epiverse-trace · pratikunterwegs · Jun 12, 2024 · Jun 10, 2024 · Jun 10, 2024 · Jun 10, 2024
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -63,11 +63,9 @@ 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@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/dependency-change.yaml b/.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-              "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"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+              "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"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.")

diff --git a/.github/workflows/lint-changed-files.yaml b/.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
 
@@ -17,7 +22,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -29,6 +34,7 @@ jobs:
             any::gh
             any::lintr
             any::purrr
+            any::cyclocomp
             epiverse-trace/etdev
           needs: check
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -54,7 +54,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -71,9 +71,14 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      - name: Check website links
+        uses: untitaker/hyperlink@0.1.32
+        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@v4.6.1
         with:
           # We clean on releases because we want to remove old vignettes,
           # figures, etc. that have been deleted from the `main` branch.

diff --git a/.github/workflows/render_readme.yml b/.github/workflows/render_readme.yml
@@ -1,26 +1,55 @@
-# Name of the workflow
+# 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: macos-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repos
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -29,25 +58,29 @@ jobs:
 
       - 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"), 
+              "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 = ".")
+          rmarkdown::render(
+            "README_expanded.Rmd",
+            output_file = "README.md",
+            output_dir = "."
+          )
         shell: Rscript {0}
-        
+
       - name: Commit files
         run: |
           git config --local user.email "action@github.com"
@@ -59,4 +92,5 @@ jobs:
             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"
diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml
@@ -6,31 +6,25 @@
 on:
   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'
-      - '**'
+      - main
     paths:
       - DESCRIPTION
       - inst/CITATION
       - .github/workflows/update-citation-cff.yaml
   workflow_dispatch:
 
 name: Update CITATION.cff
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
 permissions:
   contents: write
+  pull-requests: write
 
 jobs:
   update-citation-cff:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -53,12 +47,13 @@ jobs:
           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 "action@github.com"
-          git config --local user.name "GitHub Action"
-          git add CITATION.cff
-          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
-          git pull --rebase origin ${{ github.ref.name }}
-          git push origin || echo "No changes to commit"
+            Please verify the changes before merging. 
+          branch: update-citation-cff
diff --git a/.github/workflows/update-copyright-year.yml b/.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})?
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,13 +2,13 @@ Package: finalsize
 Title: Calculate the Final Size of an Epidemic
 Version: 0.2.1.9000
 Authors@R: c(
-    person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = c("aut", "cre", "cph"),
+    person("Pratik", "Gupte", , "pratik.gupte@lshtm.ac.uk", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0001-5294-7819")),
     person("Edwin", "Van Leeuwen", , "edwin.vanleeuwen@ukhsa.gov.uk", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0002-2383-5305")),
     person("Adam", "Kucharski", , "adam.kucharski@lshtm.ac.uk", role = c("aut", "cph"),
            comment = c(ORCID = "0000-0001-8814-9421")),
-    person("Rosalind", "Eggo", , "r.eggo@lshtm.ac.uk", role = "ctb",
+    person("Rosalind", "Eggo", , "r.eggo@lshtm.ac.uk", role = c("ctb", "cre"),
            comment = c(ORCID = "0000-0002-0362-6717")),
     person("Hugo", "Gruson", , "hugo.gruson@data.org", role = "ctb",
            comment = c(ORCID = "0000-0002-4094-1476")),
@@ -61,4 +61,4 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2024
 COPYRIGHT HOLDER: finalsize authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2022 finalsize authors
+Copyright (c) 2024 finalsize authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,17 @@
 # finalsize (development version)
 
+Maintainer is changing to @rozeggo (#212).
+
+1. Updated all GitHub Actions workflows in line with {epiverse-trace/packagetemplate} (#212).
+
+2. Updated DESCRIPTION and license files with new maintainer and new copyright year (#212).
+
+3. Added `R/dev-utils.R` for extra release issue bullet points, and added `tools/check.env` for global environment checks (#212).
+
+4. Corrected internal article links in vignettes (#212).
+
+5. Added continuous benchmarking workflows using {touchstone} following the pattern of {epiforecasts/EpiNow2} (#212).
+
 # finalsize 0.2.1
 
 This patch adds:

diff --git a/R/dev-utils.R b/R/dev-utils.R
@@ -0,0 +1,8 @@
+# This unexported function adds a custom item to `usethis::use_release_issue()`
+release_bullets <- function() {
+  c(
+    "Run `goodpractice::gp()`",
+    "Review [WORDLIST](https://docs.cran.dev/spelling#wordlist)",
+    "Check if `# nolint` comments are still needed with recent lintr releases"
+  )
+}
diff --git a/README.md b/README.md
@@ -184,7 +184,7 @@ citation("finalsize")
 #> To cite package 'finalsize' in publications use:
 #> 
 #>   Gupte P, Van Leeuwen E, Kucharski A (2024). _finalsize: Calculate the
-#>   Final Size of an Epidemic_. R package version 0.2.1,
+#>   Final Size of an Epidemic_. R package version 0.2.1.9000,
 #>   https://epiverse-trace.github.io/finalsize/,
 #>   <https://github.com/epiverse-trace/finalsize>.
 #> 
@@ -194,7 +194,7 @@ citation("finalsize")
 #>     title = {finalsize: Calculate the Final Size of an Epidemic},
 #>     author = {Pratik Gupte and Edwin {Van Leeuwen} and Adam Kucharski},
 #>     year = {2024},
-#>     note = {R package version 0.2.1, 
+#>     note = {R package version 0.2.1.9000, 
 #> https://epiverse-trace.github.io/finalsize/},
 #>     url = {https://github.com/epiverse-trace/finalsize},
 #>   }

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -7,6 +7,7 @@ Cppcheck
 Cpplint
 Dylanger
 Eigen
+EpiNow
 Epiverse
 Github
 Kwok
@@ -41,7 +42,9 @@ doi
 dt
 dx
 eff
+epiforecasts
 episoap
+epiverse
 frac
 gh
 github