Migrate CI to GitHub Actions

.Rbuildignore

@@ -2,7 +2,6 @@
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^packrat/
 ^\.Rprofile$
 ^cran-comments.md$
@@ -14,3 +13,4 @@
 ^doc$
 ^CRAN-RELEASE$
 ^customSettings$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,46 @@
+# Run R CMD Check on PR to dev
+
+on:
+  pull_request:
+    branches:
+      - dev
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Find PhantomJS path
+        id: phantomjs
+        run: |
+          echo "::set-output name=path::$(Rscript -e 'cat(shinytest:::phantom_paths()[[1]])')"
+      - name: Cache PhantomJS
+        uses: actions/cache@v2
+        with:
+          path: ${{ steps.phantomjs.outputs.path }}
+          key: ${{ matrix.config.os }}-phantomjs
+          restore-keys: ${{ matrix.config.os }}-phantomjs
+      - name: Install PhantomJS
+        shell: Rscript {0}
+        run: |
+          options(install.packages.check.source = "no")
+          if (!shinytest::dependenciesInstalled()) shinytest::installDependencies()
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

DESCRIPTION

@@ -8,9 +8,8 @@ Authors@R: c(
 	person("Xiao","Ni", role = "aut"),
 	person("James","Buchanan", role="aut"),
 	person("Susan","Duke", role="aut"),
-	person("Interactive Safety Graphics Working Group", role = "aut"),
-	person("Rho Inc.", role = "cph"))
-Maintainer: Jeremy Wildfire <jeremy_wildfire@rhoworld.com>
+	person("Interactive Safety Graphics Working Group", role = "aut"))
+Maintainer: Jeremy Wildfire <jeremy_wildfire@gmail.com>
 Description: A framework for evaluation of clinical trial safety. Users can interactively explore their data using the 'Shiny' application or create standalone 'htmlwidget' charts. Interactive charts are built using 'd3.js' and 'webcharts.js' 'JavaScript' libraries.
 URL: https://github.com/SafetyGraphics/safetyGraphics
 BugReports: https://github.com/SafetyGraphics/safetyGraphics/issues
@@ -20,32 +19,30 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1
 Suggests:
-    testthat,
-    shinytest,
-    knitr,
+    fs, 
     ggplot2,
-    plotly
+    knitr,
+    plotly,
+    rstudioapi,
+    rprojroot,
+    shinydashboard,
+    shinyFiles,
+    shinytest,
+    testthat,
+    usethis
 Imports:
     dplyr,
+    DT,
     esquisse,
     htmlwidgets,
-    purrr,
-    stringr,
     jsonlite,
+    listviewer,
+    purrr,
+    rlang,
     shiny,
-    magrittr,
-    DT,
     shinyjs,
-    rmarkdown,
-    rlang,
-    tibble,
-    utils,
-    haven,
     shinyWidgets,
-    tidyr,
-    shinybusy,
-    listviewer,
-    shinyFiles,
-    rprojroot
+    stringr,
+    yaml
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(add_chart)
 export(app_server)
+export(app_startup)
 export(app_ui)
 export(chart_template)
 export(chartsNav)
@@ -37,46 +38,24 @@ export(settingsData)
 export(settingsDataUI)
 export(settingsMapping)
 export(settingsMappingUI)
-import(clisymbols)
 import(dplyr)
 import(esquisse)
 import(listviewer)
-import(magrittr)
 import(shiny)
-import(shinyFiles)
-import(tools)
 import(yaml)
-importFrom(DT,DTOutput)
 importFrom(DT,renderDT)
-importFrom(fs,dir_copy)
-importFrom(fs,file_create)
-importFrom(fs,file_exists)
-importFrom(fs,path)
-importFrom(fs,path_abs)
-importFrom(haven,read_sas)
 importFrom(listviewer,jsonedit)
 importFrom(listviewer,jsoneditOutput)
 importFrom(listviewer,renderJsonedit)
-importFrom(magrittr,"%>%")
-importFrom(purrr,keep)
 importFrom(purrr,map)
-importFrom(purrr,transpose)
 importFrom(rlang,.data)
-importFrom(rprojroot,find_root)
-importFrom(rprojroot,is_rstudio_project)
-importFrom(rstudioapi,isAvailable)
-importFrom(rstudioapi,openProject)
 importFrom(shiny,dataTableOutput)
 importFrom(shiny,renderDataTable)
-importFrom(shinyWidgets,materialSwitch)
 importFrom(shinyWidgets,progressBar)
 importFrom(shinyWidgets,updateProgressBar)
 importFrom(shinyjs,html)
 importFrom(shinyjs,useShinyjs)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_split)
 importFrom(stringr,str_to_upper)
-importFrom(tidyr,gather)
-importFrom(usethis,create_project)
-importFrom(utils,globalVariables)
 importFrom(yaml,write_yaml)

