From e33f9bb78df3901fafefd74cc4ac97e45fc45698 Mon Sep 17 00:00:00 2001
From: mtwesley <mlen.too.wesley@gmail.com>
Date: Mon, 25 Nov 2024 12:04:34 -0500
Subject: [PATCH] more granular updates to workflow actions

---
 .github/workflows/R-CMD-check.yaml   | 34 ++++++++++++++--------------
 .github/workflows/test-coverage.yaml | 19 ++++++----------
 2 files changed, 24 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 92e1692..1050325 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -46,7 +46,16 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install Homebrew (macOS only)
+      - name: Install system dependencies (Linux only)
+        if: runner.os == 'Linux'
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            any::sessioninfo
+            any::remotes
+
+      - name: Install Homebrew and qpdf (macOS only)
         if: runner.os == 'macOS'
         uses: Homebrew/actions/setup-homebrew@master
 
@@ -69,28 +78,19 @@ jobs:
       - name: Install greta and dependencies
         shell: Rscript {0}
         run: |
-          install.packages("remotes", repos = "https://cloud.r-project.org")
-          install.packages("rcmdcheck", repos = "https://cloud.r-project.org")
-          install.packages("sessioninfo", repos = "https://cloud.r-project.org")
+          install.packages("greta", repos = c("https://greta-dev.r-universe.dev", "https://cloud.r-project.org"))
           library(greta)
           install_greta_deps(timeout = 120)
 
-      - name: Verify Greta Environment
+      - name: Verify Greta environment
+        shell: Rscript {0}
         run: |
           library(greta)
           greta::greta_sitrep()
-        shell: Rscript {0}
 
-      - name: Install package + deps
-        run: |
-          
-          remotes::install_local(dependencies = TRUE, force = TRUE)
-
-      - name: R CMD check
-        run: rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '--no-manual --as-cran'
 
       - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
\ No newline at end of file
+        run: sessioninfo::session_info()
\ No newline at end of file
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index f60be1e..0ac7579 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -6,13 +6,16 @@ on:
 
 name: test-coverage
 
-permissions: read-all
+permissions:
+  contents: read
+  actions: write
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RETICULATE_AUTOCONFIGURE: 'FALSE'
 
     steps:
       - uses: actions/checkout@v4
@@ -53,21 +56,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Test coverage
-        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: r-lib/actions/test-coverage@v2
+        with:
+          type: covr
 
       - 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