9a0dd631d5
* new package: BART This PR adds the BART (Berkeley Advanced Reconstruction Toolset) package. Despite the presence of CMake files, this package builds with a Makefile. It looks like the project is moving away from cmake. The patch for MKL has been committed upstream so should only be necessary for this version of BART. The Makefile patch is meant for working with Spack and would not be useful upstream. The bart scripts are still setup to use bart with the subcommands being individual binaries. This patches those to use the single binary with built-in subcommands and assumes that spack is providing the TOOLBOX environment variable and setting PATH. * Update var/spack/repos/builtin/packages/bart/package.py Yes, '==' make more sense for a single string. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * The python dependencies are run time only. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
85 lines
2.9 KiB
Python
85 lines
2.9 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Bart(MakefilePackage, CudaPackage):
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"""BART: Toolbox for Computational Magnetic Resonance Imaging"""
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homepage = "https://mrirecon.github.io/bart/"
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url = "https://github.com/mrirecon/bart/archive/v0.5.00.tar.gz"
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version('0.5.00', sha256='30eedcda0f0ef3808157542e0d67df5be49ee41e4f41487af5c850632788f643')
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# patch to fix build with MKL
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patch('https://github.com/mrirecon/bart/commit/b62ca4972d5ac41a44217a5c27123c15daae74db.patch',
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sha256='8fd1be181da928448da750b32d45ee6dce7ba6af0424617c4f8d653cf3f05445',
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when='@0.5.00')
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# patch to fix Makefile for openblas and cuda
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patch('Makefile.patch')
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# patch to set path to bart
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patch('bart_path.patch')
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depends_on('libpng')
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depends_on('fftw')
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depends_on('blas')
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depends_on('lapack')
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depends_on('py-numpy', type='run')
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depends_on('py-matplotlib', type='run')
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extends('python')
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conflicts('^atlas', msg='BART does not currently support atlas')
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def edit(self, spec, prefix):
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env['PREFIX'] = prefix
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env['FFTW_BASE'] = spec['fftw'].prefix
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if spec['blas'].name == 'openblas':
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env['OPENBLAS'] = '1'
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if spec['blas'].name in ['intel-mkl', 'intel-parallel-studio']:
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env['MKL'] = '1'
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env['MKL_BASE'] = env['MKLROOT']
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else:
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env['BLAS_BASE'] = spec['blas'].prefix
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if '^netlib-lapack+lapacke' not in spec:
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env['NOLAPACKE'] = '1'
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if '+cuda' in spec:
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cuda_arch = self.spec.variants['cuda_arch'].value
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env['CUDA'] = '1'
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env['CUDA_BASE'] = spec['cuda'].prefix
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env['GPUARCH_FLAGS'] = ' '.join(self.cuda_flags(cuda_arch))
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def install(self, spec, prefix):
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python_dir = join_path(prefix,
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spec['python'].package.site_packages_dir)
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make('install')
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install_tree('scripts', prefix.scripts)
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install_tree('matlab', prefix.matlab)
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install('startup.m', prefix)
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install('python/bart.py', python_dir)
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install('python/cfl.py', python_dir)
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install('python/wslsupport.py', python_dir)
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if '^python@3:' in spec:
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install('python/bartview3.py', join_path(prefix.bin, 'bartview'))
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filter_file(r'#!/usr/bin/python3', '#!/usr/bin/env python',
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prefix.bin.bartview)
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else:
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install('python/bartview.py', join_path(prefix.bin, 'bartview'))
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filter_file(r'#!/usr/bin/python', '#!/usr/bin/env python',
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prefix.bin.bartview)
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def setup_run_environment(self, env):
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env.set('TOOLBOX_PATH', self.prefix)
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