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player1537-forks/spack
|
var/spack/repos/builtin/packages/py-configargparse/package.py
|
# 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 import *
class PyConfigargparse(PythonPackage):
"""Applications with more than a handful of user-settable
options are best configured through a combination of
command line args, config files, hard-coded defaults, and
in some cases, environment variables.
Python's command line parsing modules such as argparse have
very limited support for config files and environment
variables, so this module extends argparse to add these
features."""
homepage = "https://github.com/bw2/ConfigArgParse"
url = "https://github.com/bw2/ConfigArgParse/archive/1.2.3.tar.gz"
version('1.2.3', sha256='0f1144a204e3b896d6ac900e151c1d13bde3103d6b7d541e3bb57514a94083bf')
depends_on('python@2.2:2,3.5:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-dorng/package.py
|
# 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 import *
class RDorng(RPackage):
"""Generic Reproducible Parallel Backend for 'foreach' Loops.
Provides functions to perform reproducible parallel foreach loops, using
independent random streams as generated by L'Ecuyer's combined
multiple-recursive generator (L'Ecuyer (1999),
<doi:10.1287/opre.47.1.159>). It enables to easily convert standard
%dopar% loops into fully reproducible loops, independently of the number of
workers, the task scheduling strategy, or the chosen parallel environment
and associated foreach backend."""
cran = "doRNG"
version('1.8.2', sha256='33e9d45b91b0fde2e35e911b9758d0c376049121a98a1e4c73a1edfcff11cec9')
version('1.7.1', sha256='27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9')
version('1.6.6', sha256='939c2282c72c0b89fc7510f4bff901a4e99007dc006f46762c8f594c0ecbd876')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-foreach', type=('build', 'run'))
depends_on('r-rngtools@1.3:', type=('build', 'run'))
depends_on('r-rngtools@1.5:', type=('build', 'run'), when='@1.8.2:')
depends_on('r-iterators', type=('build', 'run'))
depends_on('r-pkgmaker@0.20:', type=('build', 'run'), when='@:1.7.1')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py
|
<filename>var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py<gh_stars>10-100
# 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 import *
class PerlStatisticsDescriptive(PerlPackage):
"""Module of basic descriptive statistical functions."""
homepage = "https://metacpan.org/pod/Statistics::Descriptive"
url = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz"
version('3.0612', sha256='772413148e5e00efb32f277c4254aa78b9112490a896208dcd0025813afdbf7a')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/curl/package.py
|
<reponame>player1537-forks/spack
# 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)
import re
import sys
from spack import *
class Curl(AutotoolsPackage):
"""cURL is an open source command line tool and library for
transferring data with URL syntax"""
homepage = "https://curl.se/"
# URL must remain http:// so Spack can bootstrap curl
url = "http://curl.haxx.se/download/curl-7.78.0.tar.bz2"
executables = ['^curl$']
version('7.81.0', sha256='1e7a38d7018ec060f1f16df839854f0889e94e122c4cfa5d3a37c2dc56f1e258')
version('7.80.0', sha256='dd0d150e49cd950aff35e16b628edf04927f0289df42883750cf952bb858189c')
version('7.79.1', sha256='de62c4ab9a9316393962e8b94777a570bb9f71feb580fb4475e412f2f9387851')
version('7.79.0', sha256='d607a677f473f79f96c964100327125a6204a39d835dc00dab7fc0129b959f42')
version('7.78.0', sha256='98530b317dc95ccb324bbe4f834f07bb642fbc393b794ddf3434f246a71ea44a')
version('7.77.0', sha256='6c0c28868cb82593859fc43b9c8fdb769314c855c05cf1b56b023acf855df8ea')
version('7.76.1', sha256='7a8e184d7d31312c4ebf6a8cb59cd757e61b2b2833a9ed4f9bf708066e7695e9')
version('7.76.0', sha256='e29bfe3633701590d75b0071bbb649ee5ca4ca73f00649268bd389639531c49a')
version('7.75.0', sha256='50552d4501c178e4cc68baaecc487f466a3d6d19bbf4e50a01869effb316d026')
version('7.74.0', sha256='0f4d63e6681636539dc88fa8e929f934cd3a840c46e0bf28c73be11e521b77a5')
version('7.73.0', sha256='cf34fe0b07b800f1c01a499a6e8b2af548f6d0e044dca4a29d88a4bee146d131')
version('7.72.0', sha256='ad91970864102a59765e20ce16216efc9d6ad381471f7accceceab7d905703ef')
version('7.71.0', sha256='600f00ac2481a89548a4141ddf983fd9386165e1960bac91d0a1c81dca5dd341')
version('7.68.0', sha256='207f54917dd6a2dc733065ccf18d61bb5bebeaceb5df49cd9445483e8623eeb9')
version('7.64.0', sha256='d573ba1c2d1cf9d8533fadcce480d778417964e8d04ccddcc76e591d544cf2eb')
version('7.63.0', sha256='9bab7ed4ecff77020a312d84cc5fb7eb02d58419d218f267477a724a17fd8dd8')
version('7.60.0', sha256='897dfb2204bd99be328279f88f55b7c61592216b0542fcbe995c60aa92871e9b')
version('7.59.0', sha256='b5920ffd6a8c95585fb95070e0ced38322790cb335c39d0dab852d12e157b5a0')
version('7.56.0', sha256='de60a4725a3d461c70aa571d7d69c788f1816d9d1a8a2ef05f864ce8f01279df')
version('7.54.0', sha256='f50ebaf43c507fa7cc32be4b8108fa8bbd0f5022e90794388f3c7694a302ff06')
version('7.53.1', sha256='1c7207c06d75e9136a944a2e0528337ce76f15b9ec9ae4bb30d703b59bf530e8')
version('7.52.1', sha256='d16185a767cb2c1ba3d5b9096ec54e5ec198b213f45864a38b3bda4bbf87389b')
version('7.50.3', sha256='7b7347d976661d02c84a1f4d6daf40dee377efdc45b9e2c77dedb8acf140d8ec')
version('7.50.2', sha256='0c72105df4e9575d68bcf43aea1751056c1d29b1040df6194a49c5ac08f8e233')
version('7.50.1', sha256='3c12c5f54ccaa1d40abc65d672107dcc75d3e1fcb38c267484334280096e5156')
version('7.49.1', sha256='eb63cec4bef692eab9db459033f409533e6d10e20942f4b060b32819e81885f1')
version('7.47.1', sha256='ddc643ab9382e24bbe4747d43df189a0a6ce38fcb33df041b9cb0b3cd47ae98f')
version('7.46.0', sha256='b7d726cdd8ed4b6db0fa1b474a3c59ebbbe4dcd4c61ac5e7ade0e0270d3195ad')
version('7.45.0', sha256='65154e66b9f8a442b57c436904639507b4ac37ec13d6f8a48248f1b4012b98ea')
version('7.44.0', sha256='1e2541bae6582bb697c0fbae49e1d3e6fad5d05d5aa80dbd6f072e0a44341814')
version('7.43.0', sha256='baa654a1122530483ccc1c58cc112fec3724a82c11c6a389f1e6a37dc8858df9')
version('7.42.1', sha256='e2905973391ec2dfd7743a8034ad10eeb58dab8b3a297e7892a41a7999cac887')
default_tls = 'openssl'
if sys.platform == 'darwin':
default_tls = 'secure_transport'
# TODO: add dependencies for other possible TLS backends
values_tls = [
# 'amissl',
# 'bearssl',
'gnutls',
'mbedtls',
# 'mesalink',
'nss',
'openssl',
# 'rustls',
# 'schannel',
'secure_transport',
# 'wolfssl',
]
variant('tls', default=default_tls, description='TLS backend', values=values_tls, multi=True)
variant('nghttp2', default=False, description='build nghttp2 library (requires C++11)')
variant('libssh2', default=False, description='enable libssh2 support')
variant('libssh', default=False, description='enable libssh support') # , when='7.58:')
variant('gssapi', default=False, description='enable Kerberos support')
variant('librtmp', default=False, description='enable Rtmp support')
variant('ldap', default=False, description='enable ldap support')
variant('libidn2', default=False, description='enable libidn2 support')
conflicts('+libssh', when='@:7.57')
# on OSX and --with-ssh the configure steps fails with
# one or more libs available at link-time are not available run-time
# unless the libssh are installed externally (e.g. via homebrew), even
# though spack isn't supposed to know about such a libssh installation.
# C.f. https://github.com/spack/spack/issues/7777
conflicts('platform=darwin', when='+libssh2')
conflicts('platform=darwin', when='+libssh')
conflicts('platform=cray', when='tls=secure_transport', msg='Only supported on macOS')
conflicts('platform=linux', when='tls=secure_transport', msg='Only supported on macOS')
conflicts('tls=mbedtls', when='@:7.45')
depends_on('gnutls', when='tls=gnutls')
depends_on('mbedtls@3:', when='@7.79: tls=mbedtls')
depends_on('mbedtls@:2', when='@:7.78 tls=mbedtls')
depends_on('nss', when='tls=nss')
depends_on('openssl', when='tls=openssl')
depends_on('libidn2', when='+libidn2')
depends_on('zlib')
depends_on('nghttp2', when='+nghttp2')
depends_on('libssh2', when='+libssh2')
depends_on('libssh', when='+libssh')
depends_on('krb5', when='+gssapi')
# curl queries pkgconfig for openssl compilation flags
depends_on('pkgconfig', type='build')
@classmethod
def determine_version(cls, exe):
curl = Executable(exe)
output = curl('--version', output=str, error=str)
match = re.match(r'curl ([\d.]+)', output)
return match.group(1) if match else None
@classmethod
def determine_variants(cls, exes, version):
for exe in exes:
variants = ''
curl = Executable(exe)
output = curl('--version', output=str, error='str')
if 'nghttp2' in output:
variants += '+nghttp2'
protocols_match = re.search(r'Protocols: (.*)\n', output)
if protocols_match:
protocols = protocols_match.group(1).strip().split(' ')
if 'ldap' in protocols:
variants += '+ldap'
features_match = re.search(r'Features: (.*)\n', output)
if features_match:
features = features_match.group(1).strip().split(' ')
if 'GSS-API' in features:
variants += '+gssapi'
# TODO: Determine TLS backend if needed.
# TODO: Determine more variants.
return variants
def configure_args(self):
spec = self.spec
args = [
'--with-zlib=' + spec['zlib'].prefix,
# Prevent unintentional linking against system libraries: we could
# add variants for these in the future
'--without-brotli',
'--without-libgsasl',
'--without-libpsl',
'--without-zstd',
]
# Make gnutls / openssl decide what certs are trusted.
# TODO: certs for other tls options.
if spec.satisfies('tls=gnutls') or spec.satisfies('tls=openssl'):
args.extend([
'--without-ca-bundle',
'--without-ca-path',
'--with-ca-fallback',
])
# https://daniel.haxx.se/blog/2021/06/07/bye-bye-metalink-in-curl/
# We always disable it explicitly, but the flag is gone in newer
# versions.
if spec.satisfies('@:7.77'):
args.append('--without-libmetalink')
if spec.satisfies('+gssapi'):
args.append('--with-gssapi=' + spec['krb5'].prefix)
else:
args.append('--without-gssapi')
args += self.with_or_without('tls')
args += self.with_or_without('libidn2', 'prefix')
args += self.with_or_without('librtmp')
args += self.with_or_without('nghttp2')
args += self.with_or_without('libssh2')
args += self.with_or_without('libssh')
args += self.enable_or_disable('ldap')
return args
def with_or_without_gnutls(self, activated):
if activated:
return '--with-gnutls=' + self.spec['gnutls'].prefix
else:
return '--without-gnutls'
def with_or_without_mbedtls(self, activated):
if self.spec.satisfies('@7.46:'):
if activated:
return '--with-mbedtls=' + self.spec['mbedtls'].prefix
else:
return '--without-mbedtls'
def with_or_without_nss(self, activated):
if activated:
return '--with-nss=' + self.spec['nss'].prefix
else:
return '--without-nss'
def with_or_without_openssl(self, activated):
if self.spec.satisfies('@7.77:'):
if activated:
return '--with-openssl=' + self.spec['openssl'].prefix
else:
return '--without-openssl'
else:
if activated:
return '--with-ssl=' + self.spec['openssl'].prefix
else:
return '--without-ssl'
def with_or_without_secure_transport(self, activated):
if self.spec.satisfies('@7.65:'):
if activated:
return '--with-secure-transport'
else:
return '--without-secure-transport'
else:
if activated:
return '--with-darwinssl'
else:
return '--without-darwinssl'
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-blosc/package.py
|
# 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 import *
class PyBlosc(PythonPackage):
"""A Python wrapper for the extremely fast Blosc compression library"""
homepage = "http://python-blosc.blosc.org"
url = "https://github.com/Blosc/python-blosc/archive/v1.9.1.tar.gz"
git = "https://github.com/Blosc/python-blosc.git"
version('1.9.1', sha256='ffc884439a12409aa4e8945e21dc920d6bc21807357c51d24c7f0a27ae4f79b9')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-scikit-build', type='build')
depends_on('py-cmake@3.11:', type='build')
depends_on('py-ninja', type='build')
# depends_on('c-blosc') # shipped internally
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-biocversion/package.py
|
# 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 import *
class RBiocversion(RPackage):
"""Set the appropriate version of Bioconductor packages.
This package provides repository information for the appropriate
version of Bioconductor."""
bioc = "BiocVersion"
version('3.14.0', commit='aa56d93d0ea5dcdbf301f120502981740fd91e1e')
version('3.12.0', commit='<PASSWORD>')
depends_on('r@4.0.0:', type=('build', 'run'))
depends_on('r@4.1.0:', type=('build', 'run'), when='@3.14.0:')
|
player1537-forks/spack
|
lib/spack/spack/compilers/rocmcc.py
|
<reponame>player1537-forks/spack
# 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)
import re
import llnl.util.lang
import spack.compilers.clang
class Rocmcc(spack.compilers.clang.Clang):
# Subclasses use possible names of C compiler
cc_names = ['amdclang']
# Subclasses use possible names of C++ compiler
cxx_names = ['amdclang++']
# Subclasses use possible names of Fortran 77 compiler
f77_names = ['amdflang']
# Subclasses use possible names of Fortran 90 compiler
fc_names = ['amdflang']
PrgEnv = 'PrgEnv-amd'
PrgEnv_compiler = 'amd'
@property
def link_paths(self):
link_paths = {'cc': 'rocmcc/amdclang',
'cxx': 'rocmcc/amdclang++',
'f77': 'rocmcc/amdflang',
'fc': 'rocmcc/amdflang'}
return link_paths
@property
def cxx11_flag(self):
return "-std=c++11"
@property
def cxx14_flag(self):
return "-std=c++14"
@property
def cxx17_flag(self):
return "-std=c++17"
@property
def c99_flag(self):
return '-std=c99'
@property
def c11_flag(self):
return "-std=c11"
@classmethod
@llnl.util.lang.memoized
def extract_version_from_output(cls, output):
match = re.search(
r'llvm-project roc-(\d+)[._](\d+)[._](\d+)',
output
)
if match:
return '.'.join(match.groups())
@classmethod
def fc_version(cls, fortran_compiler):
return cls.default_version(fortran_compiler)
@classmethod
def f77_version(cls, f77):
return cls.fc_version(f77)
@property
def stdcxx_libs(self):
return ('-lstdc++', )
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/libelf/package.py
|
<filename>var/spack/repos/builtin.mock/packages/libelf/package.py
# 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 import *
class Libelf(Package):
homepage = "http://www.mr511.de/software/english.html"
url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"
version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
version('0.8.10', '9db4d36c283d9790d8fa7df1f4d7b4d9')
patch('local.patch', when='@0.8.10')
def install(self, spec, prefix):
touch(prefix.libelf)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/mstk/package.py
|
# 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 import *
class Mstk(CMakePackage):
"""MSTK is a mesh framework that allows users to represent,
manipulate and query unstructured 3D arbitrary topology meshes
in a general manner without the need to code their own data
structures. MSTK is a flexible framework in that it allows a
variety of underlying representations for the mesh while
maintaining a common interface. It allows users to choose from
different mesh representations either at initialization (implemented)
or during the program execution (not yet implemented) so that the
optimal data structures are used for the particular algorithm.
The interaction of users and applications with MSTK is through a
functional interface that acts as though the mesh always contains
vertices, edges, faces and regions and maintains connectivity between
all these entities."""
