Merge branch 'master' into 134-animint2pages-default-branch

animint · Aug 30, 2024 · f98f9d9 · f98f9d9
2 parents a3516e6 + 994006d
commit f98f9d9
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diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        test-suite: [ renderer1,renderer2,renderer3,compiler,CRAN]
+        test-suite: [ renderer, compiler, CRAN ]
 
     name: Test Suite ${{ matrix.test-suite }}
     env: 
@@ -21,17 +21,12 @@ jobs:
       GH_ACTION: "ENABLED"
     steps:
       - uses: actions/checkout@v3
-      - name: Start Selenium Docker
-        run: docker run -d --network="host" selenium/standalone-firefox-debug:2.53.0
       - name: install and update texlive
         run: /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt update -y -qq
-      - run: /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt install texlive texlive-fonts-extra -y
+      - run: /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt install tidy texlive texlive-fonts-extra -y
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
-        with: 
-          extra-packages: digest, RJSONIO, gtable, plyr, reshape2, scales, knitr
-
-
+
       - name: install package
         run: R CMD INSTALL .
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: animint2
 Title: Animated Interactive Grammar of Graphics
-Version: 2024.3.12
+Version: 2024.8.29
 URL: https://animint.github.io/animint2/
 BugReports: https://github.com/animint/animint2/issues
 Authors@R: c(
@@ -50,12 +50,12 @@ Authors@R: c(
     person("Yufan", "Fei",
      role="aut",
      comment="Animint2 GSoC 2022"),
-	person("Jocelyne", "Chen",
-	 role="aut",
-	 comment="Animint2 GSoC 2023"),
-	 person("Siddhesh", "Deodhar",
-	 role="aut",
-	 comment="Animint2 GSoC 2024"))
+    person("Jocelyne", "Chen",
+     role="aut",
+     comment="Animint2 GSoC 2023"),
+    person("Siddhesh", "Deodhar",
+     role="aut",
+     comment="Animint2 GSoC 2024"))
 Description: Functions are provided for defining animated,
  interactive data visualizations in R code, and rendering
  on a web page. The 2018 Journal of Computational and 
@@ -87,7 +87,7 @@ Suggests:
     htmltools,
     rmarkdown,
     testthat,
-    RSelenium, XML,
+    XML,
     devtools,
     httr,
     maps,
@@ -100,8 +100,8 @@ Suggests:
     nlme,
     rpart,
     svglite,
-    ggplot2
-Remotes: ropensci/[email protected]
+    ggplot2,
+    chromote
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
@@ -280,6 +280,6 @@ Collate:
     'z_scales.R'
     'z_theme_animint.R'
     'z_transformShape.R'
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Config/Needs/website: tidyverse/tidytemplate
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -507,10 +507,13 @@ import(plyr)
 import(scales)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,rgb)
+importFrom(grid,arrow)
+importFrom(grid,unit)
 importFrom(knitr,knit_print)
 importFrom(methods,is)
 importFrom(plyr,as.quoted)
 importFrom(plyr,defaults)
+importFrom(scales,alpha)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)
 importFrom(utils,browseURL)

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,23 @@
+# Changes in version 2024.8.29 (PR#147)
+
+- animint2pages initial commit README.md uses viz title.
+- animint2pages gains owner argument, with default taken from `gh::gh_whoami` (same as before, always returns user, even when token has permissions on an org); this allows user to specify an org where the user/token has write permissions. This is used in a new test-compiler-ghpages.R, which now assumes `PAT_GITHUB` has Administration and Contents permissions for all repos in `animint-test` org, so our test code can delete the `animint2pages_test_repo`, create a new one, and then use animint2pages twice, to test the results of creation/update.
+
+# Changes in version 2024.8.27 (PR#144)
+
+- Remove selenium, combine renderer tests into single CI job.
+
+# Changes in version 2024.6.6 (PR#126)
+
+- Add chromote as headless browser for testing and remove phantomjs/firefox support
+
 # Changes in version 2024.3.12 (PR#119)
 
-  - Add validation checks for duplicate args passed geom and aes
+- Add validation checks for duplicate args passed geom and aes
 
 # Changes in version 2024.2.4 (PR#116)
 
-  - Add validation checks for duplicate and missing args passed to animint.
+- Add validation checks for duplicate and missing args passed to animint.
 
