ci: Format with air, check detritus, better handling of extra-packages

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

@@ -250,6 +250,8 @@ jobs:
       fail-fast: false
       matrix: ${{fromJson(needs.rcc-smoke.outputs.versions-matrix)}}
 
+    timeout-minutes: 240
+
     steps:
       - uses: actions/checkout@v4
         with:
@@ -289,6 +291,7 @@ jobs:
           results: ${{ runner.os }}-r${{ matrix.r }}
 
       - uses: ./.github/workflows/covr
+        timeout-minutes: 240
         if: ${{ matrix.covr }}
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/covr/action.yml

@@ -1,4 +1,5 @@
 name: "Actions to run covr for an R package"
+description: "Run covr to check code coverage for an R package and upload results to Codecov."
 inputs:
   token:
     description: codecov token

.github/workflows/install/action.yml

@@ -60,6 +60,7 @@ runs:
         # echo "_R_CHECK_CRAN_INCOMING_=true" | tee -a $GITHUB_ENV
         echo "_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_=true" | tee -a $GITHUB_ENV
         echo "_R_CHECK_FORCE_SUGGESTS_=false" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_THINGS_IN_OTHER_DIRS_=true" | tee -a $GITHUB_ENV
       shell: bash
 
     - name: Set environment variables (non-Windows only)
@@ -94,7 +95,7 @@ runs:
     - id: get-extra
       run: |
         set -x
-        packages=$( ( grep Config/gha/extra-packages DESCRIPTION || true ) | cut -d " " -f 2)
+        packages=$( ( grep Config/gha/extra-packages DESCRIPTION || true ) | cut -d " " -f 2-)
         echo packages=$packages >> $GITHUB_OUTPUT
       shell: bash
 
@@ -105,7 +106,7 @@ runs:
         pak-version: stable
         needs: ${{ inputs.needs }}
         packages: ${{ inputs.packages }}
-        extra-packages: ${{ inputs.extra-packages }} ${{ ( matrix.covr && 'covr xml2' ) || '' }} ${{ steps.get-extra.outputs.packages }}
+        extra-packages: ${{ inputs.extra-packages }} ${{ ( matrix.covr && 'r-lib/covr#611 xml2' ) || '' }} ${{ steps.get-extra.outputs.packages }}
         cache-version: ${{ inputs.cache-version }}
 
     - name: Add pkg.lock to .gitignore

.github/workflows/style/action.yml

@@ -3,69 +3,29 @@ name: "Action to auto-style a package"
 runs:
   using: "composite"
   steps:
-    - name: Check styler options
+    - name: Check air.toml
       id: check
       run: |
         set -x
-        scope=$( ( grep Config/autostyle/scope DESCRIPTION || true ) | cut -d " " -f 2)
-        strict=$( ( grep Config/autostyle/strict DESCRIPTION || true ) | cut -d " " -f 2)
-        rmd=$( ( grep Config/autostyle/rmd DESCRIPTION || true ) | cut -d " " -f 2)
-        echo scope=$scope >> $GITHUB_OUTPUT
-        echo strict=$strict >> $GITHUB_OUTPUT
-        echo rmd=$rmd >> $GITHUB_OUTPUT
+        if [ -f air.toml ]; then
+          echo enabled=true >> $GITHUB_OUTPUT
+        else
+          echo enabled=false >> $GITHUB_OUTPUT
+        fi
       shell: bash
 
-    - uses: actions/cache@v4
-      if: ${{ steps.check.outputs.scope }}
-      with:
-        path: |
-          ~/.cache/R/R.cache
-        key: ${{ runner.os }}-2-${{ github.run_id }}-
-        restore-keys: |
-          ${{ runner.os }}-2-
+    - name: Install air
+      if: ${{ steps.check.outputs.enabled == 'true' }}
+      uses: posit-dev/setup-air@v1
 
-    - name: Imprint run ID
-      if: ${{ steps.check.outputs.scope }}
+    - name: Run air
+      if: ${{ steps.check.outputs.enabled == 'true' }}
       run: |
-        mkdir -p ~/.cache/R/R.cache/styler
-        touch ~/.cache/R/R.cache/${{ github.run_id }}
+        air format .
       shell: bash
 
-    - name: Show cache
-      if: ${{ steps.check.outputs.scope }}
+    - name: Check Git status
+      if: ${{ steps.check.outputs.enabled == 'true' }}
       run: |
-        ls -l ~/.cache/R/R.cache
-        ls -l ~/.cache/R/R.cache/styler
-      shell: bash
-
-    - name: Enable styler cache
-      if: ${{ steps.check.outputs.scope }}
-      run: |
-        styler::cache_activate(verbose = TRUE)
-      shell: Rscript {0}
-
-    - name: Run styler
-      if: ${{ steps.check.outputs.scope }}
-      run: |
-        strict <- as.logical("${{ steps.check.outputs.strict }}")
-        if (is.na(strict)) {
-          strict <- FALSE
-        }
-        rmd <- as.logical("${{ steps.check.outputs.rmd }}")
-        if (is.na(rmd)) {
-          rmd <- TRUE
-        }
-        styler::style_pkg(
-          scope = "${{ steps.check.outputs.scope }}",
-          strict = strict,
-          filetype = c("R", "Rprofile", if (rmd) c("Rmd", "Rmarkdown", "Rnw", "Qmd"))
-        )
-      shell: Rscript {0}
-
-    - name: Show cache again
-      if: ${{ steps.check.outputs.scope }}
-      run: |
-        ls -l ~/.cache/R/R.cache
-        ls -l ~/.cache/R/R.cache/styler
-        gdu -s --inodes ~/.cache/R/R.cache/styler/* || du -s --inodes ~/.cache/R/R.cache/styler/*
+        git status
       shell: bash