homepage = "https://github.com/MeshToolkit/MSTK"
git = "https://github.com/MeshToolkit/MSTK"
url = "https://github.com/MeshToolkit/MSTK/archive/3.3.6.tar.gz"
maintainers = ['raovgarimella', 'julienloiseau']
version('master', branch='master')
version('3.3.6', sha256='30041ee6f32d754e5d9b46db8f62609bb66d2686f8e6e16ad254f552849cb0f1')
version('3.3.5', sha256='64c976e12d1393aafd086ef941b176add6cfb963f463c33259596e7ef641cdd8')
version('3.3.4', sha256='bd34d31fc1fc468147a51e8d837d6bf9902ca8d38c7c0615e7f20968d4659da2')
version('3.3.3', sha256='54ea7929c9046915472f38367c83f75af634a6989ce0b89aad17fb9f4a25023e')
version('3.3.2', sha256='fb4ffa97af4d0a0d4771c8585d0b27538b013d8b1cfaff992e5e054fef62af0b')
version('3.3.1', sha256='9fdb0c33c1b68714d708b355d963547cf41332812658d4560d4db43904fc78de')
version('3.3.0', sha256='205c48fb5619937b5dd83788da739b7c2060155b7c41793e29ce05422b8f7dfb')
version('3.2.1', sha256='09bc6684abb576e34c324322db6f71f8987c6ec436a54256b85ef4db40185470')
version('3.2.0', sha256='57e58c5a7a456dbc608ce9f834a06c212a1aa64ac3ebc880ea0b8a19b000dab0')
version('3.1.3', sha256='03f6901cd6d563e1705a173c1a2fbbef10ab9a43f533f6ba758e357c03bdfa16')
version('3.1.2', sha256='1eb44c29554f45695f875fc60ab81554a2c46a041ef58a7224f3767d30e2846e')
version('3.1.1', sha256='5a03873c69fb38acd7ce27f2a5fa0643dd1cfcc3e214cff4aa26ee717651cc0b')
version('3.1.0', sha256='70e68d8a90cd2367015e0ab3459ed230a7995ad2297671742d9be6e28bc03dcf')
version('3.0.4', sha256='99e4c996bf22fd325335ed1391dfe735b0a338e8e4d733204d56dde7ef4eedf3')
version('3.0.3', sha256='618e371a48077f2b4ccfafd4d174c05f007b2ea7a51e0399df67442639409518')
version('3.0.2', sha256='b0172cd68e5137b8585d82c37b8a4af4b7e884f04d1b7d006a399d39447fe89e')
version('3.0.1', sha256='d44e4bf01b118b1d19710aa839b3f5f0c1a8391264a435f641ba4bd23bcf45ec')
version('3.0.0', sha256='d993ff5fc6c431067eb97e4089835c7790397d9c1ad88a56523c0591d451df19')
variant('exodusii', default=False, description='Enable ExodusII')
variant('use_markers', default=True, description='Enable use of markers')
variant('parallel', default=False, description='Enable Parallel Support')
variant('partitioner', default='none',
values=('none', 'metis', 'zoltan', 'all'),
multi=False, description='Choose partitioner')
conflicts('partitioner=none', when='+parallel')
conflicts('partitioner=all', when='-parallel')
conflicts('partitioner=zoltan', when='-parallel')
# MSTK turns on METIS only for parallel builds
conflicts('partitioner=metis', when='-parallel')
# dependencies
depends_on('cmake@3.11:', type='build')
#
depends_on('mpi', when='+parallel')
depends_on('zoltan -fortran', when='partitioner=zoltan')
depends_on('zoltan -fortran', when='partitioner=all')
depends_on('metis', when='partitioner=metis')
depends_on('metis', when='partitioner=all')
# Exodusii variant
# The default exodusii build with mpi support
depends_on('exodusii', when='+exodusii')
# Unit testing variant
depends_on('unittest-cpp', type='test')
def cmake_args(self):
options = []
if '+use_markers' in self.spec:
options.append('-DMSTK_USE_MARKERS=ON')
else:
options.append('-DMSTK_USE_MARKERS=OFF')
# Parallel variant
if '+parallel' in self.spec:
options.append('-DENABLE_PARALLEL=ON')
else:
options.append('-DENABLE_PARALLEL=OFF')
if 'partitioner=none' in self.spec:
options.append('-DENABLE_METIS=OFF')
options.append('-DENABLE_ZOLTAN=OFF')
else:
if 'zoltan' in self.spec:
options.append('-DENABLE_ZOLTAN=ON')
else:
options.append('-DENABLE_ZOLTAN=OFF')
if 'metis' in self.spec:
options.append('-DENABLE_METIS=ON')
else:
options.append('-DENABLE_METIS=OFF')
# ExodusII variant
if '+exodusii' in self.spec:
options.append('-DENABLE_ExodusII=ON')
else:
options.append('-DENABLE_ExodusII=OFF')
# Unit test variant
if self.run_tests:
options.append('-DENABLE_Tests=ON')
else:
options.append('-DENABLE_Tests=OFF')
return options
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/bowtie2/package.py
|
# 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)
class Bowtie2(MakefilePackage):
"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences"""
homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
version('2.4.2', sha256='4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e')
version('2.4.1', sha256='566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22')
version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')
depends_on('tbb', when='@2.3.0:')
depends_on('readline', when='@2.3.1:')
depends_on('perl', type='run')
depends_on('python', type='run')
depends_on('zlib', when='@2.3.1:')
depends_on('simde', when='@2.4.0: target=aarch64:', type='link')
depends_on('simde', when='@2.4.0: target=ppc64le:', type='link')
patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
# seems to have trouble with 6's -std=gnu++14
conflicts('%gcc@6:', when='@:2.3.1')
conflicts('^intel-oneapi-tbb', when='@:2.3.5.1')
conflicts('@:2.3.5.0', when='target=aarch64:')
conflicts('@2.4.1', when='target=aarch64:')
def edit(self, spec, prefix):
kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
match = '^#!/usr/bin/env perl'
perl = spec['perl'].command
substitute = "#!{perl}".format(perl=perl)
files = ['bowtie2', ]
filter_file(match, substitute, *files, **kwargs)
match = '^#!/usr/bin/env python.*'
python = spec['python'].command
substitute = "#!{python}".format(python=python)
files = ['bowtie2-build', 'bowtie2-inspect']
filter_file(match, substitute, *files, **kwargs)
if (self.spec.satisfies('@2.4.0:2.4.2 target=aarch64:') or
self.spec.satisfies('@2.4.0:2.4.2 target=ppc64le:')):
match = '-Ithird_party/simde'
simdepath = spec['simde'].prefix.include
substitute = "-I{simdepath}".format(simdepath=simdepath)
files = ['Makefile']
filter_file(match, substitute, *files, **kwargs)
@property
def build_targets(self):
make_arg = ['PREFIX={0}'.format(self.prefix)]
if self.spec.satisfies('target=aarch64:'):
make_arg.append('POPCNT_CAPABILITY=0')
return make_arg
@property
def install_targets(self):
if self.spec.satisfies('@:2.3.9'):
return ['prefix={0}'.format(self.prefix), 'install']
else:
return ['PREFIX={0}'.format(self.prefix), 'install']
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-lifelines/package.py
|
# 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)
class PyLifelines(PythonPackage):
"""Survival analysis was originally developed and applied heavily
by the actuarial and medical community. Its purpose was to answer
*why do events occur now versus later* under uncertainty (where
*events* might refer to deaths, disease remission,
etc.). *lifelines* is a pure Python implementation of the best
parts of survival analysis."""
homepage = "https://github.com/CamDavidsonPilon/lifelines"
pypi = "lifelines/lifelines-0.25.5.tar.gz"
version('0.25.5', sha256='f24260aa371829354440dfc2c1be8d59d9e841cce7a933230213cecd67787b89')
version('0.9.4', sha256='0f19a8b18ace80c231de60487b2b1a3de3eb418445c6a6d0d72c1110d860f676')
depends_on('py-setuptools', type='build')
depends_on('py-numpy', type=('build', 'run'), when='@0.9.4')
depends_on('py-scipy', type=('build', 'run'), when='@0.9.4')
depends_on('py-pandas@0.18.0:', type=('build', 'run'), when='@0.9.4')
depends_on('python@3.6:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-pandas@0.23.0:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-scipy@1.2.0:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-numpy@1.14:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-pandas@0.23.0:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-matplotlib@3.0:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-autograd@1.3:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-autograd-gamma@0.3:', type=('build', 'run'), when='@0.25.5:')
depends_on('py-patsy@0.5.0:', type=('build', 'run'), when='@0.25.5:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/minc-toolkit/package.py
|
<filename>var/spack/repos/builtin/packages/minc-toolkit/package.py
# 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 import *
class MincToolkit(CMakePackage):
"""Bundles multiple MINC-related packages"""
homepage = "https://github.com/BIC-MNI/minc-toolkit-v2"
git = "https://github.com/BIC-MNI/minc-toolkit-v2.git"
version('1.9.18.1', commit="<PASSWORD>",
submodules=True)
variant('shared', default=True,
description="Build shared libraries")
variant('visualisation', default=False,
description="Build visual tools (Display, register, etc.)")
depends_on('perl')
# included Perl packages are not added to the Perl path by default.
# rather than inheriting from both CMakePackage and PerlPackage,
# it seems clean just to add them as dependencies:
depends_on('perl-text-format', type=('build', 'run'))
depends_on('perl-getopt-tabular', type=('build', 'run'))
depends_on('perl-mni-perllib', type=('build', 'run'))
depends_on('flex', type='build')
depends_on('bison', type='build')
depends_on('zlib', type='link')
depends_on('freeglut', when="+visualisation")
def cmake_args(self):
return [self.define_from_variant('MT_BUILD_SHARED_LIBS', 'shared'),
self.define_from_variant('MT_BUILD_VISUAL_TOOLS', 'visualisation'),
# newer ANTs packaged separately
"-DMT_BUILD_ANTS=OFF",
# newer c3d packaged separately
"-DMT_BUILD_C3D=OFF",
# should be packaged separately with newer ITK
"-DMT_BUILD_ELASTIX=OFF"
]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/pkgconf/package.py
|
# 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 import *
class Pkgconf(AutotoolsPackage):
"""pkgconf is a program which helps to configure compiler and linker
flags for development frameworks. It is similar to pkg-config from
freedesktop.org, providing additional functionality while also
maintaining compatibility."""
homepage = "http://pkgconf.org/"
# URL must remain http:// so Spack can bootstrap curl
url = "https://distfiles.dereferenced.org/pkgconf/pkgconf-1.6.3.tar.xz"
version('1.8.0', sha256='ef9c7e61822b7cb8356e6e9e1dca58d9556f3200d78acab35e4347e9d4c2bbaf')
version('1.7.4', sha256='d73f32c248a4591139a6b17777c80d4deab6b414ec2b3d21d0a24be348c476ab')
version('1.7.3', sha256='b846aea51cf696c3392a0ae58bef93e2e72f8e7073ca6ad1ed8b01c85871f9c0')
version('1.6.3', sha256='61f0b31b0d5ea0e862b454a80c170f57bad47879c0c42bd8de89200ff62ea210')
version('1.6.1', sha256='22b9ee38438901f9d60f180e5182821180854fa738fd071f593ea26a81da208c')
version('1.6.0', sha256='6135a3abb576672ba54a899860442ba185063f0f90dae5892f64f7bae8e1ece5')
version('1.5.4', sha256='9c5864a4e08428ef52f05a41c948529555458dec6d283b50f8b7d32463c54664')
version('1.4.2', sha256='bab39371d4ab972be1d539a8b10b6cc21f8eafc97f617102e667e82bd32eb234')
version('1.4.0', sha256='1d112ff35dad516ffbfbdb013df3a035140618fe7632ec44ffa894a9c713301b')
version('1.3.10', sha256='62577d265fa9415a57a77a59dede5526b7ece3ef59a750434b281b262f0c1da9')
version('1.3.8', sha256='fc06f058e6905435481f649865ca51000192c91808f307b1053ca5e859cb1488')
provides('pkgconfig')
# https://github.com/spack/spack/issues/11704
patch('nvhpc.patch', when='@1.7.3%nvhpc')
# TODO: Add a package for the kyua testing framework
# depends_on('kyua', type='test')
# https://github.com/spack/spack/issues/3525
conflicts('%pgi')
tags = ['build-tools']
executables = ['^pkgconf$', '^pkg-config$']
@classmethod
def determine_version(cls, exe):
exe = Executable(exe)
# Make sure this is actually pkgconf, not pkg-config
if 'usage: pkgconf' not in exe('--help', output=str, error=str):
return None
version = exe('--version', output=str, error=str).rstrip()
return version
def setup_dependent_build_environment(self, env, dependent_spec):
"""Adds the ACLOCAL path for autotools."""
env.append_path('ACLOCAL_PATH', self.prefix.share.aclocal)
def check(self):
# TODO: running the checks needs kyua (a package not yet in spack)
# see TODO above
# thus disable the tests to be able to run --test=all for other specs
pass
@run_after('install')
def link_pkg_config(self):
symlink('pkgconf', '{0}/pkg-config'.format(self.prefix.bin))
symlink('pkgconf.1',
'{0}/pkg-config.1'.format(self.prefix.share.man.man1))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ocl-icd/package.py
|
# 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 import *
class OclIcd(AutotoolsPackage):
"""This package aims at creating an Open Source alternative to vendor specific
OpenCL ICD loaders."""
homepage = "https://github.com/OCL-dev/ocl-icd"
url = "https://github.com/OCL-dev/ocl-icd/archive/v2.2.12.tar.gz"
maintainers = ['lorddavidiii']
version('2.3.1', sha256='a32b67c2d52ffbaf490be9fc18b46428ab807ab11eff7664d7ff75e06cfafd6d')
version('2.3.0', sha256='469f592ccd9b0547fb7212b17e1553b203d178634c20d3416640c0209e3ddd50')
version('2.2.14', sha256='46df23608605ad548e80b11f4ba0e590cef6397a079d2f19adf707a7c2fbfe1b')
version('2.2.13', sha256='f85d59f3e8327f15637b91e4ae8df0829e94daeff68c647b2927b8376b1f8d92')
version('2.2.12', sha256='17500e5788304eef5b52dbe784cec197bdae64e05eecf38317840d2d05484272')
version('2.2.11', sha256='c1865ef7701b8201ebc6930ed3ac757c7e5cb30f3aa4c1e742a6bc022f4f2292')
version('2.2.10', sha256='d0459fa1421e8d86aaf0a4df092185ea63bc4e1a7682d3af261ae5d3fae063c7')
version('2.2.9', sha256='88da749bc2bd75149f0bb6e72eb4a9d74401a54f4508bc730f13cc03c57a17ed')
version('2.2.8', sha256='8a8a405c7d659b905757a358dc467f4aa3d7e4dff1d1624779065764d962a246')
version('2.2.7', sha256='b8e68435904e1a95661c385f24d6924ed28f416985c6db5a3c7448698ad5fea2')
version('2.2.6', sha256='4567cae92f58c1d6ecfc771c456fa95f206d8a5c7c5d6c9010ec688a9fd83750')
version('2.2.5', sha256='50bf51f4544f83e69a5a2f564732a2adca63fbe9511430aba12f8d6f3a53ae59')
version('2.2.4', sha256='92853137ffff393cc74f829357fdd80ac46a82b46c970e80195db86164cca316')
version('2.2.3', sha256='46b8355d90f8cc240555e4e077f223c47b950abeadf3e1af52d6e68d2efc2ff3')
variant("headers", default=False, description="Install also OpenCL headers to use this as OpenCL provider")
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
depends_on('ruby', type='build')
depends_on('asciidoc-py3', type='build')
depends_on('xmlto', type='build')
depends_on('opencl-headers@3.0:', when='+headers')
provides('opencl@:3.0', when='@2.2.13:+headers')
provides('opencl@:2.2', when='@2.2.12+headers')
provides('opencl@:2.1', when='@2.2.8:2.2.11+headers')
provides('opencl@:2.0', when='@2.2.3:2.2.7+headers')
# upstream patch to fix compatibility with the latest version of the
# official khronos OpenCL C headers release, ie opencl-c-headers@2021.04.29
patch('https://github.com/OCL-dev/ocl-icd/commit/aed1832c81c0971ea001e12d41e04df834257f94.patch',
sha256='c6bb2813e2a59ac9b79b86d7f421c3e6446c0f9d8a4c850e5641fb7273ab3b43', when='@2.3.0')
def flag_handler(self, name, flags):
if name == 'cflags' and self.spec.satisfies('@:2.2.12'):
# https://github.com/OCL-dev/ocl-icd/issues/8
# this is fixed in version grater than 2.2.12
flags.append('-O2')
# gcc-10 change the default from -fcommon to fno-common
# This is fixed in versions greater than 2.2.12:
# https://github.com/OCL-dev/ocl-icd/commit/4667bddd365bcc1dc66c483835971f0083b44b1d
if self.spec.satisfies('%gcc@10:'):
flags.append('-fcommon')
return (flags, None, None)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/apktool/package.py
|
# 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 import *
class Apktool(Package):
"""A tool for reverse engineering 3rd party, closed, binary
Android apps."""
homepage = "https://ibotpeaches.github.io/Apktool/"
url = "https://github.com/iBotPeaches/Apktool/archive/refs/tags/v2.6.0.tar.gz"
version('2.6.0', sha256='74739cdb1434ca35ec34e51ca7272ad3f378ae3ed0a2d5805d9a2fab5016037f')
depends_on('java@8:', type=('build', 'run'))
phases = ['build', 'install']
def setup_build_environment(self, env):
env.set('LC_ALL', 'en_US.UTF-8')
def build(self, spec, prefix):
gradlew = Executable('./gradlew')
gradlew('--info', '--debug', 'build', 'shadowJar')
def install(self, spec, prefix):
ln = which('ln')
mkdir(join_path(prefix, 'bin'))
install(
join_path('brut.apktool', 'apktool-cli', 'build', 'libs',
'apktool-cli-all.jar'),
join_path(prefix, 'bin'))
install(
join_path('scripts', 'linux', 'apktool'),
join_path(prefix, 'bin'))
ln(
'-s',
join_path(prefix, 'bin', 'apktool-cli-all.jar'),
join_path(prefix, 'bin', 'apktool.jar'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-argh/package.py
|
# 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 import *
class PyArgh(PythonPackage):
"""An argparse wrapper that doesn't make you say "argh" each time
you deal with it.
Building a command-line interface? Found yourself uttering "argh!"
while struggling with the API of argparse? Don't like the complexity
but need the power? Argh is a smart wrapper for argparse. Argparse is
a very powerful tool; Argh just makes it easy to use."""
homepage = "https://github.com/neithere/argh/"
pypi = "argh/argh-0.26.2.tar.gz"
maintainers = ['dorton21']
version('0.26.2', sha256='e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65')
depends_on('py-setuptools', type='build')
depends_on('py-argparse', when='^python@:2.6,3.0:3.1', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gdsfmt/package.py
|
# 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 import *
class RGdsfmt(RPackage):
"""R Interface to CoreArray Genomic Data Structure (GDS) Files.
This package provides a high-level R interface to CoreArray Genomic Data
Structure (GDS) data files, which are portable across platforms with
hierarchical structure to store multiple scalable array-oriented data
sets with metadata information. It is suited for large-scale datasets,
especially for data which are much larger than the available random-
access memory. The gdsfmt package offers the efficient operations
specifically designed for integers of less than 8 bits, since a diploid
genotype, like single-nucleotide polymorphism (SNP), usually occupies
fewer bits than a byte. Data compression and decompression are available
with relatively efficient random access. It is also allowed to read a
GDS file in parallel with multiple R processes supported by the package
parallel."""
bioc = "gdsfmt"
version('1.30.0', commit='<KEY>')
version('1.26.1', commit='<KEY>')
version('1.20.0', commit='<KEY>')
version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9')
version('1.16.0', commit='49b011452585e432b983b68466a230c9b71d8a95')
version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
version('1.12.0', commit='d705a95b0bea7be2a2b37e939f45017337ba0fb6')
depends_on('r@2.15.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-python-box/package.py
|
# 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 import *
class PyPythonBox(PythonPackage):
"""Advanced Python dictionaries with dot notation access
Box will automatically make otherwise inaccessible keys safe to access as
an attribute. You can always pass conversion_box=False to Box to disable
that behavior. Also, all new dict and lists added to a Box or BoxList
object are converted automatically."""
homepage = "https://github.com/cdgriffith/Box"
pypi = "python-box/python-box-5.3.0.tar.gz"
version('5.3.0', sha256='4ed4ef5d34de505a65c01e3f1911de8cdb29484fcae0c035141dce535c6c194a')
variant('extras',
default=False,
description='install the "extras" packages')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-ruamel-yaml', when='+extras')
depends_on('py-toml', when='+extras')
depends_on('py-msgpack', when='+extras')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-biopandas/package.py
|
# 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 import *
class PyBiopandas(PythonPackage):
"""Working with molecular structures in pandas DataFrames"""
homepage = "https://rasbt.github.io/biopandas"
pypi = "biopandas/biopandas-0.2.5.tar.gz"
git = "https://github.com/rasbt/biopandas.git"
# Note that the source package on PyPi is broken as it
# is missing the requirements.txt so we have to download
# from github
version('0.2.5', branch="v0.2.5")
depends_on('python@3.5:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-pandas@0.24.2:', type=('build', 'run'))
depends_on('py-numpy@1.16.2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-goplot/package.py
|
<filename>var/spack/repos/builtin/packages/r-goplot/package.py
# 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 import *
class RGoplot(RPackage):
"""Visualization of Functional Analysis Data.
