added installer bash

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

@@ -59,3 +59,9 @@ jobs:
         with:
           args: 'c("--no-manual")'
           upload-snapshots: false
+
+      - name: Check installation
+        if: runner.os != 'Windows'
+        run: |
+          chmod a+x ./inst/installer.sh
+          ./inst/installer.sh

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ravemanager
 Title: Manage 'RAVE' Packages
-Version: 1.0.35
+Version: 1.0.36
 Authors@R: 
     person("Zhengjia", "Wang", email = "[email protected]", 
            role = c("aut", "cre"))
@@ -14,6 +14,8 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 URL: https://dipterix.org/ravemanager/,
     http://dipterix.org/ravemanager/
+Imports:
+    utils
 Suggests: 
     learnr,
     pkgload,

NAMESPACE

@@ -12,6 +12,7 @@ export(ravemanager_version)
 export(remove_conda)
 export(run_tutorials)
 export(system_requirements)
+export(uninstall)
 export(update_rave)
 export(upgrade_installer)
 export(validate_python)

R/check.R

@@ -6,17 +6,10 @@ is_installed <- function(pkg) {
 }
 
 #' Print out 'RAVE' version information
-#' @param nightly whether to check 'nightly' build which contains the newest
-#' experimental features. However, 'nightly' builds are not stable. This
-#' option is only recommended for zero-day bug fixes.
 #' @param vanilla whether to use vanilla packages in this function
 #' @export
-version_info <- function(nightly = FALSE, vanilla = FALSE) {
-  if( nightly ) {
-    options("ravemanager.nightly" = TRUE)
-  } else {
-    options("ravemanager.nightly" = FALSE)
-  }
+version_info <- function(vanilla = FALSE) {
+  options("ravemanager.nightly" = FALSE)
 
   versions <- new.env()
   versions$ravemanager <- list(
@@ -102,10 +95,10 @@ version_info <- function(nightly = FALSE, vanilla = FALSE) {
         # message('    lib_path <- Sys.getenv("RAVE_LIB_PATH", unset = Sys.getenv("R_LIBS_USER", unset = .libPaths()[[1]]))')
         # message('    loadNamespace("ravemanager", lib.loc = lib_path)')
         cli$cli_text(cli$col_cyan(sprintf('loadNamespace("ravemanager", lib.loc = "%s")', get_libpaths(first = TRUE, check = TRUE))))
-        if( nightly ) {
-          cli$cli_text(cli$col_cyan('ravemanager::update_rave(nightly = TRUE)'))
-        } else {
+        if( isFALSE(ravemanager_needsUpdate) ) {
           cli$cli_text(cli$col_cyan('ravemanager::update_rave()'))
+        } else {
+          cli$cli_text(cli$col_cyan('ravemanager::update_rave(allow_cache = FALSE)'))
         }
         cat("\n")
       }
@@ -136,9 +129,9 @@ version_info <- function(nightly = FALSE, vanilla = FALSE) {
           '    lib_path <- Sys.getenv("RAVE_LIB_PATH", unset = Sys.getenv("R_LIBS_USER", unset = .libPaths()[[1]]))',
           '    loadNamespace("ravemanager", lib.loc = lib_path)',
           ifelse(
-            nightly,
-            '    ravemanager::update_rave(nightly = TRUE)',
-            '    ravemanager::update_rave()'
+            isFALSE(ravemanager_needsUpdate),
+            '    ravemanager::update_rave()',
+            '    ravemanager::update_rave(allow_cache = FALSE)'
           ),
           sep = "\n"
         ),

R/install.R

@@ -3,7 +3,7 @@
 #' @description Installs the newest version of 'RAVE' and its dependence
 #' packages; executes the scripts to finalize installation to update
 #' configuration files.
-#' @param nightly whether to install the nightly build
+#' @param allow_cache whether to allow cache; default is true
 #' @param upgrade_manager whether to upgrade the installer (\code{ravemanager})
 #' before updating other packages
 #' @param force whether to force updating packages even the installed have
@@ -306,11 +306,25 @@ assert_r_version <- function(min = "4.0.0") {
   return(TRUE)
 }
 
+pak_cache_dir <- function() {
+  tools <- asNamespace("tools")
+  tools$R_user_dir("ravemanager", which = "cache")
+}
+
+pak_cache_remove <- function() {
+  cache_path <- pak_cache_dir()
+  if(file.exists(cache_path)) {
+    message("Removing package cache...")
+    unlink(cache_path, recursive = TRUE)
+  }
+  invisible()
+}
+
 try_setup_pak <- function(lib_path = get_libpaths(check = TRUE)) {
   cdir <- NULL
   tryCatch({
-    tools <- asNamespace("tools")
-    cdir <- dir_create2(tools$R_user_dir("ravemanager", which = "cache"))
+
+    cdir <- dir_create2(pak_cache_dir())
 
