Merge pull request #193 from olivroy/ellipsis

Drop ellipsis dependency + avoid tidyselect deprecated syntax

Author: thackl

.github/workflows/pkgdown.yaml

@@ -1,74 +1,49 @@
+# 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: master
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 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: r-lib/actions/setup-r@v2
-        with:
-          r-version: 4.3.1
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
-      
-      - name: Install dependencies
-        run: |
-          sudo apt-get install --yes libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
-      
-      - name: Install XQuartz
-        if: runner.os == 'macOS'
-        run: brew cask install xquartz
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ubuntu-r-4.0-4-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ubuntu-r-4.0-4-
+          use-public-rspm: true
 
-      - name: Install dependencies
-        run: |
-          install.packages("BiocManager")
-          BiocManager::install("IRanges")
-          BiocManager::install("ggtree")
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          install.packages('pkgdown')
-          install.packages('devtools')
-          remotes::install_dev("dplyr")
-          install.packages("Hmisc")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
-      - name: Session Info
-        run: |
-          library(gggenomes)
-          print(sessionInfo())
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-#      - name: Setup upterm session
-#        uses: lhotari/action-upterm@v1
-
-      - name: Configure git user
-        run: |
-          git config --global user.name "github-actions[bot]"
-          git config --global user.email "github-actions[bot]@users.noreply.github.com"
-
-      - name: Deploy package
-        run: pkgdown::deploy_to_branch(new_process = FALSE, lazy=FALSE)
-        shell: Rscript {0}
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -12,20 +12,20 @@ Description: An extension of 'ggplot2' for creating complex genomic
  implements a layout concept inspired by 'ggraph' and introduces tracks to bring
  tidiness to the mess that is genomics data.
 License: MIT + file LICENSE
-URL: https://github.com/thackl/gggenomes
+URL: https://thackl.github.io/gggenomes/, https://github.com/thackl/gggenomes
 BugReports: https://github.com/thackl/gggenomes/issues
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Depends:
-    R (>= 3.4.2),
+    R (>= 3.5.0),
     ggplot2 (>= 3.5.0),
 Imports:
     vctrs,
     rlang,
-    dplyr,
+    dplyr (>= 1.1.0),
     tidyr,
     readr (>= 2.0.0),
     purrr,
@@ -39,8 +39,7 @@ Imports:
     tidyselect,
     colorspace,
     methods,
-    utils,
-    ellipsis
+    utils
 Suggests:
     testthat,
     ggtree,

NAMESPACE

@@ -205,7 +205,6 @@ export(width)
 export(width0)
 export(write_gff3)
 import(dplyr)
-import(ellipsis)
 import(ggplot2)
 import(grid)
 import(rlang)

R/aaa.R

@@ -45,11 +45,6 @@ ex <- function(file = NULL) {
   }
 }
 
-# are there any arguments in ...
-has_dots <- function(env = parent.frame()) {
-  length(ellipsis__dots(env)) > 0
-}
-
 shared_names <- function(x, ...) {
   names <- c(...)
   names[names %in% names2(x)]
@@ -127,18 +122,10 @@ qc <- function(...) sapply(match.call()[-1], deparse)
 # CRAN Workaround for unexported useful tidyverse internals
 # https://stackoverflow.com/questions/32535773/using-un-exported-function-from-another-r-package
 ggplot2__ggname <- utils::getFromNamespace("ggname", "ggplot2")
-ggplot2__rd_aesthetics <- \(x, y) utils::getFromNamespace("rd_aesthetics", "ggplot2")(x, y) |> stringr::str_replace(stringr::fixed("link[="), "link[ggplot2:")
+ggplot2__rd_aesthetics <- function(x, y) utils::getFromNamespace("rd_aesthetics", "ggplot2")(x, y) |> stringr::str_replace(stringr::fixed("link[="), "link[ggplot2:")
 ggplot2__scales_list <- utils::getFromNamespace("scales_list", "ggplot2")
 ggplot2__guides_list <- utils::getFromNamespace("guides_list", "ggplot2")
 ggplot2__make_labels <- utils::getFromNamespace("make_labels", "ggplot2")
-ellipsis__dots <- utils::getFromNamespace("dots", "ellipsis")
 scales__force_all <- utils::getFromNamespace("force_all", "scales")
 purrr__as_mapper.default <- utils::getFromNamespace("as_mapper.default", "purrr")
 
