Merge pull request #102 from stemangiola/drop-printing

remove deprecated print method, and adjust NAMESPACE. Add startup mes…

Author: stemangiola

.DS_Store

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySummarizedExperiment
 Title: Brings SummarizedExperiment to the Tidyverse 
-Version: 1.19.1
+Version: 1.19.2
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")) )
 Description: The tidySummarizedExperiment package provides a set of tools for creating and

DESCRIPTION

@@ -20,7 +20,6 @@ S3method(pivot_longer,SummarizedExperiment)
 S3method(pivot_wider,SummarizedExperiment)
 S3method(plot_ly,SummarizedExperiment)
 S3method(plot_ly,tbl_df)
-S3method(print,SummarizedExperiment)
 S3method(pull,SummarizedExperiment)
 S3method(rename,SummarizedExperiment)
 S3method(right_join,SummarizedExperiment)
@@ -32,7 +31,6 @@ S3method(separate,SummarizedExperiment)
 S3method(slice,SummarizedExperiment)
 S3method(summarise,SummarizedExperiment)
 S3method(summarize,SummarizedExperiment)
-S3method(tbl_format_header,tidySummarizedExperiment)
 S3method(tidy,RangedSummarizedExperiment)
 S3method(tidy,SummarizedExperiment)
 S3method(unite,SummarizedExperiment)
@@ -52,15 +50,13 @@ importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,"elementMetadata<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,assay)
-importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,cbind)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,elementMetadata)
 importFrom(SummarizedExperiment,rbind)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
-importFrom(cli,col_br_black)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
@@ -86,7 +82,6 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_used)
-importFrom(fansi,strwrap_ctl)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,ggplot)
 importFrom(lifecycle,deprecate_warn)
@@ -98,10 +93,6 @@ importFrom(methods,.hasSlot)
 importFrom(methods,as)
 importFrom(methods,getMethod)
 importFrom(methods,is)
-importFrom(pillar,align)
-importFrom(pillar,get_extent)
-importFrom(pillar,style_subtle)
-importFrom(pillar,tbl_format_header)
 importFrom(pkgconfig,get_config)
 importFrom(purrr,imap)
 importFrom(purrr,map)
@@ -120,11 +111,9 @@ importFrom(rlang,enquos)
 importFrom(rlang,expr)
 importFrom(rlang,flatten_if)
 importFrom(rlang,is_spliced)
-importFrom(rlang,names2)
 importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
-importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
@@ -148,4 +137,3 @@ importFrom(ttservice,bind_rows)
 importFrom(ttservice,plot_ly)
 importFrom(utils,packageDescription)
 importFrom(utils,tail)
-importFrom(vctrs,new_data_frame)

NAMESPACE

@@ -1,28 +1,4 @@
 #' @importFrom methods getMethod
-setMethod(
-    f="show",
-    signature="SummarizedExperiment",
-    definition=function(object) {
-        if (isTRUE(x=getOption(x="restore_SummarizedExperiment_show",
-            default = FALSE)) |         
-            # If the object is a SingleCellExperiment
-            # # From BioC 3_14 SingleCellExperiment is SummarizedExperiment and 
-            # # we don't want to process with tidySummarizedExperiment
-            is(object, "SingleCellExperiment")
-        ) {
-            f <- getMethod(
-                f="show",
-                signature="SummarizedExperiment",
-                where=asNamespace(ns="SummarizedExperiment")
-            )
-            f(object=object)
-        } else {
-            object %>%
-                print()
-        }
-    }
-)
-
 setClass("tidySummarizedExperiment",
     contains=c("SummarizedExperiment", "RangedSummarizedExperiment"))
 

R/methods.R

@@ -1,27 +1 @@
-NBSP <- "\U00A0"
 
-pillar___format_comment <- function (x, width)
-{
-    if (length(x) == 0L) {
-        return(character())
-    }
-    map_chr(x, pillar___wrap, prefix="# ",
-        width=min(width, cli::console_width()))
-}
-
-#' @importFrom fansi strwrap_ctl
-pillar___strwrap2 <- function (x, width, indent)
-{
-    fansi::strwrap_ctl(x, width=max(width, 0), indent=indent,
-        exdent=indent + 2)
-}
-
-
-pillar___wrap <- function (..., indent=0, prefix="", width)
-{
-    x <- paste0(..., collapse="")
-    wrapped <- pillar___strwrap2(x, width - get_extent(prefix), indent)
-    wrapped <- paste0(prefix, wrapped)
-    wrapped <- gsub(NBSP, " ", wrapped)
-    paste0(wrapped, collapse="\n")
-}

R/pillar_utilities.R

@@ -1286,22 +1286,6 @@ split_SummarizedExperiment_by_feature_to_list <- function(.data) {
   map(1:nrow(.data), ~ .data[.x,])
 }
 
-#' Add attribute to abject
-#'
-#' @keywords internal
-#' @noRd
-#'
-#'
-#' @param var A tibble
-#' @param attribute An object
-#' @param name A character name of the attribute
-#'
-#' @return A tibble with an additional attribute
-add_attr <- function(var, attribute, name) {
-  attr(var, name) <- attribute
-  var
-}
-
 is_filer_columns_in_column_selection <- function(.data, ...) {
   # columns = enquos(columns)
   tryCatch({

R/print_method.R

@@ -1,4 +1,11 @@
 #' @importFrom utils packageDescription
 .onAttach <- function(libname, pkgname) {
     attached <- tidyverse_attach()
+    
+    # Print loading message about printing
+    packageStartupMessage(
+        "tidySummarizedExperiment says: Printing is now handled externally. ",
+        "If you want to visualize the data in a tidy way, do library(tidyprint). ",
+        "See https://github.com/tidyomics/tidyprint for more information."
+    )
 }

R/utilities.R

@@ -1,10 +1,11 @@
 \name{NEWS}
 \title{News for Package \pkg{tidySummarizedExperiment}}
 
-\section{Changes in version 1.16.0, Bioconductor 3.22 Release}{
+\section{Changes in version 1.19.2, Bioconductor 3.22 Release}{
 \itemize{
     \item Updated documentation to properly reflect S3 method structure.
     \item Simplified ggplot2 compatibility - S3 method continues to work with ggplot2 4.0.0.
+    \item Users are now directed to library(tidyprint) for tidy visualization and https://github.com/tidyomics/tidyprint for more information.
 }}
 
 \section{Changes in version 1.4.0, Bioconductor 3.14 Release}{