RF: Add env var checks to removeFSLWrapper. Add more documentation for

create/removeFSLWrapper scripts.

share/fsl/sbin/createFSLWrapper

@@ -3,26 +3,31 @@
 # Create wrapper scripts in $FSLDIR/share/fsl/bin/ which invoke commands that
 # are installed in $FSLDIR/bin/.
 #
-# This script is used to create isolated versions of all executables
-# provided by FSL projects, so they can be added to the user $PATH without
-# any other executables that are installed into the conda environment that
-# is $FSLDIR/bin (for example, python, pip, tcl, etc).
+# This script is used to create isolated versions of all executables provided
+# by FSL projects, so they can be added to the user $PATH without any other
+# executables that are installed into the FSL conda environment (for example,
+# python, pip, tcl, etc).
 #
 # This script should only be invoked when FSL is being installed via the
-# fslinstaller.py script - it is not intended to be used when individual
-# FSL projects are explicitly installed into a custom conda environment.
+# fslinstaller script - it is not intended to be used when individual FSL
+# projects are explicitly installed into a custom conda environment.
+#
+# The fslinstaller script should ensure that the FSLDIR and
+# FSL_CREATE_WRAPPER_SCRIPTS variables are set appropriately before creating
+# the FSL conda environment.
+#
+# This script is intended to be called by the post-link.sh script of the conda
+# recipe for each FSL project that provides executable commands.
 #
 # Wrapper scripts will only be created if the following conditions are met:
+#
 #  - The $FSLDIR and $PREFIX environment variables are set, and
 #    are equivalent
 #  - The $FSL_CREATE_WRAPPER_SCRIPTS environment variable is set and is not
 #    empty.
-#  -
 #
-# Early versions of this script would create symlinks from $FSLDIR/bin/ into
-# $FSLDIR/fslpython/envs/fslpython/bin/ (and, later, into
-# $FSLDIR/share/fsl/bin/). However, wrapper scripts are now used instead to
-# work around a couple of problems:
+# Wrapper scripts, and not sym-links, are used to avoid a couple of potential
+# problems:
 #
 #  - We need python executables to exclusively use the libraries installed in
 #    the FSL conda environment. Users may have other Python environments
@@ -37,6 +42,11 @@
 #    to have a shebang line pointing to $FSLDIR/bin/python which does not
 #    exceed 127 characters.
 
+# Names of all executables for which wrapper
+# scripts are to be created are passed as
+# arguments
+targets="$@"
+
 # Only create wrappers if the FSL_CREATE_WRAPPER_SCRIPTS
 # environment variable is set
 if [ -z "$FSL_CREATE_WRAPPER_SCRIPTS" ]; then
@@ -53,10 +63,6 @@ if [ "$FSLDIR" != "$PREFIX" ]; then
   exit 0
 fi
 
-# Names of all executables for which wrapper
-# scripts are to be created are passed as
-# arguments
-targets=$@
 
 for script in $targets; do
   sourceScript="${PREFIX}/bin/$script"

share/fsl/sbin/removeFSLWrapper

@@ -3,21 +3,36 @@
 # Remove wrapper script/links in $FSLDIR/share/fsl/bin/ which invoke commands
 # that are installed in $FSLDIR/bin/.  See createFSLWrapper for more
 # information.
+#
+# This script is intended to be called by the pre-unlink.sh script of the
+# conda recipe for each FSL project that provides executable commands.
 
+# Names of all executables for which wrapper
+# scripts are to be created are passed as
+# arguments
 targets="$@"
 
-if [ -z "$FSLDIR" ]; then
-  exit 1
+# Note that we don't check the FSL_CREATE_WRAPPER_SCRIPTS environment variable
+# here. Wrapper scripts in $FSLDIR/share/fsl/bin/ will exist only if a
+# FSL conda packages was installed in an environment where thenb
+# FSL_CREATE_WRAPPER_SCRIPTS variable was set, so this script will simply
+# delete any wrapper scripts that exist.
+
+# Only remove wrappers if FSLDIR exists
+if [ ! -d "$FSLDIR" ]; then
+  exit 0
 fi
 
-# Only remove if scripts are in subdirectory of FSLDIR
-case "$PREFIX" in "$FSLDIR"*)
+# and if FSLDIR == PREFIX
+if [ "$FSLDIR" != "$PREFIX" ]; then
+  exit 0
+fi
 
- for script in $targets; do
-    targetScript="${FSLDIR}/share/fsl/bin/$script"
+# Only remove if scripts are in subdirectory of FSLDIR
+for script in $targets; do
+  targetScript="${FSLDIR}/share/fsl/bin/$script"
 
-    if [ -f "$targetScript" ]; then
-      rm "$targetScript"
-    fi
-  done
-esac
+  if [ -f "$targetScript" ]; then
+    rm "$targetScript"
+  fi
+done