From 7f432bca3f9b3d461a3d802cd0f9de283f7fb0f3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Dec 2021 13:12:46 +0000
Subject: [PATCH 1/4] RF: Change variable names to make script easier to follow
---
share/fsl/sbin/createFSLWrapper | 70 ++++++++++++++++++---------------
1 file changed, 38 insertions(+), 32 deletions(-)
diff --git a/share/fsl/sbin/createFSLWrapper b/share/fsl/sbin/createFSLWrapper
index 5ad8a0b..07dfab0 100755
--- a/share/fsl/sbin/createFSLWrapper
+++ b/share/fsl/sbin/createFSLWrapper
@@ -48,7 +48,7 @@
# file systems are usually case-sensitive.
#
# To work around this, and to not accidentally create a link called <Command>
-# to <command>, the FSL package post link scripts should only specify
+# to <command>, the FSL package post link scripts must only specify
# "<Command>_gui", and *not* "<Command>". This script will create a wrapper
# script for the appropriate variant ("<Command>_gui" on macOS, or "<Command>"
# on Linux).
@@ -60,60 +60,66 @@ targets="$@"
# Only create wrappers if the FSL_CREATE_WRAPPER_SCRIPTS
# environment variable is set
-if [ -z "$FSL_CREATE_WRAPPER_SCRIPTS" ]; then
+if [ -z "${FSL_CREATE_WRAPPER_SCRIPTS}" ]; then
exit 0
fi
# Only create wrappers if FSLDIR exists
-if [ ! -d "$FSLDIR" ]; then
+if [ ! -d "${FSLDIR}" ]; then
exit 0
fi
# and if FSLDIR == PREFIX
-if [ "$FSLDIR" != "$PREFIX" ]; then
+if [ "${FSLDIR}" != "${PREFIX}" ]; then
exit 0
fi
-for script in $targets; do
- sourceScript="${PREFIX}/bin/$script"
+for targetName in ${targets}; do
- # Wrapper script for a FSL TCL GUI - here, we
- # remove the _gui suffix if no source file
- # exists (in which we are likely running on
- # Linux).
- if [[ "$script" == *"_gui" ]] && [ ! -f "$sourceScript" ]; then
- script=${script/_gui/}
- sourceScript="${PREFIX}/bin/$script"
- fi
+ target="${PREFIX}/bin/${targetName}"
- targetScript="${FSLDIR}/share/fsl/bin/$script"
+ # Wrapper script for a FSL TCL GUI - here,
+ # we remove the _gui suffix if the target
+ # file does not exist (in which case we are
+ # likely running on Linux).
+ if [[ "${targetName}" == *"_gui" ]] && [ ! -f "${target}" ]; then
+ targetName=${targetName/%_gui}
+ target=${target/%_gui}
+ fi
- if [ ! -f "$sourceScript" ]; then
+ # Don't create wrapper scripts for non-
+ # existent targets (e.g. the post-link.sh
+ # script for a package may be out-dated,
+ # and request wrappers for commmands that
+ # have been removed).
+ if [ ! -f "${target}" ]; then
continue
fi
+ wrapper="${FSLDIR}/share/fsl/bin/${targetName}"
+
# create share/fsl/bin/ if it doesn't
# already exist
- if [ ! -e "$FSLDIR/share/fsl/bin" ]; then
- mkdir -p "$FSLDIR/share/fsl/bin"
+ if [ ! -e "${FSLDIR}/share/fsl/bin" ]; then
+ mkdir -p "${FSLDIR}/share/fsl/bin"
fi
- # remove target script if it already exists
- if [ -e "$targetScript" ]; then
- rm "$targetScript"
+ # remove wrapper script if it already exists
+ if [ -e "${wrapper}" ]; then
+ rm "${wrapper}"
fi
# Figure out whether this is a python
# executable or some other type of
# executable.
- id=$(head -c 1024 "$sourceScript" | grep -e '^#!.*pythonw\?$')
+ id=$(head -c 1024 "${target}" | grep -e '^#!.*pythonw\?$')
# Non-python executable - use
# a pass-through script
- if [ -z "$id" ]; then
- echo "#!/usr/bin/env bash" > "$targetScript"
- echo "$FSLDIR/bin/$script "'"$@"' >> "$targetScript"
+ if [ -z "${id}" ]; then
+ echo "#!/usr/bin/env bash" > "${wrapper}"
+ echo "${target} "'"$@"' >> "${wrapper}"
