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player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ggbio/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 RGgbio(RPackage):
"""Visualization tools for genomic data.
The ggbio package extends and specializes the grammar of graphics for
biological data. The graphics are designed to answer common scientific
questions, in particular those often asked of high throughput genomics
data. All core Bioconductor data structures are supported, where
appropriate. The package supports detailed views of particular genomic
regions, as well as genome-wide overviews. Supported overviews include
ideograms and grand linear views. High-level plots include sequence
fragment length, edge-linked interval to data view, mismatch pileup, and
several splicing summaries."""
bioc = "ggbio"
version('1.42.0', commit='3<PASSWORD>')
version('1.38.0', commit='<KEY>')
version('1.32.0', commit='<KEY>')
version('1.30.0', commit='<KEY>')
version('1.28.5', commit='594521ca556ef7d97cf4882ecfa54d22c2a2faba')
version('1.26.1', commit='<KEY>')
version('1.24.1', commit='<KEY>')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-ggplot2@1.0.0:', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'))
depends_on('r-scales', type=('build', 'run'))
depends_on('r-reshape2', type=('build', 'run'))
depends_on('r-gtable', type=('build', 'run'))
depends_on('r-hmisc', type=('build', 'run'))
depends_on('r-biovizbase@1.23.3:', type=('build', 'run'))
depends_on('r-biovizbase@1.28.2:', type=('build', 'run'), when='@1.28.5:')
depends_on('r-biovizbase@1.29.2:', type=('build', 'run'), when='@1.30.0:')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.26.1:')
depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.21.10:', type=('build', 'run'))
depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.26.1:')
depends_on('r-summarizedexperiment', type=('build', 'run'))
depends_on('r-biostrings', type=('build', 'run'))
depends_on('r-rsamtools@1.17.28:', type=('build', 'run'))
depends_on('r-genomicalignments@1.1.16:', type=('build', 'run'))
depends_on('r-bsgenome', type=('build', 'run'))
depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
depends_on('r-rtracklayer@1.25.16:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.17.13:', type=('build', 'run'))
depends_on('r-genomicfeatures@1.29.11:', type=('build', 'run'), when='@1.26.1:')
depends_on('r-organismdbi', type=('build', 'run'))
depends_on('r-ggally', type=('build', 'run'))
depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-annotationfilter', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'), when='@1.28.5:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-pinfsc50/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 RPinfsc50(RPackage):
"""Sequence ('FASTA'), Annotation ('GFF') and Variants ('VCF') for 17
Samples of 'P. Infestans" and 1 'P. Mirabilis'.
Genomic data for the plant pathogen "Phytophthora infestans." It includes a
variant file ('VCF'), a sequence file ('FASTA') and an annotation file
('GFF'). This package is intended to be used as example data for packages
that work with genomic data."""
cran = "pinfsc50"
maintainers = ['dorton21']
version('1.2.0', sha256='ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794')
depends_on('r@3.2.1:', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/schema/compilers.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)
"""Schema for compilers.yaml configuration file.
.. literalinclude:: _spack_root/lib/spack/spack/schema/compilers.py
:lines: 13-
"""
import spack.schema.environment
#: Properties for inclusion in other schemas
properties = {
'compilers': {
'type': 'array',
'items': [{
'type': 'object',
'additionalProperties': False,
'properties': {
'compiler': {
'type': 'object',
'additionalProperties': False,
'required': [
'paths', 'spec', 'modules', 'operating_system'],
'properties': {
'paths': {
'type': 'object',
'required': ['cc', 'cxx', 'f77', 'fc'],
'additionalProperties': False,
'properties': {
'cc': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'cxx': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'f77': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'fc': {'anyOf': [{'type': 'string'},
{'type': 'null'}]}}},
'flags': {
'type': 'object',
'additionalProperties': False,
'properties': {
'cflags': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'cxxflags': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'fflags': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'cppflags': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'ldflags': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'ldlibs': {'anyOf': [{'type': 'string'},
{'type': 'null'}]}}},
'spec': {'type': 'string'},
'operating_system': {'type': 'string'},
'target': {'type': 'string'},
'alias': {'anyOf': [{'type': 'string'},
{'type': 'null'}]},
'modules': {'anyOf': [{'type': 'string'},
{'type': 'null'},
{'type': 'array'}]},
'implicit_rpaths': {
'anyOf': [
{'type': 'array',
'items': {'type': 'string'}},
{'type': 'boolean'}
]
},
'environment': spack.schema.environment.definition,
'extra_rpaths': {
'type': 'array',
'default': [],
'items': {'type': 'string'}
}
}
}
}
}]
}
}
#: Full schema with metadata
schema = {
'$schema': 'http://json-schema.org/draft-07/schema#',
'title': 'Spack compiler configuration file schema',
'type': 'object',
'additionalProperties': False,
'properties': properties,
}
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-pygelf/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 PyPygelf(PythonPackage):
"""Python logging handlers with GELF (Graylog Extended Log Format)
support."""
homepage = "https://github.com/keeprocking/pygelf"
pypi = "pygelf/pygelf-0.3.6.tar.gz"
# notify when the package is updated.
maintainers = ['victorusu', 'vkarak']
version('0.4.0', sha256='3693da38794561d42b0556a78af7dcb22d92ea450125577e58089ab89a890ee5')
version('0.3.6', sha256='3e5bc59e3b5a754556a76ff2c69fcf2003218ad7b5ff8417482fa1f6a7eba5f9')
depends_on('python', type=('build', 'run'))
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-graph/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 RGraph(RPackage):
"""A package to handle graph data structures.
A package that implements some simple graph handling capabilities."""
bioc = "graph"
version('1.72.0', commit='<KEY>')
version('1.68.0', commit='<PASSWORD>')
version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3')
version('1.60.0', commit='e2aecb0a862f32091b16e0036f53367d3edf4c1d')
version('1.58.2', commit='<KEY>')
version('1.56.0', commit='c4abe227dac525757679743e6fb4f49baa34acad')
version('1.54.0', commit='<KEY>')
depends_on('r@2.10:', type=('build', 'run'))
depends_on('r-biocgenerics@0.13.11:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gawk/package.py
|
<filename>var/spack/repos/builtin/packages/gawk/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 re
class Gawk(AutotoolsPackage, GNUMirrorPackage):
"""If you are like many computer users, you would frequently like to make
changes in various text files wherever certain patterns appear, or
extract data from parts of certain lines while discarding the
rest. To write a program to do this in a language such as C or
Pascal is a time-consuming inconvenience that may take many lines
of code. The job is easy with awk, especially the GNU
implementation: gawk.
The awk utility interprets a special-purpose programming language
that makes it possible to handle simple data-reformatting jobs
with just a few lines of code.
