added local get_ss3_exe function to resolve gh::gh SAML token issues …

…downloading ss3 from nfms-ost (#109, #110)

DESCRIPTION

@@ -27,6 +27,7 @@ Imports:
     r4ss (== 1.49.3),
     randtests,
     reshape2,
+    gh,
     rlang
 Suggests:
     knitr,

NAMESPACE

@@ -19,7 +19,9 @@ export(SSretroComps)
 export(SSrmse)
 export(SSrunstest)
 export(SSsettingsBratioF)
+export(get_ss3_exe)
 export(ssruns_sig3)
+import(gh)
 importFrom(gplots,ci2d)
 importFrom(grDevices,adjustcolor)
 importFrom(grDevices,dev.new)

R/get_ss3_exe.R

@@ -0,0 +1,217 @@
+#' Download the Stock Synthesis (SS3) executable
+#'
+#' Downloads the SS3 executable according to specified version and the user
+#' operating system.
+#'
+#' @param dir The directory that you would like the executable downloaded to.
+#' @param version A character string of the executable version tag to download
+#' (e.g.'v3.30.20' or 'v3.30.18'). A list of tags is available at
+#' https://github.com/nmfs-ost/ss3-source-code/tags
+#' @return A string of the file path to the downloaded executable
+#' @author Elizabeth F. Gugliotti
+#' @export
+#' @import gh
+#' @examples
+#' \dontrun{
+#' get_ss3_exe()
+#' get_ss3_exe(version = "v3.30.18")
+#' }
+#' @description The `get_ss3_exe()` function uses the `gh` package to get either
+#' the latest release (if version = NULL) or the specified version of the Stock
+#' Synthesis executable for the appropriate operating system to the directory `dir`
+#' (if dir = NULL, then the executable is downloaded to the working directory).
+#' To view the version tags available go to
+#' https://github.com/nmfs-ost/ss3-source-code/tags
+
+get_ss3_exe <- function(dir = NULL, version = NULL) {
+  # Get latest release if version not specified
+  if (is.null(version)) {
+    latest_release <- gh::gh("GET /repos/nmfs-ost/ss3-source-code/releases/latest", page = 1, .token = NA_character_)
+    tag <- latest_release[["tag_name"]]
+  } else {
+    # Otherwise get specified version
+    all_tags <- gh::gh("GET /repos/nmfs-ost/ss3-source-code/tags", .token = NA_character_)
+    df_tags <- as.data.frame(do.call(rbind, all_tags))
+    tags <- unlist(df_tags[["name"]])
+
+    if (!version %in% tags) {
+      warning("The version tag that you entered is invalid or not in the right format,
+              please go to https://github.com/nmfs-ost/ss3-source-code/tags
+              to get a correct version tag or version tag format")
+    } else {
+      tag <- version
+    }
+  }
+
+  if (is.null(dir)) {
+    dir <- getwd()
+    message("No directory provided, the executable will be downloaded to the working directory")
+  }
+
+  if (!dir.exists(dir)) {
+    stop("Directory doesn't exist: ", dir)
+  }
+
+  #if (.Platform[["OS.type"]] == "windows") {
+  if(R.version[["os"]] == "mingw32") {
+
+    download_location <- ss3_exe_windows(dir, tag)
+
+  } else if(substr(R.version[["os"]], 1, 6) == "darwin") {
+
+    download_location <- ss3_exe_darwin(dir, tag, R.version[["arch"]])
+  } else if(R.version[["os"]] == "linux-gnu") {
+
+    download_location <- ss3_exe_linux(dir, tag)
+  } else {
+
+    stop("The Stock Synthesis executable is not available for ", R.version[["os"]], ".") # nocov end
+  }
+
+  return(invisible(download_location))
+}
+
+
+
+
+#' @rdname get_ss3_exe
+#' 
+#' @param dir Target Directory
+#' @param tag Target ss3 Version release 
+#' 
+#' @return A string of the file path to the downloaded executable
+#'
+#' @keywords internal
+#' 
+ss3_exe_windows <- function (dir, tag) {
+  if (.Platform[["r_arch"]] == "x32") { # nocov start
+    warning(
+      "Stock Synthesis binary is not available for 32-bit ",
+      .Platform[["OS.type"]], "."
+    )
+  } else {
+    url <- paste0(
+      "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+      tag, "/ss3_win.exe"
+    )
+    try_ss <- tryCatch(
+      suppressWarnings(utils::download.file(url, destfile = file.path(dir, "ss3.exe"), mode = "wb")),
+      error = function(e) "ss3 name not right for this version, trying ss"
+    )
+
+    if (try_ss == "ss3 name not right for this version, trying ss") {
+      url <- paste0(
+        "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+        tag, "/ss_win.exe"
+      )
