0ce8b9d398
* Make boost composable Currently Boost enables a few components through variants by default, which means that if you want to use only what you need and no more, you have to explicitly disable these variants, leading to concretization errors whenever a second package explicitly needs those components. For instance if package A only needs `+component_a` it might depend on `boost +component_a ~component_b`. And if packge B only needs `+component_b` it might depend on `boost ~component_a +component_b`. If package C now depends on both A and B, this leads to unsatisfiable variants and hence a concretization error. However, if we default to disabling all components, package A can simply depend on `boost +component_a` and package B on `boost +component_b` and package C will concretize to depending on `boost +component_a +component_b`, and whatever you install, you get the bare minimum. * Fix style * Added composable boost dependencies for folly * fixing akantu merge issue * hpctoolkit boost dependencies already defined * Fix Styles * Fixup style once more * Adding isort fix * isort one more time * Fix for package audit issue Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Ryan O'Malley <rd.omalley@comcast.net>
43 lines
1.6 KiB
Python
43 lines
1.6 KiB
Python
# Copyright 2013-2022 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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from spack.pkg.builtin.boost import Boost
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class Tophat(AutotoolsPackage):
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"""Spliced read mapper for RNA-Seq."""
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homepage = "https://ccb.jhu.edu/software/tophat/index.shtml"
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url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
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version('2.1.2', sha256='15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1')
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version('2.1.1', sha256='991b1b7c840a5f5c4e9a15b2815983257d2b0748246af0b9094c7d07552b023e')
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depends_on('autoconf', type='build')
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# 2.1.1 only builds with automake@1.15.1. There's a patch here:
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# https://github.com/spack/spack/pull/8244, which was incorporated
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# upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
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depends_on('automake', type='build')
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depends_on('automake@1.15.1', when='@:2.1.1', type='build')
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depends_on('libtool', type='build')
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depends_on('m4', type='build')
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depends_on('boost@1.47:')
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# TODO: replace this with an explicit list of components of Boost,
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# for instance depends_on('boost +filesystem')
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# See https://github.com/spack/spack/pull/22303 for reference
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depends_on(Boost.with_default_variants)
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depends_on('bowtie2', type='run')
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parallel = False
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def setup_build_environment(self, env):
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env.append_flags("CFLAGS", self.compiler.cxx98_flag)
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def configure_args(self):
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return ["--with-boost={0}".format(self.spec['boost'].prefix)]
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