"""
homepage = "https://www.gnu.org/software/gawk/"
gnu_mirror_path = "gawk/gawk-4.1.4.tar.xz"
executables = ['^gawk$']
tags = ['build-tools', 'core-packages']
version('5.1.1', sha256='d87629386e894bbea11a5e00515fc909dc9b7249529dad9e6a3a2c77085f7ea2')
version('5.1.0', sha256='cf5fea4ac5665fd5171af4716baab2effc76306a9572988d5ba1078f196382bd')
version('5.0.1', sha256='8e4e86f04ed789648b66f757329743a0d6dfb5294c3b91b756a474f1ce05a794')
version('4.1.4', sha256='53e184e2d0f90def9207860531802456322be091c7b48f23fdc79cda65adc266')
depends_on('gettext')
depends_on('libsigsegv')
depends_on('readline')
depends_on('mpfr')
depends_on('gmp')
provides('awk')
build_directory = 'spack-build'
@classmethod
def determine_version(cls, exe):
output = Executable(exe)('--version', output=str, error=str)
match = re.search(r'GNU Awk\s+([\d\.]+)', output)
return match.group(1) if match else None
|
player1537-forks/spack
|
lib/spack/spack/analyzers/analyzer_base.py
|
<filename>lib/spack/spack/analyzers/analyzer_base.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)
"""An analyzer base provides basic functions to run the analysis, save results,
and (optionally) interact with a Spack Monitor
"""
import os
import llnl.util.tty as tty
import spack.config
import spack.hooks
import spack.monitor
import spack.util.path
def get_analyzer_dir(spec, analyzer_dir=None):
"""
Given a spec, return the directory to save analyzer results.
We create the directory if it does not exist. We also check that the
spec has an associated package. An analyzer cannot be run if the spec isn't
associated with a package. If the user provides a custom analyzer_dir,
we use it over checking the config and the default at ~/.spack/analyzers
"""
# An analyzer cannot be run if the spec isn't associated with a package
if not hasattr(spec, "package") or not spec.package:
tty.die("A spec can only be analyzed with an associated package.")
# The top level directory is in the user home, or a custom location
if not analyzer_dir:
analyzer_dir = spack.util.path.canonicalize_path(
spack.config.get('config:analyzers_dir', '~/.spack/analyzers'))
# We follow the same convention as the spec install (this could be better)
package_prefix = os.sep.join(spec.package.prefix.split('/')[-3:])
meta_dir = os.path.join(analyzer_dir, package_prefix)
return meta_dir
class AnalyzerBase(object):
def __init__(self, spec, dirname=None):
"""
Verify that the analyzer has correct metadata.
An Analyzer is intended to run on one spec install, so the spec
with its associated package is required on init. The child analyzer
class should define an init function that super's the init here, and
also check that the analyzer has all dependencies that it
needs. If an analyzer subclass does not have dependencies, it does not
need to define an init. An Analyzer should not be allowed to proceed
if one or more dependencies are missing. The dirname, if defined,
is an optional directory name to save to (instead of the default meta
spack directory).
"""
self.spec = spec
self.dirname = dirname
self.meta_dir = os.path.dirname(spec.package.install_log_path)
for required in ["name", "outfile", "description"]:
if not hasattr(self, required):
tty.die("Please add a %s attribute on the analyzer." % required)
def run(self):
"""
Given a spec with an installed package, run the analyzer on it.
"""
raise NotImplementedError
@property
def output_dir(self):
"""
The full path to the output directory.
This includes the nested analyzer directory structure. This function
does not create anything.
"""
if not hasattr(self, "_output_dir"):
output_dir = get_analyzer_dir(self.spec, self.dirname)
self._output_dir = os.path.join(output_dir, self.name)
return self._output_dir
def save_result(self, result, overwrite=False):
"""
Save a result to the associated spack monitor, if defined.
This function is on the level of the analyzer because it might be
the case that the result is large (appropriate for a single request)
or that the data is organized differently (e.g., more than one
request per result). If an analyzer subclass needs to over-write
this function with a custom save, that is appropriate to do (see abi).
"""
# We maintain the structure in json with the analyzer as key so
# that in the future, we could upload to a monitor server
if result[self.name]:
outfile = os.path.join(self.output_dir, self.outfile)
# Only try to create the results directory if we have a result
if not os.path.exists(self._output_dir):
os.makedirs(self._output_dir)
# Don't overwrite an existing result if overwrite is False
if os.path.exists(outfile) and not overwrite:
tty.info("%s exists and overwrite is False, skipping." % outfile)
else:
tty.info("Writing result to %s" % outfile)
spack.monitor.write_json(result[self.name], outfile)
# This hook runs after a save result
spack.hooks.on_analyzer_save(self.spec.package, result)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-rq/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/py-rq/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 PyRq(PythonPackage):
"""RQ (Redis Queue) is a simple Python library for queueing
jobs and processing them in the background with workers."""
homepage = "https://github.com/rq/rq"
url = "https://github.com/rq/rq/archive/v1.5.2.tar.gz"
version('1.5.2', sha256='e8e7b6ffc4a962837eaff8eb0137514346e629633bf08550a1649771cdc4ace6')
version('1.5.1', sha256='36ca5cd2762b5b15bb176943f77da933fac6c2f4e5b5d47a0475f918c167fd4c')
version('1.5.0', sha256='97443acd8aab1c273710f74db197838f68a0678f9cabb64c3598dfb816d35e13')
version('1.4.3', sha256='a971aa16d346d1c145442af3bfb171ea620f375d240fbade3c42c2246d3d698a')
version('1.4.2', sha256='478bd19ac4f66d3066459f5e8253cf5f477bfe128f69ed952f7565cb530ac6a4')
version('1.4.1', sha256='fe158e3d9d4efe533f5698738f14e975656e396cd280c6acfd45952dc5ddfc66')
version('1.4.0', sha256='03cd39392d31d00205bd1d84930e9b7aefc5d3ac9770c59092bdd8a94fc8a47d')
version('1.3.0', sha256='ce94d07125b96313e8c4512b30c62da290ae6f5eeff60b8c3e2a0a08055f5608')
version('1.2.2', sha256='ea71f805d4e3b972b4df5545529044df4bc0fbae30814a48bc28d8d0a39c0068')
version('1.2.1', sha256='0b38344cda68710e572df9c70b733e95f1cdf13ce727a970f68307cedc98376a')
depends_on('python@3.5:3.8', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-redis@3.5.0:', type=('build', 'run'))
depends_on('py-click@5.0.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/setserial/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 Setserial(AutotoolsPackage):
"""A utility for configuring serial ports."""
homepage = "http://setserial.sourceforge.net"
url = "https://udomain.dl.sourceforge.net/project/setserial/setserial/2.17/setserial-2.17.tar.gz"
version('2.17', sha256='7e4487d320ac31558563424189435d396ddf77953bb23111a17a3d1487b5794a')
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.usr.man.man8)
make('install', 'DESTDIR={0}'.format(prefix))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/perl-getopt-tabular/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 PerlGetoptTabular(PerlPackage):
"""Getopt::Tabular is a Perl 5 module for table-driven argument parsing,
vaguely inspired by <NAME>'s Tk_ParseArgv."""
homepage = "https://metacpan.org/pod/Getopt::Tabular"
url = "https://cpan.metacpan.org/authors/id/G/GW/GWARD/Getopt-Tabular-0.3.tar.gz"
version('0.3', sha256='9bdf067633b5913127820f4e8035edc53d08372faace56ba6bfa00c968a25377')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-tidyverse/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 RTidyverse(RPackage):
"""Easily Install and Load the 'Tidyverse'.
