From 4b41d56bc346c2c2e1ab1eaeb2eebd209456fde4 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Thu, 17 Sep 2020 15:25:08 -0500
Subject: [PATCH] Add bart-0.6.00 (#18717)

This PR adds version 0.6.00 of bart.
---
 ...bart_path.patch => bart_path-0.5.00.patch} |   0
 .../packages/bart/bart_path-0.6.00.patch      | 107 ++++++++++++++++++
 .../repos/builtin/packages/bart/package.py    |   4 +-
 3 files changed, 110 insertions(+), 1 deletion(-)
 rename var/spack/repos/builtin/packages/bart/{bart_path.patch => bart_path-0.5.00.patch} (100%)
 create mode 100644 var/spack/repos/builtin/packages/bart/bart_path-0.6.00.patch

diff --git a/var/spack/repos/builtin/packages/bart/bart_path.patch b/var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch
similarity index 100%
rename from var/spack/repos/builtin/packages/bart/bart_path.patch
rename to var/spack/repos/builtin/packages/bart/bart_path-0.5.00.patch
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/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')