concurrency:
+      group: readme-${{ github.event_name != 'pull_request' }}
+      cancel-in-progress: true
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_DOCS }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+          needs: render
+
+      - name: Render README
+        run: Rscript -e 'rmarkdown::render("README.Rmd", output_format="md_document")'
+
+      - name: Commit rendered README
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add README.md man/figures/README-*
+          git commit -m "Re-build README.md" || echo "No changes to commit"
+          git push origin master || echo "No changes to commit"
+          

.gitignore

@@ -2,9 +2,6 @@
 .git
 .project
 
-# github actions
-.github
-
 # History files
 .Rhistory
 .Rapp.history