Merge pull request #116 from tidymodels/2023-spring-cleaning

2023 spring cleaning
tidymodels · Oct 31, 2023 · 103e3f5 · 103e3f5
2 parents 4e33df6 + a842994
commit 103e3f5
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
@@ -22,24 +22,25 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {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'}
 
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
+          - {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@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,9 +52,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: 
-            any::rcmdcheck,
-            randomForest=?ignore-before-r=4.1.0
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,6 +1,5 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
-# Add Config/Needs/website: tidyverse/tidytemplate to DESCRIPTION
 on:
   push:
     branches: [main, master]
@@ -15,10 +14,15 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -31,8 +35,14 @@ jobs:
           extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
 on:
   issue_comment:
@@ -8,28 +8,30 @@ name: Commands
 
 jobs:
   document:
-    if: startsWith(github.event.comment.body, '/document')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/pr-fetch@v1
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: roxygen2
+          extra-packages: any::roxygen2
+          needs: pr-document
 
       - name: Document
-        run: Rscript -e 'roxygen2::roxygenise()'
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
 
       - name: commit
         run: |
@@ -38,30 +40,32 @@ jobs:
           git add man/\* NAMESPACE
           git commit -m 'Document'
 
-      - uses: r-lib/actions/pr-push@v1
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
   style:
-    if: startsWith(github.event.comment.body, '/style')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
     name: style
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/pr-fetch@v1
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - name: Install dependencies
-        run: Rscript -e 'install.packages("styler")'
+        run: install.packages("styler")
+        shell: Rscript {0}
 
       - name: Style
-        run: Rscript -e 'styler::style_pkg()'
+        run: styler::style_pkg()
+        shell: Rscript {0}
 
       - name: commit
         run: |
@@ -70,6 +74,6 @@ jobs:
           git add \*.R
           git commit -m 'Style'
 
-      - uses: r-lib/actions/pr-push@v1
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
 on:
   push:
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,5 +27,24 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE)
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,10 @@
 Package: tidypredict
 Title: Run Predictions Inside the Database
 Version: 0.5
-Authors@R:
-    c(
-      person("Edgar", "Ruiz", email = "[email protected]", role = c("aut", "cre")),
-      person("Max", "Kuhn", email = "[email protected]", role = c("aut"))
-    )
+Authors@R: c(
+    person("Edgar", "Ruiz", , "[email protected]", role = c("aut", "cre")),
+    person("Max", "Kuhn", , "[email protected]", role = "aut")
+  )
 Description: It parses a fitted 'R' model object, and returns a formula in
     'Tidy Eval' code that calculates the predictions.  It works with
     several databases back-ends because it leverages 'dplyr' and 'dbplyr'
@@ -17,13 +16,14 @@ URL: https://tidypredict.tidymodels.org,
     https://github.com/tidymodels/tidypredict
 BugReports: https://github.com/tidymodels/tidypredict/issues
 Depends:
-    R (>= 3.1)
+    R (>= 3.6)
 Imports:
+    cli,
     dplyr (>= 0.7),
     generics,
     knitr,
     purrr,
-    rlang,
+    rlang (>= 1.1.1),
     tibble,
     tidyr
 Suggests:
@@ -42,13 +42,12 @@ Suggests:
     ranger,
     rmarkdown,
     RSQLite,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     xgboost,
     yaml
 VignetteBuilder: 
     knitr
-Config/Needs/website: 
-    tidyverse/tidytemplate
+Config/Needs/website: tidyverse/tidytemplate
+Config/testthat/edition: 3
 Encoding: UTF-8
 RoxygenNote: 7.2.3
-Config/testthat/edition: 3
diff --git a/R/acceptable.R b/R/acceptable.R
@@ -28,12 +28,11 @@ acceptable_formula.glm <- function(model) {
 }
 
 ## As suggested by @topepo, brought in from the `pryr` package
-## via the `recepies` package
+## via the `recipes` package
 fun_calls <- function(f) {
   if (is.function(f)) {
     fun_calls(body(f))
-  } 
-  else if (is.call(f)) {
+  } else if (is.call(f)) {
     fname <- as.character(f[[1]])
     # Calls inside .Internal are special and shouldn't be included
     if (identical(fname, ".Internal")) {
@@ -49,7 +48,7 @@ acceptable_lm <- function(model) {
     contr <- model$contrasts
     contr <- contr[!("contr.treatment" %in% contr)]
     if (length(contr) > 0) {
-      stop(
+      cli::cli_abort(
         "The treatment contrast is the only one supported at this time. Field(s) with an invalid contrast are: ",
         paste0("`", names(contr), "`", collapse = ","),
         call. = FALSE
@@ -63,7 +62,7 @@ acceptable_lm <- function(model) {
   if (length(funs) > 0) {
     contains_offset <- any(funs == "offset")
     contains_other <- funs[funs != "offset"]
-    stop(
+    cli::cli_abort(
       paste0(
         "Functions inside the formula are not supported.",
         if (contains_offset) "\n- Offset detected.  Try using offset as an argument instead.",

diff --git a/R/as-parsed-model.R b/R/as-parsed-model.R
@@ -1,7 +1,7 @@
 #' Prepares parsed model object
-#' 
+#'
 #' @param x A parsed model object
-#' 
+#'
 #' @export
 as_parsed_model <- function(x) {
   UseMethod("as_parsed_model")

diff --git a/R/model-cubist.R b/R/model-cubist.R
@@ -3,7 +3,7 @@ parse_model.cubist <- function(model) {
   coefs <- model$coefficients
   splits <- model$splits
   splits$variable <- as.character(splits$variable)
-  splits$dir <- as.character(splits$dir)  
+  splits$dir <- as.character(splits$dir)
 
   committees2 <- map(
     unique(coefs$committee),
@@ -13,7 +13,7 @@ parse_model.cubist <- function(model) {
         coefs$rule[coefs$committee == comm],
         ~ {
           cc <- coefs[coefs$rule == .x & coefs$committee == comm, ]
-          if(!is.null(model$splits)) {
+          if (!is.null(model$splits)) {
             cs <- splits[splits$rule == .x & splits$committee == comm, ]
             tcs <- transpose(cs)
             mcs <- map(