Implementation of multilayered visualizations for enhanced graphical
representation of functional analysis data. It combines and integrates
omics data derived from expression and functional annotation enrichment
analyses. Its plotting functions have been developed with an hierarchical
structure in mind: starting from a general overview to identify the most
enriched categories (modified bar plot, bubble plot) to a more detailed one
displaying different types of relevant information for the molecules in a
given set of categories (circle plot, chord plot, cluster plot, Venn
diagram, heatmap)."""
cran = "GOplot"
version('1.0.2', sha256='3ddaa2b6d1297ad6daad30d18af708adf43d86e8804b1b92fa29dfbf26d80df9')
depends_on('r@3.2.3:', type=('build', 'run'))
depends_on('r-ggplot2@2.0.0:', type=('build', 'run'))
depends_on('r-ggdendro@0.1-17:', type=('build', 'run'))
depends_on('r-gridextra@2.0.0:', type=('build', 'run'))
depends_on('r-rcolorbrewer@1.1-2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-qiskit-aer/package.py
|
# 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)
class PyQiskitAer(PythonPackage, CudaPackage):
"""Aer is a high performance simulator for quantum circuits that
includes noise models"""
homepage = "https://github.com/Qiskit/qiskit-aer"
pypi = "qiskit-aer/qiskit-aer-0.9.1.tar.gz"
version('0.9.1', sha256='3bf5f615aaae7cc5f816c39a4e9108aabaed0cc894fb6f841e48ffd56574e7eb')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools@40.1.0:', type='build')
depends_on('py-numpy@1.16.3:', type=('build', 'run'))
depends_on('py-pybind11@2.6:', type='build')
depends_on('py-qiskit-terra@0.17.0:', type=('build', 'run'))
depends_on('py-scipy@1.0:', type=('build', 'run'))
depends_on('py-scikit-build@0.11.0:', type='build')
depends_on('py-cmake@:3.16,3.18:', type='build')
depends_on('mpi', when='+mpi')
depends_on('nlohmann-json@3.1.1:')
depends_on('spdlog@1.5.0:')
depends_on('muparserx@4.0.8:')
depends_on('blas')
depends_on('cuda@10.1:', when='+cuda')
variant('mpi', default=True, description='Enable MPI support')
variant('gdr', default=True, description='Enable GDR support')
def setup_build_environment(self, env):
env.set('DISABLE_CONAN', 'ON')
env.set('DISABLE_DEPENDENCY_INSTALL', '1')
env.set("CUDAHOSTCXX", spack_cxx)
def install_options(self, spec, prefix):
args = []
args.append('-DDISABLE_CONAN=ON')
if '~gdr' in self.spec:
args.append('-DAER_DISABLE_GDR=True')
else:
args.append('-DAER_DISABLE_GDR=False')
if '+mpi' in self.spec:
args.append('-DAER_MPI=True')
else:
args.append('-DAER_MPI=False')
if '+cuda' in self.spec:
args.append('-DAER_THRUST_BACKEND=CUDA')
cuda_archs = spec.variants['cuda_arch'].value
if 'none' not in cuda_archs:
args.append('-DCUDA_NVCC_FLAGS={0}'.
format(' '.join(self.cuda_flags(cuda_archs))))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/minigmg/package.py
|
<reponame>player1537-forks/spack
# 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)
class Minigmg(Package):
"""miniGMG is a compact benchmark for understanding the performance
challenges associated with geometric multigrid solvers
found in applications built from AMR MG frameworks
like CHOMBO or BoxLib when running
on modern multi- and manycore-based supercomputers.
It includes both productive reference examples as well as
highly-optimized implementations for CPUs and GPUs.
It is sufficiently general that it has been used to evaluate
a broad range of research topics including PGAS programming models
and algorithmic tradeoffs inherit in multigrid. miniGMG was developed
under the CACHE Joint Math-CS Institute.
Note, miniGMG code has been supersceded by HPGMG. """
homepage = "http://crd.lbl.gov/departments/computer-science/PAR/research/previous-projects/miniGMG/"
url = "https://crd.lbl.gov/assets/Uploads/FTG/Projects/miniGMG/miniGMG.tar.gz"
version('master', sha256='1c2d27496a881f655f5e849d6a7a132625e535739f82575991c511cc2cf899ac')
variant('vec', default='ompif', description='Which method of vectorisation to use',
values=('ompif', 'sse', 'avx', 'simde'), multi=False)
variant('opt', default=False, description='Enable optimization flags for improved OpenMP')
depends_on('mpi')
# Set up SIMD Everywhere config
depends_on('simde', when='vec=simde')
patch('simde.patch', when='vec=simde')
# Patch to add timer for Aarch64 rather than rdtsc
patch('aarch64_time.patch', when='target=aarch64:')
# Replaces inline with inline static, for correct syntax
patch('inline_static.patch')
phases = ['build', 'install']
def build(self, spec, prefix):
cc = Executable(spec['mpi'].mpicc)
args = []
# Default optimisation level
if spec.satisfies('+opt'):
if self.spec.satisfies('%nvhpc'):
args.append('-fast')
else:
args.append('-Ofast')
else:
args.append('-O3')
# Add OpenMP flag
args += [self.compiler.openmp_flag]
args += ['miniGMG.c', 'mg.c', 'box.c', 'solver.c']
# Set the correct operators file - using the vec variant
if spec.satisfies('vec=sse'):
args += ['operators.sse.c']
elif spec.satisfies('vec=avx'):
args += ['operators.avx.c']
elif spec.satisfies('vec=simde'):
args += ['operators.simde.c']
else:
args += ['operators.ompif.c']
# Switch out timer file (depends on patch)
if spec.satisfies('target=aarch64:'):
args += ['timer.aarch64.c']
else:
args += ['timer.x86.c']
args += ['-D__MPI']
if spec.satisfies('+opt'):
args += ['-D__PREFETCH_NEXT_PLANE_FROM_DRAM']
args += ['-D__FUSION_RESIDUAL_RESTRICTION']
else:
args += ['-D__COLLABORATIVE_THREADING=6']
args += ['-D__TEST_MG_CONVERGENCE', '-D__PRINT_NORM', '-D__USE_BICGSTAB']
args += ['-o', 'run.miniGMG', '-lm']
cc(*args)
def install(self, spec, prefix):
mkdir(prefix.bin)
install('run.miniGMG', prefix.bin)
mkdir(prefix.jobs)
install('job*', prefix.jobs)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-parsl/package.py
|
# 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 import *
class PyParsl(PythonPackage):
"""
Simple data dependent workflows in Python
"""
homepage = "https://github.com/Parsl/parsl"
url = "https://github.com/Parsl/parsl/archive/refs/tags/1.1.0.tar.gz"
maintainers = ['hategan']
version('1.1.0', sha256='6a623d3550329f028775950d23a2cafcb0f82b199f15940180410604aa5d102c')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-pyzmq@17.1.2:', type=('build', 'run'))
depends_on('py-typeguard@2.10:', type=('build', 'run'))
depends_on('py-typing-extensions', type=('build', 'run'))
depends_on('py-globus-sdk', type=('build', 'run'))
depends_on('py-dill', type=('build', 'run'))
depends_on('py-tblib', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-paramiko', type=('build', 'run'))
depends_on('py-psutil@5.5.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-binaryornot/package.py
|
<gh_stars>10-100
# 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 import *
class PyBinaryornot(PythonPackage):
"""Ultra-lightweight pure Python package to check if a file is binary or text.
"""
homepage = "https://binaryornot.readthedocs.io"
url = "https://github.com/audreyr/binaryornot/archive/0.4.0.tar.gz"
version('0.4.4', sha256='8cca04876a5e9d01f0dda79390e99089da87f3c1948ab2720661ba379d1b23f2')
depends_on('py-setuptools', type='build')
depends_on('py-chardet')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-storm/package.py
|
# 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 import *
class PyStorm(PythonPackage):
"""Storm is an object-relational mapper (ORM) for Python"""
homepage = "https://storm.canonical.com/"
pypi = 'storm/storm-0.25.tar.gz'
version('0.25', sha256='ec7cc8897638f94f6b75c6a2af74aa9b31f5492d7a2f9482c08a8dd7b46adb14')
version('0.23', sha256='01c59f1c898fb9891333abd65519ba2dd5f68623ac8e67b54932e99ce52593d3',
url='https://files.pythonhosted.org/packages/source/s/storm/storm-0.23.tar.bz2')
version('0.20', sha256='35f5883e93a262002ca59dbb39645c67434a182d758543c4a2467ff690ac23a5')
depends_on('py-setuptools', type='build')
depends_on('py-six', type=('build', 'run'), when='@0.23:')
depends_on('py-zope-interface@4:', type=('build', 'run'))
depends_on('python@2.7:2.8', type=('build', 'run'), when='@:0.20')
depends_on('python@2.7:2.8,3.5:', type=('build', 'run'), when='@0.21:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libmnl/package.py
|
# 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 import *
class Libmnl(AutotoolsPackage):
"""libmnl is a minimalistic user-space library oriented to Netlink
developers.There are a lot of common tasks in parsing, validating,
constructing of both the Netlink header and TLVs that are repetitive
and easy to get wrong.This library aims to provide simple helpers
that allows you to re-use code and to avoid re-inventing the wheel."""
homepage = "https://github.com/threatstack/libmnl"
url = "https://github.com/threatstack/libmnl/archive/libmnl-1.0.3.tar.gz"
version('1.0.3', sha256='14405da1bb3a679c24e0fe1f2845d47359ed2de8055e588df4b6b19cab68e901')
version('1.0.2', sha256='2caec4716aceb245130f4e42f8c118b92618e37db8bb94e2799aff42b95c269f')
version('1.0.1', sha256='60fe2a6ce59f6118b75b598dc11fc89b97e20ff8633fbea26fc568c45bbb672b')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-survey/package.py
|
<gh_stars>10-100
# 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 import *
class RSurvey(RPackage):
"""Analysis of Complex Survey Samples.
Summary statistics, two-sample tests, rank tests, generalised linear
models, cumulative link models, Cox models, loglinear models, and general
maximum pseudolikelihood estimation for multistage stratified,
cluster-sampled, unequally weighted survey samples. Variances by Taylor
series linearisation or replicate weights. Post-stratification,
calibration, and raking. Two-phase subsampling designs. Graphics. PPS
sampling without replacement. Principal components, factor analysis."""
cran = "survey"
version('4.1-1', sha256='05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52')
version('4.0', sha256='b053f40f4cfa90507ca524f72d3b3a4b4869def52f11f907a14f1c6d90063de1')
version('3.36', sha256='90f32e9d2b52eacf881e6717a4b5edfc5a3beb5da516f8372293549589d79475')
version('3.35-1', sha256='11e5ddde9c8c21dfaed0b1247036e068ad32782c76ff71f7937eb7585dd364db')
version('3.30-3', sha256='be45d00b22d857e66905789031f2db1037505f80ce15d4b0ea84dabb03bc9e6d')
depends_on('r@2.14.0:', type=('build', 'run'))
depends_on('r@2.16.0:', type=('build', 'run'), when='@3.32:')
depends_on('r@3.1.0:', type=('build', 'run'), when='@3.35:')
depends_on('r@3.5.0:', type=('build', 'run'), when='@4.1-1:')
depends_on('r-matrix', type=('build', 'run'), when='@3.31:')
depends_on('r-survival', type=('build', 'run'), when='@3.31:')
depends_on('r-lattice', type=('build', 'run'), when='@3.31:')
depends_on('r-minqa', type=('build', 'run'), when='@3.34:')
depends_on('r-numderiv', type=('build', 'run'), when='@3.34:')
depends_on('r-mitools@2.4:', type=('build', 'run'), when='@3.36:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/fujitsu-frontistr/package.py
|
<reponame>player1537-forks/spack
# 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 import *
from spack.pkg.builtin.frontistr import FrontistrBase
class FujitsuFrontistr(FrontistrBase):
"""This is a fork repository of the FrontISTR tuned for A64FX."""
_name = 'fujitsu-frontistr'
homepage = "https://www.frontistr.com/"
url = "https://github.com/fujitsu/FrontISTR/archive/refs/tags/v5.2_tuned.tar.gz"
git = "https://github.com/fujitsu/FrontISTR"
maintainers = ['kinagaki-fj', 'kinagaki', 'm-shunji']
version('master', branch='fj-master')
version('5.2', sha256='ebf73a96c33ae7c9e616c99f9ce07ec90d802764dbf6abf627b0083c3bbd2b2e')
version('5.0', sha256='7a3a2dd0f834048fb71cc254c9da6c2637fb23110e79b5efaf208d6f69a5b30a')
variant('static', default=True, description='Build with static linkage')
depends_on('metis ~shared', when='+static')
depends_on('mumps ~shared', when='+static')
depends_on('trilinos ~shared', when='+static')
def url_for_version(self, version):
url = "https://github.com/fujitsu/FrontISTR/archive/refs/tags/v{0}_tuned.tar.gz"
return url.format(version)
def cmake_args(self):
define = CMakePackage.define
args = super(FujitsuFrontistr, self).cmake_args()
if self.spec.satisfies('%fj'):
args.extend([
define('CMAKE_C_FLAGS',
'-Kcmodel=large -Nlst=t -Kocl -Kfast -Kzfill -Koptmsg=2'),
define('CMAKE_CXX_FLAGS',
'-Kcmodel=large -Nlst=t -Kocl -Kfast -Kzfill -Koptmsg=2'),
define('CMAKE_Fortran_FLAGS',
'-Kcmodel=large -Nlst=t -Kocl -Kfast -Kzfill -Koptmsg=2'),
define('CMAKE_Fortran_MODDIR_FLAG', 'M'),
define('OpenMP_C_FLAGS', '-Kopenmp'),
define('OpenMP_CXX_FLAGS', '-Kopenmp'),
define('OpenMP_Fortran_FLAGS', '-Kopenmp')
])
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ade4/package.py
|
# 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 import *
class RAde4(RPackage):
"""Analysis of Ecological Data : Exploratory and Euclidean Methods in
Environmental Sciences.
Tools for multivariate data analysis. Several methods are provided for the
analysis (i.e., ordination) of one-table (e.g., principal component
analysis, correspondence analysis), two-table (e.g., coinertia analysis,
redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g.,
STATIS, multiple coinertia analysis). The philosophy of the package is
described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>."""
cran = "ade4"
version('1.7-18', sha256='ecb6f4c42c60f39702aa96f454bb536a333049c9608ee2b6bdf8795e059cc525')
version('1.7-16', sha256='9bd7a25ff4fe30a32fd8f6b71909f4c638a0e2f002fc8303c0a4795423385590')
version('1.7-13', sha256='f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b')
version('1.7-11', sha256='4ccd799ae99bd625840b866a697c4a48adb751660470bf0d6cf9207b1927a572')
version('1.7-6', sha256='80848e1650dcc0ec921c130efa6f7e9b307f0d107c63e49faa52296eda19cc52')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-pixmap', type=('build', 'run'), when='@1.7-16:')
depends_on('r-sp', type=('build', 'run'), when='@1.7-16:')
depends_on('r-progress', type=('build', 'run'), when='@1.7-16')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/stc/package.py
|
<filename>var/spack/repos/builtin/packages/stc/package.py
# 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 import *
class Stc(AutotoolsPackage):
"""STC: The Swift-Turbine Compiler"""
homepage = 'http://swift-lang.org/Swift-T'
url = 'https://swift-lang.github.io/swift-t-downloads/spack/stc-0.9.0.tar.gz'
git = "https://github.com/swift-lang/swift-t.git"
tags = ['e4s']
version('master', branch='master')
version('0.9.0', sha256='edf187344ce860476473ab6599f042cd22ed029aa186d512135990accb9d260f')
version('0.8.3', sha256='d61ca80137a955b12e84e41cb8a78ce1a58289241a2665076f12f835cf68d798')
version('0.8.2', sha256='13f0f03fdfcca3e63d2d58d7e7dbdddc113d5b9826c9357ab0713b63e8e42c5e')
depends_on('java', type=('build', 'run'))
depends_on('ant', type='build')
depends_on('turbine', type=('build', 'run'))
depends_on('turbine@master', type=('build', 'run'), when='@master')
depends_on('zsh', type=('build', 'run'))
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
@property
def configure_directory(self):
if self.version == Version('master'):
return 'stc/code'
else:
return '.'
def configure_args(self):
args = ['--with-turbine=' + self.spec['turbine'].prefix]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gsettings-desktop-schemas/package.py
|
<reponame>player1537-forks/spack
# 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 import *
class GsettingsDesktopSchemas(MesonPackage):
"""gsettings-desktop-schemas contains a collection of GSettings schemas
for settings shared by various components of a desktop."""
homepage = "https://github.com/GNOME/gsettings-desktop-schemas/"
url = "https://github.com/GNOME/gsettings-desktop-schemas/archive/3.38.0.tar.gz"
version('3.38.0', sha256='b808bd285ac7176f2e9e3a8763c3913121ab9f109d2988c70e3f1f8e742a630d')
version('3.37.92', sha256='5f5dd0421ed2f3746674b8bb6e0c652784915133c7f2d133339bf5e4140d8d1d')
version('3.37.2', sha256='1dacdfeecfc57468da7c598a01b635f82ecd088e1d78d5aa840e47256026654d')
depends_on('glib')
depends_on('gobject-introspection', type='build')
depends_on('gettext', type='build')
def setup_dependent_build_environment(self, env, dependent_spec):
env.prepend_path('XDG_DATA_DIRS', self.prefix.share)
def setup_dependent_run_environment(self, env, dependent_spec):
env.prepend_path('XDG_DATA_DIRS', self.prefix.share)
def setup_build_environment(self, env):
env.prepend_path("XDG_DATA_DIRS", self.prefix.share)
def setup_run_environment(self, env):
env.prepend_path("XDG_DATA_DIRS", self.prefix.share)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-codetools/package.py
|
# 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 import *
class RCodetools(RPackage):
"""Code analysis tools for R."""
cran = "codetools"
version('0.2-18', sha256='1a9ea6b9792dbd1688078455929385acc3a5e4bef945c77bec1261fa4a084c28')
version('0.2-16', sha256='c276757c3adabaf700f2ea25835892b09bc1bd438ebd17c805ea9073ed8a74b6')
version('0.2-15', sha256='4e0798ed79281a614f8cdd199e25f2c1bd8f35ecec902b03016544bd7795fa40')
version('0.2-14', sha256='270d603b89076081af8d2db0256927e55ffeed4c27309d50deea75b444253979')
depends_on('r@2.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/octave-io/package.py
|
<filename>var/spack/repos/builtin/packages/octave-io/package.py
# 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 import *
class OctaveIo(OctavePackage, SourceforgePackage):
"""The IO package is part of the Octave Forge project
and provides input/output from/in external formats."""
homepage = "https://octave.sourceforge.io/io/"
sourceforge_mirror_path = "octave/io-2.6.3.tar.gz"
version('2.6.3', sha256='6bc63c6498d79cada01a6c4446f793536e0bb416ddec2a5201dd8d741d459e10')
version('2.6.2', sha256='01dbf8885a8011e76c919e271727c1d44f625bf6b217948b79438039ba368ceb')
version('2.6.1', sha256='83253561f883c96ca3021a771223d23795122dc4cb800766e9cb893c6f8262dd')
version('2.6.0', sha256='27f26273ced0b42c098e900136bb0ab2e542baf98d02bc0176cf47edbd0e6d7f')
version('2.2.7', sha256='4eed2ee4c89b49ab160546c77ed66a384598f3bbb1c6e3833529c2c55aa479b6')
extends('octave@4.2.0:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-klar/package.py
|
<gh_stars>10-100
# 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 import *
class RKlar(RPackage):
"""Classification and Visualization.
Miscellaneous functions for classification and visualization, e.g.
regularized discriminant analysis, sknn() kernel-density naive Bayes, an
interface to 'svmlight' and stepclass() wrapper variable selection for
supervised classification, partimat() visualization of classification rules
and shardsplot() of cluster results as well as kmodes() clustering for
categorical data, corclust() variable clustering, variable extraction from
different variable clustering models and weight of evidence
preprocessing."""
cran = "klaR"
version('0.6-15', sha256='5bfe5bc643f8a64b222317732c26e9f93be297cdc318a869f15cc9ab0d9e0fae')
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-combinat', type=('build', 'run'))
depends_on('r-questionr', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ps/package.py
|
# 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 import *
class RPs(RPackage):
"""List, Query, Manipulate System Processes.
