update actions

epiforecasts · Feb 2, 2024 · 0d54c93 · 0d54c93
1 parent 2414824
commit 0d54c93
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Showing 5 changed files with 37 additions and 18 deletions.
diff --git a/.github/workflows/R-CMD-as-cran-check.yaml b/.github/workflows/R-CMD-as-cran-check.yaml
@@ -36,9 +36,17 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          dependencies: NA
+          extra-packages: |
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          upload-snapshots: true
+          upload-snapshots: true
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -47,13 +47,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install cmdstan Linux system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev || true
-          sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true
-          sudo apt-get install -y libpng-dev || true
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -65,8 +58,16 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          dependencies: NA
+          extra-packages: |
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:

diff --git a/.github/workflows/lint-only-changed-files.yaml b/.github/workflows/lint-only-changed-files.yaml
@@ -21,11 +21,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: NA
           extra-packages: |
             any::gh
             any::lintr
             any::purrr
-          needs: check
 
       - name: Add lintr options
         run: |
@@ -44,4 +44,4 @@ jobs:
           lintr::lint_package(exclusions = exclusions_list)
         shell: Rscript {0}
         env:
-          LINTR_ERROR_ON_LINT: true
+          LINTR_ERROR_ON_LINT: true
diff --git a/.github/workflows/synthetic-validation.yaml b/.github/workflows/synthetic-validation.yaml
@@ -24,6 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          dependencies: NA
           extra-packages: |
             dplyr
             tidyr
@@ -48,4 +49,4 @@ jobs:
         with:
           name: fits
           retention-days: 5
-          path: synthetic.rds
+          path: synthetic.rds
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -26,9 +26,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
-          needs: coverage
+          dependencies: NA
+          extra-packages: |
+            covr
+            stan-dev/cmdstanr
+            testthat
+
+      - name: Install cmdstan
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
+        shell: Rscript {0}
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
-        shell: Rscript {0}
+        shell: Rscript {0}