The 'tidyverse' is a set of packages that work in harmony because they
share common data representations and 'API' design. This package is
designed to make it easy to install and load multiple 'tidyverse' packages
in a single step. Learn more about the 'tidyverse' at
<https://tidyverse.org>."""
cran = "tidyverse"
version('1.3.1', sha256='83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632')
version('1.3.0', sha256='6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09')
version('1.2.1', sha256='ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b')
depends_on('r+X', type=('build', 'run'))
depends_on('r@3.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r@3.3:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-broom@0.4.2:', type=('build', 'run'))
depends_on('r-broom@0.5.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-broom@0.7.6:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-cli@1.0.0:', type=('build', 'run'))
depends_on('r-cli@1.1.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-cli@2.4.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-crayon@1.3.4:', type=('build', 'run'))
depends_on('r-crayon@1.4.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-dbplyr@1.1.0:', type=('build', 'run'))
depends_on('r-dbplyr@1.4.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-dbplyr@2.1.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-dplyr@0.7.4:', type=('build', 'run'))
depends_on('r-dplyr@0.8.3:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-dplyr@1.0.5:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-dtplyr@1.1.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-forcats@0.2.0:', type=('build', 'run'))
depends_on('r-forcats@0.4.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-forcats@0.5.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-googledrive@1.0.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-googlesheets4@0.3.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
depends_on('r-ggplot2@3.2.1:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-ggplot2@3.3.3:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-haven@1.1.0:', type=('build', 'run'))
depends_on('r-haven@2.2.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-haven@2.3.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-hms@0.3:', type=('build', 'run'))
depends_on('r-hms@0.5.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-hms@1.0.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-httr@1.3.1:', type=('build', 'run'))
depends_on('r-httr@1.4.1:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-httr@1.4.2:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-jsonlite@1.5:', type=('build', 'run'))
depends_on('r-jsonlite@1.6:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-jsonlite@1.7.2:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-lubridate@1.7.1:', type=('build', 'run'))
depends_on('r-lubridate@1.7.4:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-lubridate@1.7.10:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-magrittr@1.5:', type=('build', 'run'))
depends_on('r-magrittr@2.0.1:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-modelr@0.1.1:', type=('build', 'run'))
depends_on('r-modelr@0.1.5:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-modelr@0.1.8:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-pillar@1.4.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-pillar@1.6.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-purrr@0.2.4:', type=('build', 'run'))
depends_on('r-purrr@0.3.3:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-purrr@0.3.4:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-readr@1.1.1:', type=('build', 'run'))
depends_on('r-readr@1.3.1:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-readr@1.4.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-readxl@1.0.0:', type=('build', 'run'))
depends_on('r-readxl@1.3.1:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-reprex@0.1.1:', type=('build', 'run'))
depends_on('r-reprex@0.3.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-reprex@2.0.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-rlang@0.1.4:', type=('build', 'run'))
depends_on('r-rlang@0.4.1:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-rlang@0.4.10:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-rstudioapi@0.7:', type=('build', 'run'))
depends_on('r-rstudioapi@0.10:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-rstudioapi@0.13:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-rvest@0.3.2:', type=('build', 'run'))
depends_on('r-rvest@0.3.5:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-rvest@1.0.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-stringr@1.2.0:', type=('build', 'run'))
depends_on('r-stringr@1.4.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-tibble@1.3.4:', type=('build', 'run'))
depends_on('r-tibble@2.1.3:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-tibble@3.1.0:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-tidyr@0.7.2:', type=('build', 'run'))
depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-tidyr@1.1.3:', type=('build', 'run'), when='@1.3.1:')
depends_on('r-xml2@1.1.1:', type=('build', 'run'))
depends_on('r-xml2@1.2.2:', type=('build', 'run'), when='@1.3.0:')
depends_on('r-xml2@1.3.2:', type=('build', 'run'), when='@1.3.1:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-assertive-base/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 RAssertiveBase(RPackage):
"""A Lightweight Core of the 'assertive' Package.
A minimal set of predicates and assertions used by the assertive package.
This is mainly for use by other package developers who want to include
run-time testing features in their own packages. End-users will usually
want to use assertive directly."""
cran = "assertive.base"
version('0.0-9', sha256='4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e')
version('0.0-7', sha256='f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7')
version('0.0-1', sha256='6a5fb06ad912f01cd8aaf2aa7c8ca03b8ebbb1c5eb2be47fa145930f15f4d258')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@0.0-9:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-crcmod/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 PyCrcmod(PythonPackage):
"""Python module for generating objects that
compute the Cyclic Redundancy Check (CRC)"""
homepage = "http://crcmod.sourceforge.net/"
pypi = "crcmod/crcmod-1.7.tar.gz"
version('1.7', sha256='dc7051a0db5f2bd48665a990d3ec1cc305a466a77358ca4492826f41f283601e')
version('1.6', sha256='56d27d035ea029c6ed96779ca042c0136d39d106e3c30baa6422738c7d86aaa5')
depends_on('python@2.4:2.7,3.1:', type=('build', 'run'))
depends_on('py-setuptools@40.0.0:', type='build')
|
player1537-forks/spack
|
lib/spack/spack/cmd/versions.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 __future__ import print_function
import sys
import llnl.util.tty as tty
from llnl.util.tty.colify import colify
import spack.cmd.common.arguments as arguments
import spack.repo
from spack.version import infinity_versions, ver
description = "list available versions of a package"
section = "packaging"
level = "long"
def setup_parser(subparser):
output = subparser.add_mutually_exclusive_group()
output.add_argument('-s', '--safe', action='store_true',
help='only list safe versions of the package')
output.add_argument('--safe-only', action='store_true',
help='[deprecated] only list safe versions '
'of the package')
output.add_argument('-r', '--remote', action='store_true',
help='only list remote versions of the package')
output.add_argument('-n', '--new', action='store_true',
help='only list remote versions newer than '
'the latest checksummed version')
subparser.add_argument(
'-c', '--concurrency', default=32, type=int,
help='number of concurrent requests'
)
arguments.add_common_arguments(subparser, ['package'])
def versions(parser, args):
pkg = spack.repo.get(args.package)
safe_versions = pkg.versions
if args.safe_only:
tty.warn('"--safe-only" is deprecated. Use "--safe" instead.')
args.safe = args.safe_only
if not (args.remote or args.new):
if sys.stdout.isatty():
tty.msg('Safe versions (already checksummed):')
if not safe_versions:
if sys.stdout.isatty():
tty.warn('Found no versions for {0}'.format(pkg.name))
tty.debug('Manually add versions to the package.')
else:
colify(sorted(safe_versions, reverse=True), indent=2)
if args.safe:
return
fetched_versions = pkg.fetch_remote_versions(args.concurrency)
if args.new:
if sys.stdout.isatty():
tty.msg('New remote versions (not yet checksummed):')
numeric_safe_versions = list(filter(
lambda v: str(v) not in infinity_versions,
safe_versions))
highest_safe_version = max(numeric_safe_versions)
remote_versions = set([ver(v) for v in set(fetched_versions)
if v > highest_safe_version])
else:
if sys.stdout.isatty():
tty.msg('Remote versions (not yet checksummed):')
remote_versions = set(fetched_versions).difference(safe_versions)
if not remote_versions:
if sys.stdout.isatty():
if not fetched_versions:
tty.warn('Found no versions for {0}'.format(pkg.name))
tty.debug('Check the list_url and list_depth attributes of '
'the package to help Spack find versions.')
else:
tty.warn('Found no unchecksummed versions for {0}'.format(
pkg.name))
else:
colify(sorted(remote_versions, reverse=True), indent=2)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libraw1394/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/libraw1394/package.py
# Copyright 2013-2021 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 Libraw1394(AutotoolsPackage):
"""libbraw1394 provides direct access to the IEEE 1394 bus through the
Linux 1394 subsystem's raw1394 user space interface."""