 # Changes in version 2024.1.24 (PR#112)
 

diff --git a/R/data.R b/R/data.R
@@ -173,7 +173,7 @@
 #' Housing sales in TX.
 #'
 #' Information about the housing market in Texas provided by the TAMU
-#' real estate center, \url{https://www.recenter.tamu.edu/}.
+#' real estate center.
 #'
 #' @format A data frame with 8602 observations and 9 variables:
 #' \describe{

diff --git a/R/stat-unique.r b/R/stat-unique.r
@@ -1,8 +1,5 @@
 #' Remove duplicates.
 #'
-#' @section Aesthetics:
-#' \Sexpr[results=rd,stage=build]{animint2:::rd_aesthetics("stat", "unique")}
-#'
 #' @export
 #' @inheritParams layer
 #' @inheritParams geom_point

diff --git a/R/z_facets.R b/R/z_facets.R
@@ -1,4 +1,3 @@
-
 # Determine titles to put on facet panels.
 # The implementation here is a modified version of facet_strips.
 getStrips <- function(facet, panel, ...)
@@ -36,7 +35,6 @@ build_strip <- function(panel, label_df, labeller, side = "right", ...) {
   labels <- matrix(list(), nrow = nrow(label_df), ncol = ncol(label_df))
   labels <- lapply(labeller(label_df), cbind)
   labels <- do.call("cbind", labels)
-
   # unlike ggplot2, we collapse "layers" of strips into 1 layer
   apply(labels, 1, paste, collapse = "; ")
 }

diff --git a/R/z_pages.R b/R/z_pages.R
@@ -8,6 +8,7 @@
 #' @param plot.list A named list of ggplots and option lists.
 #' @param github_repo The name of the GitHub repository to which the
 #'   files will be pushed.
+#' @param owner The user/org under which the repo will be created, default comes from \code{gh::gh_whoami}.
 #' @param commit_message A string specifying the commit message for
 #'   the pushed files.
 #' @param private A logical flag indicating whether the GitHub
@@ -35,7 +36,7 @@
 #' }
 #'
 #' @export
-animint2pages <- function(plot.list, github_repo, commit_message = "Commit from animint2pages", private = FALSE, required_opts = c("title","source"), ...) {
+animint2pages <- function(plot.list, github_repo, owner=NULL, commit_message = "Commit from animint2pages", private = FALSE, required_opts = c("title","source"), ...) {
   for(opt in required_opts){
     if(!opt %in% names(plot.list)){
       stop(sprintf("plot.list does not contain option named %s, which is required by animint2pages", opt))
@@ -61,8 +62,10 @@ animint2pages <- function(plot.list, github_repo, commit_message = "Commit from
     stop("The github_repo argument should not contain '/'.")
   }
   # Check for existing repository
-  whoami <- suppressMessages(gh::gh_whoami())
-  owner <- whoami[["login"]]
+  if(is.null(owner)){
+    whoami <- suppressMessages(gh::gh_whoami())
+    owner <- whoami[["login"]]
+  }
   viz_owner_repo <- paste0(owner, "/", github_repo)
   local_clone <- tempfile()
   if (!check_no_github_repo(owner, github_repo)) {
@@ -86,18 +89,20 @@ animint2pages <- function(plot.list, github_repo, commit_message = "Commit from
     silent = TRUE
   )
   if (!has_commits) {
-    initial_commit(local_clone, repo, viz_url)
+    title <- plot.list[["title"]]
+    if(!is.character(title))title <- "New animint visualization"
+    initial_commit(local_clone, repo, viz_url, title)
   }
   # Handle gh-pages branch
   manage_gh_pages(repo, owner, to_post, local_clone, commit_message)
   message(sprintf(
     "Visualization will be available at %s\nDeployment via GitHub Pages may take a few minutes...", viz_url))
-  viz_owner_repo
+  list(owner_repo=viz_owner_repo, local_clone=local_clone, viz_url=viz_url, gh_pages_url=sprintf("https://github.com/%s/tree/gh-pages", viz_owner_repo))
 }
 
