From 4b41d56bc346c2c2e1ab1eaeb2eebd209456fde4 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Thu, 17 Sep 2020 15:25:08 -0500 Subject: Add bart-0.6.00 (#18717) This PR adds version 0.6.00 of bart. --- .../builtin/packages/bart/bart_path-0.5.00.patch | 107 +++++++++++++++++++++ .../builtin/packages/bart/bart_path-0.6.00.patch | 107 +++++++++++++++++++++ .../repos/builtin/packages/bart/bart_path.patch | 107 --------------------- var/spack/repos/builtin/packages/bart/package.py | 4 +- 4 files changed, 217 insertions(+), 108 deletions(-) create mode 100644 var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch create mode 100644 var/spack/repos/builtin/packages/bart/bart_path-0.6.00.patch delete mode 100644 var/spack/repos/builtin/packages/bart/bart_path.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch b/var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch new file mode 100644 index 0000000000..c1b6c98da5 --- /dev/null +++ b/var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch @@ -0,0 +1,107 @@ +diff -ru a/matlab/bart.m b/matlab/bart.m +--- a/matlab/bart.m 2020-04-10 18:50:50.056248692 -0500 ++++ b/matlab/bart.m 2020-04-10 18:52:20.541178180 -0500 +@@ -11,7 +11,7 @@ + return + end + +- bart_path = getenv('TOOLBOX_PATH'); ++ bart_path = [getenv('TOOLBOX_PATH') '/bin']; + isWSL = false; + + if isempty(bart_path) +diff -ru a/python/bart.py b/python/bart.py +--- a/python/bart.py 2020-04-10 18:50:50.056248692 -0500 ++++ b/python/bart.py 2020-04-10 19:18:09.481950358 -0500 +@@ -19,7 +19,7 @@ + return None + + try: +- bart_path = os.environ['TOOLBOX_PATH'] + '/bart ' ++ bart_path = os.environ['TOOLBOX_PATH'] + '/bin ' + except: + bart_path = None + isWSL = False +diff -ru a/scripts/espirit_econ.sh b/scripts/espirit_econ.sh +--- a/scripts/espirit_econ.sh 2020-04-10 18:50:50.055248693 -0500 ++++ b/scripts/espirit_econ.sh 2020-04-10 19:13:06.463193324 -0500 +@@ -56,8 +56,6 @@ + fi + + +-export PATH=$TOOLBOX_PATH:$PATH +- + input=$(readlink -f "$1") + output=$(readlink -f "$2") + +@@ -67,7 +65,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +diff -ru a/scripts/grasp.sh b/scripts/grasp.sh +--- a/scripts/grasp.sh 2020-04-10 18:50:50.055248693 -0500 ++++ b/scripts/grasp.sh 2020-04-10 19:13:31.461173327 -0500 +@@ -90,8 +90,6 @@ + fi + + +-export PATH=$TOOLBOX_PATH:$PATH +- + input=$(readlink -f "$1") + output=$(readlink -f "$2") + +@@ -101,7 +99,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +diff -ru a/scripts/octview.m b/scripts/octview.m +--- a/scripts/octview.m 2020-04-10 18:50:50.055248693 -0500 ++++ b/scripts/octview.m 2020-04-10 19:14:33.386123750 -0500 +@@ -1,6 +1,6 @@ + #! /usr/bin/octave -qf + +-addpath(strcat(getenv("TOOLBOX_PATH"), "/matlab")); ++addpath(strcat(getenv("TOOLBOX_PATH"), "/bin", "/matlab")); + arg_list = argv(); + + +diff -ru a/scripts/profile.sh b/scripts/profile.sh +--- a/scripts/profile.sh 2020-04-10 18:50:50.055248693 -0500 ++++ b/scripts/profile.sh 2020-04-10 19:15:00.723101850 -0500 +@@ -45,7 +45,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +@@ -57,7 +57,7 @@ + cd $WORKDIR + + +-nm --defined-only $TOOLBOX_PATH/bart | cut -c11-16,19- | sort > bart.syms ++nm --defined-only $TOOLBOX_PATH/bin/bart | cut -c11-16,19- | sort > bart.syms + + + cat $in | grep "^TRACE" \ +diff -ru a/startup.m b/startup.m +--- a/startup.m 2020-04-10 18:50:50.048248699 -0500 ++++ b/startup.m 2020-04-10 18:51:40.390209486 -0500 +@@ -1,4 +1,3 @@ + % set Matlab path and TOOLBOX_PATH environment variable +-addpath(fullfile(pwd, 'matlab')); +-setenv('TOOLBOX_PATH', pwd); ++addpath(fullfile(getenv('TOOLBOX_PATH'), 'matlab')); + diff --git a/var/spack/repos/builtin/packages/bart/bart_path-0.6.00.patch b/var/spack/repos/builtin/packages/bart/bart_path-0.6.00.patch new file mode 100644 index 0000000000..e5e2d200a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/bart/bart_path-0.6.00.patch @@ -0,0 +1,107 @@ +diff -ru a/matlab/bart.m b/matlab/bart.m +--- a/matlab/bart.m 2020-09-17 12:25:18.371980782 -0500 ++++ b/matlab/bart.m 2020-09-17 12:26:49.859905950 -0500 +@@ -28,7 +28,7 @@ + end + + % Check bart toolbox path +- bart_path = getenv('TOOLBOX_PATH'); ++ bart_path = [getenv('TOOLBOX_PATH') '/bin']; + isWSL = false; + if isempty(bart_path) + if exist('/usr/local/bin/bart', 'file') +diff -ru a/python/bart.py b/python/bart.py +--- a/python/bart.py 2020-09-17 12:25:18.371980782 -0500 ++++ b/python/bart.py 2020-09-17 12:27:34.161869637 -0500 +@@ -19,7 +19,7 @@ + return None + + try: +- bart_path = os.environ['TOOLBOX_PATH'] + '/bart ' ++ bart_path = os.environ['TOOLBOX_PATH'] + '/bin ' + except: + bart_path = None + isWSL = False +diff -ru a/scripts/espirit_econ.sh b/scripts/espirit_econ.sh +--- a/scripts/espirit_econ.sh 2020-09-17 12:25:18.370980783 -0500 ++++ b/scripts/espirit_econ.sh 2020-09-17 12:29:14.464787254 -0500 +@@ -56,8 +56,6 @@ + fi + + +-export PATH=$TOOLBOX_PATH:$PATH +- + input=$(readlink -f "$1") + output=$(readlink -f "$2") + +@@ -67,7 +65,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +diff -ru a/scripts/grasp.sh b/scripts/grasp.sh +--- a/scripts/grasp.sh 2020-09-17 12:25:18.370980783 -0500 ++++ b/scripts/grasp.sh 2020-09-17 12:29:56.699752498 -0500 +@@ -90,8 +90,6 @@ + fi + + +-export PATH=$TOOLBOX_PATH:$PATH +- + input=$(readlink -f "$1") + output=$(readlink -f "$2") + +@@ -101,7 +99,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +diff -ru a/scripts/octview.m b/scripts/octview.m +--- a/scripts/octview.m 2020-09-17 12:25:18.370980783 -0500 ++++ b/scripts/octview.m 2020-09-17 12:30:45.414712364 -0500 +@@ -1,6 +1,6 @@ + #! /usr/bin/octave -qf + +-addpath(strcat(getenv("TOOLBOX_PATH"), "/matlab")); ++addpath(strcat(getenv("TOOLBOX_PATH"), "/bin", "/matlab")); + arg_list = argv(); + + +diff -ru a/scripts/profile.sh b/scripts/profile.sh +--- a/scripts/profile.sh 2020-09-17 12:25:18.370980783 -0500 ++++ b/scripts/profile.sh 2020-09-17 12:31:53.517656180 -0500 +@@ -45,7 +45,7 @@ + exit 1 + fi + +-if [ ! -e $TOOLBOX_PATH/bart ] ; then ++if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then + echo "\$TOOLBOX_PATH is not set correctly!" >&2 + exit 1 + fi +@@ -57,7 +57,7 @@ + cd $WORKDIR + + +-nm --defined-only $TOOLBOX_PATH/bart | cut -c11-16,19- | sort > bart.syms ++nm --defined-only $TOOLBOX_PATH/bin/bart | cut -c11-16,19- | sort > bart.syms + + + cat $in | grep "^TRACE" \ +diff -ru a/startup.m b/startup.m +--- a/startup.m 2020-09-17 12:25:18.343980805 -0500 ++++ b/startup.m 2020-09-17 12:34:28.968538214 -0500 +@@ -1,4 +1,3 @@ + % set Matlab path and TOOLBOX_PATH environment variable +-addpath(fullfile(pwd, 'matlab')); +-setenv('TOOLBOX_PATH', pwd); ++addpath(fullfile(getenv('TOOLBOX_PATH'), 'matlab')); + diff --git a/var/spack/repos/builtin/packages/bart/bart_path.patch b/var/spack/repos/builtin/packages/bart/bart_path.patch deleted file mode 100644 index c1b6c98da5..0000000000 --- a/var/spack/repos/builtin/packages/bart/bart_path.