homepage = "https://sourceforge.net/projects/libraw1394/"
url = "https://sourceforge.net/projects/libraw1394/files/libraw1394/1.2.0/libraw1394-1.2.0.tar.gz"
version(
"1.2.0",
sha256="1fdcfa4c5a0938705b925d06f17da9be6ec3f8f065040bb7f33082ef3fc63fad",
)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/rocm-smi-lib/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 os
import shutil
from spack import *
class RocmSmiLib(CMakePackage):
"""It is a C library for Linux that provides a user space interface
for applications to monitor and control GPU applications."""
homepage = "https://github.com/RadeonOpenCompute/rocm_smi_lib"
git = "https://github.com/RadeonOpenCompute/rocm_smi_lib.git"
url = "https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/rocm-4.3.0.tar.gz"
maintainers = ['srekolam', 'arjun-raj-kuppala']
version('master', branch='master')
version('4.5.2', sha256='d4a34db26852defb62817aa44f08ef96d678c63a6f33425bc9d48c18e5e37b7a')
version('4.5.0', sha256='43a2cc2ec548cc28698ca4fa01a947a4414febd433936a8d9770bf6f6ed55e4f')
version('4.3.1', sha256='ea2f9d8a9999e4aac1cb969e6bf2a9f0b6d02f29d0c319b36cce26412ab8a8b0')
version('4.3.0', sha256='c3ff56a14d334cb688a2e9a748dac46d9c2f7f576fe1f53416b1a0edbe842f8b')
version('4.2.0', sha256='c31bf91c492f00d0c5ab21e45afbd7baa990e4a8d7ce9b01e3b988e5fdd53f50')
version('4.1.0', sha256='0c1d2152e40e14bb385071ae16e7573290fb9f74afa5ab887c54f4dd75849a6b', deprecated=True)
version('4.0.0', sha256='93d19229b5a511021bf836ddc2a9922e744bf8ee52ee0e2829645064301320f4', deprecated=True)
version('3.10.0', sha256='8bb2142640d1c6bf141f19accf809e61377a6e0c0222e47ac4daa5da2c85ddac', deprecated=True)
version('3.9.0', sha256='b2934b112542af56de2dc1d5bffff59957e21050db6e3e5abd4c99e46d4a0ffe', deprecated=True)
version('3.8.0', sha256='86250c9ae9dfb18d4f7259a5f2f09b21574d4996fe5034a739ce63a27acd0082', deprecated=True)
version('3.7.0', sha256='72d2a3deda0b55a2d92833cd648f50c7cb64f8341b254a0badac0152b26f1391', deprecated=True)
version('3.5.0', sha256='a5d2ec3570d018b60524f0e589c4917f03d26578443f94bde27a170c7bb21e6e', deprecated=True)
variant('build_type', default='Release', values=("Release", "Debug", "RelWithDebInfo"), description='CMake build type')
variant('shared', default=True, description='Build shared or static library')
depends_on('cmake@3:', type='build')
depends_on('python@3:', type=('build', 'run'), when='@3.9.0:')
patch('disable_pdf_generation_with_doxygen_and_latex.patch', when='@4.5.2:')
def cmake_args(self):
return [
self.define_from_variant('BUILD_SHARED_LIBS', 'shared')
]
@run_after('install')
def post_install(self):
shutil.rmtree(self.prefix.lib)
install_tree(self.prefix.rocm_smi, self.prefix)
shutil.rmtree(self.prefix.rocm_smi)
os.remove(join_path(self.prefix.bin, 'rsmiBindings.py'))
symlink('../bindings/rsmiBindings.py',
join_path(self.prefix.bin, 'rsmiBindings.py'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/fermi/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 Fermi(MakefilePackage):
"""A WGS de novo assembler based on the FMD-index for large genomes."""
homepage = "https://github.com/lh3/fermi"
url = "https://github.com/downloads/lh3/fermi/fermi-1.1.tar.bz2"
version('1.1', sha256='f1351b52a4ff40e5d708899e90ecf747e7af8d4eac795f6968e5b58c2ba11a67')
depends_on('zlib')
depends_on('perl', type='run')
depends_on('sse2neon', when='target=aarch64:')
patch('ksw_for_aarch64.patch', when='target=aarch64:')
def install(self, spec, prefix):
mkdir(prefix.bin)
install('fermi', prefix.bin)
install('run-fermi.pl', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-whisker/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 RWhisker(RPackage):
"""{{mustache}} for R, Logicless Templating.
Implements 'Mustache' logicless templating."""
cran = "whisker"
version('0.4', sha256='7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8')
version('0.3-2', sha256='484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/parquet-format/package.py
|
<filename>var/spack/repos/builtin/packages/parquet-format/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 ParquetFormat(MavenPackage):
"""ParquetFormat is a columnar storage format that supports nested data."""
homepage = "https://github.com/apache/parquet-format/"
url = "https://github.com/apache/parquet-format/archive/apache-parquet-format-2.8.0.tar.gz"
version('2.8.0', sha256='345c044cea73997162e0c38ae830509ee424faf49c90974e4f244079a3df01b0')
version('2.7.0', sha256='e821ffc67f61b49afce017ce2d1d402b4df352ca49dbeae167b06c4d3264b6ba')
depends_on('thrift@0.12.0', when='@2.7.0:')
depends_on('java@8', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/test/util/unparse/__init__.py
|
# Copyright (c) 2014-2021, <NAME> and Spack Project Developers.
#
# SPDX-License-Identifier: Python-2.0
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/logstash/package.py
|
<filename>var/spack/repos/builtin/packages/logstash/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 Logstash(Package):
"""
Logstash is part of the Elastic Stack along with Beats, Elasticsearch
and Kibana. Logstash is a server-side data processing pipeline that
ingests data from a multitude of sources simultaneously, transforms it,
and then sends it to your favorite "stash.
"""
homepage = "https://artifacts.elastic.co"
url = "https://artifacts.elastic.co/downloads/logstash/logstash-6.6.0.tar.gz"
version('6.6.0', sha256='5a9a8b9942631e9d4c3dfb8d47075276e8c2cff343841145550cc0c1cfe7bba7')
def install(self, spec, prefix):
install_tree('.', prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-misc3d/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 RMisc3d(RPackage):
"""Miscellaneous 3D Plots.
A collection of miscellaneous 3d plots, including isosurfaces."""
cran = "misc3d"
version('0.9-1', sha256='a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65')
version('0.9-0', sha256='a1e9291d625bd1312bae5b0e26d48b9362f66a8a0fabbf48891ba1d2432e4e82')
version('0.8-4', sha256='75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62')
depends_on('r+X', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gmsh/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 Gmsh(CMakePackage):
"""Gmsh is a free 3D finite element grid generator with a built-in CAD engine
and post-processor. Its design goal is to provide a fast, light and
user-friendly meshing tool with parametric input and advanced visualization
capabilities. Gmsh is built around four modules: geometry, mesh, solver and
post-processing. The specification of any input to these modules is done
either interactively using the graphical user interface or in ASCII text
files using Gmsh's own scripting language.