List, query and manipulate all system processes, on 'Windows', 'Linux' and
'macOS'."""
cran = "ps"
version('1.6.0', sha256='89ad7ddc5e0818bccacfd0673ddf2da0892ac2a3b4d3a821e40884ab1e96bf31')
version('1.5.0', sha256='7461a196f55557feda569a9791ad851c884f9a2dd71671655ed17cb048fafe96')
version('1.3.0', sha256='289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1')
version('1.2.1', sha256='bd7207164e6557a9e4213c4b00dc5dc23d7705ab290569765998640b16a3beff')
version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe')
version('1.0.0', sha256='9bdaf64aaa44ae11866868402eb75bf56c2e3022100476d9b9dcd16ca784ffd8')
depends_on('r@3.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-matr/package.py
|
# 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 import *
class RMatr(RPackage):
"""Metagenomics Analysis Tools.
Package matR (Metagenomics Analysis Tools for R) is an analysis client for
the MG-RAST metagenome annotation engine, part of the US Department of
Energy (DOE) Systems Biology Knowledge Base (KBase). Customized analysis
and visualization tools securely access remote data and metadata within the
popular open source R language and environment for statistical
computing."""
cran = "matR"
version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3')
version('0.9', sha256='5750e6a876cf85fe66038292adefbfcb18e2584fa2e841f39dbe67f3c51b3052')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-mgraster', type=('build', 'run'))
depends_on('r-biom-utils', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-clikit/package.py
|
<gh_stars>10-100
# 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 import *
class PyClikit(PythonPackage):
"""CliKit is a group of utilities to build beautiful and testable
command line interfaces."""
homepage = "https://github.com/sdispater/clikit"
pypi = "clikit/clikit-0.6.2.tar.gz"
version('0.6.2', sha256='442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59')
depends_on('python@2.7,3.4:3', type=('build', 'run'))
depends_on('py-poetry-core@1:', type='build')
depends_on('py-pastel@0.2.0:0.2', type=('build', 'run'))
depends_on('py-pylev@1.3:1', type=('build', 'run'))
depends_on('py-crashtest@0.3.0:0.3', when='^python@3.6:3', type=('build', 'run'))
depends_on('py-typing@3.6:3', when='^python@2.7,3.4', type=('build', 'run'))
depends_on('py-typing-extensions@3.6:3', when='^python@3.5.0:3.5.3', type=('build', 'run'))
depends_on('py-enum34@1.1:1', when='^python@2.7', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/stinger/package.py
|
<gh_stars>10-100
# 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 import *
class Stinger(CMakePackage):
"""The STINGER in-memory graph store and dynamic graph analysis
platform. Millions to billions of vertices and edges at thousands
to millions of updates per second."""
homepage = "http://www.stingergraph.com/"
git = "https://github.com/stingergraph/stinger.git"
version('master', branch='master')
parallel = False
def install(self, spec, prefix):
with working_dir(self.build_directory):
install_tree('./bin', prefix.bin)
install_tree('./lib', prefix.lib)
install_tree('./include', prefix.include)
install_tree('./share', prefix.share)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rinside/package.py
|
<gh_stars>10-100
# 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 import *
class RRinside(RPackage):
"""C++ Classes to Embed R in C++ (and C) Applications.
C++ classes to embed R in C++ applications The 'RInside' packages makes it
easier to have "R inside" your C++ application by providing a C++
wrapperclass providing the R interpreter. As R itself is embedded into your
application, a shared library build of R is required. This works on Linux,
OS X and even on Windows provided you use the same tools used to build R
itself. Numerous examples are provided in the eight subdirectories of the
examples/ directory of the installed package: standard, mpi (for parallel
computing) qt (showing how to embed 'RInside' inside a Qt GUI application),
wt (showing how to build a "web-application" using the Wt toolkit),
armadillo (for 'RInside' use with 'RcppArmadillo') and eigen (for 'RInside'
use with 'RcppEigen'). The example use GNUmakefile(s) with GNU extensions,
so a GNU make is required (and will use the GNUmakefile automatically).
Doxygen-generated documentation of the C++ classes is available at the
'RInside' website as well."""
cran = "RInside"
version('0.2.16', sha256='7ae4ade128ea05f37068d59e610822ff0b277f9d39d8900f7eb31759ad5a2a0e')
version('0.2.15', sha256='1e1d87a3584961f3aa4ca6acd4d2f3cda26abdab027ff5be2fd5cd76a98af02b')
version('0.2.14', sha256='8de5340993fe879ca00fa559c5b1b27b408ba78bfc5f67d36d6f0b8d8e8649cf')
version('0.2.13', sha256='be1da861f4f8c1292f0691bce05978e409a081f24ad6006ae173a6a89aa4d031')
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/resource.py
|
# 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)
"""Describes an optional resource needed for a build.
Typically a bunch of sources that can be built in-tree within another
package to enable optional features.
"""
class Resource(object):
"""Represents an optional resource to be fetched by a package.
Aggregates a name, a fetcher, a destination and a placement.
"""
def __init__(self, name, fetcher, destination, placement):
self.name = name
self.fetcher = fetcher
self.destination = destination
self.placement = placement
|
player1537-forks/spack
|
lib/spack/spack/test/config_values.py
|
# 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)
import pytest
import spack.spec
import spack.store
@pytest.mark.parametrize('hash_length', [1, 2, 3, 4, 5, 9])
@pytest.mark.usefixtures('mock_packages')
def test_set_install_hash_length(hash_length, mutable_config, tmpdir):
mutable_config.set('config:install_hash_length', hash_length)
mutable_config.set('config:install_tree', {'root': str(tmpdir)})
# The call below is to reinitialize the directory layout associated
# with the store according to the configuration changes above (i.e.
# with the shortened hash)
store = spack.store._store()
with spack.store.use_store(store):
spec = spack.spec.Spec('libelf').concretized()
prefix = spec.prefix
hash_str = prefix.rsplit('-')[-1]
assert len(hash_str) == hash_length
@pytest.mark.usefixtures('mock_packages')
def test_set_install_hash_length_upper_case(mutable_config, tmpdir):
mutable_config.set('config:install_hash_length', 5)
mutable_config.set(
'config:install_tree',
{
'root': str(tmpdir),
'projections': {
'all': '{name}-{HASH}'
}
}
)
# The call below is to reinitialize the directory layout associated
# with the store according to the configuration changes above (i.e.
# with the shortened hash and projection)
store = spack.store._store()
with spack.store.use_store(store):
spec = spack.spec.Spec('libelf').concretized()
prefix = spec.prefix
hash_str = prefix.rsplit('-')[-1]
assert len(hash_str) == 5
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rapiserialize/package.py
|
<filename>var/spack/repos/builtin/packages/r-rapiserialize/package.py
# 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 import *
class RRapiserialize(RPackage):
"""R API Serialization.
This package provides other packages with access to the internal R
serialization code. Access to this code is provided at the C function level
by using the registration of native function mechanism. Client packages
simply include a single header file RApiSerializeAPI.h provided by this
package. This packages builds on the Rhpc package by <NAME> and Ei-ji
Nakama which also includes a (partial) copy of the file
src/main/serialize.c from R itself. The R Core group is the original author
of the serialization code made available by this package."""
cran = "RApiSerialize"
maintainers = ['dorton21']
version('0.1.0', sha256='324d42c655c27b4647d194bfcd7c675da95c67ea3a74ce99853502022792a23e')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/er/package.py
|
<filename>var/spack/repos/builtin/packages/er/package.py
# 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 import *
class Er(CMakePackage):
"""Encoding and redundancy on a file set"""
homepage = "https://github.com/ecp-veloc/er"
url = "https://github.com/ecp-veloc/er/archive/v0.0.3.tar.gz"
git = "https://github.com/ecp-veloc/er.git"
tags = ['ecp']
maintainers = ['CamStan', 'gonsie']
version('main', branch='main')
version('0.1.0', sha256='543afc1c48bb2c67f48c32f6c9efcbf7bb27f2e622ff76f2c2ce5618c77aacfc')
version('0.0.4', sha256='c456d34719bb57774adf6d7bc2fa9917ecb4a9de442091023c931a2cb83dfd37')
version('0.0.3', sha256='243b2b46ea274e17417ef5873c3ed7ba16dacdfdaf7053d1de5434e300de796b')
depends_on('mpi')
depends_on('kvtree+mpi')
depends_on('rankstr', when='@0.0.4:')
depends_on('redset')
depends_on('shuffile')
depends_on('zlib', type='link')
variant('shared', default=True, description='Build with shared libraries')
deps = ['kvtree', 'rankstr', 'redset', 'shuffile']
for dep in deps:
depends_on(dep + '+shared', when='@0.1: +shared')
depends_on(dep + '~shared', when='@0.1: ~shared')
def cmake_args(self):
spec = self.spec
args = []
args.append(self.define('MPI_C_COMPILER', spec['mpi'].mpicc))
args.append(self.define('WITH_KVTREE_PREFIX', spec['kvtree'].prefix))
args.append(self.define('WITH_REDSET_PREFIX', spec['redset'].prefix))
args.append(
self.define('WITH_SHUFFILE_PREFIX', spec['shuffile'].prefix)
)
if spec.satisfies('@0.0.4:'):
args.append(
self.define('WITH_RANKSTR_PREFIX', spec['rankstr'].prefix)
)
if spec.satisfies('@0.1.0:'):
args.append(self.define_from_variant('BUILD_SHARED_LIBS', 'shared'))
else:
if spec.satisfies('platform=cray'):
args.append(self.define('ER_LINK_STATIC', True))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/oclint/package.py
|
<gh_stars>10-100
# 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 import *
class Oclint(Package):
"""OClint: a static analysis tool for C, C++, and Objective-C code
OCLint is a static code analysis tool for improving quality and
reducing defects by inspecting C, C++ and Objective-C code and
looking for potential problems"""
homepage = "https://oclint.org/"
url = "https://github.com/oclint/oclint/archive/v0.13.tar.gz"
version('0.13', sha256='a0fd188673863e6357d6585b9bb9c3affe737df134b9383a1a5ed021d09ed848')
depends_on('python', type=('build'))
depends_on('py-argparse', type=('build'), when='^python@:2.6,3.0:3.1')
depends_on('git', type=('build'))
depends_on('subversion', type=('build'))
depends_on('cmake', type=('build'))
depends_on('ninja', type=('build'))
depends_on('llvm@5.0.0:')
# Needed to fix a bug in oclint-scripts/bundle script, which
# attempts to install c++ headers in the wrong location
# contributed upstream as
# https://github.com/oclint/oclint/pull/492
patch('bundle.patch', level=0)
def install(self, spec, prefix):
# Build from source via directions from
# https://docs.oclint.org/en/stable/intro/build.html,
cd('oclint-scripts')
# ...but instead of using oclint-scripts/make, execute the
# commands in oclint-scripts/makeWithSystemLLVM so that
# oclint links to spack-installed LLVM
build_script = Executable(join_path('.', 'build'))
bundle_script = Executable(join_path('.', 'bundle'))
# Add the '-no-analytics' argument to the build script because
# 1) it doesn't detect properly a spack install of OpenSSL,
# and throws an error due to missing OpenSSL headers
# 2) the bespoke build system is a pain to patch as it is
# 3) many sites don't allow software that communicates analytics data
build_script('-release',
'-clean',
'-llvm-root={0}'.format(spec['llvm'].prefix),
'-use-system-compiler',
'-no-analytics',
'all')
bundle_script('-release', '-llvm-root={0}'.format(spec['llvm'].prefix))
# Copy install tree into the correct locations using the
# directory layout described in
cd(join_path('..', 'build'))
install_tree(join_path('oclint-release', 'include'), prefix.include)
install_tree(join_path('oclint-release', 'lib'), prefix.lib)
install_tree(join_path('oclint-release', 'bin'), prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/conserver/package.py
|
# 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 import *
class Conserver(AutotoolsPackage):
"""Conserver is an application that allows multiple users to
watch a serial console at the same time. """
homepage = "https://www.conserver.com/"
url = "https://github.com/bstansell/conserver/releases/download/v8.2.5/conserver-8.2.5.tar.gz"
version('8.2.5', sha256='7db192f304126d7e5c15421c4c83cd5c08039f2f2b3c61b2998e71881ae47eea')
version('8.2.4', sha256='a591eabb4abb632322d2f3058a2f0bd6502754069a99a153efe2d6d05bd97f6f')
version('8.2.3', sha256='764443b2798047f7429747510eeb3207240260590551700d13dbbad8a5bdee08')
version('8.2.2', sha256='05ea1693bf92b42ad2f0a9389c60352ccd35c2ea93c8fc8e618d0153362a7d81')
version('8.2.1', sha256='251ae01997e8f3ee75106a5b84ec6f2a8eb5ff2f8092438eba34384a615153d0')
def setup_run_environment(self, env):
env.prepend_path('PATH', self.prefix.sbin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-pbdzmq/package.py
|
<reponame>player1537-forks/spack<gh_stars>10-100
# 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 import *
class RPbdzmq(RPackage):
"""Programming with Big Data -- Interface to 'ZeroMQ'.
'ZeroMQ' is a well-known library for high-performance asynchronous
messaging in scalable, distributed applications. This package provides high
level R wrapper functions to easily utilize 'ZeroMQ'. We mainly focus on
interactive client/server programming frameworks. For convenience, a
minimal 'ZeroMQ' library (4.1.0 rc1) is shipped with 'pbdZMQ', which can be
used if no system installation of 'ZeroMQ' is available. A few wrapper
functions compatible with 'rzmq' are also provided."""
cran = "pbdZMQ"
version('0.3-6', sha256='9944c8c44221aed1dbd7763ad9ec52c0ad2611d37bee25971ca16f02e8e8c37b')
version('0.3-4', sha256='07794bd6858e093f8b6b879ddd5ab0195449b47a41b70cab2f60603f0a53b129')
version('0.3-3', sha256='ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca')
version('0.3-2', sha256='ece2a2881c662f77126e4801ba4e01c991331842b0d636ce5a2b591b9de3fc37')
version('0.2-4', sha256='bfacac88b0d4156c70cf63fc4cb9969a950693996901a4fa3dcd59949ec065f6')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.2.0:', type=('build', 'run'), when='@0.2-6:')
depends_on('r@3.5.0:', type=('build', 'run'), when='@0.3-4:')
depends_on('libzmq@4.0.4:')
depends_on('r-r6', type=('build', 'run'), when='@:0.2-6')
|
player1537-forks/spack
|
lib/spack/spack/test/spec_yaml.py
|
<filename>lib/spack/spack/test/spec_yaml.py
# 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)
"""Test YAML serialization for specs.
YAML format preserves DAG information in the spec.
"""
import ast
import inspect
import os
import pytest
from llnl.util.compat import Iterable, Mapping
import spack.hash_types as ht
import spack.spec
import spack.util.spack_json as sjson
import spack.util.spack_yaml as syaml
import spack.version
from spack import repo
from spack.spec import Spec, save_dependency_specfiles
from spack.util.mock_package import MockPackageMultiRepo
from spack.util.spack_yaml import SpackYAMLError, syaml_dict
def check_yaml_round_trip(spec):
yaml_text = spec.to_yaml()
spec_from_yaml = Spec.from_yaml(yaml_text)
assert spec.eq_dag(spec_from_yaml)
def check_json_round_trip(spec):
json_text = spec.to_json()
spec_from_json = Spec.from_json(json_text)
assert spec.eq_dag(spec_from_json)
def test_simple_spec():
spec = Spec('mpileaks')
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_normal_spec(mock_packages):
spec = Spec('mpileaks+debug~opt')
spec.normalize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
@pytest.mark.parametrize(
"invalid_yaml",
[
"playing_playlist: {{ action }} playlist {{ playlist_name }}"
]
)
def test_invalid_yaml_spec(invalid_yaml):
with pytest.raises(SpackYAMLError) as e:
Spec.from_yaml(invalid_yaml)
exc_msg = str(e.value)
assert exc_msg.startswith("error parsing YAML spec:")
assert invalid_yaml in exc_msg
@pytest.mark.parametrize(
"invalid_json, error_message",
[
("{13:", "Expecting property name")
]
)
def test_invalid_json_spec(invalid_json, error_message):
with pytest.raises(sjson.SpackJSONError) as e:
Spec.from_json(invalid_json)
exc_msg = str(e.value)
assert exc_msg.startswith("error parsing JSON spec:")
assert error_message in exc_msg
def test_external_spec(config, mock_packages):
spec = Spec('externaltool')
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
spec = Spec('externaltest')
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_ambiguous_version_spec(mock_packages):
spec = Spec('mpileaks@1.0:5.0,6.1,7.3+debug~opt')
spec.normalize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_concrete_spec(config, mock_packages):
spec = Spec('mpileaks+debug~opt')
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_yaml_multivalue(config, mock_packages):
spec = Spec('multivalue-variant foo="bar,baz"')
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_yaml_subdag(config, mock_packages):
spec = Spec('mpileaks^mpich+debug')
spec.concretize()
yaml_spec = Spec.from_yaml(spec.to_yaml())
json_spec = Spec.from_json(spec.to_json())
for dep in ('callpath', 'mpich', 'dyninst', 'libdwarf', 'libelf'):
assert spec[dep].eq_dag(yaml_spec[dep])
assert spec[dep].eq_dag(json_spec[dep])
def test_using_ordered_dict(mock_packages):
""" Checks that dicts are ordered
Necessary to make sure that dag_hash is stable across python
versions and processes.
"""
def descend_and_check(iterable, level=0):
if isinstance(iterable, Mapping):
assert isinstance(iterable, syaml_dict)
return descend_and_check(iterable.values(), level=level + 1)
max_level = level
for value in iterable:
if isinstance(value, Iterable) and not isinstance(value, str):
nlevel = descend_and_check(value, level=level + 1)
if nlevel > max_level:
max_level = nlevel
return max_level
specs = ['mpileaks ^zmpi', 'dttop', 'dtuse']
for spec in specs:
dag = Spec(spec)
dag.normalize()
level = descend_and_check(dag.to_node_dict())
# level just makes sure we are doing something here
assert level >= 5
@pytest.mark.parametrize("hash_type", [
ht.dag_hash,
ht.build_hash,
ht.full_hash
])
def test_ordered_read_not_required_for_consistent_dag_hash(
hash_type, config, mock_packages
):
"""Make sure ordered serialization isn't required to preserve hashes.
For consistent hashes, we require that YAML and json documents
have their keys serialized in a deterministic order. However, we
don't want to require them to be serialized in order. This
ensures that is not required.