     # Try to install package `pak`
     if(system.file(package = "pak") == "") {
@@ -357,6 +371,11 @@ installer_unload_packages <- function() {
 install_internal <- function(nightly = FALSE, upgrade_manager = FALSE,
                              finalize = TRUE, force = FALSE, python = FALSE, ...) {
 
+  # DIPSAUS DEBUG START
+  # list2env(list(nightly = FALSE, upgrade_manager = FALSE,
+  #               finalize = TRUE, force = FALSE, python = FALSE), envir=.GlobalEnv)
+
+
   if( nightly ) {
     options("ravemanager.nightly" = TRUE)
   } else {
@@ -472,8 +491,15 @@ install_internal <- function(nightly = FALSE, upgrade_manager = FALSE,
 
 #' @rdname RAVE-install
 #' @export
-install <- function(nightly = FALSE, upgrade_manager = FALSE,
+install <- function(allow_cache = TRUE, upgrade_manager = FALSE,
                     finalize = TRUE, force = FALSE, python = FALSE, ...) {
+
+  if(!allow_cache) {
+    pak_cache_remove()
+  }
+
+
+  nightly <- FALSE
   tryCatch({
     install_internal(
       nightly = nightly,
@@ -597,3 +623,110 @@ upgrade_installer <- function(reload = TRUE) {
   }
   return(invisible(FALSE))
 }
+
+#' Uninstall RAVE components
+#' @description
+#' Remove cache, python, and/or all settings. Please be aware that
+#' R, 'RStudio', and already installed R packages will not be uninstalled.
+#' Please carefully read printed messages.
+#' @param components which component to remove, see example for choices.
+#' @examples
+#'
+#' if( FALSE ) {
+#'
+#'   # remove cache only
+#'   ravemanager::uninstall("cache")
+#'
+#'   # remove python environment
+#'   ravemanager::uninstall("python")
+#'
+#'   # remove all sample data, settings files
+#'   ravemanager::uninstall("all")
+#'
+#' }
+#'
+#'
+#' @export
+uninstall <- function(components = c("cache", "python", "all")) {
+  components <- match.arg(components)
+  remove_cache <- components %in% c("cache", "all")
+  remove_python <- components %in% c("python", "all")
+  remove_all <- components %in% c("all")
+
+  if( remove_all ) {
+    ans <- utils::askYesNo("You are uninstalling RAVE. Please enter Y or yes to confirm: ")
+    if(!isTRUE(ans)) {
+      return(invisible())
+    }
+  }
+
+  tools <- asNamespace("tools")
+  R_user_dir <- tools$R_user_dir
+
+  remove_files <- function(paths) {
+    lapply(paths, function(path) {
+      if(!file.exists(path)) { return() }
+      if(dir.exists(path)) {
+        unlink(path, recursive = TRUE)
+      } else {
+        unlink(path)
+      }
+      return()
+    })
+  }
+  if( remove_cache ) {
+    message("Removing cache...")
+
+    # ravemanager
+    pak_cache_remove()
+
+    # raveio
+    d <- R_user_dir(package = "raveio", which = "data")
+    fs <- list.files(d, pattern = "^(dipterix|rave-ieeg)-rave-pipelines", include.dirs = TRUE, full.names = TRUE, recursive = FALSE)
+    remove_files(fs)
+    if(is_installed("raveio")) {
+      raveio <- asNamespace("raveio")
+      raveio$clear_cached_files()
+    }
+  }
+
+  if( remove_python ) {
+    message("Removing python...")
+    remove_conda(ask = FALSE)
+
+    # rpymat
+    d <- R_user_dir(package = "rpymat", which = "config")
+    remove_files(file.path(d, "jupyter-configurations"))
+  }
+
+  if( remove_all ) {
+    message("Uninstalling RAVE (we are sorry to say goodbye)...")
+
+    # remove ~/rave_modules
+    remove_files("~/rave_modules")
+
+    remove_files( R_user_dir("raveio", "data") )
+    remove_files( R_user_dir("rpyANTs", "data") )
+    remove_files( R_user_dir("threeBrain", "data") )
+
+    remove_files( R_user_dir("raveio", "config") )
+    remove_files( R_user_dir("ravemanager", "config") )
+    remove_files( R_user_dir("rpymat", "config") )
+
+    remove_files( R_user_dir("dipsaus", "cache") )
+    remove_files( R_user_dir("ravemanager", "cache") )
+    remove_files( R_user_dir("readNSx", "cache") )
+
+    message("R and RStudio are not managed by RAVE. Please uninstall them by yourself if necessary.")
+    msg <- paste(
+      c(
+        "There are some files that may contain your data or used other packages. ",
+        "Please check them manually:\n",
+        .libPaths(),
+        normalizePath("~/rave_data", mustWork = FALSE)
+      ),
+      collapse = "\n"
+    )
+    message(msg)
+  }
+}

