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# Copyright 2013-2023 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"
license("BSD-3-Clause")
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"
elif spec["blas"].name in INTEL_MATH_LIBRARIES:
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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