-# Additional fix for seamingly unused package in imports due to the workaround above
-# https://forum.posit.co/t/new-r-cmd-check-note-in-r-4-2-0-for-imports-field/143153/4
-#' @import ellipsis
-#' @noRd
-dummy <- function() {
-  ellipsis::safe_median
-}

R/clusters.R

@@ -32,7 +32,7 @@ add_clusters.gggenomes <- function(x, ..., .track_id = "genes") {
 #' @importFrom rlang .data
 #' @export
 add_clusters.gggenomes_layout <- function(x, ..., .track_id = "genes") {
-  if (!has_dots()) {
+  if (...length() == 0) {
     warn("No clusters data provided - check your arguments")
     return(x)
   }

R/feats.R

@@ -45,7 +45,7 @@ as_feats.tbl_df <- function(x, seqs, ..., everything = TRUE) {
   }
 
   other_vars <- if (everything) tidyselect::everything else function() NULL
-  x <- as_tibble(select(x, vars, other_vars()))
+  x <- as_tibble(select(x, dplyr::all_of(vars), other_vars()))
   # TODO: mutate_at - if at all
   x %<>% mutate_if(is.factor, as.character)
 
@@ -90,7 +90,7 @@ layout_feats <- function(
 
   # project feats onto new layout and clean up aux vars (.seq)
   x <- project_feats(x) %>%
-    select(.data$y, .data$x, .data$xend, .data$bin_id, everything(), -starts_with(".seq"))
+    select("y", "x", "xend", "bin_id", everything(), -starts_with(".seq"))
   x
 }
 
@@ -128,7 +128,7 @@ add_feats.gggenomes <- function(x, ...) {
 
 #' @export
 add_feats.gggenomes_layout <- function(x, ...) {
-  if (!has_dots()) {
+  if (...length() == 0) {
     return(x)
   }
   dot_exprs <- enexprs(...) # defuse before list(...)
@@ -145,8 +145,8 @@ add_feat_layout_scaffold <- function(x, seqs) {
   scaffold <- seqs %>%
     ungroup() %>%
     select(
-      .data$seq_id, .data$bin_id, .data$y,
-      .seq_strand = .data$strand, .seq_x = .data$x, .seq_start = .data$start, .seq_end = .data$end
+      "seq_id", "bin_id", "y",
+      .seq_strand = "strand", .seq_x = "x", .seq_start = "start", .seq_end = "end"
     )
 
   inner_join(x, scaffold, by = shared_names(x, "seq_id", "bin_id"))

R/flip.R

@@ -64,7 +64,7 @@ flip.gggenomes <- function(x, ..., .bin_track = seqs) {
 }
 #' @export
 flip.gggenomes_layout <- function(x, ..., .bin_track = seqs) {
-  if (!has_dots()) {
+  if (...length() == 0) {
     return(x)
   }
   flip_impl(x, bins = c(...), bin_track = {{ .bin_track }})
@@ -84,7 +84,7 @@ flip_seqs.gggenomes <- function(x, ..., .bins = everything(), .seq_track = seqs,
 }
 #' @export
 flip_seqs.gggenomes_layout <- function(x, ..., .bins = everything(), .seq_track = seqs, .bin_track = seqs) {
-  if (!has_dots()) {
+  if (...length()  == 0) {
     return(x)
   }
   flip_impl(x, bins = {{ .bins }}, seqs = c(...), bin_track = {{ .bin_track }}, seq_track = {{ .seq_track }})
@@ -111,8 +111,8 @@ sync.gggenomes_layout <- function(x, link_track = 1, min_support = 0) {
   s0 <- ungroup(pull_seqs(x))
 
   f0 <- l0 |>
-    dplyr::left_join(select(s0, .data$seq_id, seq_strand = .data$strand), by = "seq_id") |>
-    dplyr::left_join(select(s0, seq_id2 = .data$seq_id, seq_strand2 = .data$strand), by = "seq_id2") |>
+    dplyr::left_join(select(s0, "seq_id", seq_strand = "strand"), by = "seq_id") |>
+    dplyr::left_join(select(s0, seq_id2 = "seq_id", seq_strand2 = "strand"), by = "seq_id2") |>
     dplyr::mutate(
       bin_id = ifelse(.data$y < .data$yend, .data$bin_id, .data$bin_id2), # chose the lower bin id
       bin_id2 = ifelse(.data$y < .data$yend, .data$bin_id2, .data$bin_id), # chose the lower bin id
@@ -129,7 +129,7 @@ sync.gggenomes_layout <- function(x, link_track = 1, min_support = 0) {
 
