{simulist} v0.3.0 full package review

.Rbuildignore

@@ -9,3 +9,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^CITATION\.cff$
+^doc$
+^Meta$
+^tools$

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

@@ -22,6 +22,7 @@ on:
  - 'LICENSE'
  - '.Rbuildignore'
  - '.github/workflows/R-CMD-check.yaml'
+ merge_group:
  pull_request:
  paths:
  - 'data/**'
@@ -62,11 +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
 
@@ -85,6 +84,7 @@ 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

@@ -0,0 +1,82 @@
+# 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:
+ pull_request:
+ paths:
+ - 'DESCRIPTION'
+
+name: Analyze dependency changes
+
+concurrency:
+ group: ${{ github.workflow }}-${{ github.ref }}
+ cancel-in-progress: true
+
+permissions:
+ pull-requests: write
+
+jobs:
+ dependency-changes:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - name: Setup R
+ uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - name: Install dependencies
+ uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ packages: any::pak, glue, gh
+
+ - name: Analyze dependency changes
+ shell: Rscript {0}
+ run: |
+ deps_base <- pak::pkg_deps("${{ github.repository }}@${{ github.base_ref }}", dependencies = TRUE) |>
+ subset(!directpkg) |>
+ subset(is.na(priority))
+ # We install from PR number rather than branch to deal with the case
+ # of PR coming from forks
+ deps_head <- pak::pkg_deps("${{ github.repository }}#${{ github.event.number }}", dependencies = TRUE) |>
+ subset(!directpkg) |>
+ subset(is.na(priority))
+
+ deps_added <- deps_head |>
+ subset(!ref %in% deps_base$ref)
+
+ deps_removed <- deps_base |>
+ subset(!ref %in% deps_head$ref)
+
+ if (nrow(deps_added) + nrow(deps_removed) > 0) {
+
+ message("Dependencies have changed! Analyzing...")
+
+ if (nrow(deps_added) > 0) {
+ nudge <- "Reach out on slack (`#code-review` or `#help` channels) to double check if there are base R alternatives to the new dependencies.\n"
+ } else {
+ nudge <- ""
+ }
+
+ msg <- glue::glue(
+ .sep = "\n",
+ "This pull request:",
+ "- Adds {nrow(deps_added)} new dependencies (direct and indirect)",
+ "- Adds {length(unique(deps_added$sysreqs))} new system dependencies",
+ "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
+ "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
+ "",
+ nudge,
+ "(Note that results may be inaccurate if you branched from an outdated version of the target branch.)"
+ )
+
+ message("Posting results as a pull request comment.")
+
+ gh::gh(
+ "POST /repos/{repo}/issues/{issue_number}/comments",
+ repo = "${{ github.repository }}",
+ issue_number = "${{ github.event.number }}",
+ body = msg
+ )
+
+ }

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

@@ -0,0 +1,52 @@
+# 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: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: |
+ any::gh
+ any::lintr
+ any::purrr
+ epiverse-trace/etdev
+ needs: check
+
+ - name: Install package
+ run: R CMD INSTALL .
+
+ - name: Extract and lint files changed by this PR
+ run: |
+ files <- gh::gh("/repos/${{ 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

@@ -21,6 +21,7 @@ on:
  - 'DESCRIPTION'
  - '.Rbuildignore'
  - '.github/**'
+ merge_group:
  pull_request:
  paths:
  - 'README.Rmd'
@@ -44,15 +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
 
@@ -69,9 +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 != 'pull_request'
- uses: JamesIves/github-pages-deploy-action@4.1.4
+ if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
+ uses: JamesIves/github-pages-deploy-action@v4.6.0
  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

@@ -26,6 +26,10 @@ name: render-readme
 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'
@@ -34,6 +38,9 @@ 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:
@@ -42,7 +49,7 @@ jobs:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
  steps:
  - name: Checkout repos
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
 
  - name: Setup R
  uses: r-lib/actions/setup-r@v2
@@ -85,4 +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"

.github/workflows/test-coverage.yaml

@@ -16,6 +16,7 @@ on:
  - 'inst/**'
  - 'DESCRIPTION'
  - '.github/workflows/test-coverage.yaml'
+ merge_group:
  pull_request:
  paths:
  - 'R/**'
@@ -31,24 +32,54 @@ concurrency:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
  test-coverage:
  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
  with:
  use-public-rspm: true
 
  - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- extra-packages: any::covr
+ extra-packages: any::covr, any::xml2
  needs: coverage
 
  - name: Test coverage
- run: covr::codecov(quiet = FALSE)
+ run: |
+ cov <- covr::package_coverage(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+ )
+ covr::to_cobertura(cov)
  shell: Rscript {0}
+
+ - uses: codecov/codecov-action@v4
+ with:
+ fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+ file: ./cobertura.xml
+ plugin: noop
+ disable_search: true
+ token: ${{ secrets.CODECOV_TOKEN }}
+
+ - name: Show testthat output
+ if: always()
+ run: |
+ ## --------------------------------------------------------------------
+ find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
+
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v4
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package

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

@@ -1,28 +1,30 @@
 # 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:
  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:
@@ -45,11 +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 "[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