R/python.R

@@ -159,12 +159,11 @@ system_pkgpath <- function(package, ..., alternative = TRUE) {
 
 #' @rdname configure-python
 #' @export
-configure_python <- function(python_ver = "3.9", verbose = TRUE) {
+configure_python <- function(python_ver = "auto", verbose = TRUE) {
 
   if(!is_installed("rpymat")) {
     install_packages("rpymat")
   }
-
   rpymat <- asNamespace("rpymat")
 
   # Install conda and create a conda environment

inst/installer.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -e
+set -u
+
+SCRIPT_DIR=$(dirname "$0")
+R_CMD=$(which Rscript || echo $1)
+OS_TYPE=$(/usr/bin/uname)
+
+if [ "$2" == "--skip-sysreq" ]; then
+  echo "Skipping system requisites"
+elif [ "$OS_TYPE" == "Darwin" ]; then
+    echo "Operating System: macOS"
+    . "${SCRIPT_DIR}/shell/installer-prerequisites-osx.sh"
+elif [ "$OS_TYPE" == "Linux" ]; then
+    echo "Operating System: Linux"
+    # . "${SCRIPT_DIR}/shell/installer-prerequisites-linux.sh"
+fi
+
+
+# Load installer commons
+. "${SCRIPT_DIR}/shell/installer-common.sh"
+
+
+ohai "Operating System: ${OS_TYPE}"
+ohai "R binary path: ${R_CMD}"
+
+
+# Create a temporary directory
+tmpdir=$(mktemp -d -t "rave-installer")
+cd "${tmpdir}"
+
+ohai "Current directory: ${tmpdir}"
+
+# Install ravemanager
+lib_path=$(${R_CMD} --no-save --no-restore -e 'cat(Sys.getenv("RAVE_LIB_PATH", unset = Sys.getenv("R_LIBS_USER", unset = .libPaths()[[1]])))')
+
+ohai "R Library path: $lib_path"
+
+mkdir -p "$lib_path"
+
+
+cmd_str="
+lib_path <- '$lib_path'
+if( system.file(package = 'ravemanager', lib.loc = lib_path) == '' ) {
+  install.packages('ravemanager', repos = 'https://rave-ieeg.r-universe.dev', lib = lib_path)
+}
+loadNamespace('ravemanager', lib.loc = lib_path)
+ravemanager::install(allow_cache = FALSE)
+"
+ohai "Running R command: ${cmd_str}"
+${R_CMD} --no-save --no-restore -e "${cmd_str}"
+
+
+

inst/shell/installer-prerequisites-osx.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -u
+
+SCRIPT_DIR=$(dirname "$0")
+
+# Load installer commons
+. "${SCRIPT_DIR}/installer-common.sh"
+
+ohai "Checking sudo access (may require your password): "
+have_sudo_access true
+
+UNAME_MACHINE="$(/usr/bin/uname -m)"
+if [[ "$UNAME_MACHINE" == "arm64" ]]; then
+  # On ARM macOS, this script installs to /opt/homebrew only
+  HOMEBREW_PREFIX="/opt/homebrew"
+  HOMEBREW_REPOSITORY="${HOMEBREW_PREFIX}"
+else
+  # On Intel macOS, this script installs to /usr/local only
+  HOMEBREW_PREFIX="/usr/local"
+  HOMEBREW_REPOSITORY="${HOMEBREW_PREFIX}/Homebrew"
+fi
+
+# Install brew
+execute_sudo echo | /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+
+
+# Add brew to zsh (z-shell), bash, and sh
+# execute echo "eval \"\$($HOMEBREW_PREFIX/bin/brew shellenv)\"" >> "$HOME/.zprofile"
+# execute echo "eval \"\$($HOMEBREW_PREFIX/bin/brew shellenv)\"" >> "$HOME/.bash_profile"
+# execute echo "eval \"\$($HOMEBREW_PREFIX/bin/brew shellenv)\"" >> "$HOME/.profile"
+# Activate brew
+eval "$($HOMEBREW_PREFIX/bin/brew shellenv)"
+
+execute $HOMEBREW_PREFIX/bin/brew install hdf5 fftw libgit2 libxml2 pkg-config libjpeg libpng libtiff cmake