Upkeep 2024-09 (#479)

* Update snapshots
* `use_tidy_github_actions()`
* Bump required R version
* Re-document & fix S3 method exports
* Eliminate dplyr warning

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

@@ -10,7 +10,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -25,24 +27,22 @@ jobs:
           - {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'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          # 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: 'oldrel-4'}
 
     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
 
@@ -60,3 +60,4 @@ 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

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +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(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

@@ -15,8 +15,8 @@ Description: Provides a data.table backend for 'dplyr'. The goal of
 License: MIT + file LICENSE
 URL: https://dtplyr.tidyverse.org, https://github.com/tidyverse/dtplyr
 BugReports: https://github.com/tidyverse/dtplyr/issues
-Depends: 
-    R (>= 3.6)
+Depends:
+    R (>= 4.0)
 Imports:
     cli (>= 3.4.0),
     data.table (>= 1.13.0),
@@ -35,10 +35,10 @@ Suggests:
     testthat (>= 3.1.2),
     tidyr (>= 1.1.0),
     waldo (>= 0.3.1)
-VignetteBuilder: 
+VignetteBuilder:
     knitr
 Config/Needs/website: tidyverse/tidytemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: {library(tidyr); list(markdown = TRUE)}
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -17,9 +17,11 @@ S3method(distinct,dtplyr_step)
 S3method(do,dtplyr_step)
 S3method(dt_call,dtplyr_step)
 S3method(dt_call,dtplyr_step_assign)
+S3method(dt_call,dtplyr_step_call)
 S3method(dt_call,dtplyr_step_first)
 S3method(dt_call,dtplyr_step_join)
 S3method(dt_call,dtplyr_step_modify)
+S3method(dt_call,dtplyr_step_mutate)
 S3method(dt_call,dtplyr_step_set)
 S3method(dt_call,dtplyr_step_subset)
 S3method(dt_has_computation,dtplyr_step)

R/step-call.R

@@ -16,6 +16,7 @@ step_call <- function(parent, fun, args = list(), vars = parent$vars, in_place =
   )
 }
 
+#' @export
 dt_call.dtplyr_step_call <- function(x, needs_copy = x$needs_copy) {
   call2(x$fun, dt_call(x$parent, needs_copy), !!!x$args)
 }

R/step-join.R

@@ -82,7 +82,7 @@ dt_call.dtplyr_step_join <- function(x, needs_copy = x$needs_copy) {
     anti = call2("[", lhs, call2("!", rhs), on = on),
     semi = call2("[", lhs, call2("unique", call2("[", lhs, rhs, which = TRUE, nomatch = NULL, on = on)))
   )
-  
+
   if (x$style == "full") {
     default_suffix <- c(".x", ".y")
     if (!identical(x$suffix, default_suffix)) {
@@ -133,7 +133,6 @@ right_join.dtplyr_step <- function(x, y, ..., by = NULL, copy = FALSE, suffix =
   step_join(x, y, by, style = "right", copy = copy, suffix = suffix)
 }
 
-
 #' @importFrom dplyr inner_join
 #' @export
 inner_join.dtplyr_step <- function(x, y, ..., by = NULL, copy = FALSE, suffix = c(".x", ".y")) {

R/step-mutate.R

@@ -26,6 +26,7 @@ step_mutate <- function(parent, new_vars = list(), use_braces = FALSE, by = new_
   out
 }
 
+#' @export
 dt_call.dtplyr_step_mutate <- function(x, needs_copy = x$needs_copy) {
   # i is always empty because we never mutate a subset
   if (is_empty(x$new_vars)) {

README.Rmd

@@ -17,8 +17,8 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/dtplyr)](https://cran.r-project.org/package=dtplyr)
-[![R-CMD-check](https://github.com/tidyverse/dtplyr/workflows/R-CMD-check/badge.svg)](https://github.com/tidyverse/dtplyr/actions)
-[![Codecov test coverage](https://codecov.io/gh/tidyverse/dtplyr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/dtplyr?branch=main)
+[![R-CMD-check](https://github.com/tidyverse/dtplyr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidyverse/dtplyr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/tidyverse/dtplyr/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/dtplyr)
 <!-- badges: end -->
 
 ## Overview
@@ -52,7 +52,7 @@ library(dtplyr)
 library(dplyr, warn.conflicts = FALSE)
 ```
 
-Then use `lazy_dt()` to create a "lazy" data table that tracks the operations performed on it. 
+Then use `lazy_dt()` to create a "lazy" data table that tracks the operations performed on it.
 
