Merge branch 'main' into opt1_theme_classic_update

Author: teunbrand

.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:
@@ -25,15 +27,15 @@ 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: '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 }}
@@ -46,7 +48,7 @@ jobs:
       VDIFFR_LOG_PATH: "../vdiffr.Rout.fail"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -62,9 +64,10 @@ jobs:
           extra-packages: >
             any::rcmdcheck,
             Hmisc=?ignore-before-r=4.1.0,
-            quantreg=?ignore-before-r=4.3.0,
+            quantreg=?ignore-before-r=4.3.0
           needs: check
 
       - 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:
@@ -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

CONTRIBUTING.md

@@ -61,20 +61,19 @@ Each of these steps are described in more detail below. This might feel
 overwhelming the first time you get set up, but it gets easier with practice. 
 If you get stuck at any point, please reach out for help on the [ggplot2-dev](https://groups.google.com/forum/#!forum/ggplot2-dev) mailing list.
 
-If you're not familiar with git or github, please start by reading <http://r-pkgs.had.co.nz/git.html>
+If you're not familiar with git or github, please start by reading <https://r-pkgs.org/software-development-practices.html>
 
 <!--
 * [ ] Motivate the change in one paragraph, and include it in NEWS.
       In parentheses, reference your github user name and this issue:
       `(@hadley, #1234)`
 * [ ] Check pull request only includes relevant changes.
-* [ ] Use the [official style](http://adv-r.had.co.nz/Style.html).
+* [ ] Use the [official style](https://style.tidyverse.org).
 * [ ] Update documentation and re-run roxygen2
 * [ ] Add test, if bug in non-graphical function
 * [ ] Add visual test, if bug in graphical function
 * [ ] Add minimal example, if new graphical feature
 
-See http://docs.ggplot2.org/dev/vignettes/development.html for more details.
 --->
 
 Pull requests will be evaluated against a seven point checklist:
@@ -100,20 +99,16 @@ Pull requests will be evaluated against a seven point checklist:
     and don't submit any others until the first one has been processed.
 
 1.  __Use ggplot2 coding style__. Please follow the
-    [official tidyverse style](http://style.tidyverse.org). Maintaining
+    [official tidyverse style](https://style.tidyverse.org). Maintaining
     a consistent style across the whole code base makes it much easier to
     jump into the code. If you're modifying existing ggplot2 code that
     doesn't follow the style guide, a separate pull request to fix the
     style would be greatly appreciated.
 
 1.  If you're adding new parameters or a new function, you'll also need
-    to document them with [roxygen](https://github.com/klutometis/roxygen).
+    to document them with [roxygen2](https://github.com/r-lib/roxygen2).
     Make sure to re-run `devtools::document()` on the code before submitting.
 
-    Currently, ggplot2 uses the development version of roxygen2, which you
-    can get with `install_github("klutometis/roxygen")`. This will be
-    available on CRAN in the near future.
-
 1.  If fixing a bug or adding a new feature to a non-graphical function,
     please add a [testthat](https://github.com/r-lib/testthat) unit test.
 

DESCRIPTION

@@ -33,7 +33,6 @@ Depends:
     R (>= 3.5)
 Imports: 
     cli,
-    glue,
     grDevices,
     grid,
     gtable (>= 0.1.1),
@@ -79,7 +78,7 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate: 
     'ggproto.R'
     'ggplot-global.R'

NAMESPACE

@@ -427,6 +427,7 @@ export(get_last_plot)
 export(get_layer_data)
 export(get_layer_grob)
 export(get_panel_scales)
+export(get_strip_labels)
 export(get_theme)
 export(gg_dep)
 export(gg_par)
@@ -512,6 +513,8 @@ export(remove_missing)
 export(render_axes)
 export(render_strips)
 export(replace_theme)
+export(reset_geom_defaults)
+export(reset_stat_defaults)
 export(reset_theme_settings)
 export(resolution)
 export(scale_alpha)
@@ -727,8 +730,6 @@ import(gtable)
 import(rlang)
 import(scales)
 import(vctrs)
-importFrom(glue,glue)
-importFrom(glue,glue_collapse)
 importFrom(grid,arrow)
 importFrom(grid,unit)
 importFrom(lifecycle,deprecated)

NEWS.md

@@ -1,7 +1,44 @@
 # ggplot2 (development version)
 
