Update package based on the Epiverse template

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

@@ -54,20 +54,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          # Test with the 3 R versions and the 3 platforms from CRAN checks
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: '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: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      # Exists since R 4.3.0 but `false` by default
-      _R_CHECK_LENGTH_COLON_: true
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/dependency-change.yaml

@@ -52,6 +52,12 @@ jobs:
 
             message("Dependencies have changed! Analyzing...")
 
+            if (nrow(deps_added) > 0) {
+              nudge <- "Reach out on slack (`#code-review` or `#help` channels) to double check if there are base R alternatives to the new dependencies.\n"
+            } else {
+              nudge <- ""
+            }
+
             msg <- glue::glue(
               .sep = "\n",
               "This pull request:",
@@ -60,7 +66,8 @@ jobs:
               "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
               "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
               "",
-              "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"
+              nudge,
+              "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"
             )
 
             message("Posting results as a pull request comment.")

.github/workflows/lint-changed-files.yaml

@@ -0,0 +1,53 @@
+# 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:
+  workflow_dispatch:
+  pull_request:
+    branches: [main, master]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - '**/.lintr'
+      - '**/.lintr.R'
+
+name: lint-changed-files
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+            any::cyclocomp
+            epiverse-trace/etdev
+          needs: check
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          changed_files <- purrr::map_chr(files, "filename")
+          all_files <- list.files(recursive = TRUE)
+          exclusions_list <- as.list(setdiff(all_files, changed_files))
+          lintr::lint_package(exclusions = exclusions_list)
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -8,7 +8,7 @@
 # ```
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, master]
     paths:
       - 'README.Rmd'
       - 'README.md'
@@ -45,15 +45,16 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: write
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -70,9 +71,14 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      - name: Check website links
+        uses: untitaker/[email protected]
+        with:
+          args: docs/
+
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.7.2
         with:
           # We clean on releases because we want to remove old vignettes,
           # figures, etc. that have been deleted from the `main` branch.

.github/workflows/render_readme.yml

@@ -0,0 +1,96 @@
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rmarkdown", "any::usethis", "."))
+# writeLines(
+#   knitr::knit_expand(
+#     "README.Rmd",
+#     packagename = read.dcf("DESCRIPTION", "Package"),
+#     gh_repo = usethis:::github_remote_list()$repo_spec
+#   ),
+#   "README_expanded.Rmd"
+# )
+# rmarkdown::render(
+#   "README_expanded.Rmd",
+#   output_file = "README.md",
+#   output_dir = "."
+# )
+# unlink("README_expanded.Rmd")
+# ```
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+#
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      # This may seem like a no-op but it prevents triggering on tags
+      # We use '**' rather '*' to accomodate names like 'dev/branch-1'
+      - '**'
+    paths:
+      - 'README.Rmd'
+      - '.github/workflows/render_readme.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd",
+              packagename = read.dcf("DESCRIPTION", "Package"),
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ),
+            "README_expanded.Rmd"
+          )
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir = "."
+          )
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git pull --rebase origin ${{ github.ref.name }}
+          git push origin || echo "No changes to push"

.github/workflows/test-coverage.yaml

@@ -8,7 +8,7 @@
 # ```
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, master]
     paths:
       - 'R/**'
       - 'src/**'
@@ -62,11 +62,11 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
-          file: ./cobertura.xml
-          plugin: noop
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -82,4 +82,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          path: ${{ runner.temp }}/package

.github/workflows/update-citation-cff.yaml

@@ -48,7 +48,7 @@ jobs:
 
         shell: Rscript {0}
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           commit-message: Update `CITATION.cff`
           title: Update `CITATION.cff`

.github/workflows/update-copyright-year.yml

@@ -0,0 +1,37 @@
+name: Update copyright year(s) in license file
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 3 1 1 *'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: FantasticFiasco/action-update-license-year@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          path: | 
+            LICENSE.md
+          prBody: >
+           This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+           ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+      - uses: FantasticFiasco/action-update-license-year@v3
+        with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+            path: | 
+              LICENSE
+            prBody: >
+             This PR updates the copyright license for this new year! If you're reading this while you're celebrating, enjoy! Don't worry about this one :blush:
+
+             ![Happy new year!](https://media.giphy.com/media/HyDfNCZlTn5iU/giphy.gif?cid=ecf05e4777yl7dbo1xfha6bx1z5lrl13uq7biv6rs9dqsyoh&ep=v1_gifs_search&rid=giphy.gif&ct=g)
+            transform: (?<=YEAR:\s)(?<from>\d{4})?-?(\d{4})?