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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Bart(MakefilePackage, CudaPackage):
"""BART: Toolbox for Computational Magnetic Resonance Imaging"""
homepage = "https://mrirecon.github.io/bart/"
url = "https://github.com/mrirecon/bart/archive/v0.5.00.tar.gz"
maintainers = ['glennpj']
version('0.7.00', sha256='a16afc4b632c703d95b5c34e47acd82fafc19f51f9aff442373eecfef08bfc41')
version('0.6.00', sha256='dbbd33d1e3ed3324fe21f90a3b62cb51765fe369f21df100b46a32004928f18d')
version('0.5.00', sha256='30eedcda0f0ef3808157542e0d67df5be49ee41e4f41487af5c850632788f643')
# patch to fix build with MKL
patch('https://github.com/mrirecon/bart/commit/b62ca4972d5ac41a44217a5c27123c15daae74db.patch?full_index=1',
sha256='501ca985df2324fc02e32cc4ffb32ce5c235fe83a59f5b853eb78ad0f2d6629c',
when='@0.5.00')
# patch to fix Makefile for openblas and cuda
patch('Makefile.patch', when='@:0.6.00')
patch('Makefile-0.7.00.patch', when='@0.7.00:')
# patch to set path to bart
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')
depends_on('blas')
depends_on('lapack')
depends_on('py-numpy', type='run')
depends_on('py-matplotlib', type='run')
extends('python')
conflicts('^atlas', msg='BART does not currently support atlas')
def edit(self, spec, prefix):
env['PREFIX'] = prefix
env['FFTW_BASE'] = spec['fftw'].prefix
if spec['blas'].name == 'openblas':
env['OPENBLAS'] = '1'
if '^mkl' in spec:
env['MKL'] = '1'
env['MKL_BASE'] = spec['mkl'].prefix.mkl
else:
env['BLAS_BASE'] = spec['blas'].prefix
if '^netlib-lapack+lapacke' not in spec:
env['NOLAPACKE'] = '1'
if '+cuda' in spec:
cuda_arch = self.spec.variants['cuda_arch'].value
env['CUDA'] = '1'
env['CUDA_BASE'] = spec['cuda'].prefix
env['GPUARCH_FLAGS'] = ' '.join(self.cuda_flags(cuda_arch))
def install(self, spec, prefix):
make('install')
install_tree('scripts', prefix.scripts)
install_tree('matlab', prefix.matlab)
install('startup.m', prefix)
install('python/bart.py', python_platlib)
install('python/cfl.py', python_platlib)
install('python/wslsupport.py', python_platlib)
if '^python@3:' in spec:
install('python/bartview3.py', join_path(prefix.bin, 'bartview'))
filter_file(r'#!/usr/bin/python3', '#!/usr/bin/env python',
prefix.bin.bartview)
else:
install('python/bartview.py', join_path(prefix.bin, 'bartview'))
filter_file(r'#!/usr/bin/python', '#!/usr/bin/env python',
prefix.bin.bartview)
def setup_run_environment(self, env):
env.set('TOOLBOX_PATH', self.prefix)
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