R/add_chart.R

@@ -21,16 +21,18 @@
 #' @param type Type of chart: `plot`, `module`, or `htmlwidget`. Default is `plot` (static)
 #' @param domain associated data domain, for example `aes`, `labs`, or `multiple`
 #' @param package optional, R package that this chart is associated with.
-#' @param chart_template chart template function
+#' @param workflow list of workflow functions appropriate for chart YAML
+#' @param open boolean 
+#' @param ... additional parameters for chart_template
 #' 
 #' @seealso [chart_template()]
 #' 
-#' @importFrom rprojroot find_root is_rstudio_project
-#' @importFrom fs path file_create file_exists
 #' @importFrom yaml write_yaml
 #' 
 #' @export
+
 add_chart <- function(
+  path,
   name = "newplot",
   label = "New Static Plot",
   type = "plot",
@@ -41,9 +43,20 @@ add_chart <- function(
   ...
 ){
 
-  proj_root <- rprojroot::find_root(rprojroot::is_rstudio_project)
+  if (!requireNamespace("rprojroot", quietly = TRUE)) {
+    stop("Package \"rprojroot\" needed for this function to work. Please install it.",
+      call. = FALSE)
+  }
 
-  path <- file.path(proj_root, "config")
+  if (!requireNamespace("fs", quietly = TRUE)) {
+    stop("Package \"fs\" needed for this function to work. Please install it.",
+      call. = FALSE)
+  }
+  proj_root <- rprojroot::find_root(rprojroot::is_rstudio_project)
+  if(missing(path)){
+    path <- file.path(proj_root, "config")
+  }
+
 
   yaml_where <- file.path(
     path, paste0(name, ".yaml")

R/aes.R

@@ -3,11 +3,6 @@
 #' A dataset containing anonymized AE data from a clinical trial in the CDISC ADaM format. The structure is 1 record per measure per adverse event. See a full description of the ADaM data standard \href{https://www.cdisc.org/standards/foundational/adam/adam-implementation-guide-v11}{here}.
 #'
 #' @format A data frame with 10288 rows and 46 variables.
-#' \describe{
-#'    \item{STUDYID}{Study Identifier}
-#'    \item{SUBJID}{Subject Identifier for the Study}
-#'    \item{USUBJID}{Unique Subject Identifier}
-#' }    
 #' @source \url{https://github.com/RhoInc/data-library}
 #' 
 "aes"

R/app_init_addin.R

@@ -1,14 +1,15 @@
 #' RStudio Add-in for constructing lean ADLB and ADAE data
 #' 
-#' 
 #' @import shiny
-#' @import shinyFiles
 #' @import listviewer
-#' 
 
 
 app_init_addin <- function(){
-
+  if (!requireNamespace("shinyFiles", quietly = TRUE)) {
+    stop("Package \"shinyFiles\" needed for this function to work. Please install it.",
+      call. = FALSE)
+  }
+
 
   ui <- bootstrapPage(
 
@@ -133,11 +134,11 @@ app_init_addin <- function(){
       chartSettingsPaths = NULL
     ){
 
-      config <- safetyGraphics:::app_startup(domainData, meta, charts, mapping, chartSettingsPaths)
+      config <- safetyGraphics::app_startup(domainData, meta, charts, mapping, chartSettingsPaths)
 
       app <- shinyApp(
         ui =  app_ui(config$meta, config$domainData, config$mapping, config$standards),
-        server = app_server(input, output, session, config$meta, config$mapping, config$domainData, config$charts)
+        server = app_server(config$meta, config$mapping, config$domainData, config$charts)
       )
     }
 