-* `theme_classic()` now has black ticks and text instead of dark gray. In 
-  addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978).
+* New `reset_geom_defaults()` and `reset_stat_defaults()` to restore all geom or
+  stat default aesthetics at once (@teunbrand, #5975).
+* `facet_wrap()` can have `space = "free_x"` with 1-row layouts and 
+  `space = "free_y"` with 1-column layouts (@teunbrand)
+* Secondary axes respect `n.breaks` setting in continuous scales (@teunbrand, #4483).
+* Layers can have names (@teunbrand, #4066).
+* (internal) improvements to `pal_qualitative()` (@teunbrand, #5013)
+* `coord_radial(clip = "on")` clips to the panel area when the graphics device
+  supports clipping paths (@teunbrand, #5952).
+* (internal) Panel clipping responsibility moved from Facet class to Coord 
+  class through new `Coord$draw_panel()` method.
+* `theme(strip.clip)` now defaults to `"on"` and is independent of Coord 
+  clipping (@teunbrand, 5952).
+* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand).
+* Axis labels are now justified across facet panels (@teunbrand, #5820)
+* Fixed bug in `stat_function()` so x-axis title now produced automatically 
+  when no data added. (@phispu, #5647).
+* geom_sf now accepts shape names (@sierrajohnson, #5808)
+* Added `gg` class to `labs()` (@phispu, #5553).
+* Missing values from discrete palettes are no longer translated 
+  (@teunbrand, #5929).
+* Fixed bug in `facet_grid(margins = TRUE)` when using expresssions 
+  (@teunbrand, #1864).
+* `geom_step()` now supports the `orientation` argument (@teunbrand, #5936).
+* `position_dodge()` and `position_jitterdodge()` now have a `reverse` argument 
+  (@teunbrand, #3610)
+* `coord_radial(r.axis.inside)` can now take a numeric value to control 
+  placement of internally placed radius axes (@teunbrand, #5805).
+* (internal) default labels are derived in `ggplot_build()` rather than
+  in `ggplot_add.Layer()` (@teunbrand, #5894)
+* An attempt is made to use a variable's label attribute as default label 
+  (@teunbrand, #4631)
+* Themes gain an additional `header_family` argument to easily set the font
+  for headers and titles (#5886).
+* The `plot.subtitle`, `plot.caption` and `plot.tag` theme elements now inherit 
+  from the root `text` element instead of the `title` element (#5886).
+* ggplot2 no longer imports {glue} (@teunbrand, #5986).
+* `geom_rect()` can now derive the required corners positions from `x`/`width`
+  or `y`/`height` parameterisation (@teunbrand, #5861).
 * All position scales now use the same definition of `x` and `y` aesthetics.
   This lets uncommon aesthetics like `xintercept` expand scales as usual.
   (#3342, #4966, @teunbrand)
@@ -106,8 +143,21 @@
   the `nbin` argument (@teunbrand, #5882, #5036)
 * `after_stat()` and `after_scale()` throw warnings when the computed aesthetics
   are not of the correct length (#5901).
+* `guide_colourbar()` now correctly hands off `position` and `available_aes`
+  parameters downstream (@teunbrand, #5930)
 * `geom_hline()` and `geom_vline()` now have `position` argument
   (@yutannihilation, #4285).
+* New function `get_strip_labels()` to retrieve facet labels (@teunbrand, #4979)
+* Fixed bug in `position_dodge2()`'s identification of range overlaps 
+  (@teunbrand, #5938, #4327).
+* Fixed bug where empty discrete scales weren't recognised as such 
+  (@teunbrand, #5945).
+* (internal) The summary function of `stat_summary()` and `stat_summary_bin()` 
+  is setup once in total instead of once per group (@teunbrand, #5971)
+* `facet_grid(space = "free")` can now be combined with `coord_fixed()` 
+  (@teunbrand, #4584).
+* `theme_classic()` now has black ticks and text instead of dark gray. In 
+  addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978).
 
 # ggplot2 3.5.1
 

R/aes-evaluation.R

@@ -231,9 +231,9 @@ is_calculated <- function(x, warn = FALSE) {
   } else if (is.symbol(x)) {
     res <- is_dotted_var(as.character(x))
     if (res && warn) {
-      what <- I(glue("The dot-dot notation (`{x}`)"))
+      what <- I(paste0("The dot-dot notation (`", x, "`)"))
       var <- gsub(match_calculated_aes, "\\1", as.character(x))
-      with <- I(glue("`after_stat({var})`"))
+      with <- I(paste0("`after_stat(", var, ")`"))
       deprecate_warn0("3.4.0", what, with, id = "ggplot-warn-aes-dot-dot")
     }
     res
@@ -242,9 +242,9 @@ is_calculated <- function(x, warn = FALSE) {
   } else if (is.call(x)) {
     if (identical(x[[1]], quote(stat))) {
       if (warn) {
-        what <- I(glue("`{expr_deparse(x)}`"))
+        what <- I(paste0("`", expr_deparse(x), "`"))
         x[[1]] <- quote(after_stat)
-        with <- I(glue("`{expr_deparse(x)}`"))
+        with <- I(paste0("`", expr_deparse(x), "`"))
         deprecate_warn0("3.4.0", what, with, id = "ggplot-warn-aes-stat")
       }
       TRUE

R/annotation-logticks.R

@@ -165,7 +165,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
 
       names(xticks)[names(xticks) == "value"] <- x_name   # Rename to 'x' for coordinates$transform
       xticks <- coord$transform(xticks, panel_params)
-      xticks = xticks[xticks$x <= 1 & xticks$x >= 0,]
+      xticks <- xticks[xticks$x <= 1 & xticks$x >= 0,]
 
       if (outside)
         xticks$end = -xticks$end
@@ -203,7 +203,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
 
       names(yticks)[names(yticks) == "value"] <- y_name   # Rename to 'y' for coordinates$transform
       yticks <- coord$transform(yticks, panel_params)
-      yticks = yticks[yticks$y <= 1 & yticks$y >= 0,]
+      yticks <- yticks[yticks$y <= 1 & yticks$y >= 0,]
 
       if (outside)
         yticks$end = -yticks$end
@@ -238,7 +238,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
 # - start: on the other axis, start position of the line (usually 0)
 # - end: on the other axis, end position of the line (for example, .1, .2, or .3)
 calc_logticks <- function(base = 10, ticks_per_base = base - 1,
-    minpow = 0, maxpow = minpow + 1, start = 0, shortend = .1, midend = .2, longend = .3) {
+    minpow = 0, maxpow = minpow + 1, start = 0, shortend = 0.1, midend = 0.2, longend = 0.3) {
 
   # Number of blocks of tick marks
   reps <- maxpow - minpow