R/attach.R

In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

core <- c("xcms", "mzR", "MSnbase")

core_unloaded <- function() {
  search <- paste0("package:", core)
  core[!search %in% search()]
}

# Attach the package from the same package library it was
same_library <- function(pkg) {
  loc <- if (pkg %in% loadedNamespaces()) dirname(getNamespaceInfo(pkg, "path"))
  do.call(
    "library",
    list(pkg, lib.loc = loc, character.only = TRUE, warn.conflicts = FALSE)
  )
}

metflow2_attach <- function() {
  to_load <- core_unloaded()
  if (length(to_load) == 0)
    return(invisible())
  
  # msg(
  #   cli::rule(
  #     left = crayon::bold("Attaching packages"),
  #     right = paste0("metflow2 ", package_version("metflow2"))
  #   ),
  #   startup = TRUE
  # )
  
  versions <- vapply(to_load, package_version, character(1))
  packages <- paste0(
    crayon::green(cli::symbol$tick), " ", crayon::blue(format(to_load)), " ",
    crayon::col_align(versions, max(crayon::col_nchar(versions)))
  )
  
  if (length(packages) %% 2 == 1) {
    packages <- append(packages, "")
  }
  col1 <- seq_len(length(packages) / 2)
  info <- paste0(packages[col1], "     ", packages[-col1])
  
  msg(paste(info, collapse = "\n"), startup = TRUE)
  
  suppressPackageStartupMessages(
    lapply(to_load, same_library)
  )
  
  invisible()
}

package_version <- function(x) {
  version <- as.character(unclass(utils::packageVersion(x))[[1]])
  
  if (length(version) > 3) {
    version[4:length(version)] <- crayon::red(as.character(version[4:length(version)]))
  }
  paste0(version, collapse = ".")
}


msg <- function(..., startup = FALSE) {
  if (startup) {
    if (!isTRUE(getOption("metflow2.quiet"))) {
      packageStartupMessage(text_col(...))
    }
  } else {
    message(text_col(...))
  }
}

text_col <- function(x) {
  # If RStudio not available, messages already printed in black
  if (!rstudioapi::isAvailable()) {
    return(x)
  }
  
  if (!rstudioapi::hasFun("getThemeInfo")) {
    return(x)
  }
  
  theme <- rstudioapi::getThemeInfo()
  
  if (isTRUE(theme$dark)) crayon::white(x) else crayon::black(x)
  
}

#' List all packages in the metflow2
#'
#' @param include_self Include metflow2 in the list?
#' @export
#' @examples
#' metflow2_packages()
metflow2_packages <- function(include_self = TRUE) {
  raw <- utils::packageDescription("metflow2")$Imports
  imports <- strsplit(raw, ",")[[1]]
  parsed <- gsub("^\\s+|\\s+$", "", imports)
  names <- vapply(strsplit(parsed, "\\s+"), "[[", 1, FUN.VALUE = character(1))
  
  if (include_self) {
    names <- c(names, "metflow2")
  }
  
  names
}

invert <- function(x) {
  if (length(x) == 0) return()
  stacked <- utils::stack(x)
  tapply(as.character(stacked$ind), stacked$values, list)
}


style_grey <- function(level, ...) {
  crayon::style(
    paste0(...),
    crayon::make_style(grDevices::grey(level), grey = TRUE)
  )
}