"""
homepage = 'https://gmsh.info'
url = 'https://gmsh.info/src/gmsh-4.4.1-source.tgz'
git = 'https://gitlab.onelab.info/gmsh/gmsh.git'
version('master', branch='master')
version('4.8.4', sha256='760dbdc072eaa3c82d066c5ba3b06eacdd3304eb2a97373fe4ada9509f0b6ace')
version('4.7.1', sha256='c984c295116c757ed165d77149bd5fdd1068cbd7835e9bcd077358b503891c6a')
version('4.7.0', sha256='e27f32f92b374ba2a746a9d9c496401c13f66ac6e3e70753e16fa4012d14320e')
version('4.6.0', sha256='0f2c55e50fb6c478ebc8977f6341c223754cbf3493b7b0d683b4395ae9f2ad1c')
version('4.5.6', sha256='46eaeb0cdee5822fdaa4b15f92d8d160a8cc90c4565593cfa705de90df2a463f')
version('4.5.5', sha256='899d3cded664124fa387da57b6f170f47a7e712c7744aa3562779897e2b9e251')
version('4.5.4', sha256='ccf8c74f43cbe3c371abe79862025d41642b3538a0148f018949494e3b3e2ecd')
version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc')
version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc')
version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f')
version('3.0.6', sha256='9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b')
version('3.0.1', sha256='830b5400d9f1aeca79c3745c5c9fdaa2900cdb2fa319b664a5d26f7e615c749f')
version('2.16.0', sha256='e829eaf32ea02350a385202cc749341f2a3217c464719384b18f653edd028eea')
version('2.15.0', sha256='992a4b580454105f719f5bc05441d3d392ab0b4b80d4ea07b61ca3bdc974070a')
variant('external', default=False,
description='Use system versions of contrib libraries, when possible')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('mpi', default=False, description='Builds MPI support for parser and solver')
variant('openmp', default=False, description='Enable OpenMP support')
variant('fltk', default=True, description='Enables the build of the FLTK GUI')
variant('hdf5', default=False, description='Enables HDF5 support')
variant('gmp', default=True, description='Enable GMP for Kbipack (advanced)')
variant('cairo', default=False, description='Enable Cairo to render fonts (experimental)')
variant('compression', default=True, description='Enables IO compression through zlib')
variant('med', default=True, description='Build with MED(HDF5)')
variant('mmg', default=True, description='Build with Mmg3d')
variant('netgen', default=True, description='Build with Netgen (built-in)')
variant('opencascade', default=False, description='Build with OpenCASCADE')
variant('oce', default=False, description='Build with OCE')
variant('petsc', default=False, description='Build with PETSc')
variant('slepc', default=False, description='Build with SLEPc (only when PETSc is enabled)')
variant('tetgen', default=False, description='Build with Tetgen (built-in)')
variant('metis', default=True, description='Build with Metis (built-in)')
variant('privateapi', default=False, description='Enable the private API')
variant('alglib', default=True, description='Build with Alglib (built-in or 3rd party)')
variant('eigen', default=False, description='Build with Eigen (built-in or 3rd party)')
variant('voropp', default=True, description='Build with voro++ (built-in or 3rd party')
variant('cgns', default=True, description='Build with CGNS')
# https://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
# We make changes to the GMSH default, such as external blas.
depends_on('blas', when='~eigen')
depends_on('lapack', when='~eigen')
depends_on('eigen@3:', when='+eigen+external')
depends_on('alglib', when='+alglib+external')
depends_on('voropp', when='+voropp+external')
depends_on('cmake@2.8:', type='build')
depends_on('gmp', when='+gmp')
depends_on('mpi', when='+mpi')
depends_on('fltk+gl', when='+fltk')
depends_on('gl', when='+fltk')
depends_on('glu', when='+fltk')
depends_on('cairo', when='+cairo')
depends_on('hdf5', when='+hdf5')
depends_on('hdf5', when='+med')
depends_on('med', when='+med')
depends_on('mmg', when='+mmg')
depends_on('opencascade', when='+opencascade')
depends_on('oce', when='+oce')
depends_on('freetype', when='+oce')
depends_on('freetype', when='+opencascade')
depends_on('petsc+mpi', when='+petsc+mpi')
depends_on('petsc', when='+petsc~mpi')
depends_on('slepc', when='+slepc+petsc')
depends_on('zlib', when='+compression')
depends_on('metis', when='+metis+external')
depends_on('cgns', when='+cgns')
# Gmsh's high quality vector PostScript, PDF and SVG output is produced by GL2PS.
# But Gmsh ships with its own version of this library, so it is not a
# dependency of this package.
# See https://gitlab.onelab.info/gmsh/gmsh/-/blob/master/Graphics/gl2ps.h
# and https://gitlab.onelab.info/gmsh/gmsh/-/blob/master/Graphics/gl2ps.cpp
conflicts('+slepc', when='~petsc')
conflicts('+oce', when='+opencascade')
conflicts('+metis', when='+external',
msg="External Metis cannot build with GMSH")
def cmake_args(self):
spec = self.spec
options = [
self.define_from_variant('ENABLE_ALGLIB', 'alglib'),
self.define_from_variant('ENABLE_CAIRO', 'cairo'),
self.define_from_variant('ENABLE_CGNS', 'cgns'),
self.define_from_variant('ENABLE_EIGEN', 'eigen'),
self.define_from_variant('ENABLE_FLTK', 'fltk'),
self.define_from_variant('ENABLE_GMP', 'gmp'),
self.define_from_variant('ENABLE_MED', 'med'),
self.define_from_variant('ENABLE_METIS', 'metis'),
self.define_from_variant('ENABLE_MMG', 'mmg'),
self.define_from_variant('ENABLE_MPI', 'mpi'),
self.define_from_variant('ENABLE_NETGEN', 'netgen'),
self.define_from_variant('ENABLE_OPENMP', 'openmp'),
self.define_from_variant('ENABLE_PETSC', 'petsc'),
self.define_from_variant('ENABLE_PRIVATE_API', 'privateapi'),
self.define_from_variant('ENABLE_SLEPC', 'slepc'),
self.define_from_variant('ENABLE_VOROPP', 'voropp'),
]
# Use system versions of contrib libraries, when possible:
if '+external' in spec:
options.append(self.define('ENABLE_SYSTEM_CONTRIB', True))
# Make sure native file dialogs are used
options.append('-DENABLE_NATIVE_FILE_CHOOSER=ON')
options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' % self.prefix.lib)
# Prevent GMsh from using its own strange directory structure on OSX
options.append('-DENABLE_OS_SPECIFIC_INSTALL=OFF')
# Make sure GMSH picks up correct BlasLapack by providing linker flags
if '~eigen' in spec:
options.append('-DENABLE_BLAS_LAPACK=ON')
blas_lapack = spec['lapack'].libs + spec['blas'].libs
options.append(
'-DBLAS_LAPACK_LIBRARIES={0}'.format(blas_lapack.ld_flags))
if '+oce' in spec:
options.append('-DENABLE_OCC=ON')
elif '+opencascade' in spec:
options.append('-DENABLE_OCC=ON')
else:
options.append('-DENABLE_OCC=OFF')
if '@:3.0.6' in spec:
options.append(self.define_from_variant('ENABLE_TETGEN', 'tetgen'))
if '@:4.6' in spec:
options.append(self.define_from_variant('ENABLE_MMG3D', 'mmg'))
if '+shared' in spec:
# Builds dynamic executable and installs shared library
options.append(self.define('ENABLE_BUILD_SHARED', True))
options.append(self.define('ENABLE_BUILD_DYNAMIC', True))
else:
# Builds and installs static library
options.append(self.define('ENABLE_BUILD_LIB', True))
if '+compression' in spec:
options.append(self.define('ENABLE_COMPRESSED_IO', True))
return options
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-queryablelist/package.py
|
<filename>var/spack/repos/builtin/packages/py-queryablelist/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 PyQueryablelist(PythonPackage):
"""Python module to add support for ORM-style filtering to any list of
items"""
homepage = "https://github.com/kata198/QueryableList"
pypi = "queryablelist/QueryableList-3.1.0.tar.gz"
version('3.1.0', sha256='8891dccbadc69a35f5944e1826d8f8db224522aa3af913e301a7a448f5b411e9')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/xlc/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 collections
import re
import llnl.util.tty as tty
import spack.compiler
class Xlc(Package):
"""IBM XL C/C++ is an advanced, high-performance compiler that can be
used for developing complex, computationally intensive programs, including
interlanguage calls with C and Fortran programs.
