Merge pull request #14 from dzhang32/fix-unit_tests

1.0.0: update ggtranscript to interoperate with the latest versions of R, ggplot2 and ggrepel
dzhang32 · Aug 24, 2024 · 682a0df · 682a0df
2 parents b99da0d + d7a9f4b
commit 682a0df
Show file tree

Hide file tree

Showing 35 changed files with 1,304 additions and 1,239 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -1,25 +1,3 @@
-## Read more about GitHub actions the features of this GitHub Actions workflow
-## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
-##
-## For more details, check the biocthis developer notes vignette at
-## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
-##
-## You can add this workflow to other packages using:
-## > biocthis::use_bioc_github_action()
-##
-## Using GitHub Actions exposes you to many details about how R packages are
-## compiled and installed in several operating system.s
-### If you need help, please follow the steps listed at
-## https://github.com/r-lib/actions#where-to-find-help
-##
-## If you found an issue specific to biocthis's GHA workflow, please report it
-## with the information that will make it easier for others to help you.
-## Thank you!
-
-## Acronyms:
-## * GHA: GitHub Action
-## * OS: operating system
-
 on:
   push:
   pull_request:
@@ -28,35 +6,25 @@ name: R-CMD-check-bioc
 
 ## These environment variables control whether to run GHA code later on that is
 ## specific to testthat, covr, and pkgdown.
-##
-## If you need to clear the cache of packages, update the number inside
-## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
-## Note that you can always run a GHA test without the cache by using the word
-## "/nocache" in the commit message.
 env:
   has_testthat: 'true'
   run_covr: 'true'
   run_pkgdown: 'true'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
-  run_docker: 'false'
 
 jobs:
   build-check:
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
-    ## Environment variables unique to this job.
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.1', bioc: '3.14'}
-          - { os: windows-latest, r: '4.1', bioc: '3.14'}
-          ## Check https://github.com/r-lib/actions/tree/master/examples
-          ## for examples using the http-user-agent
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -67,32 +35,25 @@ jobs:
 
     steps:
 
-      ## Set the R library to the directory matching the
-      ## R packages cache step further below when running on Docker (Linux).
       - name: Set R Library home on Linux
         if: runner.os == 'Linux'
         run: |
           mkdir /__w/_temp/Library
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
 
-      ## Most of these steps are the same as the ones in
-      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
-      ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
-      ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -102,15 +63,15 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
@@ -123,32 +84,6 @@ jobs:
           echo $sysreqs
           sudo -s eval "$sysreqs"
 
-      - name: Install macOS system dependencies
-        if: matrix.config.os == 'macOS-latest'
-        run: |
-          ## Enable installing XML from source if needed
-          brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
-          ## Required for tcltk
-          brew install xquartz --cask
-
-      - name: Install Windows system dependencies
-        if: runner.os == 'Windows'
-        run: |
-          ## Edit below if you have any Windows system dependencies
-        shell: Rscript {0}
-
       - name: Install BiocManager
         run: |
           message(paste('****', Sys.time(), 'installing BiocManager ****'))
@@ -306,13 +241,3 @@ jobs:
         with:
           name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results
           path: check
-
-      - uses: docker/build-push-action@v1
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: dzhang32/ggtranscript
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ggtranscript
 Title: Visualizing Transcript Structure and Annotation using 'ggplot2'
-Version: 0.99.9
+Version: 1.0.0
 Authors@R:
     c(
     person("David", "Zhang", , "dyzhang32@gmail.com", 
@@ -27,7 +27,7 @@ URL: https://github.com/dzhang32/ggtranscript
 BugReports: https://github.com/dzhang32/ggtranscript/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Suggests: 
     BiocStyle,
     covr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+
+# ggtranscript 1.0.0
+
+## Fixes
+
+* Updates `geom`s to work with the latest version of `ggplot2` and `ggrepel` (R version `4.4`). 
+* Fixes all unit tests.
+* Fixes CI workflow issues and simplifies testing to linux-only.
+
 # ggtranscript 0.99.9
 
 ## NEW FEATURES

diff --git a/R/geom_intron.R b/R/geom_intron.R
@@ -63,7 +63,7 @@
 #' # the functionality from the parameters and aesthetics in ggplot2
 #' base + geom_intron(
 #'     aes(colour = transcript_name),
-#'     size = 1
+#'     linewidth = 1
 #' )
 #'
 #' # together, geom_range() and geom_intron() are designed to visualize
@@ -132,7 +132,7 @@ GeomIntron <- ggplot2::ggproto("GeomIntron", ggplot2::GeomSegment,
     required_aes = c("xstart", "xend", "y"),
     default_aes = aes(
         colour = "black",
-        size = 0.5,
+        linewidth = 0.5,
         linetype = 1,
         alpha = NA,
         strand = "+"

