Update workflows to match packagetemplate

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

@@ -1,5 +1,12 @@
+
 # 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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rcmdcheck", "."), dependencies = "Config/Needs/check")
+# rcmdcheck::rcmdcheck()
+# ```
 on:
   push:
     branches: [main, master]
@@ -16,8 +23,8 @@ on:
       - 'LICENSE'
       - '.Rbuildignore'
       - '.github/workflows/R-CMD-check.yaml'
+  merge_group:
   pull_request:
-    branches: [main, master]
     paths:
       - 'data/**'
       - 'R/**'
@@ -48,7 +55,7 @@ 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'}
@@ -57,8 +64,6 @@ jobs:
     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@v4
@@ -80,6 +85,7 @@ jobs:
         id: rcmdcheck
         with:
           upload-snapshots: true
+          error-on: '"note"'
 
       # fail-fast but only if rcmdcheck step fails
       - name: Manual fail-fast

.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-              "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"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+              "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"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

@@ -4,6 +4,11 @@ on:
   workflow_dispatch:
   pull_request:
     branches: [main, master]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - '**/.lintr'
+      - '**/.lintr.R'
 
 name: lint-changed-files
 

.github/workflows/pkgdown.yaml

@@ -21,6 +21,7 @@ on:
       - 'DESCRIPTION'
       - '.Rbuildignore'
       - '.github/**'
+  merge_group:
   pull_request:
     paths:
       - 'README.Rmd'
@@ -44,13 +45,14 @@ 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@v4
 
@@ -69,8 +71,13 @@ 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 != 'pull_request'
+        if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
         uses: JamesIves/[email protected]
         with:
           # We clean on releases because we want to remove old vignettes,

.github/workflows/test-coverage.yaml

@@ -1,5 +1,11 @@
 # 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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak("any::covr", dependencies = "Config/Needs/coverage")
+# covr::codecov(quiet = FALSE)
+# ```
 on:
   push:
     branches: [main, master]
@@ -10,8 +16,8 @@ on:
       - 'inst/**'
       - 'DESCRIPTION'
       - '.github/workflows/test-coverage.yaml'
+  merge_group:
   pull_request:
-    branches: [main, master]
     paths:
       - 'R/**'
       - 'src/**'

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

@@ -1,20 +1,23 @@
+
 # Workflow derived from https://github.com/r-lib/actions/tree/master/examples
 # The action runs when:
-# - A new release is published
 # - The DESCRIPTION or inst/CITATION are modified
 # - Can be run manually
 # For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
 on:
-  release:
-    types: [published]
   push:
+    branches:
+      - main
     paths:
       - DESCRIPTION
       - inst/CITATION
       - .github/workflows/update-citation-cff.yaml
   workflow_dispatch:
 
 name: Update CITATION.cff
+permissions:
+  contents: write
+  pull-requests: write
 
 jobs:
   update-citation-cff:
@@ -29,21 +32,29 @@ jobs:
           extra-packages: |
             any::cffr
             any::V8
+
       - name: Update CITATION.cff
         run: |
+
           library(cffr)
+
           # Customize with your own code
           # See https://docs.ropensci.org/cffr/articles/cffr.html
+
           # Write your own keys
           mykeys <- list()
+
           # Create your CITATION.cff file
           cff_write(keys = mykeys)
+
         shell: Rscript {0}
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v6
+        with:
+          commit-message: Update `CITATION.cff`
+          title: Update `CITATION.cff`
+          body: |
+            This pull request updates the citation file, ensuring all authors are credited and there are no discrepancies.
 
-      - name: Commit results
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Action"
-          git add CITATION.cff
-          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
-          git push origin || echo "No changes to commit"
+            Please verify the changes before merging.
+          branch: 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})?

README.Rmd

@@ -240,8 +240,7 @@ To report a bug please open an [issue](https://github.com/epiverse-trace/epichai
 
 ## Contribute
 
-We welcome contributions to enhance the package's functionalities. If you 
-wish to do so, please follow the [package contributing guide](https://github.com/epiverse-trace/epichains/blob/main/.github/CONTRIBUTING.md).
+Contributions to {epichains} are welcomed. Please follow the [package contributing guide](https://github.com/epiverse-trace/.github/blob/main/CONTRIBUTING.md).
 
 ## Code of conduct