   bins_to_flip <- f0 |>
     dplyr::filter(.data$needs_flip) |>
-    dplyr::pull(.data$bin_id)
+    dplyr::pull("bin_id")
 
   if (!length(bins_to_flip)) {
     inform(str_glue(

R/focus.R

@@ -215,8 +215,8 @@ locate_impl <- function(
   # => mirror links to seq1 to ensure seq2 links are accounted for
   if (track_type(x, {{ .track_id }}) == "links") {
     targets2 <- dplyr::rename(targets,
-      seq_id = .data$seq_id2, seq_id2 = .data$seq_id,
-      start = .data$start2, start2 = .data$start, end = .data$end2, end2 = .data$end
+      seq_id = "seq_id2", seq_id2 = "seq_id",
+      start = "start2", start2 = "start", end = "end2", end2 = "end"
     )
     targets <- bind_rows(targets, targets2)
   }
@@ -250,9 +250,9 @@ focus_feats <- function(track, seqs, bin_id) {
 add_feat_focus_scaffold <- function(track, seqs) {
   scaffold <- seqs %>%
     ungroup() %>%
-    dplyr::select(
-      .data$seq_id, .data$bin_id, .data$locus_id, .data$y,
-      .seq_strand = .data$strand, .seq_x = .data$x, .seq_start = .data$start, .seq_end = .data$end
+    select(
+      "seq_id", "bin_id", "locus_id", "y",
+      .seq_strand = "strand", .seq_x = "x", .seq_start = "start", .seq_end = "end"
     )
 
   inner_join(track, scaffold, by = shared_names(track, "seq_id", "bin_id", "locus_id"))
@@ -278,14 +278,14 @@ add_link_focus_scaffold <- function(track, seqs) {
   scaffold <- seqs %>%
     ungroup() %>%
     select(
-      seq_id = .data$seq_id, bin_id = .data$bin_id, locus_id = .data$locus_id, y = .data$y, .seq_strand = .data$strand, .seq_x = .data$x,
-      .seq_start = .data$start, .seq_end = .data$end
+      seq_id = "seq_id", bin_id = "bin_id", locus_id = "locus_id", y = "y", .seq_strand = "strand", .seq_x = "x",
+      .seq_start = "start", .seq_end = "end"
     )
   scaffold2 <- seqs %>%
     ungroup() %>%
     select(
-      seq_id2 = .data$seq_id, bin_id2 = .data$bin_id, locus_id2 = .data$locus_id, yend = .data$y, .seq_strand2 = .data$strand, .seq_x2 = .data$x,
-      .seq_start2 = .data$start, .seq_end2 = .data$end
+      seq_id2 = "seq_id", bin_id2 = "bin_id", locus_id2 = "locus_id", yend = "y", .seq_strand2 = "strand", .seq_x2 = "x",
+      .seq_start2 = "start", .seq_end2 = "end"
     )
 
   track <- inner_join(track, scaffold, by = shared_names(track, "seq_id", "bin_id", "locus_id"))

R/geom_gene.R

@@ -238,7 +238,7 @@ makeContent.genetree <- function(x) {
   coord_flipped <- FALSE
   if (names(data)[1] == "x") {
     coord_flipped <- TRUE
-    data <- rename(data, y = .data$x, x = .data$y, xend = .data$yend)
+    data <- rename(data, y = "x", x = "y", xend = "yend")
   }
 
   s <- x$sizes

R/gggenomes.R

@@ -263,7 +263,7 @@ infer_seqs_from_feats <- function(
       .start = {{ infer_start }},
       .end = {{ infer_end }}
     ) %>%
-    dplyr::rename(start = .data$.start, end = .data$.end) # this is necessary, so {{ infer_end }} does
+    dplyr::rename(start = ".start", end = ".end") # this is necessary, so {{ infer_end }} does
   # not already use the "start" from {{ infer_start }}
 
   dplyr::ungroup(seqs)
@@ -289,7 +289,7 @@ infer_seqs_from_links <- function(
       .start = {{ infer_start }},
       .end = {{ infer_end }}
     ) %>%
-    dplyr::rename(start = .data$.start, end = .data$.end)
+    dplyr::rename(start = ".start", end = ".end")
 
   dplyr::ungroup(seqs)
 }