else
# Python executable - run it via
@@ -121,21 +127,21 @@ for script in $targets; do
# mode. Under macOS, GUI apps are
# invoked with pythonw, so we need
# to preserve the interpreter.
- if [[ "$id" == *"pythonw" ]]; then
+ if [[ "${id}" == *"pythonw" ]]; then
interp="pythonw"
else
interp="python"
fi
- echo "#!/usr/bin/env bash" > "$targetScript"
- echo "${FSLDIR}/bin/${interp} -I $sourceScript "'"$@"' >> "$targetScript"
+ echo "#!/usr/bin/env bash" > "${wrapper}"
+ echo "${FSLDIR}/bin/${interp} -I ${target} "'"$@"' >> "${wrapper}"
fi
# Preserve file permissions
- if [[ "$OSTYPE" == "darwin"* ]]; then
- perms=$(stat -f "%A" "$sourceScript")
- chmod ${perms} "$targetScript"
+ if [[ "${OSTYPE}" == "darwin"* ]]; then
+ perms=$(stat -f "%A" "${target}")
+ chmod ${perms} "${wrapper}"
else
- chmod --reference="$sourceScript" "$targetScript"
+ chmod --reference="${target}" "${wrapper}"
fi
done
--
GitLab
From 5ab211b1bf233746e0aabb1814aad3f34e93c737 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Dec 2021 17:12:50 +0000
Subject: [PATCH 2/4] ENH: New option in createFSLWrapper to generate wrapper
script with different name to executable
---
share/fsl/sbin/createFSLWrapper | 75 +++++++++------------------------
share/fsl/sbin/removeFSLWrapper | 29 +++++++++----
2 files changed, 41 insertions(+), 63 deletions(-)
diff --git a/share/fsl/sbin/createFSLWrapper b/share/fsl/sbin/createFSLWrapper
index 07dfab0..5093df3 100755
--- a/share/fsl/sbin/createFSLWrapper
+++ b/share/fsl/sbin/createFSLWrapper
@@ -1,57 +1,15 @@
#!/usr/bin/env bash
#
# Create wrapper scripts in $FSLDIR/share/fsl/bin/ which invoke commands that
-# are installed in $FSLDIR/bin/.
+# are installed in $FSLDIR/bin/. Calling this script like:
#
-# 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).
+# createFSLWrapper command1 command2 command3
#
-# 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.
+# will cause wrapper scripts to be created in $FSLDIR/share/fsl/bin/, which
+# call the commands of the same name in $FSLDIR/bin/, i.e.:
#
-# This script should only be invoked when FSL is being installed via the
-# 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.
-#
-# 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.
-#
-# 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
-# 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.
-#
-# Wrapper scripts are created for *all* FSL commands, including FSL TCL GUI
-# commands (e.g. "fsl", "Flirt", "Flirt_gui", etc). FSL TCL GUIs are called
-# (e.g.) "<Command>" om Linux, but "<Command>_gui" on macOS, because macOS
-# file systems are usually case-sensitive.
-#
-# To work around this, and to not accidentally create a link called <Command>
-# to <command>, the FSL package post link scripts must only specify
-# "<Command>_gui", and *not* "<Command>". This script will create a wrapper
-# script for the appropriate variant ("<Command>_gui" on macOS, or "<Command>"
-# on Linux).
+# $FSLDIR/share/fsl/bin/command1 calls $FSLDIR/bin/command1
+# $FSLDIR/share/fsl/bin/command2 calls $FSLDIR/bin/command2
# Names of all executables for which wrapper
# scripts are to be created are passed as
@@ -75,16 +33,27 @@ if [ "${FSLDIR}" != "${PREFIX}" ]; then
fi
-for targetName in ${targets}; do
+for target in ${targets}; do
+
+ # A wrapper script with a different
+ # name to the target can be created
+ # by passing "targetName=wrapperName"
+ if [[ "${target}" == *"="* ]]; then
+ wrapper=${target#*=}
+ target=${target%=*}
+ else
+ wrapper=${target}
+ fi
- target="${PREFIX}/bin/${targetName}"
+ target="${FSLDIR}/bin/${target}"
+ wrapper="${FSLDIR}/share/fsl/bin/${wrapper}"
# Wrapper script for a FSL TCL GUI - here,
# we remove the _gui suffix if the target
# file does not exist (in which case we are
# likely running on Linux).
- if [[ "${targetName}" == *"_gui" ]] && [ ! -f "${target}" ]; then
- targetName=${targetName/%_gui}
+ if [[ "${target}" == *"_gui" ]] && [ ! -f "${target}" ]; then
+ wrapper=${wrapper/%_gui}
target=${target/%_gui}
fi
@@ -97,8 +66,6 @@ for targetName in ${targets}; do
continue
fi
- wrapper="${FSLDIR}/share/fsl/bin/${targetName}"