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff -ru a/matlab/bart.m b/matlab/bart.m ---- a/matlab/bart.m 2020-04-10 18:50:50.056248692 -0500 -+++ b/matlab/bart.m 2020-04-10 18:52:20.541178180 -0500 -@@ -11,7 +11,7 @@ - return - end - -- bart_path = getenv('TOOLBOX_PATH'); -+ bart_path = [getenv('TOOLBOX_PATH') '/bin']; - isWSL = false; - - if isempty(bart_path) -diff -ru a/python/bart.py b/python/bart.py ---- a/python/bart.py 2020-04-10 18:50:50.056248692 -0500 -+++ b/python/bart.py 2020-04-10 19:18:09.481950358 -0500 -@@ -19,7 +19,7 @@ - return None - - try: -- bart_path = os.environ['TOOLBOX_PATH'] + '/bart ' -+ bart_path = os.environ['TOOLBOX_PATH'] + '/bin ' - except: - bart_path = None - isWSL = False -diff -ru a/scripts/espirit_econ.sh b/scripts/espirit_econ.sh ---- a/scripts/espirit_econ.sh 2020-04-10 18:50:50.055248693 -0500 -+++ b/scripts/espirit_econ.sh 2020-04-10 19:13:06.463193324 -0500 -@@ -56,8 +56,6 @@ - fi - - --export PATH=$TOOLBOX_PATH:$PATH -- - input=$(readlink -f "$1") - output=$(readlink -f "$2") - -@@ -67,7 +65,7 @@ - exit 1 - fi - --if [ ! -e $TOOLBOX_PATH/bart ] ; then -+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then - echo "\$TOOLBOX_PATH is not set correctly!" >&2 - exit 1 - fi -diff -ru a/scripts/grasp.sh b/scripts/grasp.sh ---- a/scripts/grasp.sh 2020-04-10 18:50:50.055248693 -0500 -+++ b/scripts/grasp.sh 2020-04-10 19:13:31.461173327 -0500 -@@ -90,8 +90,6 @@ - fi - - --export PATH=$TOOLBOX_PATH:$PATH -- - input=$(readlink -f "$1") - output=$(readlink -f "$2") - -@@ -101,7 +99,7 @@ - exit 1 - fi - --if [ ! -e $TOOLBOX_PATH/bart ] ; then -+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then - echo "\$TOOLBOX_PATH is not set correctly!" >&2 - exit 1 - fi -diff -ru a/scripts/octview.m b/scripts/octview.m ---- a/scripts/octview.m 2020-04-10 18:50:50.055248693 -0500 -+++ b/scripts/octview.m 2020-04-10 19:14:33.386123750 -0500 -@@ -1,6 +1,6 @@ - #! /usr/bin/octave -qf - --addpath(strcat(getenv("TOOLBOX_PATH"), "/matlab")); -+addpath(strcat(getenv("TOOLBOX_PATH"), "/bin", "/matlab")); - arg_list = argv(); - - -diff -ru a/scripts/profile.sh b/scripts/profile.sh ---- a/scripts/profile.sh 2020-04-10 18:50:50.055248693 -0500 -+++ b/scripts/profile.sh 2020-04-10 19:15:00.723101850 -0500 -@@ -45,7 +45,7 @@ - exit 1 - fi - --if [ ! -e $TOOLBOX_PATH/bart ] ; then -+if [ ! -e $TOOLBOX_PATH/bin/bart ] ; then - echo "\$TOOLBOX_PATH is not set correctly!" >&2 - exit 1 - fi -@@ -57,7 +57,7 @@ - cd $WORKDIR - - --nm --defined-only $TOOLBOX_PATH/bart | cut -c11-16,19- | sort > bart.syms -+nm --defined-only $TOOLBOX_PATH/bin/bart | cut -c11-16,19- | sort > bart.syms - - - cat $in | grep "^TRACE" \ -diff -ru a/startup.m b/startup.m ---- a/startup.m 2020-04-10 18:50:50.048248699 -0500 -+++ b/startup.m 2020-04-10 18:51:40.390209486 -0500 -@@ -1,4 +1,3 @@ - % set Matlab path and TOOLBOX_PATH environment variable --addpath(fullfile(pwd, 'matlab')); --setenv('TOOLBOX_PATH', pwd); -+addpath(fullfile(getenv('TOOLBOX_PATH'), 'matlab')); - diff --git a/var/spack/repos/builtin/packages/bart/package.py b/var/spack/repos/builtin/packages/bart/package.py index 954a4e6930..43b2c1e566 100644 --- a/var/spack/repos/builtin/packages/bart/package.py +++ b/var/spack/repos/builtin/packages/bart/package.py @@ -12,6 +12,7 @@ class Bart(MakefilePackage, CudaPackage): homepage = "https://mrirecon.github.io/bart/" url = "https://github.com/mrirecon/bart/archive/v0.5.00.tar.gz" + version('0.6.00', sha256='dbbd33d1e3ed3324fe21f90a3b62cb51765fe369f21df100b46a32004928f18d') version('0.5.00', sha256='30eedcda0f0ef3808157542e0d67df5be49ee41e4f41487af5c850632788f643') # patch to fix build with MKL @@ -23,7 +24,8 @@ class Bart(MakefilePackage, CudaPackage): patch('Makefile.patch') # patch to set path to bart - patch('bart_path.patch') + patch('bart_path-0.5.00.patch', when='@0.5.00') + patch('bart_path-0.6.00.patch', when='@0.6.00') depends_on('libpng') depends_on('fftw') -- cgit v1.2.3-70-g09d2