"""
specs = ['mpileaks ^zmpi', 'dttop', 'dtuse']
for spec in specs:
spec = Spec(spec)
spec.concretize()
#
# Dict & corresponding YAML & JSON from the original spec.
#
spec_dict = spec.to_dict(hash=hash_type)
spec_yaml = spec.to_yaml(hash=hash_type)
spec_json = spec.to_json(hash=hash_type)
#
# Make a spec with reversed OrderedDicts for every
# OrderedDict in the original.
#
reversed_spec_dict = reverse_all_dicts(spec.to_dict(hash=hash_type))
#
# Dump to YAML and JSON
#
yaml_string = syaml.dump(spec_dict, default_flow_style=False)
reversed_yaml_string = syaml.dump(reversed_spec_dict,
default_flow_style=False)
json_string = sjson.dump(spec_dict)
reversed_json_string = sjson.dump(reversed_spec_dict)
#
# Do many consistency checks
#
# spec yaml is ordered like the spec dict
assert yaml_string == spec_yaml
assert json_string == spec_json
# reversed string is different from the original, so it
# *would* generate a different hash
assert yaml_string != reversed_yaml_string
assert json_string != reversed_json_string
# build specs from the "wrongly" ordered data
round_trip_yaml_spec = Spec.from_yaml(yaml_string)
round_trip_json_spec = Spec.from_json(json_string)
round_trip_reversed_yaml_spec = Spec.from_yaml(
reversed_yaml_string
)
round_trip_reversed_json_spec = Spec.from_yaml(
reversed_json_string
)
# Strip spec if we stripped the yaml
spec = spec.copy(deps=hash_type.deptype)
# specs are equal to the original
assert spec == round_trip_yaml_spec
assert spec == round_trip_json_spec
assert spec == round_trip_reversed_yaml_spec
assert spec == round_trip_reversed_json_spec
assert round_trip_yaml_spec == round_trip_reversed_yaml_spec
assert round_trip_json_spec == round_trip_reversed_json_spec
# dag_hashes are equal
assert spec.dag_hash() == round_trip_yaml_spec.dag_hash()
assert spec.dag_hash() == round_trip_json_spec.dag_hash()
assert spec.dag_hash() == round_trip_reversed_yaml_spec.dag_hash()
assert spec.dag_hash() == round_trip_reversed_json_spec.dag_hash()
# full_hashes are equal if we round-tripped by build_hash or full_hash
if hash_type in (ht.build_hash, ht.full_hash):
spec.concretize()
round_trip_yaml_spec.concretize()
round_trip_json_spec.concretize()
round_trip_reversed_yaml_spec.concretize()
round_trip_reversed_json_spec.concretize()
assert spec.full_hash() == round_trip_yaml_spec.full_hash()
assert spec.full_hash() == round_trip_json_spec.full_hash()
assert spec.full_hash() == round_trip_reversed_yaml_spec.full_hash()
assert spec.full_hash() == round_trip_reversed_json_spec.full_hash()
@pytest.mark.parametrize("module", [
spack.spec,
spack.version,
])
def test_hashes_use_no_python_dicts(module):
"""Coarse check to make sure we don't use dicts in Spec.to_node_dict().
Python dicts are not guaranteed to iterate in a deterministic order
(at least not in all python versions) so we need to use lists and
syaml_dicts. syaml_dicts are ordered and ensure that hashes in Spack
are deterministic.
This test is intended to handle cases that are not covered by the
consistency checks above, or that would be missed by a dynamic check.
This test traverses the ASTs of functions that are used in our hash
algorithms, finds instances of dictionaries being constructed, and
prints out the line numbers where they occur.
"""
class FindFunctions(ast.NodeVisitor):
"""Find a function definition called to_node_dict."""
def __init__(self):
self.nodes = []
def visit_FunctionDef(self, node): # noqa
if node.name in ("to_node_dict", "to_dict", "to_dict_or_value"):
self.nodes.append(node)
class FindDicts(ast.NodeVisitor):
"""Find source locations of dicts in an AST."""
def __init__(self, filename):
self.nodes = []
self.filename = filename
def add_error(self, node):
self.nodes.append(
"Use syaml_dict instead of dict at %s:%s:%s"
% (self.filename, node.lineno, node.col_offset)
)
def visit_Dict(self, node): # noqa
self.add_error(node)
def visit_Call(self, node): # noqa
name = None
if isinstance(node.func, ast.Name):
name = node.func.id
elif isinstance(node.func, ast.Attribute):
name = node.func.attr
if name == 'dict':
self.add_error(node)
find_functions = FindFunctions()
module_ast = ast.parse(inspect.getsource(module))
find_functions.visit(module_ast)
find_dicts = FindDicts(module.__file__)
for node in find_functions.nodes:
find_dicts.visit(node)
# fail with offending lines if we found some dicts.
assert [] == find_dicts.nodes
def reverse_all_dicts(data):
"""Descend into data and reverse all the dictionaries"""
if isinstance(data, dict):
return syaml_dict(reversed(
[(reverse_all_dicts(k), reverse_all_dicts(v))
for k, v in data.items()]))
elif isinstance(data, (list, tuple)):
return type(data)(reverse_all_dicts(elt) for elt in data)
else:
return data
def check_specs_equal(original_spec, spec_yaml_path):
with open(spec_yaml_path, 'r') as fd:
spec_yaml = fd.read()
spec_from_yaml = Spec.from_yaml(spec_yaml)
return original_spec.eq_dag(spec_from_yaml)
def test_save_dependency_spec_jsons_subset(tmpdir, config):
output_path = str(tmpdir.mkdir('spec_jsons'))
default = ('build', 'link')
mock_repo = MockPackageMultiRepo()
g = mock_repo.add_package('g', [], [])
f = mock_repo.add_package('f', [], [])
e = mock_repo.add_package('e', [], [])
d = mock_repo.add_package('d', [f, g], [default, default])
c = mock_repo.add_package('c', [], [])
b = mock_repo.add_package('b', [d, e], [default, default])
mock_repo.add_package('a', [b, c], [default, default])
with repo.use_repositories(mock_repo):
spec_a = Spec('a')
spec_a.concretize()
b_spec = spec_a['b']
c_spec = spec_a['c']
spec_a_json = spec_a.to_json(hash=ht.build_hash)
save_dependency_specfiles(spec_a_json, output_path, ['b', 'c'])
assert check_specs_equal(b_spec, os.path.join(output_path, 'b.json'))
assert check_specs_equal(c_spec, os.path.join(output_path, 'c.json'))
def test_legacy_yaml(tmpdir, install_mockery, mock_packages):
"""Tests a simple legacy YAML with a dependency and ensures spec survives
concretization."""
yaml = """
spec:
- a:
version: '2.0'
arch:
platform: linux
platform_os: rhel7
target: x86_64
compiler:
name: gcc
version: 8.3.0
namespace: builtin.mock
parameters:
bvv: true
foo:
- bar
foobar: bar
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
dependencies:
b:
hash: iaapywazxgetn6gfv2cfba353qzzqvhn
type:
- build
- link
hash: obokmcsn3hljztrmctbscmqjs3xclazz
full_hash: avrk2tqsnzxeabmxa6r776uq7qbpeufv
build_hash: obokmcsn3hljztrmctbscmqjs3xclazy
- b:
version: '1.0'
arch:
platform: linux
platform_os: rhel7
target: x86_64
compiler:
name: gcc
version: 8.3.0
namespace: builtin.mock
parameters:
cflags: []
cppflags: []
cxxflags: []
fflags: []
ldflags: []
ldlibs: []
hash: iaapywazxgetn6gfv2cfba353qzzqvhn
full_hash: qvsxvlmjaothtpjluqijv7qfnni3kyyg
build_hash: iaapywazxgetn6gfv2cfba353qzzqvhy
"""
spec = Spec.from_yaml(yaml)
concrete_spec = spec.concretized()
assert concrete_spec.eq_dag(spec)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-backports/package.py
|
<filename>var/spack/repos/builtin/packages/r-backports/package.py
# 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 import *
class RBackports(RPackage):
"""Reimplementations of Functions Introduced Since R-3.0.0.
Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective
base version, if available. Package developers can make use of new
functions or arguments by selectively importing specific backports to
support older installations."""
cran = "backports"
version('1.4.1', sha256='845c3c59fbb05e5a892c4231b955a0afdd331d82b7cc815bcff0672023242474')
version('1.4.0', sha256='e7611565d24a852ad8b08579a7c67ad9121c1bda148bade98c7bec686e8dabbf')
version('1.2.1', sha256='a2834bbd57e305e5d8010322f1906ea1789b3b5ba5eca77c5ff4248aceb7c2d5')
version('1.1.4', sha256='ee4b5efef22fa7ef27d7983ffcd31db52f81e1fbb7189c6e89ee09b69349ff03')
version('1.1.3', sha256='e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1')
version('1.1.1', sha256='494e81a4829339c8f1cc3e015daa807e9138b8e21b929965fc7c00b1abbe8897')
version('1.1.0', sha256='c5536966ed6ca93f20c9a21d4f569cc1c6865d3352445ea66448f82590349fcd')
depends_on('r@3.0.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ggdendro/package.py
|
<gh_stars>10-100
# 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 import *
class RGgdendro(RPackage):
"""Create Dendrograms and Tree Diagrams Using 'ggplot2'.
This is a set of tools for dendrograms and tree plots using 'ggplot2'. The
'ggplot2' philosophy is to clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots directly to a plot
device without exposing the data. The 'ggdendro' package resolves this by
making available functions that extract the dendrogram plot data. The
package provides implementations for tree, rpart, as well as diana and
agnes cluster diagrams."""
cran = "ggdendro"
version('0.1.22', sha256='f0a65f3498c1abc3076df0fb56364b63bdf5d212d8931f85bcc6997510916b6a')
version('0.1-20', sha256='125cae904fa5d426cccaf32ebe9c6297e9ef0c6fd3f19f61513834d03a0cf8ff')
depends_on('r-mass', type=('build', 'run'))
depends_on('r-ggplot2@0.9.2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/shapeit/package.py
|
# 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 import *
class Shapeit(Package):
"""SHAPEIT is a fast and accurate method for estimation of haplotypes (aka
phasing) from genotype or sequencing data."""
homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html"
url = "https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.12.Linux.dynamic.tgz"
version('2.837', sha256='ec2ce728dd754452423ff5a8f7ed39c1c1218a11cedb93fab0c18428e3211874')
def url_for_version(self, version):
url = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v{0}.r{1}.GLIBCv2.12.Linux.dynamic.tgz'
return url.format(version[0], version[1])
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('bin'):
install('shapeit', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/spm/package.py
|
# 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 import *
class Spm(Package):
"""Statistical Parametric Mapping refers to the construction and assessment
of spatially extended statistical processes used to test hypotheses
about functional imaging data. These ideas have been instantiated in
software that is called SPM."""
homepage = "https://www.fil.ion.ucl.ac.uk/spm/"
url = "https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/spm12_r7219.zip"
list_url = "https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/"
version('12_r7219', sha256='b46fe8ce5ab537caeea7634c650f3a12fe2716f6a2e8ac15aa0d62b3652fe764',
url='https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip')
depends_on('zip', type='build')
depends_on('matlab', type='run')
def install(self, spec, prefix):
unzip = which('unzip')
unzip('spm12.ctf')
bash = which('bash')
bash('./run_spm12.sh')
install_tree('spm12', prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/hpccg/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/hpccg/package.py
# 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 import *
class Hpccg(MakefilePackage):
"""Proxy Application. Intended to be the 'best approximation
to an unstructured implicit finite element or finite volume
application in 800 lines or fewer.'
"""
homepage = "https://mantevo.org/about/applications/"
url = "https://downloads.mantevo.org/releaseTarballs/miniapps/HPCCG/HPCCG-1.0.tar.gz"
tags = ['proxy-app']
version('1.0', sha256='5be1b8cc3246811bfc9d6d7072be29455777d61b585675512ae52043ea64cefc')
variant('mpi', default=True, description='Build with MPI support')
variant('openmp', default=True, description='Build with OpenMP support')
# Optional dependencies
depends_on('mpi', when='+mpi')
@property
def build_targets(self):
targets = []
if '+mpi' in self.spec:
targets.append('CXX={0}'.format(self.spec['mpi'].mpicxx))
targets.append('LINKER={0}'.format(self.spec['mpi'].mpicxx))
targets.append('USE_MPI=-DUSING_MPI')
else:
targets.append('CXX=c++')
targets.append('LINKER=c++')
if '+openmp' in self.spec:
targets.append('USE_OMP=-DUSING_OMP')
targets.append('OMP_FLAGS={0}'.format(self.compiler.openmp_flag))
# Remove Compiler Specific Optimization Flags
if '%gcc' not in self.spec:
targets.append('CPP_OPT_FLAGS=')
return targets
def install(self, spec, prefix):
# Manual installation
mkdirp(prefix.bin)
mkdirp(prefix.doc)
install('test_HPCCG', prefix.bin)
install('README', prefix.doc)
install('weakScalingRunScript', prefix.bin)
install('strongScalingRunScript', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-bigmemory-sri/package.py
|
<reponame>player1537-forks/spack<gh_stars>10-100
# 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 import *
class RBigmemorySri(RPackage):
"""A shared resource interface for Bigmemory Project packages.
This package provides a shared resource interface for the bigmemory and
synchronicity packages."""
cran = "bigmemory.sri"
version('0.1.3', sha256='55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-tidyr/package.py
|
# 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 import *
class RTidyr(RPackage):
"""Tidy Messy Data.
Tools to help to create tidy data, where each column is a variable, each
row is an observation, and each cell contains a single value. 'tidyr'
contains tools for changing the shape (pivoting) and hierarchy (nesting and
'unnesting') of a dataset, turning deeply nested lists into rectangular
data frames ('rectangling'), and extracting values out of string columns.
It also includes tools for working with missing values (both implicit and
explicit)."""
cran = "tidyr"
version('1.1.4', sha256='0b0c98be98a433e15a2550f60330b31a58529a9c58bc2abd7bff6462ab761241')
version('1.1.2', sha256='08fccb67824515b33187886f3ca2cf2fe747a778514892dbbf5e565edf0dfd6c')
version('0.8.3', sha256='a18f54ec35124110058ab23f7e0a3c037a8d50f0405520cf5cc5443ec022cc37')
version('0.8.2', sha256='99a508d0539390364789c5f4835b36c4a383927f0ec1648e2a4636c1cc6e490f')
version('0.7.2', sha256='062cea2e2b57fffd500e4ce31cba6d593e65684fc0897ea49ea38d257c76009c')
version('0.5.1', sha256='dbab642ac7231cbfe3e2a0d4553fb4ffb3699c6d6b432be2bb5812dfbbdbdace')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-dplyr@0.7.0:', type=('build', 'run'))
depends_on('r-dplyr@0.8.2:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-ellipsis@0.1.0:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-glue', type=('build', 'run'))
depends_on('r-lifecycle', type=('build', 'run'), when='@1.1.2:')
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-purrr', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-tibble@2.1.1:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-tidyselect@0.2.5:', type=('build', 'run'))
depends_on('r-tidyselect@1.1.0:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-vctrs@0.3.0:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-vctrs@0.3.6:', type=('build', 'run'), when='@1.1.3:')
depends_on('r-cpp11@0.2.1:', type=('build', 'run'), when='@1.1.2:')
depends_on('r-cpp11@0.2.6:', type=('build', 'run'), when='@1.1.3:')
depends_on('r-stringi', type=('build', 'run'), when='@:0.8.3')
depends_on('r-rcpp', type=('build', 'run'), when='@:0.8.3')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/amdlibm/package.py
|
<gh_stars>10-100
# 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)
import os
from spack import *
class Amdlibm(SConsPackage):
"""AMD LibM is a software library containing a collection of basic math
functions optimized for x86-64 processor-based machines. It provides
many routines from the list of standard C99 math functions.
Applications can link into AMD LibM library and invoke math functions
instead of compiler's math functions for better accuracy and
performance."""
homepage = "https://developer.amd.com/amd-aocl/amd-math-library-libm/"
git = "https://github.com/amd/aocl-libm-ose.git"
maintainers = ["amd-toolchain-support"]
# If a user who doesn't specify a version
# amdlibm installed for commit ID:4033e02
# of master branch.
# To install amdlibm from latest master branch:
# spack install amdlibm ^amdlibm@master
version("3.1", branch="aocl-3.1")
version("3.0", branch="aocl-3.0")
version("2.2", commit="4033e022da428125747e118ccd6fdd9cee21c470")
variant("verbose", default=False,
description="Building with verbosity")
# Mandatory dependencies
depends_on("python@3.6.2", when="%aocc@3.2.0:", type=("build", "run"))
depends_on("python@3.6.1:", type=("build", "run"))
depends_on("scons@3.1.2:", type=("build"))
depends_on("mpfr", type=("link"))
patch("0001-libm-ose-Scripts-cleanup-pyc-files.patch", when="@2.2")
patch("0002-libm-ose-prevent-log-v3.c-from-building.patch", when="@2.2")
conflicts(
'%gcc@:9.1.0',
msg='Minimum required GCC version is 9.2.0')
conflicts(
'%gcc@11.2.0:',
msg='Maximum required GCC version is 11.1.0')
conflicts(
'%aocc@3.2.0',
when='@2.2:3.0',
msg='amdlibm 2.2 and 3.0 versions are not supported with AOCC 3.2.0')
def build_args(self, spec, prefix):
"""Setting build arguments for amdlibm """
args = ["--prefix={0}".format(prefix)]
# we are circumventing the use of
# Spacks compiler wrappers because
# SCons wipes out all environment variables.
if spec.satisfies("@:3.0 %aocc"):
args.append("--compiler=aocc")
var_prefix = '' if spec.satisfies("@:3.0") else 'ALM_'
args.append("{0}CC={1}".format(var_prefix, self.compiler.cc))
args.append("{0}CXX={1}".format(var_prefix, self.compiler.cxx))
if "+verbose" in spec:
args.append("--verbose=1")
else:
args.append("--verbose=0")
return args
install_args = build_args
@run_after('install')
def create_symlink(self):
"""Symbolic link for backward compatibility"""
with working_dir(self.prefix.lib):
os.symlink('libalm.a', 'libamdlibm.a')
os.symlink('libalm.so', 'libamdlibm.so')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-squarem/package.py
|
# 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 import *
class RSquarem(RPackage):
"""Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms.