-
# create share/fsl/bin/ if it doesn't
# already exist
if [ ! -e "${FSLDIR}/share/fsl/bin" ]; then
diff --git a/share/fsl/sbin/removeFSLWrapper b/share/fsl/sbin/removeFSLWrapper
index 8b42934..6e122d7 100755
--- a/share/fsl/sbin/removeFSLWrapper
+++ b/share/fsl/sbin/removeFSLWrapper
@@ -1,7 +1,7 @@
#!/usr/bin/env bash
#
# Remove wrapper script/links in $FSLDIR/share/fsl/bin/ which invoke commands
-# that are installed in $FSLDIR/bin/. See createFSLWrapper for more
+# that are installed in $FSLDIR/bin/. See createFSLWrapper for more
# information.
#
# This script is intended to be called by the pre-unlink.sh script of the
@@ -19,25 +19,36 @@ targets="$@"
# delete any wrapper scripts that exist.
# Only remove wrappers if FSLDIR exists
-if [ ! -d "$FSLDIR" ]; then
+if [ ! -d "${FSLDIR}" ]; then
exit 0
fi
# and if FSLDIR == PREFIX
-if [ "$FSLDIR" != "$PREFIX" ]; then
+if [ "${FSLDIR}" != "${PREFIX}" ]; then
exit 0
fi
# Only remove if scripts are in subdirectory of FSLDIR
-for script in $targets; do
- targetScript="${FSLDIR}/share/fsl/bin/$script"
+for target in ${targets}; do
+
+ # A wrapper script with a different
+ # name to the target can be created
+ # by passing "targetName=wrapperName"
+ if [[ "${target}" == *"="* ]]; then
+ wrapper=${target#*=}
+ target=${target%=*}
+ else
+ wrapper=${target}
+ fi
+
+ wrapper="${FSLDIR}/share/fsl/bin/${wrapper}"
# See comment about FSL GUIs in post-link.sh
- if [[ "$targetScript" == *"_gui" ]] && [ ! -f "$targetScript" ]; then
- targetScript=${targetScript/_gui/}
+ if [[ "${target}" == *"_gui" ]] && [ ! -f "${wrapper}" ]; then
+ wrapper=${wrapper/%_gui}
fi
- if [ -f "$targetScript" ]; then
- rm "$targetScript"
+ if [ -f "${wrapper}" ]; then
+ rm "${wrapper}"
fi
done
--
GitLab
From eeb2580ca43eeb40bb2143cc13c4bb090015f224 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Dec 2021 17:13:20 +0000
Subject: [PATCH 3/4] TEST: Test createFSLWrapper rename capability
---
tests/test_create_remove_wrapper.py | 40 +++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/tests/test_create_remove_wrapper.py b/tests/test_create_remove_wrapper.py
index b2abcce..624fd5e 100755
--- a/tests/test_create_remove_wrapper.py
+++ b/tests/test_create_remove_wrapper.py
@@ -305,6 +305,46 @@ def test_create_wrappers_no_handle_gui_wrappers():
assert not op.exists(wrapper)
+def test_create_wrappers_rename():
+ """Tests the renaming functionality in createFSLWrapper. If
+ $FSLDIR/bin/script exists, a wrapper with a different name
+ (e.g. $FSLDIR/share/fsl/bin/renamed_script) can be created by passing
+ "script=renamed_script".
+ """
+
+ # Keys are passed to createFSLWrapper, values
+ # are wrappers that should be created
+ scripts = {
+ 'script1=renamed_script1' : 'renamed_script1',
+ 'script2=renamed_script2' : 'renamed_script2',
+ 'script3_gui=renamed_script3_gui' : 'renamed_script3_gui',
+ 'script4_gui=renamed_script4' : 'renamed_script4'
+ }
+
+ with temp_fsldir() as (fsldir, wrapperdir):
+ for script in scripts.keys():
+ target = script.split('=')[0]
+ with open(target, 'wt') as f:
+ touch(op.join(fsldir, 'bin', target))
+
+ for wrappers in it.permutations(scripts.keys()):
+ args = ' '.join(wrappers)
+ run(f'{CREATE_WRAPPER} {args}')
+
+ for arg in wrappers:
+ target = arg.split('=')[0]
+ wrapper = op.join(wrapperdir, scripts[arg])
+
+ assert op.exists(wrapper)
+ assert get_called_command(wrapper) == target
+
+ run(f'{REMOVE_WRAPPER} {args}')
+ for arg in wrappers:
+ target = scripts[arg]
+ wrapper = op.join(wrapperdir, target)
+ assert not op.exists(wrapper)
+
+
if __name__ == '__main__':
# base dir can be speecified on command line
if len(sys.argv) > 1:
--
GitLab
From 1393d89493cf2589e6d9d34f910721fa38db7fda Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 31 Dec 2021 17:14:24 +0000
Subject: [PATCH 4/4] DOC: changelog
---
CHANGELOG.md | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1b86a7a..58f02a9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
# FSL base project changelog
+## 2112.6 (Thursday 31st December 2021)
+
+* The `createFSLWrapper` script nowe has the ability to generate a wrapper
+ script with a name different to the called executable.
+
## 2112.5 (Thursday 30th December 2021)
--
GitLab