New build system

2 files changed, 20 insertions, 167 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 685796eb6be8..57f07d5ff29b 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,50 +1,12 @@
 pkgbase = fsl
 	pkgdesc = A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
-	pkgver = 6.0.5.1
-	pkgrel = 6
+	pkgver = 6.0.6.2
+	pkgrel = 1
 	url = http://www.fmrib.ox.ac.uk/fsl/
 	arch = x86_64
 	license = custom
-	makedepends = boost
-	makedepends = fftw
-	makedepends = inetutils
-	depends = gd
-	depends = libxml2
-	depends = libxml++2.6
-	depends = gsl
-	depends = libpng
-	depends = nlopt
-	depends = newmat
-	depends = tcl
-	depends = tk
-	depends = zlib
 	depends = python
-	depends = glu
-	depends = boost-libs
-	depends = vtk
-	depends = sqlite
-	depends = fslpy>=3.7.0
-	depends = bc
-	depends = openblas
-	depends = fmt
-	depends = pugixml
-	depends = tbb
-	optdepends = cuda-9.1
-	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-sources.tar.gz
-	source = https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-feeds.tar.gz
-	source = buildSettings.mk
-	source = fsl_sub
-	source = 001-use_distribution_environment.patch
-	source = 002-fix_fsl_exec_empty_errorCode.patch
-	source = 003-fix_missing_LIB_PROB.patch
-	source = 004-fix_mist_discard.patch
-	sha256sums = d8ab2ebc87d3e33ce1097dde18d8a55f62d4a27b45efc4f68adccfb6e8e1425c
-	sha256sums = 12aadb3bf48b1f0624aebc83f7e4b9fa46fb513b816b8ca29b0dee96570405fc
-	sha256sums = 08eba697dfd9f9e9d102ab2a73b506f48a9c946a55a14393ed9743c3a0387bc5
-	sha256sums = 2516982d151ab9e450a9ac6d5a6fc87099a7acc067514d80422c69950e618170
-	sha256sums = 906ac7de8068e5a5487b083844b50b6afd7562866088a4175fd88030182affdd
-	sha256sums = 64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a
-	sha256sums = adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04
-	sha256sums = 1ea3ef517e9692ea8e95076c5eb0b759637672df41ace9619b50c2c9fa8216c2
+	source = https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
+	sha256sums = 898e53c62814d9c8df8ae4f2abc3f79ad7c91aaf497b3f36b39310a8c4a369d0
 
 pkgname = fsl
diff --git a/PKGBUILD b/PKGBUILD
index d18e32ca4146..22ab82c75819 100755
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,145 +1,36 @@
 # Maintainer: Tobias Bachmann <tobachmann@gmx.de>
 # Contributor: fishburn <frankthefishburn@gmail.com>
 