Algorithms for accelerating the convergence of slow, monotone sequences
from smooth, contraction mapping such as the EM algorithm. It can be used
to accelerate any smooth, linearly convergent acceleration scheme. A
tutorial style introduction to this package is available in a vignette on
the CRAN download page or, when the package is loaded in an R session, with
vignette("SQUAREM"). Refer to the J Stat Software article:
<doi:10.18637/jss.v092.i07>."""
cran = "SQUAREM"
version('2021.1', sha256='66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58')
version('2017.10-1', sha256='9b89905b436f1cf3faa9e3dabc585a76299e729e85ca659bfddb4b7cba11b283')
depends_on('r@3.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/perl-ffi-checklib/package.py
|
# 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 import *
class PerlFfiChecklib(PerlPackage):
"""This module checks whether a particular dynamic library is available for
FFI to use. It is modeled heavily on Devel::CheckLib, but will find dynamic
libraries even when development packages are not installed. It also
provides a find_lib function that will return the full path to the found
dynamic library, which can be feed directly into FFI::Platypus or another
FFI system."""
homepage = "https://metacpan.org/pod/FFI::CheckLib"
url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/FFI-CheckLib-0.25.tar.gz"
version('0.25', sha256='eb36b9a7cff1764a65b1b77e01e92c26207c558a3f986d0d17d2b110fa366ba4')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/userspace-rcu/package.py
|
<filename>var/spack/repos/builtin/packages/userspace-rcu/package.py
# 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 import *
class UserspaceRcu(AutotoolsPackage):
"""liburcu is a LGPLv2.1 userspace RCU (read-copy-update) library. This
data synchronization library provides read-side access which scales
linearly with the number of cores."""
homepage = "https://liburcu.org/"
url = "https://github.com/urcu/userspace-rcu/archive/v0.11.1.tar.gz"
version('0.11.1', sha256='a0ed8995edfbeac5f5eb2f152a8f3654040ecfc99a746bfe3da3bccf435b7d5d')
version('0.11.0', sha256='7834e4692565b491b9d2d258095d6c05089c9bae8a1bef280c338d15ba02e9ac')
version('0.10.2', sha256='e117c416fced894e24720cc1b38247074a13020f19d6704b38e554cbcb993d06')
version('0.9.6', sha256='4d9e4ca40c079e0b0e9f912a9092589b97fbaf80eb6537e9ae70d48c09472efa')
depends_on('m4', type='build')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
patch('examples.patch', sha256='49aa8fa99d3a1315c639d2a90014079c34a7d0a6dde110b6cbb7b02f87324742')
def autoreconf(self, spec, prefix):
bash = which('bash')
bash('./bootstrap')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/yoda/package.py
|
# 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 import *
class Yoda(AutotoolsPackage):
"""YODA - Yet more Objects for Data Analysis"""
homepage = "https://yoda.hepforge.org/"
url = "https://yoda.hepforge.org/downloads/?f=YODA-1.8.3.tar.bz2"
tags = ['hep']
version('1.9.0', sha256='9a55de12ffebbe41d1704459c5c9289eeaf0f0eb6a4d0104ea222d7ab889fdf4')
version('1.8.5', sha256='4c2e6b8571fc176271515a309b45687a2981af1b07ff3f00d0b035a597aa32fd')
version('1.8.4', sha256='9d24a41c9b7cc6eb14cab0a48f65d2fca7ec9d794afe0922ceb158d0153c150e')
version('1.8.3', sha256='d9dd0ea5e0f630cdf4893c09a40c78bd44455777c2125385ecc26fa9a2acba8a')
version('1.8.2', sha256='89558c11cf9b88b0899713e5b4bf8781fdcecc480ff155985ebbf148c6d80bdb')
version('1.8.1', sha256='51472e12065b9469f13906f0dc609e036d0c1dbd2a8e445e7d654aba73660112')
version('1.8.0', sha256='82c62bbaedb4b6b7d50cd42ce5409d453d46c1cc6724047db5efa74d34dd6dc5')
version('1.7.7', sha256='cfb64b099a79ec4d138792f0b464a8fbb04c4345143f77bbdca07acb744628ce')
version('1.7.6', sha256='864a1459c82676c991fcaed931263a415e815e3c9dc2cad2f94bda6fa4d112e5')
version('1.7.5', sha256='7b1dc7bb380d0fbadce12072f5cc21912c115e826182a3922d864e7edea131db')
version('1.7.4', sha256='3df316b89e9c0052104f8956e4f7d26c0b0b05cdace7d908be35c383361e3a71')
version('1.7.3', sha256='ebf6094733823e9cc2d1586aff06db2d8999c74a47e666baf305322f62c48058')
version('1.7.2', sha256='7f093cf947824ec118767c7c1999a50ea9343c173cf8c5062e3800ba54c2943e')
version('1.7.1', sha256='edd7971ecd272314309c800395200b07cf68547cbac3378a02d0b8c9ac03027b')
version('1.7.0', sha256='b3d6bfb0c52ed87cd240cee5e93e09102832d9ef32505d7275f4d3191a35ce3b')
version('1.6.7', sha256='2abf378573832c201bc6a9fecfff5b2006fc98c7a272540326cda8eb5bd95e16')
version('1.6.6', sha256='cf172a496d9108b93420530ea91055d07ecd514d2894d78db46b806530e91d21')
version('1.6.5', sha256='1477fe754cfe2e4e06aa363a773accf18aab960a8b899968b77834368cac14c5')
version('1.6.4', sha256='4c01f43c18b7b2e71f61dea0bb8c6fdc099c8e1a66256c510652884c4ffffbca')
version('1.6.3', sha256='1dd7e334fe54a05ff911d9e227d395abc5efd29e29d60187a036b2201f97da19')
version('1.6.2', sha256='5793cd1320694118423888801ca520f2719565fde04699ee69e1751f47cb57a8')
version('1.6.1', sha256='ec3f4cc4eb57f94fb431cc37db10eb831f025df95ffd9e516b8009199253c62b')
version('1.6.0', sha256='2920ef2588268484b650dc08438664a3539b79c65a9e80d58e3771bb699e2a6b')
version('1.5.9', sha256='1a19cc8c34c08f1797a93d355250e682eb85d62d4ab277b6714d7873b4bdde75')
version('1.5.8', sha256='011c5be5cc565f8baf02e7ebbe57a57b4d70dc6a528d5b0102700020bbf5a973')
version('1.5.7', sha256='f775df11b034154b8f5d43f12007692c3314672e60d3e554b3928fe5b0f00c29')
version('1.5.6', sha256='050e17b1b80658213281a2e4112dfecc0096f01f269cd739d601b2fd0e790a0c')
version('1.5.5', sha256='ce45df6248c6c50633953048240513dc52ca5c9144ef69ea72ada2df23bc4918')
version('1.5.4', sha256='c41853a1f3aa0794875ae09c1ba4348942eb890e798ac7cee6e3505a9b68b678')
version('1.5.3', sha256='1220ac0ae204c3ed6b22a6a35c30d9b5c1ded35a1054cff131861b4a919d4904')
version('1.5.2', sha256='ec113c53a6174b174aaea8f45802cc419184ce056123b93ab8d3f80fc1bd4986')
version('1.5.1', sha256='a8b088b3ede67d560e40f91f4f99be313f21841c46ce2f657af7692a7bbe3276')
version('1.5.0', sha256='2c2b77344854fac937a8ef07c0928c50829ff4c69bcad6e0afb92da611b7dd18')
version('1.4.0', sha256='e76a129f7c2b72b53525fe0b712606eeeab0dc145daa070ebf0728f0384eaf48')
version('1.3.1', sha256='274e196d009e3aac6dd1f2db876de9613ca1a3c21ec3364bc3662f5493bc9747')
version('1.3.0', sha256='d63197d5940b481ecb06cf4703d9c0b49388f32cad61ccae580d1b80312bd215')
version('1.2.1', sha256='e86964e91e4fbbba443d2848f55c028001de4713dcc64c40339389de053e7d8b')
version('1.2.0', sha256='143fa86cd7965d26d3897a5752307bfe08f4866c2f9a9f226a393127d19ee353')
version('1.1.0', sha256='5d2e8f3c1cddfb59fe651931c7c605fe0ed067864fa86047aed312c6a7938e01')
version('1.0.7', sha256='145c27d922c27a4e1d6d50030f4ddece5f03d6c309a5e392a5fcbb5e83e747ab')
version('1.0.6', sha256='357732448d67a593e5ff004418f2a2a263a1401ffe84e021f8a714aa183eaa21')
version('1.0.5', sha256='ba72bc3943a1b39fa63900570948199cf5ed5c7523f2c4af4740e51b098f1794')
version('1.0.4', sha256='697fe397c69689feecb2a731e19b2ff85e19343b8198c4f18a7064c4f7123950')
version('1.0.3', sha256='6a1d1d75d9d74da457726ea9463c1b0b6ba38d4b43ef54e1c33f885e70fdae4b')
variant("root", default=False, description="Enable ROOT interface")
depends_on('python', type=('build', 'run'))
depends_on('py-future', type=('build', 'run'))
depends_on('zlib')
depends_on('boost', when='@:1.6.0', type=('build', 'run'))
depends_on('py-cython@0.18:', type='build', when='@:1.4.0')
depends_on('py-cython@0.20:', type='build', when='@1.4.0:1.6.5')
depends_on('py-cython@0.23.5:', type='build', when='@1.6.5:1.8.0')
depends_on('py-cython@0.24:', type='build', when='@1.8.0:')
depends_on('py-matplotlib', when='@1.3.0:', type=('build', 'run'))
depends_on('root', type=('build', 'link', 'run'), when='+root')
patch('yoda-1.5.5.patch', level=0, when='@1.5.5')
patch('yoda-1.5.9.patch', level=0, when='@1.5.9')
patch('yoda-1.6.1.patch', level=0, when='@1.6.1')
patch('yoda-1.6.2.patch', level=0, when='@1.6.2')
patch('yoda-1.6.3.patch', level=0, when='@1.6.3')
patch('yoda-1.6.4.patch', level=0, when='@1.6.4')
patch('yoda-1.6.5.patch', level=0, when='@1.6.5')
patch('yoda-1.6.6.patch', level=0, when='@1.6.6')
patch('yoda-1.6.7.patch', level=0, when='@1.6.7')
conflicts("%gcc@10:", when="@:1.8.5",
msg="yoda up to 1.8.5 is missing a <limits> include in AnalysisObject.h."
"Use version 1.9.0 or later, or patch earlier versions if needed.")
def configure_args(self):
args = []
if self.spec.satisfies('@:1.6.0'):
args.append('--with-boost=' + self.spec['boost'].prefix)
args.extend(self.enable_or_disable('root'))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/deconseq-standalone/package.py
|
# 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 import *
class DeconseqStandalone(Package):
"""The DeconSeq tool can be used to automatically detect and efficiently
remove sequence contaminations from genomic and metagenomic datasets."""
homepage = "http://deconseq.sourceforge.net"
url = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz"
version('0.4.3', sha256='fb4050418c26a5203220f6396263da554326657590cffd65053eb8adc465ac65')
depends_on('perl@5:')
def install(self, spec, prefix):
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl', 'deconseq.pl')
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl', 'splitFasta.pl')
mkdirp(prefix.bin)
install('bwa64', prefix.bin)
install('bwaMAC', prefix.bin)
install('deconseq.pl', prefix.bin)
install('splitFasta.pl', prefix.bin)
install('DeconSeqConfig.pm', prefix)
chmod = which('chmod')
chmod('+x', join_path(prefix.bin, 'bwa64'))
chmod('+x', join_path(prefix.bin, 'bwaMAC'))
chmod('+x', join_path(prefix.bin, 'deconseq.pl'))
chmod('+x', join_path(prefix.bin, 'splitFasta.pl'))
def setup_run_environment(self, env):
env.prepend_path('PERL5LIB', self.prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ruby-terminal-table/package.py
|
<reponame>player1537-forks/spack
# 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)
class RubyTerminalTable(RubyPackage):
"""Simple, feature rich ascii table generation library"""
homepage = "https://github.com/tj/terminal-table"
url = "https://github.com/tj/terminal-table/archive/v1.8.0.tar.gz"
version('1.8.0', sha256='69b8e157f5dc3f056b5242923ab3e729a16c6f893b3a5d540e71135a973e5fbe')
depends_on('ruby-unicode-display-width@1.1.1:1', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-paleotree/package.py
|
<gh_stars>10-100
# 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 import *
class RPaleotree(RPackage):
"""Paleontological and Phylogenetic Analyses of Evolution.
Provides tools for transforming, a posteriori time-scaling, and modifying
phylogenies containing extinct (i.e. fossil) lineages"""
cran = "paleotree"
version('3.3.25', sha256='aa64b9120075581229439227a12db776d052b03eb5f9721692a16a9402ac8712')
version('3.3.0', sha256='f8f6b0228dd5290b251cad3a8626689442b5aa793d8f072c8c2c7813a063df90')
version('3.1.3', sha256='4c1cc8a5e171cbbbd88f78914f86d5e6d144ae573816fbeeff2ab54a814ec614')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-ape@4.1:', type=('build', 'run'))
depends_on('r-phangorn@2.0.0:', type=('build', 'run'))
depends_on('r-phytools@0.6-00:', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'), when='@3.3.0:')
depends_on('r-png', type=('build', 'run'), when='@3.3.0:')
depends_on('r-rcurl', type=('build', 'run'), when='@3.3.0:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-debugpy/package.py
|
<reponame>player1537-forks/spack
# 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 import *
class PyDebugpy(PythonPackage):
"""An implementation of the Debug Adapter Protocol for Python."""
homepage = "https://github.com/microsoft/debugpy/"
pypi = "debugpy/debugpy-1.4.1.zip"
# 'debugpy._vendored' requires additional dependencies, Windows-specific
import_modules = [
'debugpy', 'debugpy.adapter', 'debugpy.launcher', 'debugpy.server',
'debugpy.common'
]
version('1.5.1', sha256='d2b09e91fbd1efa4f4fda121d49af89501beda50c18ed7499712c71a4bf3452e')
version('1.4.1', sha256='889316de0b8ff3732927cb058cfbd3371e4cd0002ecc170d34c755ad289c867c')
depends_on('python@2.7:2.8,3.5:', type=('build', 'link', 'run'))
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rjava/package.py
|
# 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 import *
class RRjava(RPackage):
"""Low-Level R to Java Interface.
Low-level interface to Java VM very much like .C/.Call and friends. Allows
creation of objects, calling methods and accessing fields."""
cran = "rJava"
version('1.0-6', sha256='e290d0493317a5d6c452793e92baa914e37ef03faef19b2e436329b4ec8658c6')
version('0.9-13', sha256='5b1688f5044476b34f71d868b222ac5fce3a088f0c2b9e4591c1e48f3d8c75f4')
version('0.9-11', sha256='c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69')
version('0.9-8', sha256='dada5e031414da54eb80b9024d51866c20b92d41d68da65789fe0130bc54bd8a')
depends_on('r@2.5:', type=('build', 'run'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@1.0-6:')
depends_on('java@2:')
depends_on('gmake', type='build')
# these are not listed as dependencies but are needed
depends_on('bzip2')
depends_on('icu4c')
depends_on('libiconv')
depends_on('pcre2')
depends_on('xz')
def setup_build_environment(self, env):
spec = self.spec
env.append_flags('JAVAH', '{0}/javah'.format(
join_path(spec['java'].prefix.bin)))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-mako/package.py
|
<filename>var/spack/repos/builtin/packages/py-mako/package.py
# 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 import *
class PyMako(PythonPackage):
"""A super-fast templating language that borrows the best
ideas from the existing templating languages."""
homepage = "https://www.makotemplates.org/"
pypi = "Mako/Mako-1.0.1.tar.gz"
git = "https://github.com/sqlalchemy/mako"
version('1.1.6', sha256='4e9e345a41924a954251b95b4b28e14a301145b544901332e658907a7464b6b2')
version('1.1.5', sha256='169fa52af22a91900d852e937400e79f535496191c63712e3b9fda5a9bed6fc3')
version('1.1.4', sha256='17831f0b7087c313c0ffae2bcbbd3c1d5ba9eeac9c38f2eb7b50e8c99fe9d5ab')
version('1.0.4', sha256='fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059')
version('1.0.1', sha256='45f0869febea59dab7efd256fb451c377cbb7947bef386ff0bb44627c31a8d1c')
depends_on('python@2.7:2,3.4:', when='@1.1.0:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-markupsafe@0.9.2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-addict/package.py
|
# 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 import *
class PyAddict(PythonPackage):
"""addict is a Python module that gives you dictionaries
whose values are both gettable and settable using
attributes, in addition to standard item-syntax."""
homepage = "https://github.com/mewwts/addict"
url = "https://github.com/mewwts/addict/archive/v2.2.1.tar.gz"
version('2.2.1', sha256='398bba9e7fa25e2ce144c5c4b8ec6208e89b9445869403dfa88ab66ec110fa12')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-hmisc/package.py
|
# 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 import *
class RHmisc(RPackage):
"""Harrell Miscellaneous.
Contains many functions useful for data analysis, high-level graphics,
utility operations, functions for computing sample size and power,
importing and annotating datasets, imputing missing values, advanced table
making, variable clustering, character string manipulation, conversion of R
objects to LaTeX and html code, and recoding variables."""
cran = "Hmisc"
version('4.6-0', sha256='2c1ce906b2333c6dc946dc7f10b74cfa552bce2b12dbebf295d143163562a1ad')
version('4.4-2', sha256='490ac64dd8558868e7c6fdd9523af102e17ea536c450d62c48b04155279bfbc8')
version('4.4-0', sha256='f16ecf4c5ee2202d51f426282a54f8000ffa8b9747c3e910205f34f878556ec7')
version('4.2-0', sha256='9e9614673288dd00295f250fa0bf96fc9e9fed692c69bf97691081c1a01411d9')
version('4.1-1', sha256='991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498')
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-survival@2.40-1:', type=('build', 'run'))
depends_on('r-survival@3.1-6:', type=('build', 'run'), when='@4.4:')
depends_on('r-formula', type=('build', 'run'))
depends_on('r-ggplot2@2.2:', type=('build', 'run'))
depends_on('r-latticeextra', type=('build', 'run'))
depends_on('r-cluster', type=('build', 'run'))
depends_on('r-rpart', type=('build', 'run'))
depends_on('r-nnet', type=('build', 'run'))
depends_on('r-foreign', type=('build', 'run'))
depends_on('r-gtable', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-data-table', type=('build', 'run'))
depends_on('r-htmltable@1.11.0:', type=('build', 'run'))
depends_on('r-viridis', type=('build', 'run'))
depends_on('r-htmltools', type=('build', 'run'))
depends_on('r-base64enc', type=('build', 'run'))
depends_on('r-acepack', type=('build', 'run'), when='@:4.4-0')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-nortest/package.py
|
# 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 import *
class RNortest(RPackage):
"""Tests for Normality.
Five omnibus tests for testing the composite hypothesis of normality."""
cran = "nortest"
version('1.0-4', sha256='a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f')
|
player1537-forks/spack
|
lib/spack/spack/analyzers/config_args.py
|
<reponame>player1537-forks/spack
# 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)
"""A configargs analyzer is a class of analyzer that typically just uploads
already existing metadata about config args from a package spec install
directory."""
import os
import spack.monitor
from .analyzer_base import AnalyzerBase
class ConfigArgs(AnalyzerBase):
name = "config_args"
outfile = "spack-analyzer-config-args.json"
description = "config args loaded from spack-configure-args.txt"
def run(self):
"""
Load the configure-args.txt and save in json.
The run function will find the spack-config-args.txt file in the
package install directory, and read it into a json structure that has
the name of the analyzer as the key.
"""
config_file = os.path.join(self.meta_dir, "spack-configure-args.txt")
return {self.name: spack.monitor.read_file(config_file)}
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-leaps/package.py
|
# 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 import *
class RLeaps(RPackage):
"""Regression Subset Selection.
