Merge pull request #489 from cmu-delphi/dev

release: v0.8

.Rbuildignore

@@ -12,3 +12,7 @@
 ^pkgdown$
 ^doc$
 ^Meta$
+^.git-blame-ignore-revs$
+^.lintr$
+^DEVELOPMENT.md$
+man-roxygen

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# Move to styler
+c65876078a6f9525952b305eaea2fca003adf907
+# Move to lintr
+0c8144e0e9deb79547eb523298d782926a7337a6

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+### Checklist
+
+Please:
+
+- [ ] Make sure this PR is against "dev", not "main" (unless this is a release
+      PR).
+- [ ] Request a review from one of the current main reviewers:
+      brookslogan, nmdefries.
+- [ ] Makes sure to bump the version number in `DESCRIPTION`. Always increment
+      the patch version number (the third number), unless you are making a
+      release PR from dev to main, in which case increment the minor version
+      number (the second number).
+- [ ] Describe changes made in NEWS.md, making sure breaking changes
+      (backwards-incompatible changes to the documented interface) are noted.
+      Collect the changes under the next release number (e.g. if you are on
+      1.7.2, then write your changes under the 1.8 heading).
+- See [DEVELOPMENT.md](DEVELOPMENT.md) for more information on the development
+  process.
+
+### Change explanations for reviewer
+
+### Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch
+
+- Resolves #{issue number}

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

@@ -1,12 +1,14 @@
 # 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
 #
-# Created with usethis + edited to run on PRs to dev, use API key.
+# Modifications:
+# - API key secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, dev]
+  workflow_dispatch:
 
 name: R-CMD-check
 
@@ -17,7 +19,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/document.yaml

@@ -0,0 +1,58 @@
+# 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
+#
+# Modifications:
+# - devtools::build_readme()
+# - workflow_dispatch added to allow manual triggering of the workflow
+# - trigger branches changed
+# - API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
+on:
+  push:
+    paths: ["R/**", "README.Rmd"]
+  workflow_dispatch:
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::devtools
+            any::roxygen2
+          needs: |
+            devtools
+            roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Build README.md from README.Rmd
+        run: Rscript -e 'if (file.exists("README.Rmd")) devtools::build_readme()'
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add README.md
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "docs: document (GHA)" || echo "No changes to commit"
+          git pull --rebase
+          git push origin

.github/workflows/lint.yaml

@@ -0,0 +1,39 @@
+# 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
+#
+# Modifications:
+#   * workflow_dispatch added to allow manual triggering of the workflow
+#   * trigger branches changed
+#   * API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+  workflow_dispatch:
+
+name: Lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
+    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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -1,12 +1,15 @@
 # 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
 #
-# Created with usethis + edited to run on PRs to dev, use API key.
+# Modifications:
+#   * workflow_dispatch added to allow manual triggering of the workflow
+#   * trigger branches changed
+#   * API key secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY
 on:
   push:
-    branches: [main, master]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -23,6 +26,7 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
     steps:
       - uses: actions/checkout@v3
 
@@ -34,13 +38,31 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, local::., any::cli
           needs: website
 
       - name: Build site
-        env:
-          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        # - target_ref gets the ref from a different variable, depending on the event
+        # - override allows us to set the pkgdown mode and version_label
+        #   - mode: release is the standard build mode, devel places the site in /dev
+        #   - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
+        #                    https://bootswatch.com/cosmo/
+        # - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
+        #   https://github.com/r-lib/pkgdown/issues/2257
+        run: |
+          target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
+          override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
+            list(development = list(mode = "release", version_label = "light"))
+          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
+            list(development = list(mode = "devel", version_label = "success"))
+          } else {
+            stop("Unexpected target_ref: ", target_ref)
+          }
+          pkg <- pkgdown::as_pkgdown(".", override = override)
+          cli::cli_rule("Cleaning files from old site...")
+          pkgdown::clean_site(pkg)
+          pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
+          pkgdown:::build_github_pages(pkg)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

.github/workflows/style.yml

@@ -0,0 +1,87 @@
+# 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
+#
+# Modifications:
+#   * workflow_dispatch added to allow manual triggering of the workflow
+#   * trigger branches changed
+#   * API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
+on:
+  push:
+    paths:
+      [
+        "**.[rR]",
+        "**.[qrR]md",
+        "**.[rR]markdown",
+        "**.[rR]nw",
+        "**.[rR]profile",
+      ]
+  workflow_dispatch:
+
+name: Style
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::styler, any::roxygen2
+          needs: styler
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "location=",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            file = Sys.getenv("GITHUB_OUTPUT"),
+            append = TRUE,
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
+              | egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
+          then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit ${FILES_TO_COMMIT[*]} -m "style: styler (GHA)"
+            git pull --rebase
+            git push origin
+          else
+            echo "No changes to commit."
+          fi

.gitignore

@@ -7,4 +7,9 @@ inst/doc
 docs
 /doc/
 /Meta/
-*.DS_Store
+*.DS_Store
+
+# Delphi custom
+renv/
+renv.lock
+.Rprofile

.lintr

@@ -0,0 +1,9 @@
+linters: linters_with_defaults(
+  line_length_linter(120),
+  cyclocomp_linter = NULL,
+  object_length_linter(length = 40L)
+  )
+exclusions: list(
+  "renv",
+  "venv"
+  )