Make cmd check run

.github/workflows/R-CMD-check.yaml

@@ -9,8 +9,11 @@ on:
     branches: [main, master]
   pull_request:
     branches: [main, master]
+  workflow_dispatch:
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,21 +28,25 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          #- {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      CXX14: g++
+      CXX14STD: -std=c++1y
+      CXX14FLAGS: -Wall -g -02
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -57,3 +64,8 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/pr-commands.yaml

@@ -4,7 +4,9 @@ on:
   issue_comment:
     types: [created]
 
-name: Commands
+name: pr-commands.yaml
+
+permissions: read-all
 
 jobs:
   document:
@@ -13,8 +15,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -50,8 +54,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - 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_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
         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

DESCRIPTION

@@ -24,10 +24,10 @@ Imports:
     generics (>= 0.1.2),
     glue (>= 1.6.2),
     hardhat (>= 1.0.0),
-    modelenv (>= 0.1.0),
+    modelenv (>= 0.2.0.9000),
     parsnip (>= 1.0.2),
     prettyunits (>= 1.1.0),
-    Rfast (>= 	2.0.6),
+    Rfast (>= 2.0.6),
     rlang (>= 1.0.6),
     rsample (>= 1.0.0),
     stats,
@@ -49,6 +49,8 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     workflows (>= 1.1.2)
+Remotes:
+    tidymodels/modelenv
 Config/Needs/website: pkgdown, tidymodels, tidyverse, palmerpenguins,
     patchwork, ggforce, tidyverse/tidytemplate
 Config/testthat/edition: 3

R/cluster_spec.R

@@ -10,7 +10,12 @@
 #' @export
 #' @keywords internal
 new_cluster_spec <- function(cls, args, eng_args, mode, method, engine) {
-  modelenv::check_spec_mode_engine_val(model = cls, mode = mode, eng = engine)
+  modelenv::check_spec_mode_engine_val(
+    model = cls, 
+    mode = mode,
+    eng = engine,
+    call = rlang::caller_env()
+  )
 
   out <- list(
     args = args, eng_args = eng_args,

tests/testthat/_snaps/arguments.md

@@ -12,29 +12,30 @@
       k_means() %>% set_mode()
     Condition
       Error in `modelenv::stop_incompatible_mode()`:
-      ! Available modes for model type k_means are: 'unknown', 'partition'
+      x Available modes for model type k_means are:
+      * "unknown" and "partition".
 
 ---
 
     Code
       k_means() %>% set_mode(2)
     Condition
-      Error in `modelenv::check_spec_mode_engine_val()`:
-      ! '2' is not a known mode for model `k_means()`.
+      Error in `set_mode()`:
+      ! 2 is not a known mode for model `k_means()`.
 
 ---
 
     Code
       k_means() %>% set_mode("haberdashery")
     Condition
-      Error in `modelenv::check_spec_mode_engine_val()`:
-      ! 'haberdashery' is not a known mode for model `k_means()`.
+      Error in `set_mode()`:
+      ! "haberdashery" is not a known mode for model `k_means()`.
 
 # can't set a mode that isn't allowed by the model spec
 
     Code
       set_mode(k_means(), "classification")
     Condition
-      Error in `modelenv::check_spec_mode_engine_val()`:
-      ! 'classification' is not a known mode for model `k_means()`.
+      Error in `set_mode()`:
+      ! "classification" is not a known mode for model `k_means()`.
 

tests/testthat/_snaps/hier_clust.md

@@ -3,8 +3,8 @@
     Code
       hier_clust(mode = "bogus")
     Condition
-      Error in `modelenv::check_spec_mode_engine_val()`:
-      ! 'bogus' is not a known mode for model `hier_clust()`.
+      Error in `hier_clust()`:
+      ! "bogus" is not a known mode for model `hier_clust()`.
 
 ---
 

tests/testthat/_snaps/k_means.md

@@ -3,8 +3,8 @@
     Code
       k_means(mode = "bogus")
     Condition
-      Error in `modelenv::check_spec_mode_engine_val()`:
-      ! 'bogus' is not a known mode for model `k_means()`.
+      Error in `k_means()`:
+      ! "bogus" is not a known mode for model `k_means()`.
 
 ---
 

tests/testthat/_snaps/tune_cluster.md

@@ -112,6 +112,9 @@
     Condition
       Warning:
       The `...` are not used in this function but one or more objects were passed: 'something'
+      Warning:
+      `grid_latin_hypercube()` was deprecated in dials 1.3.0.
+      i Please use `grid_space_filling()` instead.
     Output
       # Tuning results
       # 2-fold cross-validation