Regression subset selection, including exhaustive search."""
cran = "leaps"
version('3.1', sha256='3d7c3a102ce68433ecf167ece96a7ebb4207729e4defd0ac8fc00e7003f5c3b6')
version('3.0', sha256='55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285')
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/mvapich2/package.py
|
<filename>var/spack/repos/builtin.mock/packages/mvapich2/package.py
# 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)
class Mvapich2(Package):
homepage = "http://www.homepage.org"
url = "http://www.someurl"
version('1.5', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
variant(
'file_systems',
description='List of the ROMIO file systems to activate',
values=auto_or_any_combination_of('lustre', 'gpfs', 'nfs', 'ufs'),
)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/lazyten/package.py
|
# 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)
import os
from spack import *
class Lazyten(CMakePackage):
"""Lightweight linear algebra library based on lazy matrices"""
homepage = "https://lazyten.org"
url = "https://github.com/lazyten/lazyten/archive/v0.4.1.tar.gz"
git = "https://github.com/lazyten/lazyten.git"
maintainers = ['mfherbst']
#
# Versions
#
version("develop", branch="master")
version('0.4.1', sha256='696d151382993c13d04516c77db3ea712a70e3cb449539b9e79abc78cf245ae4')
#
# Variants
#
# Library build type
variant("build_type", default="DebugRelease",
description="The build type to build",
values=("Debug", "Release", "DebugRelease"))
variant("shared", default=True,
description="Build shared libraries (else the static one)")
# Features
variant("arpack", default=True,
description="Build with Arpack support")
# Components
variant("examples", default=False,
description="Compile examples")
#
# Conflicts
#
# Only builds on clang > 3.5 and gcc > 4.8
conflicts("%intel", msg="krims only builds with gcc and clang")
conflicts("%gcc@:4.8")
conflicts("%clang@:3.5")
#
# Dependencies
#
depends_on("cmake@3:", type="build")
depends_on("krims@develop", when="@develop")
depends_on("krims@0.2.1", when="@0.4.1")
depends_on("blas")
depends_on("lapack")
depends_on("armadillo@4:")
depends_on("arpack-ng", when="+arpack")
#
# Settings and cmake cache
#
def cmake_args(self):
spec = self.spec
args = [
"-DAUTOCHECKOUT_MISSING_REPOS=OFF",
#
"-DBUILD_SHARED_LIBS=" + str("+shared" in spec),
# TODO Hard-disable tests for now, since rapidcheck not in Spack
"-DLAZYTEN_ENABLE_TESTS=OFF",
"-DLAZYTEN_ENABLE_EXAMPLES=" + str("+examples" in spec),
]
# Tell lazyten where to look for the krims cmake config
# and targets files
krims_modules = os.path.join(spec["krims"].prefix.share, "cmake/krims")
args.append("-Dkrims_DIR=" + krims_modules)
# Add linear algebra backends
lapack_blas = spec['lapack'].libs + spec['blas'].libs
args.extend([
"-DARMADILLO_INCLUDE_DIR=" + spec["armadillo"].prefix.include,
"-DARMADILLO_LIBRARY=" + ";".join(spec["armadillo"].libs),
#
"-DLAPACK_FOUND=ON",
"-DLAPACK_LIBRARIES=" + ";".join(lapack_blas),
])
if "+arpack" in spec:
args.append("-DARPACK_DIR=" + spec["arpack-ng"].prefix)
args.append("-DARPACK_LIBRARY=" + ";".join(spec["arpack-ng"].libs))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/perl-text-unidecode/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/perl-text-unidecode/package.py
# 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 import *
class PerlTextUnidecode(PerlPackage):
"""plain ASCII transliterations of Unicode text"""
homepage = "https://metacpan.org/pod/Text::Unidecode"
url = "http://search.cpan.org/CPAN/authors/id/S/SB/SBURKE/Text-Unidecode-1.30.tar.gz"
version('1.30', sha256='6c24f14ddc1d20e26161c207b73ca184eed2ef57f08b5fb2ee196e6e2e88b1c6')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
|
# 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 import *
class RGenomeinfodbdata(RPackage):
"""for mapping between NCBI taxonomy ID and species. Used by functions
in the GenomeInfoDb package."""
bioc = "GenomeInfoDbData"
url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
version('1.2.7',
url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz',
sha256='217cbad0dd3ed8f0da6b21c7d35df5737bcbd21e317ca71d2fb6ec4c316b1987')
version('1.2.1',
url='https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz',
sha256='75e6d683a29b8baeec66ba5194aa59a6aa69b04fae5a9c718a105c155fb41711')
version('1.1.0',
url='https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz',
sha256='6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c')
version('0.99.0', sha256='457049804bbd70f218c1c84067a23e83bdecb7304a3e4d8b697fee0b16dc1888')
depends_on('r@3.5:', type=('build', 'run'), when='@1.2.1:')
depends_on('r@3.3:', type=('build', 'run'), when='@0.99.0:1.1.0')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/p4est/package.py
|
# 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 import *
class P4est(AutotoolsPackage):
"""Dynamic management of a collection (a forest) of adaptive octrees in
parallel"""
homepage = "https://www.p4est.org"
# Only use the official tarball releases provided on p4est.org or
# p4est.github.io. The automatically generated releases from the
# Github repository lack important parts.
url = "https://p4est.github.io/release/p4est-2.8.tar.gz"
maintainers = ['davydden']
version('2.8', sha256='6a0586e3abac06c20e31b1018f3a82a564a6a0d9ff6b7f6c772a9e6b0f0cc5e4')
version('2.3.2', sha256='076df9e5578e0e7fcfbe12e1a0b080104001f8c986ab1d5a69ec2220050df8e6')
version('2.3.1', sha256='be66893b039fb3f27aca3d5d00acff42c67bfad5aa09cea9253cdd628b2bdc9a')
version('2.2', sha256='1549cbeba29bee2c35e7cc50a90a04961da5f23b6eada9c8047f511b90a8e438')
version('2.1', sha256='07ab24bd63a652a30576fbca12c0fc068dffa615d888802d7f229fa994a9c1ef')
version('2.0', sha256='c522c5b69896aab39aa5a81399372a19a6b03fc6200d2d5d677d9a22fe31029a')
version('1.1', sha256='0b5327a35f0c869bf920b8cab5f20caa4eb55692eaaf1f451d5de30285b25139')
variant('mpi', default=True, description='Enable MPI')
variant('openmp', default=False, description='Enable OpenMP')
# build dependencies
depends_on('automake', when='@2.0', type='build')
depends_on('autoconf', when='@2.0', type='build')
depends_on('libtool@2.4.2:', type='build')
# other dependencies
depends_on('mpi', when='+mpi')
depends_on('zlib')
# from sc upstream, correct the default libraries
patch('https://github.com/cburstedde/libsc/commit/b506aab224b988fec210cc212469f2c4f58b2d04.patch',
sha256='e9418b1a9347a409be241cd185519b31950e42a7f55b6fb80ce53097657098ee',
working_dir='sc',
when='@2.0')
patch('https://github.com/cburstedde/libsc/commit/b45a51a7ef97883a3d4dcbd05cb2c77890a76f75.patch',
sha256='8fb829e34e3a1e28afdd6e56e0bdc1d377af569b7ccb9e9d8da0eeb5829ed27e',
working_dir='sc',
when='@2.0')
def autoreconf(self, spec, prefix):
if self.spec.satisfies('@2.0'):
bootstrap = Executable('./bootstrap')
bootstrap()
def configure_args(self):
args = [
'--enable-shared',
'--disable-vtk-binary',
'--without-blas',
'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
'CFLAGS=-O2'
]
if '~mpi' in self.spec:
args.append('--disable-mpi')
else:
args.append('--enable-mpi')
args.append('CC=%s' % self.spec['mpi'].mpicc)
args.append('CXX=%s' % self.spec['mpi'].mpicxx)
args.append('FC=%s' % self.spec['mpi'].mpifc)
args.append('F77=%s' % self.spec['mpi'].mpif77)
if '+openmp' in self.spec:
try:
args.append(
'--enable-openmp={0}'.format(self.compiler.openmp_flag))
except UnsupportedCompilerFlag:
args.append('--enable-openmp')
else:
args.append('--disable-openmp')
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-mistune/package.py
|
<gh_stars>10-100
# 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 import *
class PyMistune(PythonPackage):
"""A sane Markdown parser with useful plugins and renderers."""
homepage = "https://github.com/lepture/mistune"
pypi = "mistune/mistune-2.0.2.tar.gz"
version('2.0.2', sha256='6fc88c3cb49dba8b16687b41725e661cf85784c12e8974a29b9d336dd596c3a1')
version('0.8.4', sha256='59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e')
version('0.8.3', sha256='bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619')
version('0.8.2', sha256='c50f2fb3a058120c5696f08af9d57877a9c76e879f19af5835fb2c6a4e56a67b')
version('0.8.1', sha256='4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82')
version('0.8', sha256='dc3f43e7cf0abb95cdfecbf82d85c419108d5f13e1844b2a8a2fc0abf24c7a47')
version('0.7.4', sha256='8517af9f5cd1857bb83f9a23da75aa516d7538c32a2c5d5c56f3789a9e4cd22f')
version('0.7.3', sha256='21d0e869df3b9189f248e022f1c9763cf9069e1a2f00676f1f1852bd7f98b713')
version('0.7.2', sha256='626f2516adcde4af608eaf83635ff20ff7e577c1898ad4d0f0fcd8c094399840')
version('0.7.1', sha256='6076dedf768348927d991f4371e5a799c6a0158b16091df08ee85ee231d929a7')
version('0.7', sha256='1daa2e55f5de63ecde7c446c4677c0447006752f78ad2c9c1c3c3452d395f89f')
version('0.6', sha256='d54a69365d01bc97412a39c11674a8aae3f333586e91f38895cc1ad818e13dc5')
version('0.5.1', sha256='cc66489a28845c0e1848ae290af5b555074eb76185136ca058e8eed1faa89692')
version('0.5', sha256='d53d868cfd10cf757160e88adb5760fce95f7026a243f15a02b7c604238e5869')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/gcc/package.py
|
<filename>var/spack/repos/builtin.mock/packages/gcc/package.py
# 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 import *
class Gcc(Package):
"""Simple compiler package."""
homepage = "http://www.example.com"
url = "http://www.example.com/gcc-1.0.tar.gz"
version('1.0', '<KEY>')
version('2.0', '<KEY>')
version('3.0', '<PASSWORD>3<PASSWORD>3<PASSWORD>')
depends_on('conflict', when='@3.0')
def install(self, spec, prefix):
# Create the minimal compiler that will fool `spack compiler find`
mkdirp(prefix.bin)
with open(prefix.bin.gcc, 'w') as f:
f.write('#!/bin/bash\necho "%s"' % str(spec.version))
set_executable(prefix.bin.gcc)
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/py-extension2/package.py
|
# 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)
import os.path
from spack import *
class PyExtension2(PythonPackage):
"""A package which extends python. It also depends on another
package which extends the same package."""
homepage = "http://www.example.com"
url = "http://www.example.com/extension2-1.0.tar.gz"
# Override settings in base class
maintainers = []
extends("python")
depends_on('py-extension1', type=('build', 'run'))
version('1.0', '00000000000000000000000000000210')
def install(self, spec, prefix):
mkdirp(prefix.bin)
with open(os.path.join(prefix.bin, 'py-extension2'), 'w+') as fout:
fout.write(str(spec.version))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/rhash/package.py
|
# 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)
import os
class Rhash(MakefilePackage):
"""RHash is a console utility for computing and verifying hash sums of
files. It supports CRC32, MD4, MD5, SHA1, SHA256, SHA512, SHA3, Tiger,
TTH, Torrent BTIH, AICH, ED2K, GOST R 34.11-94, RIPEMD-160, HAS-160,
EDON-R 256/512, WHIRLPOOL and SNEFRU hash sums."""
homepage = "https://sourceforge.net/projects/rhash/"
url = "https://github.com/rhash/RHash/archive/v1.3.5.tar.gz"
version('1.4.2', sha256='600d00f5f91ef04194d50903d3c79412099328c42f28ff43a0bdb777b00bec62')
version('1.3.5', sha256='98e0688acae29e68c298ffbcdbb0f838864105f9b2bd8857980664435b1f1f2e')
# configure: fix clang detection on macOS
# Patch accepted and merged upstream, remove on next release
patch('https://github.com/rhash/RHash/commit/4dc506066cf1727b021e6352535a8bb315c3f8dc.patch?full_index=1',
when='@1.4.2', sha256='3fbfe4603d2ec5228fd198fc87ff3ee281e1f68d252c1afceaa15cba76e9b6b4')
# Intel 20xx.yy.z works just fine. Un-block it from the configure script
# https://github.com/rhash/RHash/pull/197
patch('rhash-intel20.patch')
# For macOS build instructions, see:
# https://github.com/Homebrew/homebrew-core/blob/master/Formula/rhash.rb
@when('@:1.3.5')
def build(self, spec, prefix):
# Doesn't build shared libraries by default
make('PREFIX={0}'.format(prefix))
if spec.satisfies('platform=darwin'):
make('PREFIX={0}'.format(prefix), '-C', 'librhash', 'dylib')
else:
make('PREFIX={0}'.format(prefix), 'lib-shared')
@when('@1.3.6:')
def build(self, spec, prefix):
configure('--prefix=')
make()
def check(self):
# Makefile has both `test` and `check` targets:
#
# * `test` - used to test that the build is working properly
# * `check` - used to check that the tarball is ready for upload
#
# Default implmentation is to run both `make test` and `make check`.
# `test` passes, but `check` fails, so only run `test`.
make('test')
if self.spec.satisfies('@:1.3.5'):
make('test-static-lib')
else:
make('test-lib-static')
if not self.spec.satisfies('@:1.3.5 platform=darwin'):
make('test-shared')
if self.spec.satisfies('@:1.3.5'):
make('test-shared-lib')
else:
make('test-lib-shared')
@when('@:1.3.5')
def install(self, spec, prefix):
# Some things are installed to $(DESTDIR)$(PREFIX) while other things
# are installed to $DESTDIR/etc.
make('install', 'DESTDIR={0}'.format(prefix), 'PREFIX=')
make('install-lib-static', 'DESTDIR={0}'.format(prefix), 'PREFIX=')
if spec.satisfies('platform=darwin'):
install('librhash/*.dylib', prefix.lib)
else:
make('install-lib-shared', 'DESTDIR={0}'.format(prefix), 'PREFIX=')
os.symlink(join_path(prefix.lib, 'librhash.so.0'),
join_path(prefix.lib, 'librhash.so'))
@when('@1.3.6:')
def install(self, spec, prefix):
# Intermittent issues during installation, prefix.bin directory already exists
make('install', 'DESTDIR={0}'.format(prefix), parallel=False)
make('install-pkg-config', 'DESTDIR={0}'.format(prefix))
make('install-lib-so-link', 'DESTDIR={0}'.format(prefix))
make('install-lib-headers', 'DESTDIR={0}'.format(prefix))
@run_after('install')
def darwin_fix(self):
# The shared library is not installed correctly on Darwin; fix this
if self.spec.satisfies('@1.3.6: platform=darwin'):
# Fix RPATH for <prefix>/bin/rhash
old = '/lib/librhash.0.dylib'
new = self.prefix.lib.join('librhash.dylib')
install_name_tool = Executable('install_name_tool')
install_name_tool('-change', old, new, self.prefix.bin.rhash)
# Fix RPATH for <prefix>/lib/librhash.dylib
fix_darwin_install_name(self.prefix.lib)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-spatialite/package.py
|
# 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 import *
class PySpatialite(PythonPackage):
"""Wrapper for standard Python module "sqlite3" which adds SpatiaLite
support.
"""
homepage = "https://github.com/malexer/spatialite"
pypi = "spatialite/spatialite-0.0.3.tar.gz"
version('0.0.3', sha256='a0761f239a52f326b14ce41ba61b6614dfcc808b978a0bec4a37c1de9ad9071e')
depends_on('py-setuptools', type='build')
depends_on('libspatialite')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-alpine/package.py
|
<filename>var/spack/repos/builtin/packages/r-alpine/package.py
# 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 import *
class RAlpine(RPackage):
"""alpine.
Fragment sequence bias modeling and correction for RNA-seq transcript
abundance estimation."""
bioc = "alpine"
version('1.20.0', commit='9348ef14128aa6be10cca1987736ddbc385df7e9')
version('1.16.0', commit='aee<PASSWORD>')
version('1.10.0', commit='bf<PASSWORD>')
version('1.8.0', commit='<KEY>')
version('1.6.0', commit='ea55fcb3cedb5caa20d8264bb29a4975041f5274')
version('1.4.0', commit='<KEY>')
version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
depends_on('r@3.3:', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-genomicalignments', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-genomicfeatures', type=('build', 'run'))
depends_on('r-speedglm', type=('build', 'run'))
depends_on('r-graph', type=('build', 'run'))
depends_on('r-rbgl', type=('build', 'run'))
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-genomeinfodb', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-deoptim/package.py
|
<reponame>player1537-forks/spack
# 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 import *
class RDeoptim(RPackage):
"""Global Optimization by Differential Evolution.
Implements the differential evolution algorithm for global optimization of
a real-valued function of a real-valued parameter vector."""
cran = "DEoptim"
version('2.2-6', sha256='8c63397d83a067212d003ef3e639fd81f5f00bf61e3c271b4e4999031a69e2e1')
version('2.2-5', sha256='ae12dedcd4a43994e811e7285f8c12bfdb688e7c99d65515cf7e8cb6db13955a')
version('2.2-4', sha256='0a547784090d1e9b93efc53768110621f35bed3692864f6ce5c0dda2ebd6d482')
version('2.2-3', sha256='af2120feea3a736ee7a5a93c6767d464abc0d45ce75568074b233405e73c9a5d')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/xineramaproto/package.py
|
# 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 import *
class Xineramaproto(AutotoolsPackage, XorgPackage):
"""X Xinerama Extension.
This is an X extension that allows multiple physical screens controlled
by a single X server to appear as a single screen."""
homepage = "https://cgit.freedesktop.org/xorg/proto/xineramaproto"
xorg_mirror_path = "proto/xineramaproto-1.2.1.tar.gz"
version('1.2.1', sha256='d99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1')
depends_on('pkgconfig', type='build')
depends_on('util-macros', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/octave-struct/package.py
|
# 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 import *
class OctaveStruct(OctavePackage, SourceforgePackage):
"""Additional structure manipulation functions for Octave."""
homepage = "https://octave.sourceforge.io/struct/"
sourceforge_mirror_path = "octave/struct-1.0.14.tar.gz"
version('1.0.17', sha256='0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433')
version('1.0.14', sha256='ad4e17687bc24650f032757271b20b70fe32c35513d4dd9ab1e549919df36b47')
extends('octave@2.9.7:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/lbzip2/package.py
|
# 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 import *
class Lbzip2(AutotoolsPackage):
"""Multi-threaded compression utility with support for bzip2
compressed file format"""
homepage = "https://lbzip2.org/"
url = "http://archive.lbzip2.org/lbzip2-2.5.tar.gz"
version('2.5', sha256='46c75ee93cc95eedc6005625442b2b8e59a2bef3ba80987d0491f055185650e9')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/netcdf-cxx4/package.py
|
# 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 import *
class NetcdfCxx4(AutotoolsPackage):
"""NetCDF (network Common Data Form) is a set of software libraries and
machine-independent data formats that support the creation, access, and
sharing of array-oriented scientific data. This is the C++ distribution."""
homepage = "https://www.unidata.ucar.edu/software/netcdf"
url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx4-4.3.1.tar.gz"
maintainers = ['WardF']
version('4.3.1', sha256='6a1189a181eed043b5859e15d5c080c30d0e107406fbb212c8fb9814e90f3445')
version('4.3.0', sha256='e34fbc6aba243ec82c23e9ee99db2430555ada849c54c1f3ab081b0ddd0f5f30')
# Usually the configure automatically inserts the pic flags, but we can
# force its usage with this variant.
variant('static', default=True, description='Enable building static libraries')
variant('shared', default=True, description='Enable shared library')
variant('pic', default=True, description='Produce position-independent code (for shared libs)')
variant('doxygen', default=True, description='Enable doxygen docs')
depends_on('netcdf-c')
depends_on('automake', type='build')
depends_on('autoconf', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
depends_on('doxygen', when='+doxygen', type='build')
conflicts('~shared', when='~static')
force_autoreconf = True
def flag_handler(self, name, flags):
if name == 'cflags' and '+pic' in self.spec:
flags.append(self.compiler.cc_pic_flag)
elif name == 'cppflags':
flags.append('-I' + self.spec['netcdf-c'].prefix.include)
return (None, None, flags)
@property
def libs(self):
shared = True
return find_libraries(
'libnetcdf_c++4', root=self.prefix, shared=shared, recursive=True
)
def configure_args(self):
config_args = []
if '+static' in self.spec:
config_args.append('--enable-static')
else:
config_args.append('--disable-static')
if '+shared' in self.spec:
config_args.append('--enable-shared')
else:
config_args.append('--disable-shared')
if '+pic' in self.spec:
config_args.append('--with-pic')
else:
config_args.append('--without-pic')
if '+doxygen' in self.spec:
config_args.append('--enable-doxygen')
else:
config_args.append('--disable-doxygen')
return config_args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/delly2/package.py
|
# 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 import *
class Delly2(MakefilePackage):
"""Delly2 is an integrated structural variant prediction method that can
discover, genotype and visualize deletions, tandem duplications,
inversions and translocations at single-nucleotide resolution in
short-read massively parallel sequencing data.."""
homepage = "https://github.com/dellytools/delly"
git = "https://github.com/dellytools/delly.git"
version('0.9.1', tag='v0.9.1')
version('2017-08-03', commit='<PASSWORD>', deprecated=True)
variant('openmp', default=False, description='Build with openmp support')
depends_on('htslib', type=('build', 'link'))
depends_on('boost', type=('build', 'link'))
depends_on('bcftools', type='run')
def edit(self, spec, prefix):
if '+openmp' in self.spec:
env['PARALLEL'] = '1'
# Only want to build delly source, not submodules. Build fails
# using provided submodules, succeeds with existing spack recipes.
if self.spec.satisfies('@2017-08-03'):
makefile = FileFilter('Makefile')
makefile.filter('HTSLIBSOURCES =', '#HTSLIBSOURCES')
makefile.filter('BOOSTSOURCES =', '#BOOSTSOURCES')
makefile.filter('SEQTK_ROOT ?=', '#SEQTK_ROOT')
makefile.filter('BOOST_ROOT ?=', '#BOOST_ROOT')
makefile.filter('cd src', '# cd src')
makefile.filter('.htslib ', '')
makefile.filter('.bcftools ', '')
makefile.filter('.boost ', '')
makefile.filter('.htslib:', '# .htslib:')
makefile.filter('.bcftools:', '# .bcftools:')
makefile.filter('.boost:', '# .boost:')
else:
env['EBROOTHTSLIB'] = self.spec['htslib'].prefix
filter_file('BUILT_PROGRAMS =.*$',
'BUILT_PROGRAMS = src/delly src/dpe', 'Makefile')
filter_file('${SUBMODULES}', '', 'Makefile', string=True)
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('src'):
install('delly', prefix.bin)
install('dpe', prefix.bin)
if self.spec.satisfies('@2017-08-03'):
install('cov', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/xxhash/package.py
|
<reponame>player1537-forks/spack
# 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 import *
class Xxhash(MakefilePackage):
"""xxHash is an Extremely fast Hash algorithm, running at RAM speed
limits. It successfully completes the SMHasher test suite which
evaluates collision, dispersion and randomness qualities of hash
functions. Code is highly portable, and hashes are identical on all
platforms (little / big endian).