"""
homepage = "https://www.ibm.com/support/knowledgecenter/SSXVZZ_16.1.1/com.ibm.compilers.linux.doc/welcome.html"
variant('r', default=True, description='The _r version of compilers')
def install(self, spec, prefix):
raise InstallError(
'XL compilers are not installable yet, but can be '
'detected on a system where they are supplied by vendor'
)
executables = [r'xlc', r'xlC', r'xlc\+\+']
@classmethod
def determine_version(cls, exe):
version_regex = re.compile(r'([0-9]?[0-9]\.[0-9])')
try:
output = spack.compiler.get_compiler_version_output(
exe, '-qversion'
)
# Exclude spurious Fortran compilers
if 'Fortran' in output:
return None
match = version_regex.search(output)
if match:
return match.group(1)
except spack.util.executable.ProcessError:
pass
except Exception as e:
tty.debug(str(e))
@classmethod
def determine_variants(cls, exes, version_str):
variants = collections.defaultdict(dict)
for exe in exes:
# Determine the variant of the spec
variant_str = '+r' if '_r' in exe else '~r'
if 'xlc++' in exe:
variants[variant_str]['cxx'] = exe
continue
if 'xlc' in exe:
variants[variant_str]['c'] = exe
continue
results = []
for variant_str, compilers in variants.items():
results.append((variant_str, {'compilers': compilers}))
return results
@property
def cc(self):
if self.spec.external:
return self.spec.extra_attributes['compilers']['c']
msg = "cannot retrieve C compiler [spec is not concrete]"
assert self.spec.concrete, msg
@property
def cxx(self):
if self.spec.external:
return self.spec.extra_attributes['compilers']['cxx']
msg = "cannot retrieve C compiler [spec is not concrete]"
assert self.spec.concrete, msg
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-netcdf4/package.py
|
<filename>var/spack/repos/builtin/packages/py-netcdf4/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 PyNetcdf4(PythonPackage):
"""Python interface to the netCDF Library."""
homepage = "https://github.com/Unidata/netcdf4-python"
pypi = "netCDF4/netCDF4-1.2.7.tar.gz"
maintainers = ['skosukhin']
version('1.5.3', sha256='2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be')
version('1.4.2', sha256='b934af350459cf9041bcdf5472e2aa56ed7321c018d918e9f325ec9a1f9d1a30')
version('1.2.7', sha256='0c449b60183ee06238a8f9a75de7b0eed3acaa7a374952ff9f1ff06beb8f94ba')
version('1.2.3.1', sha256='55edd74ef9aabb1f7d1ea3ffbab9c555da2a95632a97f91c0242281dc5eb919f')
variant("mpi", default=True, description="Parallel IO support")
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.19:', type='build')
depends_on('py-numpy@1.7:', type=('build', 'run'))
depends_on('py-cftime', type=('build', 'run'))
depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
depends_on('netcdf-c', when='-mpi')
depends_on('netcdf-c+mpi', when='+mpi')
depends_on('hdf5@1.8.0:+hl', when='-mpi')
depends_on('hdf5@1.8.0:+hl+mpi', when='+mpi')
# The installation script tries to find hdf5 using pkg-config. However, the
# version of hdf5 installed with Spack does not have pkg-config files.
# Therefore, if pkg-config finds hdf5.pc at all (e.g. provided by
# Ubuntu/Debian package manager), it is definitely not what we need. The
# following patch disables the usage of pkg-config at all.
patch('disable_pkgconf.patch')
# Older versions of the package get a false negative result when checking
# the version of HDF5.
patch('check_hdf5version.patch', when='@:1.2.9 ^hdf5@1.10:')
def setup_build_environment(self, env):
"""Ensure installed netcdf and hdf5 libraries are used"""
# Explicitly set these variables so setup.py won't erroneously pick up
# system versions
# See: http://unidata.github.io/netcdf4-python
env.set('USE_SETUPCFG', '0')
env.set('USE_NCCONFIG', '1')
env.set('HDF5_DIR', self.spec['hdf5'].prefix)
env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include)
env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib)
env.set('NETCDF4_DIR', self.spec['netcdf-c'].prefix)
env.set('NETCDF4_INCDIR', self.spec['netcdf-c'].prefix.include)
env.set('NETCDF4_LIBDIR', self.spec['netcdf-c'].prefix.lib)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/sparskit/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 Sparskit(MakefilePackage):
"""SPARSKIT: A basic tool-kit for sparse matrix computations (Version 2).
Made by <NAME>, University of Minnesota.
"""
homepage = "https://www-users.cse.umn.edu/~saad/software/SPARSKIT/"
version('develop', sha256='ecdd0a9968d6b45153a328710a42fe87600f0bba0e3c53896090b8ae1c113b7a',
url='http://www-users.cs.umn.edu/~saad/software/SPARSKIT/SPARSKIT2.tar.gz')
# The library uses blas routine which needs to be known when the lib is used.
# A dependent package should add self.spec['blas'].libs.ld_flags
# at the end of its link line.
# But, asis, this packages compiles without needing to know about it.
# depends_on('blas', type='run')
variant('pic', default=True,
description='Compile with position independent code.')
variant('debug', default=False,
description='Builds a debug version of the library')
# We provide the standard Make flags here:
# https://spack.readthedocs.io/en/latest/packaging_guide.html?highlight=flag_handler#compiler-flags
def flag_handler(self, name, flags):
spec = self.spec
if '+pic' in spec:
if name == 'fflags':
flags.append(self.compiler.fc_pic_flag)
if name == 'fflags':
if 'gfortran' in self.compiler.fc:
flags.append('-std=legacy')
flags.append('-Wall')
if '+debug' in spec:
if '-g' in self.compiler.debug_flags:
flags.append('-g')
if '-O0' in self.compiler.opt_flags:
flags.append('-O0')
elif '-O' in self.compiler.opt_flags:
flags.append('-O')
else:
if '-O3' in self.compiler.opt_flags:
flags.append('-O3')
elif '-O2' in self.compiler.opt_flags:
flags.append('-O2')
return (None, flags, None)
def edit(self, spec, prefix):
mkfile = FileFilter('makefile')
mkfile.filter(r'^(OPT).*=.+', r'\1= -c $(FFLAGS)')
if os.path.exists('libskit.a'):
os.unlink('libskit.a')
def build(self, spec, prefix):
make('clean')
make('F77={0}'.format(spack_fc))
def install(self, spec, prefix):
mkdirp(prefix.lib)
install('libskit.*', prefix.lib)
@property
def libs(self):
return find_libraries(
"libskit*", root=self.prefix, shared=False, recursive=True
)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-circlize/package.py
|
<filename>var/spack/repos/builtin/packages/r-circlize/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 RCirclize(RPackage):
"""Circular Visualization.