-# Set number of parallel compile jobs, default equals number of CPUs
-NJOBS=$(nproc)
-
-# Run makepkg or your usual AUR helper with CUDA=1 as an environment variable
-# or uncomment the following line ('cuda-9.1' from the AUR is needed)
-#CUDA=1
-
 pkgname=fsl
-pkgver=6.0.5.1
-pkgrel=6
+pkgver=6.0.6.2
+pkgrel=1
 pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data"
 arch=("x86_64")
 url="http://www.fmrib.ox.ac.uk/fsl/"
 license=('custom')
-depends=('gd' 'libxml2' 'libxml++2.6' 'gsl' 'libpng' 'nlopt' 'newmat' 'tcl' 'tk' 'zlib' 'python' 'glu' 'boost-libs' 'vtk' 'sqlite' 'fslpy>=3.7.0' 'bc' 'openblas' 'fmt' 'pugixml' 'tbb')
-makedepends=('boost' 'fftw' 'inetutils')
-optdepends=('cuda-9.1')
-source=("https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz"
-        "https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-feeds.tar.gz"
-	"buildSettings.mk"
-	"fsl_sub"
-	"001-use_distribution_environment.patch"
-	"002-fix_fsl_exec_empty_errorCode.patch"
-	"003-fix_missing_LIB_PROB.patch"
-	"004-fix_mist_discard.patch")
-
-sha256sums=('d8ab2ebc87d3e33ce1097dde18d8a55f62d4a27b45efc4f68adccfb6e8e1425c'
-	    '12aadb3bf48b1f0624aebc83f7e4b9fa46fb513b816b8ca29b0dee96570405fc'
-	    '08eba697dfd9f9e9d102ab2a73b506f48a9c946a55a14393ed9743c3a0387bc5'
-	    '2516982d151ab9e450a9ac6d5a6fc87099a7acc067514d80422c69950e618170'
-	    '906ac7de8068e5a5487b083844b50b6afd7562866088a4175fd88030182affdd'
-	    '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a'
-	    'adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04'
-	    '1ea3ef517e9692ea8e95076c5eb0b759637672df41ace9619b50c2c9fa8216c2')
-
-prepare() {
-	cd "${srcdir}"
-	export FSLDIR="${srcdir}/fsl"
-	. "${FSLDIR}/etc/fslconf/fsl.sh"
-	export FSLMACHTYPE=$(${FSLDIR}/etc/fslconf/fslmachtype.sh)
-        # We only create this dir to keep 'build' from complaining
-	mkdir "${FSLDIR}/config/${FSLMACHTYPE}"
-        
-	# Apply patches
-	patch -Np1 -i "${srcdir}"/001-use_distribution_environment.patch
-	# From https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e8fa48c1.1501
-	patch -Np1 -i "${srcdir}"/002-fix_fsl_exec_empty_errorCode.patch
-	# I'm not sure why -L${LIB_PROB} is missing in some Makefiles 
-	patch -Np1 -i "${srcdir}"/003-fix_missing_LIB_PROB.patch
-	# Recent glibc related upgrade (?) broke compilation of mist's shape.cpp due to binding unbindable types
-	patch -Np1 -i "${srcdir}"/004-fix_mist_discard.patch
+depends=('python')
+source=("https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py")
 
-	# Insert makepkg build flags into configuration
-	sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk"
-	sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CPPFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk"
-	sed -i '1,/${AccumulatedIncFlags}/!{s^${AccumulatedIncFlags}^& '"${CXXFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk"
-	sed -i '1,/${AccumulatedIncFlags}/!{s^${AccumulatedIncFlags}^& '"${CPPFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk"
-	sed -i 's^LDFLAGS = .*$^& '"${LDFLAGS}"'^g' "${srcdir}/fsl/config/common/vars.mk"
-        
-        echo -e "\n"
-        if [ -n "${CUDA}" ] && [ ${CUDA} -eq 1 ]; then
-            sed -i 's/COMPILE_GPU\ \=\ 0/COMPILE_GPU\ \=\ 1/g' "${srcdir}"/buildSettings.mk
-            # With CUDA enabled, ptx2 has to be compiled without --std=c++11
-            sed -i '26 a GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long' "${srcdir}"/fsl/src/ptx2/Makefile
-            echo "CUDA support is enabled. You need to install 'cuda-9.1' from the AUR first."
-        else
-            echo "CUDA support is disabled. To enable, set CUDA=1 in the PKGBUILD or as an environment variable."
-        fi
-        echo "Number of parallel compile jobs: ${NJOBS}"
-        echo -e "\n"
-	
-        cp "${srcdir}"/buildSettings.mk "${FSLDIR}"/config/
-}
+sha256sums=('898e53c62814d9c8df8ae4f2abc3f79ad7c91aaf497b3f36b39310a8c4a369d0')
 