@@ -187,7 +188,7 @@ app_init_addin <- function(){
     tblMeta <- function(charts){
 
       bbb <- purrr::map(charts, ~{
-        bb <- as_tibble(t(tibble(.x)))
+        bb <- dplyr::as_tibble(t(dplyr::tibble(.x)))
         names(bb) <- names(.x)
         bb
       })

R/app_server.R

@@ -2,15 +2,19 @@
 #'
 #' This function returns a server function suitable for use in shiny::runApp()
 #' 
-#' @param input app input 
-#' @param output app output
-#' @param session app session
+
 #' @param meta data frame containing the metadata for use in the app. See the preloaded file (\code{?safetyGraphics::meta}) for more data specifications and details. Defaults to \code{safetyGraphics::meta}. 
 #' @param domainData named list of data.frames to be loaded in to the app.
-#' @param chartsList list of charts to include in the app
+#' @param mapping current mapping
+#' @param charts list of charts to include in the app
+#' 
+#' @import shiny
+#' @import dplyr
+#' @importFrom purrr map
+#' @importFrom shinyjs html
 #' 
 #' @export
-app_server <- function(input, output, session, meta, mapping, domainData, charts){
+app_server <- function(meta, mapping, domainData, charts){
     server <- function(input, output, session) {
         #Initialize modules
 
@@ -19,8 +23,8 @@ app_server <- function(input, output, session, meta, mapping, domainData, charts
         current_mapping<-callModule(mappingTab, "mapping", meta, domainData)
 
         id_col <- reactive({
-            dm<-current_mapping()%>%filter(domain=="dm")   
-            id<-dm %>%filter(text_key=="id_col")%>%pull(current)
+            dm<-current_mapping()%>%filter(.data$domain=="dm")   
+            id<-dm %>%filter(.data$text_key=="id_col")%>%pull(.data$current)
             return(id)
         })
 
@@ -32,17 +36,17 @@ app_server <- function(input, output, session, meta, mapping, domainData, charts
             id_col=id_col
         )
 
-        callModule(settingsData, "dataSettings", domains = domainData, filtered=filtered_data)
+        callModule(settingsData, "dataSettings", domains = domainData)
         callModule(settingsMapping, "metaSettings", metaIn=meta, mapping=current_mapping)
         callModule(settingsCharts, "chartSettings",charts = charts)
         callModule(homeTab, "home")
 
         #Initialize Chart UI - Adds subtabs to chart menu - this initializes initializes chart UIs
-        charts %>% map(chartsNav)
+        charts %>% purrr::map(chartsNav)
 
         #Initialize Chart Servers
         validDomains <- tolower(names(mapping))
-        charts %>% map(
+        charts %>% purrr::map(
             ~callModule(
                 module=chartsTab,
                 id=.x$name,

R/app_startup.R

@@ -2,6 +2,12 @@
 #' 
 #' Prepare inputs for safetyGraphics app - run before app is initialized. See ?safetyGraphicsApp for parameter definitions
 #'
+#' @param domainData named list of domain level data
+#' @param meta list of configuration metadata 
+#' @param charts list of charts
+#' @param mapping initial data mapping
+#' @param chartSettingsPaths character vector with paths to chart setting yaml files
+#' 
 #' @return List of elements for used to initialize the shiny app with the following parameters
 #'  \itemize{
 #'  \item{"meta"}{ List of configuration metadata }
@@ -11,6 +17,7 @@
 #'  \item{"standards"}{ List of domain level data standards }
 #' }
 #' 
+#' @export
 app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, chartSettingsPaths=NULL){
     # Process charts metadata
     if(is.null(charts)){

R/app_ui.R

@@ -4,7 +4,9 @@
 #' @param domainData named list of data.frames to be loaded in to the app.
 #' @param mapping data.frame specifying the initial values for each data mapping. If no mapping is provided, the app will attempt to generate one via \code{detectStandard()}
 #' @param standards a list of information regarding data standards. Each list item should use the format returned by safetyGraphics::detectStandard.
-#' 
+#'
+#' @importFrom shinyjs useShinyjs
+#'  
 #' @export
 
 app_ui <- function(meta, domainData, mapping, standards){
@@ -21,7 +23,7 @@ app_ui <- function(meta, domainData, mapping, standards){
 
     #app UI using calls to modules
     ui<-tagList(
-        useShinyjs(),
+        shinyjs::useShinyjs(),
         tags$head(
             tags$style(app_css),
             tags$link(