 ```{r}
 mtcars2 <- lazy_dt(mtcars)
@@ -61,35 +61,35 @@ mtcars2 <- lazy_dt(mtcars)
 You can preview the transformation (including the generated data.table code) by printing the result:
 
 ```{r}
-mtcars2 %>% 
-  filter(wt < 5) %>% 
+mtcars2 %>%
+  filter(wt < 5) %>%
   mutate(l100k = 235.21 / mpg) %>% # liters / 100 km
-  group_by(cyl) %>% 
+  group_by(cyl) %>%
   summarise(l100k = mean(l100k))
 ```
 
 But generally you should reserve this only for debugging, and use `as.data.table()`, `as.data.frame()`, or `as_tibble()` to indicate that you're done with the transformation and want to access the results:
 
 ```{r}
-mtcars2 %>% 
-  filter(wt < 5) %>% 
+mtcars2 %>%
+  filter(wt < 5) %>%
   mutate(l100k = 235.21 / mpg) %>% # liters / 100 km
-  group_by(cyl) %>% 
-  summarise(l100k = mean(l100k)) %>% 
+  group_by(cyl) %>%
+  summarise(l100k = mean(l100k)) %>%
   as_tibble()
 ```
 
 ## Why is dtplyr slower than data.table?
 
 There are two primary reasons that dtplyr will always be somewhat slower than data.table:
 
-* Each dplyr verb must do some work to convert dplyr syntax to data.table 
-  syntax. This takes time proportional to the complexity of the input code, 
+* Each dplyr verb must do some work to convert dplyr syntax to data.table
+  syntax. This takes time proportional to the complexity of the input code,
   not the input _data_, so should be a negligible overhead for large datasets.
-  [Initial benchmarks][benchmark] suggest that the overhead should be under 
+  [Initial benchmarks][benchmark] suggest that the overhead should be under
   1ms per dplyr call.
 
-* To match dplyr semantics, `mutate()` does not modify in place by default. 
+* To match dplyr semantics, `mutate()` does not modify in place by default.
   This means that most expressions involving `mutate()` must make a copy
   that would not be necessary if you were using data.table directly.
   (You can opt out of this behaviour in `lazy_dt()` with `immutable = FALSE`).

README.md

@@ -7,9 +7,9 @@
 
 [![CRAN
 status](https://www.r-pkg.org/badges/version/dtplyr)](https://cran.r-project.org/package=dtplyr)
-[![R-CMD-check](https://github.com/tidyverse/dtplyr/workflows/R-CMD-check/badge.svg)](https://github.com/tidyverse/dtplyr/actions)
+[![R-CMD-check](https://github.com/tidyverse/dtplyr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tidyverse/dtplyr/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/tidyverse/dtplyr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/dtplyr?branch=main)
+coverage](https://codecov.io/gh/tidyverse/dtplyr/graph/badge.svg)](https://app.codecov.io/gh/tidyverse/dtplyr)
 <!-- badges: end -->
 
 ## Overview
@@ -47,6 +47,7 @@ other goodies that it provides:
 
 ``` r
 library(data.table)
+#> Warning: package 'data.table' was built under R version 4.4.1
 library(dtplyr)
 library(dplyr, warn.conflicts = FALSE)
 ```
@@ -62,10 +63,10 @@ You can preview the transformation (including the generated data.table
 code) by printing the result:
 
 ``` r
-mtcars2 %>% 
-  filter(wt < 5) %>% 
+mtcars2 %>%
+  filter(wt < 5) %>%
   mutate(l100k = 235.21 / mpg) %>% # liters / 100 km
-  group_by(cyl) %>% 
+  group_by(cyl) %>%
   summarise(l100k = mean(l100k))
 #> Source: local data table [3 x 2]
 #> Call:   `_DT1`[wt < 5][, `:=`(l100k = 235.21/mpg)][, .(l100k = mean(l100k)), 
@@ -85,11 +86,11 @@ But generally you should reserve this only for debugging, and use
 you’re done with the transformation and want to access the results:
 
 ``` r
-mtcars2 %>% 
-  filter(wt < 5) %>% 
+mtcars2 %>%
+  filter(wt < 5) %>%
   mutate(l100k = 235.21 / mpg) %>% # liters / 100 km
-  group_by(cyl) %>% 
-  summarise(l100k = mean(l100k)) %>% 
+  group_by(cyl) %>%
+  summarise(l100k = mean(l100k)) %>%
   as_tibble()
 #> # A tibble: 3 × 2
 #>     cyl l100k

tests/testthat/_snaps/step-call.md

@@ -23,6 +23,6 @@
       collect(drop_na(dt, "z"))
     Condition
       Error in `drop_na()`:
-      ! Can't subset columns that don't exist.
+      ! Can't select columns that don't exist.
       x Column `z` doesn't exist.
 

tests/testthat/test-step-join.R

@@ -346,10 +346,10 @@ test_that("performs cartesian joins as needed", {
 test_that("performs cross join", {
   df1 <- data.frame(x = 1:2, y = "a", stringsAsFactors = FALSE)
   df2 <- data.frame(x = 3:4)
+  expected <- dplyr::cross_join(df1, df2) %>% as_tibble()
 
   dt1 <- lazy_dt(df1, "dt1")
   dt2 <- lazy_dt(df2, "dt2")
-  expected <- left_join(df1, df2, by = character()) %>% as_tibble()
 
   expect_snapshot(left_join(dt1, dt2, by = character()))
   expect_equal(left_join(dt1, dt2, by = character()) %>% collect(), expected)