Update actions (#769)

* update actions * update `simulate_*` snapshots (#780) * install rstan from CRAN explicitly (#782) * use github version for cmdstanr * Revert "update `simulate_*` snapshots (#780)" This reverts commit a21fbf8. * setup pandoc * use epinowcast action --------- Co-authored-by: Sebastian Funk <[email protected]>
epiforecasts · Sep 27, 2024 · 95c3643 · 95c3643
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commit 95c3643
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Showing 7 changed files with 30 additions and 31 deletions.
diff --git a/.github/workflows/R-CMD-as-cran-check.yaml b/.github/workflows/R-CMD-as-cran-check.yaml
@@ -34,22 +34,21 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             rcmdcheck
             rmarkdown
-            cmdstanr
+            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: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
 
       - uses: r-lib/actions/check-r-package@v2
         with:

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -55,23 +55,22 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             rmarkdown
             rcmdcheck
-            cmdstanr
+            stan-dev/cmdstanr
             testthat
 
       - name: Install cmdstan
         if: runner.os != 'Windows'
-        run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
-        shell: Rscript {0}
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
 
       - 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
@@ -18,16 +18,14 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             here
             usethis
-            cmdstanr
+            stan-dev/cmdstanr
             any::gh
             any::lintr
             any::purrr

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -28,9 +28,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
-          extra-packages: |
-            epiforecasts/EpiNow2
-            pkgdown
+          extra-packages: pkgdown local::.
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

diff --git a/.github/workflows/stan-model-benchmark.yaml b/.github/workflows/stan-model-benchmark.yaml
@@ -24,21 +24,20 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           packages: |
             local::.
             here
             purrr
-            cmdstanr
+            stan-dev/cmdstanr
 
       - name: Install cmdstan
-        run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
-        shell: Rscript {0}
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
 
       - name: Checkout main branch in parallel and move to separate dir
         run: |

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -10,6 +10,10 @@ on:
 
 name: test-coverage
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test-coverage:
     runs-on: macos-latest
@@ -21,24 +25,26 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          extra-repositories: https://mc-stan.org/r-packages/
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: NA
           extra-packages: |
             covr
-            cmdstanr
+            stan-dev/cmdstanr
             testthat
 
       - name: Install cmdstan
-        run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, quiet = TRUE)
-        shell: Rscript {0}
+        if: runner.os != 'Windows'
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: 'latest'
+          num-cores: 2
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -142,7 +142,7 @@ LinkingTo:
     rstan (>= 2.26.0),
     StanHeaders (>= 2.26.0)
 Additional_repositories:
-    https://mc-stan.org/r-packages/
+    https://stan-dev.r-universe.dev
 Biarch: true
 Config/testthat/edition: 3
 Encoding: UTF-8