+      utils::download.file(url, destfile = file.path(dir, "ss3.exe"), mode = "wb")
+    }
+    download_location <- file.path(dir, "ss3.exe")
+    message(paste0(
+      "The stock synthesis executable for Windows ", tag, " was downloaded to: ",
+      download_location
+    ))
+
+    return(invisible(download_location))
+  }
+}
+
+
+#' @rdname get_ss3_exe
+#'
+#' @param dir Target Directory
+#' @param tag Target ss3 Version release 
+#' @param arch arch
+#' 
+#' @return A string of the file path to the downloaded executable
+#'
+#' @keywords internal
+#' 
+ss3_exe_darwin <- function(dir, tag, arch = c("aarch64", "x86_64" )) {
+
+  arch <- match.arg(arch)
+
+  if(arch == "aarch64"){
+    url <- paste0(
+      "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+      tag, "/ss3_osx_arm64"
+    )
+    try_arm64 <- tryCatch(
+      suppressWarnings(utils::download.file(url, destfile = file.path(dir, "ss3"), mode = "wb")),
+      error = function(e) "ss3 executable not available for macOS arm64 architecture
+            computers for versions prior to v.3.30.22.1"
+    )
+
+    if (try_arm64 == "ss3 executable not available for macOS arm64 architecture computers for
+        versions prior to v.3.30.22.1") {
+      print(try_arm64)
+    } else {
+      Sys.chmod(paths = file.path(dir, "ss3"), mode = "0700")
+      download_location <- file.path(dir, "ss3")
+      message(paste0(
+        "The stock synthesis executable for Mac ", tag, " was downloaded to: ",
+        download_location
+      ))
+    }
+  } else if (arch == "x86_64") {
+    url <- paste0(
+      "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+      tag, "/ss3_osx"
+    )
+    try_ss <- tryCatch(
+      suppressWarnings(utils::download.file(url, destfile = file.path(dir, "ss3"), mode = "wb")),
+      error = function(e) "ss3 name not right for this version, trying ss"
+    )
+
+    if (try_ss == "ss3 name not right for this version, trying ss") {
+      url <- paste0(
+        "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+        tag, "/ss_osx"
+      )
+      utils::download.file(url, destfile = file.path(dir, "ss3"), mode = "wb")
+    }
+    Sys.chmod(paths = file.path(dir, "ss3"), mode = "0700")
+    download_location <- file.path(dir, "ss3")
+    message(paste0(
+      "The stock synthesis executable for Mac ", tag, " was downloaded to: ",
+      download_location
+    ))
+  }
+  return(invisible(download_location))
+}
+
+#' @rdname get_ss3_exe
+#' 
+#' @param dir Target Directory
+#' @param tag Target ss3 Version release 
+#' 
+#' @return A string of the file path to the downloaded executable
+#'
+#' @keywords internal
+#' 
+ss3_exe_linux <- function(dir, tag) {
+  url <- paste0(
+    "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+    tag, "/ss3_linux"
+  )
+  try_ss <- tryCatch(
+    suppressWarnings(utils::download.file(url, destfile = file.path(dir, "ss3"), mode = "wb")),
+    error = function(e) "ss3 name not right for this version, trying ss"
+  )
+
+  if (try_ss == "ss3 name not right for this version, trying ss") {
+    url <- paste0(
+      "https://github.com/nmfs-ost/ss3-source-code/releases/download/",
+      tag, "/ss_linux"
+    )
+    utils::download.file(url, destfile = file.path(dir, "ss3"), mode = "wb")
+  }
+  Sys.chmod(paths = file.path(dir, "ss3"), mode = "0700")
+  Sys.chmod(paths = dir, mode = "0777")
+  download_location <- file.path(dir, "ss3")
+  message(paste0(
+    "The stock synthesis executable for Linux ", tag, " was downloaded to: ",
+    download_location
+  ))
+  return(invisible(download_location))
+}

tests/testthat.R

@@ -7,7 +7,8 @@ files_path <- system.file("extdata", package = "ss3diags")
 run_tmp <- file.path(tempdir(check = TRUE), "test-runs")
 dir.create(run_tmp, showWarnings = FALSE)
 file.copy(from = list.files(files_path, full.names = TRUE), to = run_tmp)
-r4ss::get_ss3_exe(dir = run_tmp, version = "v3.30.21")
+#r4ss::get_ss3_exe(dir = run_tmp, version = "v3.30.21")
+ss3diags::get_ss3_exe(dir = run_tmp, version = "v3.30.21")
 ## Run retrospectives
 if (file.exists(file.path(run_tmp, "ss3")) | file.exists(file.path(run_tmp, "ss3.exe"))) {
   r4ss::retro(dir = run_tmp, oldsubdir = "", newsubdir = "retrospectives", years = 0:-3, show_in_console = FALSE)