Merge pull request #747 from olivroy/upkeep

Avoid testthat deprecated features + upkeep

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

@@ -2,11 +2,12 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [develop, main]
+    branches: [main, develop]
   pull_request:
-    branches: [develop, main]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +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/test-coverage.yaml

@@ -1,54 +1,61 @@
+# 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:
-    branches:
-      - main
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     env:
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
-        id: install-r
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
         run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("covr", execute = TRUE)
+          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}
 
-      - name: Install dependencies
+      - 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: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("covr")
-        shell: Rscript {0}
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -121,7 +121,7 @@ Depends:
     R (>= 3.1.2)
 Imports:
     cli,
-    dplyr (>= 0.8.0),
+    dplyr (>= 1.0.0),
     knitr (>= 1.2),
     magrittr (>= 1.5),
     pillar (>= 1.6.4),
@@ -133,23 +133,21 @@ Imports:
     tibble (>= 2.0.0),
     tidyr (>= 1.0),
     tidyselect (>= 1.0.0),
-    vctrs
+    vctrs (>= 0.5.0)
 Suggests:
-    covr,
-    crayon,
     data.table,
     dtplyr,
     extrafont,
     haven,
     lubridate,
     rmarkdown,
-    testthat (>= 2.0.0),
+    testthat (>= 3.0.0),
     withr
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Collate:
     'deprecated.R'
     'dplyr.R'
@@ -165,3 +163,4 @@ Collate:
     'summary.R'
     'utils.R'
     'vctrs.R'
+Config/testthat/edition: 3

R/reshape.R

@@ -81,10 +81,9 @@ reconcile_skimmers <- function(data, groups, base) {
   extra_cols <- dplyr::setdiff(all_columns, with_base_columns)
   if (length(extra_cols) > 0) {
     grouped <- dplyr::group_by(data, .data$skim_type)
-    complete_by_type <- dplyr::summarize_at(
+    complete_by_type <- dplyr::summarise(
       grouped,
-      extra_cols,
-      ~ !all(is.na(.x))
+      dplyr::across(tidyselect::all_of(extra_cols),  ~ !all(is.na(.x)))
     )
     complete_cols <- purrr::pmap(
       complete_by_type,
@@ -242,12 +241,12 @@ to_long.default <- function(.data, ..., skim_fun = skim) {
 #' @describeIn  to_long Transform a skim_df to a long data frame.
 #' @export
 to_long.skim_df <- function(.data, ..., skim_fun = skim) {
-  tidyr::gather(
+  .data <- dplyr::mutate(.data, dplyr::across(dplyr::everything(), as.character))
+  tidyr::pivot_longer(
     .data,
-    key = "stat",
-    value = "formatted",
-    na.rm = TRUE,
-    -"skim_type",
-    -"skim_variable"
+    cols = c(-"skim_type", -"skim_variable"),
+    names_to = "stat",
+    values_to = "formatted",
+    values_drop_na = TRUE
   )
 }

R/skim.R

@@ -73,7 +73,7 @@
 #' iris %>%
 #'   skim() %>%
 #'   dplyr::select(numeric.mean) %>%
-#'   dplyr::top_n(5)
+#'   dplyr::slice_head(n = 5)
 #'
 #' # Which of my columns have missing values? Use the base skimmer n_missing.
 #' iris %>%

R/skim_print.R

@@ -26,7 +26,7 @@
 #'
 #' @inheritParams tibble::print.tbl
 #' @seealso [tibble::trunc_mat()] For a list of global options for customizing
-#'   print formatting. [crayon::has_color()] for the variety of issues that
+#'   print formatting. [cli::num_ansi_colors()] for the variety of issues that
 #'   affect tibble's color support.
 #' @param include_summary Whether a summary of the data frame should be printed
 #' @param summary_rule_width Width of Data Summary cli rule, defaults to 40.

R/skimr-package.R

@@ -10,16 +10,12 @@
 #' provides an API for customization. Users can change both the functions
 #' dispatched and the way the results are formatted.
 #'
-#' @importFrom rlang .data
-#' @name skimr-package
-#' @aliases skimr
-#' @docType package
-NULL
+"_PACKAGE"
 
 
 # Imports -----------------------------------------------------------------
 
-#' @importFrom rlang %||%
+#' @importFrom rlang %||% .data
 
 #' @importFrom magrittr %>%
 #' @export

README.Rmd

@@ -8,21 +8,22 @@ align="right" height="139" /></a>
 
 ```{r set-options, echo=FALSE, message=FALSE}
 library(skimr)
-options(tibble.width = Inf)
+options(pillar.width = Inf)
 options(width = 100)
 ```
 
+<!-- badges: start -->
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/)
-[![R build
-status](https://github.com/ropensci/skimr/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/skimr/actions?workflow=R-CMD-check)
-[![codecov](https://codecov.io/gh/ropensci/skimr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/skimr)
+[![R-CMD-check](https://github.com/ropensci/skimr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/skimr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/ropensci/skimr/graph/badge.svg)](https://app.codecov.io/gh/ropensci/skimr)
 [![This is an ROpenSci Peer reviewed
 package](https://badges.ropensci.org/175_status.svg)](https://github.com/ropensci/software-review/issues/175)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/skimr)](https://cran.r-project.org/package=skimr)
 [![cran
 checks](https://badges.cranchecks.info/worst/skimr.svg)](https://badges.cranchecks.info/worst/skimr.svg)
+<!-- badges: end -->
 
 
 `skimr` provides a frictionless approach to summary statistics which conforms