Improved script argument parsing (any order), plus couple tiny tweaks

README.md

@@ -236,7 +236,7 @@ scp -o sftp_server="singularity -s exec --overlay=/data/HCPsquash/hcp1200-00-100
 or more simply using the same type of wrapper described for sshfs:
 
 ```bash
-sshfs -o sftp_server="/data/HCPsquash/sing_sftpd_here" user@computer2:/HCP_1200_data/remote_file.txt localfile.txt
+scp -o sftp_server="/data/HCPsquash/sing_sftpd_here" user@computer2:/HCP_1200_data/remote_file.txt localfile.txt
 ```
 
 ### f) Extracting data using rsync

bin/sing_command

@@ -22,7 +22,7 @@
 #  sing_sftpd_here   # default sqfs and image: in install dir
 #  sing_rsync_here   # default sqfs and image: in install dir
 
-VERSION="3.0"
+VERSION="3.1"
 BASENAME=$(basename $0)
 PREFIX="" # -D option
 
@@ -51,6 +51,7 @@ RSYNC_COMMAND="rsync" # hopefully it's in the search path in the container
 
 # Documentation and usage statement
 function usage() {
+  local rc=${1:-2}  # ability to exit with a different code if provided
   cat <<USAGE 1>&2
 This is $BASENAME $VERSION by Pierre Rioux
 
@@ -60,8 +61,6 @@ program, it will run the OpenSSH 'sftp-server', or the 'rsync' command.
 
 Usage: $BASENAME [-D directory] [-I singularity_image_file] [-O overlay_file_pattern] [command...]
 
-Note: options must be provided in the order shown!
-
 where:
 
   -D directory
@@ -130,7 +129,7 @@ Examples:
  sing_sftpd -D /my/path/for/everything
 
 USAGE
-  exit 2
+  exit $rc
 }
 
 ##########################################
@@ -143,36 +142,42 @@ if test "X${BASENAME/*_here/Y}" = "XY" ; then
   PREFIX=$(dirname $(readlink -e "$0")) || exit
 fi
 
-####################################
-# Validation of arguments
-####################################
+#####################################
+# Parsing and validation of arguments
+#####################################
 
 if test -z "$PREFIX" -a $# -lt 2 ; then
   usage
 fi
 
-# Optional PREFIX in -D
-if test "X$1" = "X-D" ; then
-  PREFIX="$2"
-  shift ; shift
-  if ! test -d "$PREFIX" ; then
-    echo "Error: '$PREFIX' for option -D is not a directory." 1>&2
-    exit 2
-  fi
-fi
-
-# Option -I: the path of the singularity image
-if test "X$1" = "X-I" ; then
-  test $# -lt 2 && usage
-  SING_IMAGE="$2" # can be empty string if -D provided
-  shift ; shift
-fi
-
-# Option -O: the path (or pattern) for one or several overlay images
-if test "X$1" = "X-O" ; then
-  test $# -lt 2 && usage
-  OVERLAYS="$2";  # can also be empty if -D provided
-  shift ; shift
+SING_IMAGE="" # can be empty string if -D provided
+OVERLAYS=""   # can also be empty if -D provided
+while test -n "$1" ; do
+  case "$1" in
+    -D)
+      test $# -lt 2 && usage
+      PREFIX="$2"
+      shift ; shift ;;
+    -I)
+      test $# -lt 2 && usage
+      SING_IMAGE="$2"
+      shift ; shift ;;
+    -O)
+      test $# -lt 2 && usage
+      OVERLAYS="$2"
+      shift ; shift ;;
+    -h | -help | --help)
+      usage 0
+    *)
+      # Must be command and/or arguments, leave as is
+      break ;;
+  esac
+done
+
+# Sanity check for optional PREFIX in -D
+if ! test -d "$PREFIX" ; then
+  echo "Error: '$PREFIX' for option -D is not a directory." 1>&2
+  exit 2
 fi
 
 # Find image and overlays if necessary
@@ -209,7 +214,7 @@ fi
 # Validate overlays patterns
 if test -z "$OVERLAYS" ; then
   echo "Error: no patterns for the overlays files provided." 1>&2
-  echo "Maybe you need to provide the path with -O ?"        1>&2
+  echo "Maybe you need to provide the pattern with -O ?"        1>&2
   exit 2
 fi
 
@@ -250,11 +255,6 @@ if test "$MODE" = "shell" ; then
   fi
 fi
 
-if test "X$*" = "X-h" -o "X$*" = "X-help" -o "X$*" = "X--help" ; then
-  usage
-  exit 2
-fi
-
 if test $MODE = "exec" ; then
   # OK do the main work now.
   #
@@ -264,7 +264,7 @@ if test $MODE = "exec" ; then
   exec singularity -s exec \
     $SING_OVERLAYS         \
     $SING_IMAGE            \
-    bash -c "exec $COMMAND $*"
+    bash -c "exec $COMMAND $@"
 else # interactive shell
   exec singularity -s shell \
     $SING_OVERLAYS          \