env files need to set SIRF_PATH to where data is installed

[KrisThielemans]

SIRF-SuperBuild/env_sirf.sh.in

Line 6 in 3950a2a

SIRF_PATH=@SIRF_SOURCE_DIR@

but this means we need to have access to the source files.

Should instead be something like ${CMAKE_INSTALL_PREFIX}/share/SIRF-3.2/. see https://github.com/SyneRBI/SIRF-SuperBuild/pull/718/files#r882778578

[KrisThielemans]

SIRF finds location for install here

[KrisThielemans]

Ideally we should get rid of the use of SIRF_PATH at all. Related is SyneRBI/SIRF#904 and SyneRBI/SIRF#919

[KrisThielemans]

as we apparently haven't fixed this yet, we need to keep the sources (in #101).

@paskino, best to postpone this to 3.5 I think

[KrisThielemans]

Pending SyneRBI/SIRF#1201, so postponing

[KrisThielemans]

Likely we can now just remove SIRF_PATH completely.

[KrisThielemans]

SIRF tests still use the SIRF_PATH env variable sadly, see SyneRBI/SIRF#1235, so we cannot remove SIRF_PATH yet. However, there are a few things that probably should be resolved now.

Before going into that, note that it is currently set as

SIRF-SuperBuild/env_sirf.sh.in

Line 6 in 8ca5067

SIRF_PATH=@SIRF_SOURCE_DIR@

Also, I believe that in the new docker env, we don't have the source anymore, so SIRF_PATH will point to a non-existent path I suppose.

optionally fix now

I found a few places where SIRF_PATH is used to find the location of the gadgetron executable, but they should all use SIRF_INSTALL_PATH instead

SIRF-SuperBuild/docker/start-gadgetron-notebook.sh

Lines 31 to 34 in 8ca5067

	SB_PATH=$(dirname "$(dirname "$SIRF_PATH")")
	echo "start gadgetron"
	pushd "${SB_PATH}"
	test -x ./INSTALL/bin/gadgetron && ./INSTALL/bin/gadgetron >& ~/gadgetron.log&

SIRF-SuperBuild/.github/workflows/test_cil.sh

Line 12 in 8ca5067

$SIRF_PATH/../../INSTALL/bin/gadgetron >& ~/gadgetron.log&

SIRF-SuperBuild/docker/devel/test.sh

Lines 12 to 15 in 8ca5067

	pushd $(dirname "$(dirname "$SIRF_PATH")")
	# start gadgetron
	[ -f ./INSTALL/bin/gadgetron ] && ./INSTALL/bin/gadgetron >& gadgetron.log&

Note that these 2 VM scripts should use another way to find the location of the sources after we remove SIRF_PATH

SIRF-SuperBuild/VirtualBox/scripts/update_VM_to_full_CIL.sh

Lines 13 to 14 in 8ca5067

	if [ -z "$SIRF_PATH" -o ! -d $SIRF_PATH -o ! -d $SIRF_PATH/../STIR ]; then
	echo "Directories not found. Run update_VM.sh"

SIRF-SuperBuild/VirtualBox/scripts/update_VM_to_full_STIR.sh

Lines 14 to 15 in 8ca5067

	if [ -z "$SIRF_PATH" -o ! -d $SIRF_PATH -o ! -d $SIRF_PATH/../STIR ]; then
	echo "Directories not found. Run update_VM.sh"

fix later

I found 2 locations in the doc referring to $SIRF_PATH which will need to be adapted

SIRF-SuperBuild/README.md

Line 257 in 8ca5067

cd $SIRF_PATH

SIRF-SuperBuild/VirtualBox/documentation/Getting-started-with-SIRF.md

Line 13 in 8ca5067

cd $SIRF_PATH

long term problem?

By the way, as the docker images don't contain the build files either, I guess we don't run any SIRF tests in them (which isn't great). Is that correct, @casperdcl ?