Merge pull request #120 from tidymodels/upkeep-2024

Upkeep 2024

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

@@ -1,16 +1,13 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -23,24 +20,17 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
           - {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'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -58,3 +48,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +42,7 @@ 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/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,46 @@ 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(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

DESCRIPTION

@@ -50,4 +50,5 @@ VignetteBuilder:
 Config/Needs/website: tidyverse/tidytemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

R/model-glm.R

@@ -0,0 +1,34 @@
+# Predict ---------------------------------------
+
+#' @export
+tidypredict_fit.glm <- function(model) {
+  parsedmodel <- parse_model(model)
+  build_fit_formula(parsedmodel)
+}
+
+# Parse model --------------------------------------
+
+#' @export
+parse_model.glm <- function(model) parse_model_lm(model)
+
+# Intervals -----------------------------------------------
+
+#' @export
+tidypredict_interval.glm <- function(model, interval = 0.95) {
+  parsedmodel <- parse_model(model)
+  te_interval_glm(parsedmodel, interval)
+}
+
+te_interval_glm <- function(parsedmodel, interval = 0.95) {
+  intervals <- te_interval_lm(parsedmodel, interval)
+  family <- parsedmodel$general$family
+  link <- parsedmodel$general$link
+  assigned <- 0
+  if (family == "gaussian" && link == "identity") {
+    assigned <- 1
+  }
+  if (assigned == 0) {
+    cli::cli_abort("Combination of family and link are not supported for prediction intervals")
+  }
+  intervals
+}

R/model-lm.R

@@ -6,12 +6,6 @@ tidypredict_fit.lm <- function(model) {
   build_fit_formula(parsedmodel)
 }
 
-#' @export
-tidypredict_fit.glm <- function(model) {
-  parsedmodel <- parse_model(model)
-  build_fit_formula(parsedmodel)
-}
-
 build_fit_formula <- function(parsedmodel) {
   parsed_f <- map(
     parsedmodel$terms,
@@ -77,9 +71,6 @@ build_fit_formula <- function(parsedmodel) {
 #' @export
 parse_model.lm <- function(model) parse_model_lm(model)
 
-#' @export
-parse_model.glm <- function(model) parse_model_lm(model)
-
 parse_model_lm <- function(model) {
   acceptable_formula(model)
 
@@ -167,12 +158,6 @@ tidypredict_interval.lm <- function(model, interval = 0.95) {
   te_interval_lm(parsedmodel, interval)
 }
 
-#' @export
-tidypredict_interval.glm <- function(model, interval = 0.95) {
-  parsedmodel <- parse_model(model)
-  te_interval_glm(parsedmodel, interval)
-}
-
 get_qr_lm <- function(qr_name, parsedmodel) {
   q <- map(
     parsedmodel$terms,
@@ -225,17 +210,3 @@ te_interval_lm <- function(parsedmodel, interval = 0.95) {
   tfrac <- qt(1 - (1 - 0.95) / 2, parsedmodel$general$residual)
   expr(!!tfrac * sqrt((!!qrs) + (!!parsedmodel$general$sigma2)))
 }
-
-te_interval_glm <- function(parsedmodel, interval = 0.95) {
-  intervals <- te_interval_lm(parsedmodel, interval)
-  family <- parsedmodel$general$family
-  link <- parsedmodel$general$link
-  assigned <- 0
-  if (family == "gaussian" && link == "identity") {
-    assigned <- 1
-  }
-  if (assigned == 0) {
-    cli::cli_abort("Combination of family and link are not supported for prediction intervals")
-  }
-  intervals
-}

cran-comments.md

@@ -18,15 +18,6 @@
 
 * Having Max as the maintainer will guarantee good follow through for any communications with CRAN.  This is the reason why there is another update is such short order from the previous update in CRAN.  Thank you for your understanding.
 
-## Test environments
-
-* macOS M1.     R: 4.2.1
-* macOS         R: Release
-* Windows       R: Release
-* Windows       R: 3.6
-* Ubuntu 18.04  R: Release
-* Ubuntu 18.04  R: Devel
-
 ## R CMD check results
 
 * 0 errors | 0 warnings | 0 notes