Issue #147: Remove cmdstanr from remote (#356)

* Remove cmdstanr from Remotes * Move into Additional_repositories * Use stable release version rather than latest * Use R universe version of cmdstanr and add to GH actions * Move cmdstanr from Imports to Suggests * Remove import statement in package Former-commit-id: 6ee9839 Former-commit-id: 7d9b5e32d8be79d554b92b7f7b7bdaa3f07eeddf Former-commit-id: bde4c96ef6c5a1db1f33a65eee29cbe8a987f296 [formerly 5d1af31] Former-commit-id: a4407652c81af30af0071da5568ea77bd0e8478c
epinowcast · Oct 2, 2024 · 5c17a9d · 5c17a9d
1 parent 58747a7
commit 5c17a9d
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Showing 12 changed files with 22 additions and 9 deletions.
diff --git a/.github/workflows/R-CMD-as-cran-check.yaml b/.github/workflows/R-CMD-as-cran-check.yaml
@@ -30,6 +30,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -49,6 +49,7 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
           rtools-version: ${{ matrix.config.rtools }}
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/check-cmdstan.yaml b/.github/workflows/check-cmdstan.yaml
@@ -46,6 +46,9 @@ jobs:
           sudo apt-get install -y libpng-dev || true
 
       - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with: 

diff --git a/.github/workflows/codemeta.yaml b/.github/workflows/codemeta.yaml
@@ -19,7 +19,8 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
+          extra-repositories: 'https://stan-dev.r-universe.dev'
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::codemetar

diff --git a/.github/workflows/lint-changed-files.yaml b/.github/workflows/lint-changed-files.yaml
@@ -18,6 +18,9 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -31,7 +31,8 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
+          extra-repositories: 'https://stan-dev.r-universe.dev'
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::pkgdown, local::.

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -23,6 +23,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/.github/workflows/render-readme.yaml b/.github/workflows/render-readme.yaml
@@ -21,7 +21,10 @@ jobs:
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
-
+        with:
+          use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
+
       - name: Setup pandoc
         uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -25,6 +25,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: 'https://stan-dev.r-universe.dev'
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,6 @@ Depends:
     R (>= 3.5.0)
 Imports: 
     brms,
-    cmdstanr,
     ggplot2,
     purrr,
     stats,
@@ -50,9 +49,10 @@ Suggests:
     sf,
     tidybayes,
     modelr,
-    patchwork
-Remotes:
-    stan-dev/cmdstanr
+    patchwork,
+    cmdstanr
+Additional_repositories:
+    https://stan-dev.r-universe.dev
 Config/Needs/website:
     r-lib/pkgdown,
     epinowcast/enwtheme

diff --git a/NAMESPACE b/NAMESPACE
@@ -37,7 +37,6 @@ export(simulate_exponential_cases)
 export(simulate_gillespie)
 export(simulate_secondary)
 export(simulate_uniform_cases)
-import(cmdstanr)
 import(ggplot2)
 importFrom(brms,bf)
 importFrom(brms,prior)

diff --git a/R/epidist-package.R b/R/epidist-package.R
@@ -2,7 +2,6 @@
 "_PACKAGE"
 
 #' @import ggplot2
-#' @import cmdstanr
 
 ## usethis namespace: start
 #' @importFrom dplyr filter select