allow prerequisite run without sudo

inst/installer.sh

@@ -4,7 +4,9 @@ set -u
 
 SCRIPT_DIR=$(dirname "$0")
 OS_TYPE=$(/usr/bin/uname)
-R_CMD=$(/usr/bin/which Rscript)
+R_CMD=$(/usr/bin/which Rscript || echo "Rscript")
+
+# 0 no install; 1 assuming no sudo access; 2 have sudo
 SYSREQ="1"
 
 while getopts ":s:r:" opt; do
@@ -34,10 +36,10 @@ ohai "R binary path: ${R_CMD}"
 if [ "${SYSREQ}" == "1" ]; then
   if [ "$OS_TYPE" == "Darwin" ]; then
       ohai "Operating System: macOS"
-      . "${SCRIPT_DIR}/shell/installer-prerequisites-osx.sh"
+      . "${SCRIPT_DIR}/shell/installer-prerequisites-osx.sh" -s "${SYSREQ}"
   elif [ "$OS_TYPE" == "Linux" ]; then
       ohai "Operating System: Linux"
-      # . "${SCRIPT_DIR}/shell/installer-prerequisites-linux.sh"
+      # . "${SCRIPT_DIR}/shell/installer-prerequisites-linux.sh" -s "${SYSREQ}"
   fi
 else
   ohai "Skipping system requisites"
@@ -64,10 +66,12 @@ 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)
+ravemanager::install(allow_cache = FALSE, python = TRUE)
 "
 ohai "Running R command: ${cmd_str}"
 ${R_CMD} --no-save --no-restore -e "${cmd_str}"
 
+ohai "Check python loading"
 
+execute ${R_CMD} --no-save --no-restore -e "rpyANTs::load_ants()"
 

inst/shell/installer-prerequisites-osx.sh

@@ -2,14 +2,28 @@
 
 set -u
 
+SYSREQ="1"
+while getopts ":s:" opt; do
+  case $opt in
+    s)
+      SYSREQ="$OPTARG"
+      ;;
+    \?)
+      echo "Invalid option: -$OPTARG" >&2
+      exit 1
+      ;;
+    :)
+      echo "Option -$OPTARG requires an argument." >&2
+      exit 1
+      ;;
+  esac
+done
+
 # 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
@@ -21,8 +35,15 @@ else
   HOMEBREW_REPOSITORY="${HOMEBREW_PREFIX}/Homebrew"
 fi
 
-# Install brew
-execute_sudo echo | /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+if [ "${SYSREQ}" == "2" ]; then
+  ohai "Checking sudo access (may require your password): "
+  have_sudo_access true
+
+  # Install brew
+  execute_sudo echo | /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+fi
+
+
 
 
 # Add brew to zsh (z-shell), bash, and sh

tests/testthat/test-installation.R

@@ -1,2 +1,50 @@
 # DIPSAUS DEBUG START
 # library(testthat)
+
+remove_conda <- function() {
+  try(silent = TRUE, {
+    rpymat <- asNamespace("rpymat")
+    root <- normalizePath(rpymat$install_root(), mustWork = FALSE)
+    unlink(root, recursive = TRUE, force = TRUE)
+  })
+}
+
+get_os <- function ()
+{
+  if ("windows" %in% tolower(.Platform$OS.type)) {
+    return("windows")
+  }
+  os <- tolower(R.version$os)
+  if (startsWith(os, "darwin")) {
+    return("darwin")
+  }
+  if (startsWith(os, "linux")) {
+    return("linux")
+  }
+  if (startsWith(os, "solaris")) {
+    return("solaris")
+  }
+  if (startsWith(os, "win")) {
+    return("windows")
+  }
+  return("unknown")
+}
+
+test_that("Installation works", {
+  if(detect_gh_ci() && get_os() == "windows") {
+    ravemanager::install()
+    libpath <- .libPaths()[[1]]
+    expect_true(nzchar(system.file(package = "ravebuiltins", lib.loc = libpath)))
+    expect_true(nzchar(system.file(package = "rpyANTs", lib.loc = libpath)))
+    rpyANTs <- asNamespace("rpyANTs")
+    rpymat <- asNamespace("rpymat")
+
+    on.exit({
+      remove_conda()
+    })
+
+    # remove_conda()
+    # ravemanager::configure_python()
+    # expect_s3_class(rpyANTs$ants, c("ants.proxy", "python.builtin.module"))
+  }
+})