diff --git a/R/geom_junction.R b/R/geom_junction.R
@@ -101,11 +101,11 @@
 #' # this can be useful when mapping junction thickness to their counts
 #' base + geom_junction(
 #'     data = sod1_junctions,
-#'     aes(size = mean_count),
+#'     aes(linewidth = mean_count),
 #'     junction.y.max = 0.5,
 #'     colour = "purple"
 #' ) +
-#'     scale_size(range = c(0.1, 1))
+#'     scale_linewidth(range = c(0.1, 1))
 #'
 #' # it can be useful to combine geom_junction() with geom_half_range()
 #' sod1_exons %>%
@@ -120,12 +120,12 @@
 #'     ) +
 #'     geom_junction(
 #'         data = sod1_junctions,
-#'         aes(size = mean_count),
+#'         aes(linewidth = mean_count),
 #'         junction.y.max = 0.5,
 #'         junction.orientation = "top",
 #'         colour = "purple"
 #'     ) +
-#'     scale_size(range = c(0.1, 1))
+#'     scale_linewidth(range = c(0.1, 1))
 geom_junction <- function(mapping = NULL,
                           data = NULL,
                           stat = "identity",
@@ -256,7 +256,7 @@ GeomJunction <- ggplot2::ggproto("GeomJunction", ggplot2::GeomLine,
     junction_curve <- data.frame(
         x_points = c(x, curve_points$x, xend),
         y_points = c(y, curve_points$y, y),
-        y_orig = y
+        y_original = y
     ) %>%
         dplyr::rename(
             x = x_points,
@@ -282,17 +282,17 @@ GeomJunction <- ggplot2::ggproto("GeomJunction", ggplot2::GeomLine,
     # then divided by the sf, setting the max y
     if (junction.orientation == "top") {
         junctions <- junctions %>% dplyr::mutate(
-            y = ifelse(y == y_orig, y, y_orig + (y / max(y)) / sf)
+            y = ifelse(y == y_original, y, y_original + (y / max(y)) / sf)
         )
     } else if (junction.orientation == "bottom") {
         junctions <- junctions %>% dplyr::mutate(
-            y = ifelse(y == y_orig, y, y_orig - (y / max(y)) / sf)
+            y = ifelse(y == y_original, y, y_original - (y / max(y)) / sf)
         )
     } else if (junction.orientation == "alternating") {
         junctions <- junctions %>% dplyr::mutate(y = dplyr::case_when(
-            y == y_orig ~ y,
-            junction_index %% 2 == 0 ~ y_orig - (y / max(y) / sf),
-            junction_index %% 2 == 1 ~ y_orig + (y / max(y) / sf)
+            y == y_original ~ y,
+            junction_index %% 2 == 0 ~ y_original - (y / max(y) / sf),
+            junction_index %% 2 == 1 ~ y_original + (y / max(y) / sf)
         ))
     }
 

diff --git a/R/geom_range.R b/R/geom_range.R
@@ -58,7 +58,7 @@
 #' # the functionality from the parameters and aesthetics in ggplot2
 #' base + geom_range(
 #'     aes(fill = transcript_name),
-#'     size = 1
+#'     linewidth = 1
 #' )
 #'
 #' # together, geom_range() and geom_intron() are designed to visualize
@@ -177,7 +177,7 @@ GeomRange <- ggplot2::ggproto("GeomRange", ggplot2::GeomTile,
     default_aes = aes(
         fill = "grey",
         colour = "black",
-        size = 0.25,
+        linewidth = 0.25,
         linetype = 1,
         alpha = NA,
         height = NA
@@ -220,7 +220,7 @@ GeomRange <- ggplot2::ggproto("GeomRange", ggplot2::GeomTile,
             gp = grid::gpar(
                 col = coords$colour,
                 fill = ggplot2::alpha(coords$fill, coords$alpha),
-                lwd = coords$size * ggplot2::.pt,
+                lwd = coords$linewidth * ggplot2::.pt,
                 lty = coords$linetype,
                 linejoin = linejoin,
                 lineend = lineend

diff --git a/R/ggtranscript-package.R b/R/ggtranscript-package.R
@@ -12,7 +12,7 @@
 #'
 #' @docType package
 #' @name ggtranscript
-NULL
+"_PACKAGE"
 
 #' @importFrom rlang %||%
 #' @importFrom magrittr %>%

diff --git a/R/globals.R b/R/globals.R
@@ -41,7 +41,7 @@ utils::globalVariables(c(
     "x_points",
     "y_points",
     "y",
-    "y_orig",
+    "y_original",
     "position_nudge_repel",
     # add_utr(),
     "dummy_group"

diff --git a/README.Rmd b/README.Rmd
@@ -261,4 +261,4 @@ citation("ggtranscript")
 
 ## Credits
 
-* `ggtranscript` was developed using `r BiocStyle::Biocpkg("biocthis")`.
+* `ggtranscript` was developed using `biocthis`.