"""
homepage = "https://github.com/Cyan4973/xxHash"
url = "https://github.com/Cyan4973/xxHash/archive/v0.6.5.tar.gz"
version('0.8.0', sha256='7054c3ebd169c97b64a92d7b994ab63c70dd53a06974f1f630ab782c28db0f4f')
version('0.7.4', sha256='4d9706c9da4fbdf901598f5e3b71db0eddd4ac962e827a73ebf75d66dfd820fe')
version('0.6.5', sha256='19030315f4fc1b4b2cdb9d7a317069a109f90e39d1fe4c9159b7aaa39030eb95')
version('0.6.4', sha256='4570ccd111df6b6386502791397906bf69b7371eb209af7d41debc2f074cdb22')
version('0.6.3', sha256='d8c739ec666ac2af983a61dc932aaa2a8873df974d333a9922d472a121f2106e')
version('0.6.2', sha256='e4da793acbe411e7572124f958fa53b280e5f1821a8bf78d79ace972950b8f82')
version('0.6.1', sha256='a940123baa6c71b75b6c02836bae2155cd2f74f7682e1a1d6f7b889f7bc9e7f8')
version('0.6.0', sha256='2adee77416e1bd53d1bf689d78947ff4e9a603aa319c84c9111ccf53f1a646e8')
version('0.5.1', sha256='0171af39eefa06be1e616bc43b250d13bba417e4741135ec85c1fe8dc391997d')
version('0.5.0', sha256='9605cd18d40d798eb1262bc0c2a154e1a3c138a6a9a0c4c792e855d0c08c23e1')
@property
def build_targets(self):
targets = []
if '%nvhpc' in self.spec:
if self.spec.satisfies('%nvhpc@:20.11'):
targets.append('CFLAGS=-O1')
if 'avx512' in self.spec.target:
# Workaround AVX512 compiler issue
targets.append('CPPFLAGS=-DXXH_VECTOR=XXH_AVX2')
return targets
def edit(self, spec, prefix):
makefile = FileFilter("Makefile")
makefile.filter('/usr/local', prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rferns/package.py
|
# 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 import *
class RRferns(RPackage):
"""Random Ferns Classifier.
Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua
(2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label
classification and featuring OOB error approximation and importance measure
as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>."""
cran = "rFerns"
version('5.0.0', sha256='78da671e18dc1fb499eddcc6db7eedd69cef673ba0b46c873bd95615cbb583fb')
version('4.0.0', sha256='cc8cea0893390bf5db0fb0f59748d5bf6f29537d68bedca900268fd551489128')
version('3.0.0', sha256='35e7e31a6497e415a0fe578678cf9b2f537b21319e4c015a1e2dade00310227c')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ape/package.py
|
# 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 import *
class RApe(RPackage):
"""Analyses of Phylogenetics and Evolution.
Functions for reading, writing, plotting, and manipulating phylogenetic
trees, analyses of comparative data in a phylogenetic framework, ancestral
character analyses, analyses of diversification and macroevolution,
computing distances from DNA sequences, reading and writing nucleotide
sequences as well as importing from BioConductor, and several tools such as
Mantel's test, generalized skyline plots, graphical exploration of
phylogenetic data (alex, trex, kronoviz), estimation of absolute
evolutionary rates and clock-like trees using mean path lengths and
penalized likelihood, dating trees with non-contemporaneous sequences,
translating DNA into AA sequences, and assessing sequence alignments.
Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete distance matrices
(NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions
call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results
are returned into R."""
cran = "ape"
version('5.6-1', sha256='25401e036576eed1200e15bf68879ccd85611303a3508b989e15164cd4c0f7f7')
version('5.4-1', sha256='f0316c8e74ce900053e8b3e8c9322b9d10e7730f3be2150365f74630bee7eee4')
version('5.3', sha256='08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23')
version('5.2', sha256='27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415')
version('5.1', sha256='b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e')
version('5.0', sha256='c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960')
version('4.1', sha256='935af5ddadcba832d3f9cc032a80fc1a2e627a7ed54ef5f3773f87e06374a924')
depends_on('r@3.2:', type=('build', 'run'))
depends_on('r-nlme', type=('build', 'run'))
depends_on('r-lattice', type=('build', 'run'))
depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/modylas/package.py
|
# 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)
import os
from spack import *
class Modylas(AutotoolsPackage):
"""
The 'MOlecular DYnamics Software for LArge Systems' (MODYLAS) is
a general-purpose, molecular dynamics simulation program suited
to the simulation of very large physical, chemical,
and biological systems.
"""
homepage = "https://www.modylas.org"
url = "file://{0}/MODYLAS_1.0.4.tar.gz".format(os.getcwd())
manual_download = True
version('1.0.4', '<PASSWORD>')
variant('mpi', default=True, description='Enable MPI support')
# to define MPIPARA when +mpi
patch('makefile.patch')
# fix no width I in format
patch('gcc_format.patch', when='%gcc')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('mpi', when='+mpi')
build_directory = 'source'
configure_directory = 'source'
def setup_build_environment(self, env):
if self.spec.satisfies('+mpi'):
env.set('FC', self.spec['mpi'].mpifc, force=True)
fflags = ['-O3', self.compiler.openmp_flag]
if self.spec.satisfies('%gcc'):
fflags.append('-cpp')
elif self.spec.satisfies('%fj'):
fflags.append('-Cpp')
env.set('FCFLAGS', ' '.join(fflags))
def configure_args(self):
return self.enable_or_disable('mpi')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/perl-io-all/package.py
|
# 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 import *
class PerlIoAll(PerlPackage):
"""IO::All combines all of the best Perl IO modules into a single nifty
object oriented interface to greatly simplify your everyday Perl IO idioms.
It exports a single function called io, which returns a new IO::All object.
And that object can do it all!
The IO::All object is a proxy for IO::File, IO::Dir, IO::Socket, Tie::File,
File::Spec, File::Path, File::MimeInfo and File::ReadBackwards; as well as
all the DBM and MLDBM modules. You can use most of the methods found in
these classes and in IO::Handle (which they inherit from). IO::All adds
dozens of other helpful idiomatic methods including file stat and
manipulation functions.
IO::All is pluggable, and modules like IO::All::LWP and IO::All::Mailto add
even more functionality. Optionally, every IO::All object can be tied to
itself. This means that you can use most perl IO builtins on it: readline,
<>, getc, print, printf, syswrite, sysread, close."""
homepage = "https://metacpan.org/pod/distribution/IO-All/lib/IO/All.pod"
url = "https://cpan.metacpan.org/authors/id/F/FR/FREW/IO-All-0.87.tar.gz"
version('0.87', sha256='54e21d250c0229127e30b77a3461e10077854ec244f26fb670f1b445ed4c4d5b')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ggsci/package.py
|
# 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 import *
class RGgsci(RPackage):
"""Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'.
collection of 'ggplot2' color palettes inspired by plots in scientific
journals, data visualization libraries, science fiction movies, and TV
shows."""
cran = "ggsci"
version('2.9', sha256='4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c')
version('2.8', sha256='b4ce7adce7ef23edf777866086f98e29b2b45b58fed085bbd1ffe6ab52d74ae8')
version('2.4', sha256='9682c18176fee8e808c68062ec918aaef630d4d833e7a0bd6ae6c63553b56f00')
depends_on('r@3.0.2:', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-ggplot2@2.0.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/shapelib/package.py
|
# 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 import *
class Shapelib(CMakePackage):
"""The Shapefile C Library provides the ability to write simple C programs
for reading, writing and updating (to a limited extent) ESRI Shapefiles,
and the associated attribute file (.dbf).
"""
homepage = "http://shapelib.maptools.org/"
url = "https://github.com/OSGeo/shapelib/archive/v1.5.0.tar.gz"
version('1.5.0', sha256='48de3a6a8691b0b111b909c0b908af4627635c75322b3a501c0c0885f3558cad')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/hevea/package.py
|
<filename>var/spack/repos/builtin/packages/hevea/package.py
# 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 import *
class Hevea(MakefilePackage):
"""Hevea a fast Latex to HTML translator"""
homepage = "http://hevea.inria.fr/"
url = "https://github.com/maranget/hevea/archive/v2.35.tar.gz"
git = "https://github.com/maranget/hevea.git"
maintainers = ['scemama', 'cessenat']
version('develop', branch='master')
version('2.35', sha256='78f834cc7a8112ec59d0b8acdfbed0c8ac7dbb85f964d0be1f4eed04f25cdf54')
version('2.34', sha256='f505a2a5bafdc2ea389ec521876844e6fdcb5c1b656396b7e8421c1631469ea2')
version('2.33', sha256='122f9023f9cfe8b41dd8965b7d9669df21bf41e419bcf5e9de5314f428380d0f')
version('2.32', sha256='f0c12ee3936364a3aa26da384e3d2ad2344be0091f04f9531f04ecb1dca98aca')
# Dependency demands ocamlbuild
depends_on('ocaml')
depends_on('ocamlbuild')
def edit(self, spec, prefix):
env['PREFIX'] = self.spec.prefix
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-th-data/package.py
|
<reponame>player1537-forks/spack
# 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 import *
class RThData(RPackage):
"""TH's Data Archive.
Contains data sets used in other packages <NAME> maintains."""
cran = "TH.data"
version('1.1-0', sha256='21b37e251da5635ae91668f64b4c6f6a7ccedbe1f01af769d30fb532af83113e')
version('1.0-10', sha256='618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55')
version('1.0-9', sha256='d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f')
version('1.0-8', sha256='478f109fcc1226500ead8e3bd6e047cecde2294fde4df8ec216d38313db79a9d')
version('1.0-7', sha256='29e126344daccbebc7df68924730ae4159a0faad77f86302070920684ba6070e')
depends_on('r@2.10.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.1-0:')
depends_on('r-survival', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rcppcctz/package.py
|
# 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 import *
class RRcppcctz(RPackage):
"""'Rcpp' Bindings for the 'CCTZ' Library.
'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a C++
library for translating between absolute and civil times using the rules of
a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details."""
cran = "RcppCCTZ"
version('0.2.10', sha256='3a78188ec771270c87d5ccb8237506adac1827220c694df2f683f64002e2444a')
version('0.2.9', sha256='723f45eca1be08903234e339523daca35748fe65c1a9d59afcb583d3a17bcaae')
version('0.2.6', sha256='0e9a76055d29da24cd4c4069c78c1f44998f3461be60c7a6c3e7a35059fb79ae')
version('0.2.4', sha256='98b6867d38abe03957fe803e88b6cc2d122b85a68ef07fa86f7e1009d6c00819')
version('0.2.3', sha256='0fefcc98387b2c1a5907e5230babb46e2cc11b603424f458f515e445a3236031')
depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/shadow/package.py
|
# 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 import *
class Shadow(AutotoolsPackage):
"""Tools to help unprivileged users create uid and gid mappings in
user namespaces."""
homepage = "https://github.com/shadow-maint/shadow"
url = "https://github.com/shadow-maint/shadow/releases/download/4.7/shadow-4.7.tar.gz"
git = "https://github.com/shadow-maint/shadow.git"
version('4.8.1', sha256='3ee3081fbbcbcfea5c8916419e46bc724807bab271072104f23e7a29e9668f3a')
version('4.7', sha256='5135b0ca2a361a218fab59e63d9c1720d2a8fc1faa520c819a654b638017286f')
version('4.6', sha256='4668f99bd087399c4a586084dc3b046b75f560720d83e92fd23bf7a89dda4d31')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/heffte/package.py
|
# 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 import *
class Heffte(CMakePackage, CudaPackage, ROCmPackage):
"""Highly Efficient FFT for Exascale"""
homepage = "https://bitbucket.org/icl/heffte"
url = "https://bitbucket.org/icl/heffte/get/v1.0.tar.gz"
git = "https://bitbucket.org/icl/heffte.git"
maintainers = ['mkstoyanov']
tags = ['e4s', 'ecp']
test_requires_compiler = True
version('develop', branch='master')
version('2.2.0', sha256='aff4f5111d3d05b269a1378bb201271c40b39e9c960c05c4ef247a31a039be58')
version('2.1.0', sha256='527a3e21115231715a0342afdfaf6a8878d2dd0f02f03c92b53692340fd940b9')
version('2.0.0', sha256='12f2b49a1a36c416eac174cf0cc50e729d56d68a9f68886d8c34bd45a0be26b6')
version('1.0', sha256='0902479fb5b1bad01438ca0a72efd577a3529c3d8bad0028f3c18d3a4935ca74')
version('0.2', sha256='4e76ae60982b316c2e873b2e5735669b22620fefa1fc82f325cdb6989bec78d1')
version('0.1', sha256='d279a03298d2dc76574b1ae1031acb4ea964348cf359273d1afa4668b5bfe748')
patch('threads10.patch', when='@1.0')
patch('fortran200.patch', when='@2.0.0')
depends_on('cmake@3.10:', type=('build', 'run'))
variant('shared', default=True, description='Builds with shared libraries')
variant('fftw', default=False, description='Builds with support for FFTW backend')
variant('mkl', default=False, description='Builds with support for MKL backend')
variant('magma', default=False, description='Use helper methods from the UTK MAGMA library')
variant('python', default=False, description='Install the Python bindings')
variant('fortran', default=False, description='Install the Fortran modules')
depends_on('python@3.0:', when='+python', type=('build', 'run'))
depends_on('py-mpi4py', when='+python', type=('build', 'run'))
depends_on('py-numpy', when='+python', type=('build', 'run'))
depends_on('py-numba', when='+python+cuda', type=('build', 'run'))
extends('python', when='+python', type=('build', 'run'))
conflicts('~fftw', when='@:2.1.0~mkl~cuda') # requires at least one backend
conflicts('+fftw', when='+mkl@:1.0') # old API supports at most one CPU backend
conflicts('^openmpi~cuda', when='+cuda') # +cuda requires CUDA enabled OpenMPI
conflicts('~cuda~rocm', when='+magma') # magma requires CUDA or HIP
conflicts('+rocm', when='@:2.1.0') # heffte+rocm is in in development in spack
conflicts('+python', when="@:1.0") # python support was added post v1.0
conflicts('+fortran', when="@:1.0") # fortran support was added post v1.0
conflicts('+magma', when="@:1.0") # magma support was added post v1.0
depends_on('mpi', type=('build', 'run'))
depends_on('fftw@3.3.8:', when="+fftw", type=('build', 'run'))
depends_on('intel-mkl@2018.0.128:', when="+mkl", type=('build', 'run'))
depends_on('cuda@8.0:', when="+cuda", type=('build', 'run'))
depends_on('hip@3.8.0:', when='+rocm')
depends_on('rocfft@3.8.0:', when='+rocm')
depends_on('magma@2.5.3:', when="+cuda+magma", type=('build', 'run'))
depends_on('magma+rocm@2.6.1:',
when='+magma+rocm @2.1:', type=('build', 'run'))
depends_on('hipblas@3.8:', when='+magma+rocm', type=('build', 'run'))
depends_on('hipsparse@3.8:', when='+magma+rocm', type=('build', 'run'))
examples_src_dir = 'examples'
def cmake_args(self):
args = [
self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
self.define_from_variant('Heffte_ENABLE_CUDA', 'cuda'),
self.define_from_variant('Heffte_ENABLE_ROCM', 'rocm'),
self.define_from_variant('Heffte_ENABLE_FFTW', 'fftw'),
self.define_from_variant('Heffte_ENABLE_MKL', 'mkl'),
self.define_from_variant('Heffte_ENABLE_MAGMA', 'magma'),
self.define_from_variant('Heffte_ENABLE_FORTRAN', 'fortran'),
self.define_from_variant('Heffte_ENABLE_PYTHON', 'python'),
'-DBUILD_GPU={0:1s}'.format(
'ON' if ('+cuda' in self.spec and
'+fftw' in self.spec) else 'OFF'), ]
if '+cuda' in self.spec:
cuda_arch = self.spec.variants['cuda_arch'].value
if len(cuda_arch) > 0 or cuda_arch[0] != 'none':
nvcc_flags = ""
for nvflag in self.cuda_flags(cuda_arch):
nvcc_flags += "{0};".format(nvflag)
args.append('-DCUDA_NVCC_FLAGS={0}'.format(nvcc_flags))
if '+rocm' in self.spec:
args.append('-DCMAKE_CXX_COMPILER={0}'.format(self.spec['hip'].hipcc))
rocm_arch = self.spec.variants['amdgpu_target'].value
if 'none' not in rocm_arch:
args.append('-DCMAKE_CXX_FLAGS={0}'.format(self.hip_flags(rocm_arch)))
# See https://github.com/ROCmSoftwarePlatform/rocFFT/issues/322
if self.spec.satisfies('^cmake@3.21.0:3.21.2'):
args.append(self.define('__skip_rocmclang', 'ON'))
return args
def test(self):
# using the tests installed in <prefix>/share/heffte/testing
cmake_dir = join_path(self.prefix, 'share', 'heffte', 'testing')
test_dir = join_path(self.test_suite.current_test_cache_dir,
'test_install')
with working_dir(test_dir, create=True):
cmake(cmake_dir)
make()
make('test')
|
player1537-forks/spack
|
lib/spack/spack/cmd/reindex.py
|
# 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)
import spack.store
description = "rebuild Spack's package database"
section = "admin"
level = "long"
def reindex(parser, args):
spack.store.store.reindex()
|
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