workflow fixes, fix category name stan check, run-extended

ropensci · Feb 25, 2025 · 7afeb5d · 7afeb5d
1 parent e7d27bb
commit 7afeb5d
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Showing 5 changed files with 26 additions and 12 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -57,10 +57,12 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        needs: check
         with:
           cache-version: 2
           extra-packages: |
-            rcmdcheck
+            any::rcmdcheck
+            local::.
             BH
             RcppParallel
             RcppEigen

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -21,7 +23,7 @@ jobs:
       DYNAMITE_SCALING_TESTS: ${{contains(github.event.head_commit.message, 'run-scaling')}}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -32,6 +34,7 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache-version: 1
+          needs: coverage
           extra-packages: |
             covr
             BH
@@ -50,23 +53,33 @@ jobs:
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/R/prepare_stan_input.R b/R/prepare_stan_input.R
@@ -46,7 +46,7 @@ prepare_stan_input <- function(dformula, data, group_var, time_var,
     data[, .SD, .SDcols = resp],
     function(x) {
       cl <- class(x)
-      attr(cl, "levels") <- stan_name(levels(x))
+      attr(cl, "levels") <- stan_name(levels(x), check_first = FALSE)
       cl
     }
   )

diff --git a/R/stan_utilities.R b/R/stan_utilities.R
@@ -129,12 +129,12 @@ stan_reserved_keywords <- c(
 #'
 #' @param x A `character` vector.
 #' @noRd
-stan_name <- function(x) {
+stan_name <- function(x, check_first = TRUE) {
   x <- gsub("\\s+", "_", x)
   x <- gsub("[^a-zA-Z0-9_]", "", x)
   x <- gsub("_{2,}$", "", x)
   for (i in seq_along(x)) {
-    if (!grepl("^[a-zA-Z]", x[i])) {
+    if (check_first && !grepl("^[a-zA-Z]", x[i])) {
       x[i] <- paste0("v_", x[i])
     }
     if (tolower(x[i]) %in% stan_reserved_keywords) {

diff --git a/tests/testthat/test-extended.R b/tests/testthat/test-extended.R
@@ -222,8 +222,7 @@ test_that("time-invariant cumulative fit and predict work", {
 
   expect_error(
     fit <- dynamite(
-      dformula =
-        obs(y ~ x, family = "cumulative", link = "logit"),
+      dformula = obs(y ~ x, family = "cumulative", link = "logit"),
       data = d,
       time = "time",
       group = "id"