Merge branch 'dev' into ndefries/flusurv-new-columns

Author: nmdefries

.Rbuildignore

@@ -23,3 +23,4 @@
 ^README\.Rmd$
 ^CRAN-SUBMISSION$
 ^LICENSE\.md$
+^revdep$

.bumpversion.cfg

@@ -1 +1 @@
-* @dshemetov @brookslogan @dsweber2
+* @dshemetov @brookslogan @dsweber2 @nmdefries

.github/CODEOWNERS

@@ -0,0 +1,22 @@
+### 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 epidatr main reviewers:
+      brookslogan, dshemetov, nmdefries, dsweber2.
+- [ ] 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).
+
+### 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/pull_request_template.md

@@ -19,21 +19,26 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          # Mac latest release
           - { os: macos-latest, r: "release" }
+          # Oldest R version we claim to support
+          - { os: macos-latest, r: "3.5" }
 
+          # Windows latest release
           - { os: windows-latest, r: "release" }
-          # Use 3.6 to trigger usage of RTools35
-          - { os: windows-latest, r: "3.6" }
+          # Use 3.5 to trigger usage of RTools35
+          - { os: windows-latest, r: "3.5" }
           # use 4.1 to check with rtools40's older compiler
           - { os: windows-latest, r: "4.1" }
 
+          # Ubuntu latest release
           - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
           - { os: ubuntu-latest, r: "release" }
           - { os: ubuntu-latest, r: "oldrel-1" }
           - { os: ubuntu-latest, r: "oldrel-2" }
           - { os: ubuntu-latest, r: "oldrel-3" }
           - { os: ubuntu-latest, r: "oldrel-4" }
-          # The oldest version of R we claim to support
+          # Oldest R version we claim to support
           - { os: ubuntu-latest, r: "3.5" }
 
     env:

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

@@ -5,6 +5,7 @@ on:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
+  workflow_dispatch:
 
 name: R-CMD-check
 

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

@@ -2,7 +2,8 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    paths: ["R/**"]
+    paths: ["R/**", "README.Rmd"]
+  workflow_dispatch:
 
 name: Document
 
@@ -26,17 +27,25 @@ jobs:
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::roxygen2
-          needs: roxygen2
+          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 '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

.github/workflows/document.yaml

@@ -5,6 +5,7 @@ on:
     branches: [main, dev]
   pull_request:
     branches: [main, dev]
+  workflow_dispatch:
 
 name: lint
 

.github/workflows/lint.yaml

@@ -5,9 +5,9 @@
 # update the documentation web site on pushes to `dev` branch.
 on:
   push:
-    branches: [main]
+    branches: [main, dev]
   pull_request:
-    branches: [main]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -16,16 +16,17 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    # only build docs on the main repository and not forks
     if: github.repository_owner == 'cmu-delphi'
     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 }}
-      DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
+      DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIDATR_GHACTIONS_DELPHI_EPIDATA_KEY }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -35,18 +36,36 @@ 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: ${{ secrets.SECRET_EPIDATR_GHACTIONS_DELPHI_EPIDATA_KEY }}
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        # - target_ref gets the ref from a different variable, depending on the event
+        # - override allows us to set the pkgdown mode and version_label
+        #   - mode: release is the standard build mode, devel places the site in /dev
+        #   - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
+        #                    https://bootswatch.com/cosmo/
+        # - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
+        #   https://github.com/r-lib/pkgdown/issues/2257
+        run: |
+          target_ref <- "${{ 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"))
+          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
+            list(development = list(mode = "devel"))
+          } 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 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pkgdown.yaml

@@ -10,6 +10,7 @@ on:
         "**.[rR]nw",
         "**.[rR]profile",
       ]
+    workflow_dispatch:
 
 name: Style