USEPA · cristinamullin · Feb 10, 2023 · Feb 10, 2023
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [develop]
+    branches: develop
   pull_request:
-    branches: [develop]
+    branches: develop
 
 name: R-CMD-check
 
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,39 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: main
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    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: Install dependencies
+        run: |
+          install.packages(c("zoo", "maps", "patchwork", "leaflet"))
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,51 @@
+on:
+  issue_comment:
+    types: [created]
+name: Commands
+jobs:
+  document:
+    if: startsWith(github.event.comment.body, '/document')
+    name: document
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@develop
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@develop
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+      - name: commit
+        run: |
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@develop
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  style:
+    if: startsWith(github.event.comment.body, '/style')
+    name: style
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@develop
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@develop
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+      - name: commit
+        run: |
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@develop
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/style-and-lint.yaml b/.github/workflows/style-and-lint.yaml
@@ -0,0 +1,85 @@
+# 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
+# Only run when PR is opened to the main branch, and changes are made to these types of R files
+on:
+  pull_request:
+    paths: ["**.[rR]", "**.[rR]md", "**.[rR]markdown", "**.[rR]nw"]
+    branches: [main]
+
+name: Style and Lint
+
+jobs:
+  # First run styler and push style changes to feature branch
+  style:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::styler
+          needs: styler
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "##[set-output name=location;]",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Run styler on all files containing R code
+        run: styler::style_pkg(filetype = c(".R", ".Rmd", ".Rmarkdown", ".Rnw"))
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: Style Code
+
+  # Next run lintr to annotate the PR with anything caught by the linter that wasn't changed by styler
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Run lintr on the package
+        run: lintr::lint_package()
+        shell: Rscript {0}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,44 @@
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-4.0-2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: macOS-r-4.0-2-
+
+      - name: Install dependencies
+        run: |
+          options(pkgType = "binary")
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,7 +25,7 @@ Authors@R:
            family = "Healy",
            role = "aut")
     )
-Description: Assists data partners in performing automated assessments with
+Description: Assists data partners in performing water quality analyses with
     data from the Water Quality Portal.
 License: CC0
 Copyright: This software is in the public domain because it contains materials

diff --git a/man/PotentialDuplicateRowID.Rd b/man/PotentialDuplicateRowID.Rd