Circular layout is an efficient way for the visualization of huge amounts
of information. Here this package provides an implementation of circular
layout generation in R as well as an enhancement of available software. The
flexibility of the package is based on the usage of low-level graphics
functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for better
understanding complex patterns behind multiple dimensional data. The
package is described in Gu et al. 2014
<doi:10.1093/bioinformatics/btu393>."""
cran = "circlize"
version('0.4.13', sha256='6cbadbf8e8b1abbd71a79080677d2b95f2bdd18f2e4d707c32d5c2ff26c5369b')
version('0.4.12', sha256='b3b60caa5292cf980cf474c85f59582f6862925631a4da86a78eac05903252f4')
version('0.4.6', sha256='cec88cfc5e512a111cc37177552c25698ccc0e9bbecb0d6e60657e7b115a56fa')
version('0.4.1', sha256='204a170ae3b982f09b652c4583189907cfa42a29bc7efaba02a1e0d79f1cf1f0')
version('0.4.0', sha256='abdc1bbe264be42c1d7b65869979da7cd131032fd6fd3f11f9744dae54e83f5c')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.0:', type=('build', 'run'))
depends_on('r-globaloptions@0.1.2:', type=('build', 'run'), when='@0.4.12:')
depends_on('r-shape', type=('build', 'run'))
depends_on('r-colorspace', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-kernsmooth/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 RKernsmooth(RPackage):
"""Functions for Kernel Smoothing Supporting Wand & Jones (1995).
Functions for kernel smoothing (and density estimation) corresponding to
the book: <NAME>. and <NAME>. (1995) "Kernel Smoothing"."""
cran = "KernSmooth"
version('2.23-20', sha256='20eb75051e2473933d41eedc9945b03c632847fd581e2207d452cf317fa5ec39')
version('2.23-18', sha256='8334800c5ad2305539d2731b929ea34f50fa4269ba87277b699fd5be5b03c490')
version('2.23-15', sha256='8b72d23ed121a54af188b2cda4441e3ce2646359309885f6455b82c0275210f6')
depends_on('r@2.5.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/bracken/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 Bracken(Package):
"""Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
accurate statistical method that computes the abundance of species in DNA
sequences from a metagenomics sample."""
homepage = "https://ccb.jhu.edu/software/bracken"
url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
version('1.0.0', sha256='8ee736535ad994588339d94d0db4c0b1ba554a619f5f96332ee09f2aabdfe176')
depends_on('perl', type=('build', 'link', 'run'))
depends_on('python@2.7:', type=('build', 'link', 'run'))
depends_on('perl-exporter-tiny')
depends_on('perl-list-moreutils')
depends_on('perl-parallel-forkmanager')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_tree('sample_data', prefix.sample_data)
filter_file(
r'#!/bin/env perl',
'#!/usr/bin/env perl',
'count-kmer-abundances.pl'
)
filter_file(
r'#!/usr/bin/python',
'#!/usr/bin/env {0}'.format(
os.path.basename(self.spec['python'].command.path)),
'est_abundance.py'
)
filter_file(
r'#!/usr/bin/python',
'#!/usr/bin/env {0}'.format(
os.path.basename(self.spec['python'].command.path)),
'generate_kmer_distribution.py'
)
files = (
'count-kmer-abundances.pl',
'est_abundance.py',
'generate_kmer_distribution.py',
)
chmod = which('chmod')
for name in files:
install(name, prefix.bin)
chmod('+x', join_path(self.prefix.bin, name))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-mido/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 PyMido(PythonPackage):
"""Mido is a library for working with MIDI messages and ports. It's
designed to be as straight forward and Pythonic as possible."""
homepage = "https://mido.readthedocs.io/"
url = "https://github.com/mido/mido/archive/1.2.9.tar.gz"
version('1.2.9', sha256='6d68d7514bb3320f505ba4d7e06006c4725c0b97f281126bc983f3f7eeed697a')
version('1.2.8', sha256='4d26706430ea87dfcd950b19979d3edb97b2b113eb7e233c64290713cf7ec7b9')
version('1.2.7', sha256='7fb8d2c4b16b1d4f18b2e440654905ad63a8d24121f41b0126f39e3c7db89cf1')
version('1.2.6', sha256='870d2f470ce1123324f9ef9676b6c9f2580293dd2a07fdfe00e20a47740e8b8e')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-dipy/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 PyDipy(PythonPackage):
""" Diffusion MRI utilities in python.
DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic
methods for spatial normalization, signal processing, machine learning,
statistical analysis and visualization of medical images. Additionally, it
contains specialized methods for computational anatomy including diffusion,
perfusion and structural imaging.
"""
homepage = "https://dipy.org/"
pypi = "dipy/dipy-1.4.1.tar.gz"
version('1.4.1', sha256='b4bf830feae751f3f985d54cb71031fc35cea612838320f1f74246692b8a3cc0')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.29:', type=('build'))
depends_on('py-numpy@1.12.0:', type=('build', 'run'))
depends_on('py-scipy@1.0:', type=('build', 'run'))
depends_on('py-nibabel@3.0.0:', type=('build', 'run'))
depends_on('py-h5py@2.5.0:', type=('build', 'run'))
depends_on('py-packaging@19.0:', type=('build', 'run'))
depends_on('py-tqdm@4.30.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/mad-numdiff/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/mad-numdiff/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 MadNumdiff(CMakePackage):
"""compare unformatted text files with numerical content"""
homepage = "https://github.com/quinoacomputing/ndiff"
url = "https://github.com/quinoacomputing/ndiff/tarball/20150724"
git = "https://github.com/quinoacomputing/ndiff.git"
version('develop', branch='master')
version('20150724', sha256='33130b48416f8dcb6402acbcb8906cdec35b7242fe2f3ad49b7d7c063d75377b')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-accimage/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 PyAccimage(PythonPackage):
"""An accelerated Image loader and preprocessor leveraging Intel IPP.
accimage mimics the PIL API and can be used as a backend for torchvision.
"""
homepage = "https://github.com/pytorch/accimage"
url = "https://github.com/pytorch/accimage/archive/v0.1.1.tar.gz"
version('0.1.1', sha256='573c56866a42683c7cf25185620fe82ec2ce78468e0621c29fac8f4134a785f5')
depends_on('python', type=('build', 'link', 'run'))
# pip silently replaces distutils with setuptools
depends_on('py-setuptools', type='build')
depends_on('jpeg')
depends_on('ipp')
depends_on('py-pytest', type='test')
depends_on('py-numpy', type='test')
depends_on('py-imageio', type='test')
@run_after('install')
@on_package_attributes(run_tests=True)
def build_test(self):
pytest = which('pytest')
pytest('test.py')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/dracut/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 Dracut(AutotoolsPackage):
"""dracut is used to create an initramfs image by copying tools and
files from an installed system and combining it with the dracut
framework."""
homepage = "https://github.com/dracutdevs/dracut"
url = "https://github.com/dracutdevs/dracut/archive/050.tar.gz"
version('050', sha256='f9dbf18597e5929221365964293212c8c9ffb7d84529c5a338c834ecab06e333')
depends_on('kmod')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-assertive-reflection/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 RAssertiveReflection(RPackage):
"""Assertions for Checking the State of R.
