ENH: scripts to create/remove wrapper scripts in $FSLDIR/share/bin

etc/fslconf/createFSLWrapper.sh

+#!/bin/sh
+#
+# Create wrapper scripts in $FSLDIR/share/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 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.
+#
+# Early versions of this script would create symlinks from $FSLDIR/bin/ into
+# $FSLDIR/fslpython/envs/fslpython/bin/ (and, later, into
+# $FSLDIR/share/bin/). However, wrapper scripts are now used instead to work
+# around a couple of problems:
+#
+#  - We need python executables to exclusively use the libraries installed in
+#    the FSL conda environment. Users may have other Python environments
+#    activated, and/or libraries installed into a local site-packages
+#    directory. So we need to invoke the python interpreter in isolated mode,
+#    with the -I flag:
+#
+#        https://docs.python.org/3/using/cmdline.html#id2
+#
+#  - There is no guarantee that a shell supports shebang lines longer than 127
+#    characters. Depending on where FSL is installed, it may not be possible
+#    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 scripts
+# are in subdirectory of FSLDIR
+if [ -z "$FSLDIR" ]; then
+  exit 1
+fi
+
+case "$PREFIX" in "$FSLDIR"*)
+
+  for script in $targets; do
+    sourceScript="${PREFIX}/bin/$script"
+    targetScript="${FSLDIR}/share/bin/$script"
+
+    if [ ! -f "$sourceScript" ]; then
+      continue
+    fi
+
+    # remove target script if it already exists
+    if [ -e "$targetScript" ]; then
+      rm "$targetScript"
+    fi
+
+    # Figure out whether this is a python
+    # executable or some other type of
+    # executable. We search for these strings
+    # in source file headers to ID them as
+    # python scripts. We need to check both
+    # match "#!/usr/bin/env python" and
+    # "#!<fsldir>/bin/python...", because
+    # conda might generate one or the other
+    # in different scenarios.
+    id1=$(head -c 1024 "$sourceScript" | grep "#!/usr/bin/env python")
+    id2=$(head -c 1024 "$sourceScript" | grep "/fslpython/bin/python")
+
+    # Non-python executable - use a
+    # pass-through script
+    if [ -z "$id1" ] && [ -z "$id2" ]; then
+      echo "#!/bin/sh"                   > "$targetScript"
+      echo "$FSLDIR/bin/$script \"$@\"" >> "$targetScript"
+    else
+
+      # Python executable - run it via
+      # $FSLDIR/bin/python in isolated mode
+      echo "#!/bin/sh"                                   > "$targetScript"
+      echo "$FSLDIR/bin/python -I $sourceScript \"$@\"" >> "$targetScript"
+    fi
+
+    # Preserve file permissions
+    chmod --reference="$sourceScript" "$targetScript"
+  done
+esac

etc/fslconf/removeFSLWrapper.sh

+#!/bin/sh
+#
+# Remove wrapper script/links in $FSLDIR/share/bin/ which invoke commands
+# that are installed in $FSLDIR/bin/.  See createFSLWrapper.sh for more
+# information.
+
+targets="$@"
+
+if [ -z "$FSLDIR" ]; then
+  exit 1
+fi
+
+# Only remove if scripts are in subdirectory of FSLDIR
+case "$PREFIX" in "$FSLDIR"*)
+
+ for script in $targets; do
+    targetScript="${FSLDIR}/share/bin/$script"
+
+    if [ -f "$targetScript" ]; then
+      rm "$targetScript"
+    fi
+  done
+esac