-initial_commit <- function(local_clone, repo, viz_url) {
+initial_commit <- function(local_clone, repo, viz_url, title) {
   readme_file_path <- file.path(local_clone, "README.md")
-  header <- "## New animint visualization\n"
+  header <- sprintf("## %s\n", title)
   url_hyperlink <- sprintf("[%s](%s)\n", viz_url, viz_url)
   full_content <- paste0(header, url_hyperlink)
   writeLines(full_content, readme_file_path)

diff --git a/man/animint2pages.Rd b/man/animint2pages.Rd
diff --git a/man/position_dodge.Rd b/man/position_dodge.Rd
diff --git a/man/position_identity.Rd b/man/position_identity.Rd
diff --git a/man/position_nudge.Rd b/man/position_nudge.Rd
diff --git a/man/position_stack.Rd b/man/position_stack.Rd
diff --git a/man/stat_unique.Rd b/man/stat_unique.Rd
diff --git a/man/txhousing.Rd b/man/txhousing.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,51 +1,17 @@
 library("testthat")
 library("animint2")
-library("RSelenium");library("XML")
+library("XML")
 setwd("testthat")
 source("helper-functions.R")
 source("helper-HTML.R")
 source("helper-plot-data.r")
-
-## RSelenium does not work with all versions of firefox, TDH usually
-## tests using one of the following.
-
-## thocking@silene:~/R/animint-mine(fix-common-chunk)$ firefox --version
-## Mozilla Firefox 11.0
-## thocking@silene:~/R/animint(animation-fix)$ java -jar ~/lib/R/library/RSelenium/bin/selenium-server-standalone.jar --version
-## 10:10:58.942 INFO - Launching a standalone server
-## 10:10:58.973 INFO - Java: Sun Microsystems Inc. 23.25-b01
-## 10:10:58.973 INFO - OS: Linux 3.8.0-44-generic amd64
-## 10:10:58.987 INFO - v2.44.0, with Core v2.44.0. Built from revision 76d78cf
-## > packageVersion("RSelenium")
-## [1] ‘1.3.6’
-
-## > packageVersion("RSelenium")
-## [1] ‘1.3.5’
-## tdhock@recycled:~/R/animint(roc-bugfix)$ firefox --version
-## Mozilla Firefox 41.0
-## tdhock@recycled:~/R/animint(roc-bugfix*)$ java -jar ~/lib/R/library/RSelenium/bin/selenium-server-standalone.jar --version
-## 08:13:17.803 INFO - Launching a standalone Selenium Server
-## 08:13:17.877 INFO - Java: Oracle Corporation 24.79-b02
-## 08:13:17.877 INFO - OS: Linux 3.13.0-65-generic i386
-## 08:13:17.907 INFO - v2.47.0, with Core v2.47.0. Built from revision 0e4837e
-
 filter <- Sys.getenv("TEST_SUITE")
-# If we're running in github actions then use Firefox, since we can
-# use the Selenium docker image instead of relying on PhantomJS.
 gh.action <- Sys.getenv("GH_ACTION")
-dont.need.browser <- grepl("compiler", filter)
-use.browser <- !dont.need.browser
+use.browser <- grepl("renderer", filter)
 if(filter == ""){
   filter <- NULL
 }
 message(gh.action)
-if(FALSE){
-  tests_init("chrome")
-}else if(interactive() | (gh.action == "ENABLED")) {
-  tests_init("firefox")
-} else {
-  tests_init()
-}
-
+if(use.browser)tests_init()
 tests_run(filter=filter)
-tests_exit()
+if(use.browser)tests_exit()