CDCgov · seabbs · May 3, 2024 · May 1, 2024
@@ -1,2 +1,7 @@
 ^LICENSE$
 ^\.github$
+^\.pre-commit-config\.yaml$
+^_pkgdown\.yml$
+^codecov\.yml$
+^docs$
+^pkgdown$
@@ -0,0 +1,49 @@
+# 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:
+  pull_request:
+    branches: [main]
+  push:
+    branches:
+      - main
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
@@ -0,0 +1,12 @@
+name: Git Checks
+
+on: [pull_request]
+
+jobs:
+  block-fixup:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2.0.0
+    - name: Block Fixup Commit Merge
+      uses: 13rac1/block-fixup-merge-action@v2.0.0
@@ -0,0 +1,35 @@
+name: Check NEWS.md Update
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  check-news-md-modification:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0 # Fetch all history for all tags and branches
+
+      - name: Check for NEWS.md changes
+        run: |
+          echo "Current SHA: $GITHUB_SHA"
+          echo "Base SHA: ${{ github.event.pull_request.base.sha }}"
+
+          git fetch origin ${{ github.event.pull_request.base.ref }}
+
+          CHANGED_FILES=$(git diff --name-only $GITHUB_SHA $(git merge-base $GITHUB_SHA origin/${{ github.event.pull_request.base.ref }}))
+          echo "Changed files:"
+          echo "$CHANGED_FILES"
+
+          if echo "$CHANGED_FILES" | grep -q "NEWS.md"; then
+            echo "NEWS.md has been modified."
+          else
+            echo "::error file=NEWS.md,line=1,col=5::NEWS.md must be updated with each PR." >&2
+            exit 1
+          fi
+        shell: /usr/bin/bash -e {0}
@@ -0,0 +1,48 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+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 }}
+    permissions:
+      contents: write
+    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}
+
+      - 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
@@ -0,0 +1,79 @@
+# 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:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
@@ -1,14 +1,51 @@
 name: pre-commit
 
-on:
-  pull_request:
-  push:
-    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+
+on: [push]
 
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
+    if: >-
+      !contains(github.event.head_commit.message, 'ci skip') &&
+      (
+        startsWith(github.ref, 'refs/heads') ||
+        github.event.pull_request.draft == false
+      )
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: ./.github/actions/pre-commit
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libcurl4-openssl-dev
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+          architecture: "x64"
+      - name: Run pre-commit
+        uses: pre-commit/action@v2.0.3
+      - name: Commit files
+        if: failure() && startsWith(github.ref, 'refs/heads')
+        run: |
+          if [[ `git status --porcelain --untracked-files=no` ]]; then
+            git config --local user.email "github-actions[bot]@users.noreply.github.com"
+            git config --local user.name "github-actions[bot]"
+            git checkout -- .github/workflows
+            git commit -m "pre-commit" -a
+          fi
+      - name: Push changes
+        if: failure() && startsWith(github.ref, 'refs/heads')
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}
+    env:
+      RENV_CONFIG_CACHE_ENABLED: FALSE
@@ -0,0 +1,51 @@
+# 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: [main]
+  pull_request:
+    branches: [main]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"),
+            token = "${{ secrets.CODECOV_TOKEN }}"
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
@@ -379,3 +379,4 @@ docs/site/
 # such, it should not be committed for packages, but should be committed for
 # applications that require a static environment.
 #Manifest.toml
+docs