1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
|
# Copyright 2013-2024 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 *
from spack.pkg.builtin.boost import Boost
class Revbayes(CMakePackage):
"""Bayesian phylogenetic inference using probabilistic graphical models
and an interpreted language."""
homepage = "https://revbayes.github.io"
url = "https://github.com/revbayes/revbayes/archive/1.1.0.tar.gz"
git = "https://github.com/revbayes/revbayes.git"
license("GPL-3.0-only")
version("develop", branch="development")
version(
"1.2.2",
sha256="339f89169cc9320212c3c64d0557b66f416ec9ae25d45e21a4e9a1cafef6e423",
url="https://github.com/revbayes/revbayes/archive/refs/tags/v1.2.2.tar.gz",
)
version("1.1.1", sha256="d61293fceac817d8203ed1e828661d76c73fa16bf04458a50a37057e99fd40c0")
version("1.1.0", sha256="a9f35178d8289d0dd32c9d936f6384f260e8e81e7b80a5155169064a24666012")
version("1.0.13", sha256="e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9")
version("1.0.12", sha256="80c926bb6b37288d02e36e07b44e4663841cd1fe541e2cc0b0e44c89ca929759")
version("1.0.11", sha256="03052194baa220dde7e622a739f09f34393f67ea00a0b163b409d313d7fc7c02")
version("1.0.10", sha256="6a3cf303e7224b0b32637bd8e2c3c2cf2621f5dbe599cd74ce4b0c215d0fcd2d")
variant("mpi", default=True, description="Enable MPI parallel support")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("mpi", when="+mpi")
conflicts("%gcc@7.1.0:", when="@:1.0.12")
def url_for_version(self, version):
if version > Version("1.0.13"):
return "https://github.com/revbayes/revbayes/archive/{0}.tar.gz".format(version)
else:
return "https://github.com/revbayes/revbayes.archive/archive/v{0}.tar.gz".format(
version
)
@property
def root_cmakelists_dir(self):
if self.spec.version > Version("1.0.13"):
return "src"
else:
return "projects/cmake/build"
@when("@1.1.0:")
def cmake_args(self):
args = []
if "+mpi" in self.spec:
args.extend([self.define("MPI", "ON"), self.define("RB_EXEC_NAME", "rb-mpi")])
return args
@run_before("cmake")
def regenerate(self):
with working_dir(join_path("projects", "cmake")):
mkdirp("build")
if self.spec.version > Version("1.0.13"):
generate_version = Executable("./generate_version_number.sh")
generate_version()
dest = join_path("..", "..", "src", "revlanguage", "utils")
install("GitVersion.cpp", dest)
else:
edit = FileFilter("regenerate.sh")
edit.filter('boost="true"', 'boost="false"')
if "+mpi" in self.spec:
edit.filter('mpi="false"', 'mpi="true"')
regenerate = Executable("./regenerate.sh")
regenerate()
def install(self, spec, prefix):
mkdirp(prefix.bin)
if "+mpi" in spec:
install_path = join_path(self.build_directory, "..", "rb-mpi")
install(install_path, prefix.bin)
else:
install_path = join_path(self.build_directory, "..", "rb")
install(install_path, prefix.bin)
@when("@1.0.12:1.0.13")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_path = join_path(self.build_directory, "..", "rb")
install(install_path, prefix.bin)
|