 build() {
-        export FSLDIR="${srcdir}/fsl"
-        cd "${FSLDIR}"
-
-        MAKEOPTIONS="-j $NJOBS" ./build extras CiftiLib-master utils znzlib NewNifti fslio giftiio miscmaths newimage libvis first_lib meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc
-        MAKEOPTIONS="-j 1" ./build fslsurface # fslsurface does not like parallel compiling
-        MAKEOPTIONS="-j $NJOBS" ./build libmeshutils newmesh DiscreteOpt FastPDlib MSMRegLib misc_c topup asl_mfree avwutils basil baycest bet2 bianca cluster fsl_deface eddy fabber_core fabber_models_asl fabber_models_cest fabber_models_dce fabber_models_dsc fabber_models_dualecho fabber_models_dwi fabber_models_pet fabber_models_qbold fabber_models_t1 fast4
-        MAKEOPTIONS="-j 1" ./build fdt # fdt does not like parallel compiling and has to be built after eddy with CUDA support enabled
-        MAKEOPTIONS="-j $NJOBS" ./build feat5 film filmbabe first flameo flirt fnirt fslvbm fugue gps lesions mcflirt melodic misc_scripts miscvis mist mm MSM oxford_asl possum ptx2 qboot randomise siena slicetimer susan swe tbss verbena xtract
-
-        # Install missing binaries, which are now Python scripts and shipped with fslpy
-        /usr/bin/install -m 755 /usr/bin/{imcp,imglob,immv} "${srcdir}"/fsl/bin
-        # Install missing fsl_sub script from 6.0.4
-        /usr/bin/install -m 755 "${srcdir}"/fsl_sub "${srcdir}"/fsl/bin
-        # Create fake fslpython environment (all dependencies have been taken care of system-wide)
-        ln -s /usr/bin/python "${srcdir}"/fsl/bin/fslpython
-}
-
-
-check() {
-	export FSLDIR="${srcdir}/fsl"
-	export FEEDSDIR="${srcdir}/feeds"
-	. "${FSLDIR}/etc/fslconf/fsl.sh"
-	export PATH="${FSLDIR}/bin":${PATH}
-	cd "${FEEDSDIR}"
-	time ./RUN all
+        export TMPFSLDIR="${srcdir}/fsl"
+	mkdir -p "${TMPFSLDIR}"
+	/usr/bin/python3 "${srcdir}"/fslinstaller.py -n -o -d "${TMPFSLDIR}" -V "${pkgver}"
 }
 
 package() {
-	rm -rf "${srcdir}/fsl/src"
-	rm -rf "${srcdir}/fsl/extras/src"
-	rm -rf "${srcdir}/fsl/extras/include"
-	mkdir -p "${pkgdir}/opt/fsl"
-
-	cp -r "${srcdir}/fsl/bin"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/data"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/doc"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/etc"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/extras"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/lib"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/refdoc"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/fsl/tcl"	"${pkgdir}/opt/fsl/"
-	cp -r "${srcdir}/feeds"	        "${pkgdir}/opt/fsl/"
-
+	# Replace paths and move files in place
+	find "${TMPFSLDIR}" -type f -exec grep -Iq . {} \; -exec sed -i "s|${srcdir}|/opt|g" {} +
+	mkdir "${pkgdir}"/opt
+	mv "${TMPFSLDIR}" "${pkgdir}"/opt
+	# Copy license
+	mkdir -p "${pkgdir}"/usr/share/licenses/fsl	
+	cp "${pkgdir}"/opt/fsl/LICENCE.FSL "${pkgdir}"/usr/share/licenses/fsl/LICENSE
+	# Setup shell environment
 	mkdir -p "${pkgdir}/etc/profile.d"
 	echo 'FSLDIR=/opt/fsl' >			"${pkgdir}/etc/profile.d/fsl.sh"
 	echo '. ${FSLDIR}/etc/fslconf/fsl.sh' >>	"${pkgdir}/etc/profile.d/fsl.sh"
 	echo 'export FSLDIR' >>				"${pkgdir}/etc/profile.d/fsl.sh"
 	echo 'export PATH=$PATH:${FSLDIR}/bin' >>	"${pkgdir}/etc/profile.d/fsl.sh"
-
-	mkdir -p "${pkgdir}/usr/share/licenses/fsl"
-	grep -v \< "${srcdir}/fsl/doc/fsl/licence.html" | cat -s > "${pkgdir}/usr/share/licenses/fsl/LICENSE"
-
-	# Fix permissions
-	find "${pkgdir}" -type f -exec chmod 644 {} \;
-	find "${pkgdir}" -type d -exec chmod 755 {} \;
-	find "${pkgdir}/opt/fsl/bin" -exec chmod 755 {} \;
-	find "${pkgdir}/opt/fsl/etc/fslconf" -exec chmod 755 {} \;
-	chmod 755 "${pkgdir}/etc/profile.d/fsl.sh"
-	
-	mkdir -p "${pkgdir}/opt/fsl/feeds/results"
-	chmod -R 777 "${pkgdir}/opt/fsl/feeds/results"
-	chmod 755 "${pkgdir}/opt/fsl/feeds/RUN"
-
-	# Clean up	
-	find "${pkgdir}" -empty -delete
-	find "${pkgdir}" -type f -exec sed -i 's^/usr/local/fsl^/opt/fsl^g' "{}" \;
 }