A set of predicates and assertions for checking the state and capabilities
of R, the operating system it is running on, and the IDE being used. This
is mainly for use by other package developers who want to include run-time
testing features in their own packages. End-users will usually want to use
assertive directly."""
cran = "assertive.reflection"
version('0.0-5', sha256='c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-assertive-base@0.0-7:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-argparse/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 RArgparse(RPackage):
"""Command Line Optional and Positional Argument Parser.
A command line parser to be used with Rscript to write "#!" shebang scripts
that gracefully accept positional and optional arguments and automatically
generate usage."""
cran = "argparse"
version('2.1.3', sha256='aeda31a54a8d7a0a511cfbf7c5868637e129922671d43938165867437fb6a66e')
version('2.0.3', sha256='d26139c610ea0adf8d6632699cd34c4595ae3e7963bfc7a00cb3b7504f2059b0')
version('2.0.1', sha256='949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab')
version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b')
depends_on('r-r6', type=('build', 'run'), when='@2.0.0:')
depends_on('r-findpython', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('python@3.2:', type=('build', 'run'))
depends_on('r-proto@1:', type=('build', 'run'), when='@1.0.0:1.9.9')
depends_on('r-getopt', type=('build', 'run'), when='@1.0.0:1.9.9')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-rpy2/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 PyRpy2(PythonPackage):
"""rpy2 is a redesign and rewrite of rpy. It is providing a low-level
interface to R from Python, a proposed high-level interface,
including wrappers to graphical libraries, as well as R-like
structures and functions.
"""
pypi = "rpy2/rpy2-2.5.4.tar.gz"
version('3.0.4', sha256='2af5158a5d56af7f7bf5e54d8d7e87b6f115ff40f056d82f93cad0cbf6acc0cb')
version('3.0.0', sha256='34efc2935d9015527837d6b1de29641863d184b19d39ad415d5384be8a015bce')
version('2.9.4', sha256='be57f741d0c284b5d8785ab03dff0e829303e5ac30e548d5ceb46e05b168812e')
version('2.8.6', sha256='004d13734a7b9a85cbc1e7a93ec87df741e28db1273ab5b0d9efaac04a9c5f98')
version('2.5.6', sha256='d0d584c435b5ed376925a95a4525dbe87de7fa9260117e9f208029e0c919ad06')
version('2.5.4', sha256='d521ecdd05cd0c31ab017cb63e9f63c29b524e46ec9063a920f640b5875f8a90')
# FIXME: Missing dependencies:
# ld: cannot find -licuuc
# ld: cannot find -licui18
# All versions
depends_on('py-setuptools', type='build')
depends_on('r', type=('build', 'run'))
# @3.0.0:
depends_on('py-cffi@1.0.0:', when='@3.0.0:', type=('build', 'run'))
depends_on('py-simplegeneric', when='@3.0.0:', type=('build', 'run'))
depends_on('py-pytest', when='@3:', type=('build', 'run'))
# @2.9.0:
depends_on('r@3.3:', when='@2.9.0:', type=('build', 'run'))
depends_on('python@3.5:', when='@2.9.0:', type=('build', 'run'))
depends_on('py-jinja2', when='@2.9.0:', type=('build', 'run'))
depends_on('py-six', when='@2.9.0:2.9', type=('build', 'run'))
# @:2.8.6
depends_on('r@2.8:', when='@:2.8.6', type=('build', 'run'))
depends_on('py-singledispatch', when='^python@:2', type=('build', 'run'))
depends_on('python@2.7:2.8,3.5:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/mpitrampoline/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 Mpitrampoline(CMakePackage):
"""MPItrampoline: A forwarding MPI implementation that can use any other
MPI implementation via an MPI ABI."""
homepage = "https://github.com/eschnett/MPItrampoline"
url = "https://github.com/eschnett/MPItrampoline/archive/v1.0.1.tar.gz"
git = "https://github.com/eschnett/MPItrampoline.git"
maintainers = ['eschnett']
version('develop', branch='main')
version('2.8.0', sha256='bc2a075ced19e5f7ea547060e284887bdbb0761d34d1adb6f16d2e9e096a7d38')
version('2.7.0', sha256='b188657e41b240bba663ce5b3d7b73377a27a64edcc1e0aaa7c924cf00e30b42')
version('2.6.0', sha256='5425085f4b8772990b28a643b7dfc7ac37a399ee35ffa3d6113a06e5b508dfac')
version('2.5.0', sha256='26423749a6a45324062cbe82eb6934236b0c8ea17f9d5b594ed0c15ea8d0dbad')
version('2.4.0', sha256='e08785cf5b43c9913d890be44f6e7a551a83f34f389f6db9136db2379697fadd')
version('2.3.0', sha256='4559acb13d34b9a052752a9e0f928d31da54bfa7b05f31585bf6a66fadaceca4')
version('2.2.0', sha256='fa213a7ac03b4c54d5c9281192fb604747d4b5be4ce9b54b4c740f3da7a6aaea')
version('2.1.0', sha256='8794c07772ecc6d979ecf475653ae571a593d01ef2df51ccbc63c9f9d9c67856')
version('2.0.0', sha256='50d4483f73ea4a79a9b6d025d3abba42f76809cba3165367f4810fb8798264b6')
version('1.1.0', sha256='67fdb710d1ca49487593a9c023e94aa8ff0bec56de6005d1a437fca40833def9')
version('1.0.1', sha256='4ce91b99fb6d2dab481b5e477b6b6a0709add48cf0f287afbbb440fdf3232500')
variant('shared', default=True,
description='Build a shared version of the library')
provides("mpi @3.1")
def cmake_args(self):
return [self.define_from_variant('BUILD_SHARED_LIBS', 'shared')]
def setup_run_environment(self, env):
# Because MPI implementations provide compilers, they have to add to
# their run environments the code to make the compilers available.
env.set('MPITRAMPOLINE_CC', self.compiler.cc_names[0])
env.set('MPITRAMPOLINE_CXX', self.compiler.cxx_names[0])
env.set('MPITRAMPOLINE_FC', self.compiler.fc_names[0])
env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
env.set('MPIF77', join_path(self.prefix.bin, 'mpifc'))
env.set('MPIF90', join_path(self.prefix.bin, 'mpifc'))
def setup_dependent_build_environment(self, env, dependent_spec):
self.setup_run_environment(env)
def setup_dependent_package(self, module, dependent_spec):
self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
self.spec.mpif77 = join_path(self.prefix.bin, 'mpifc')
self.spec.mpifc = join_path(self.prefix.bin, 'mpifc')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ptw/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 RPtw(RPackage):
"""Parametric Time Warping.
Parametric Time Warping aligns patterns, i.e. it aims to put corresponding
features at the same locations. The algorithm searches for an optimal
polynomial describing the warping. It is possible to align one sample to a
reference, several samples to the same reference, or several samples to
several references. One can choose between calculating individual warpings,
or one global warping for a set of samples and one reference. Two
optimization criteria are implemented: RMS (Root Mean Square error) and WCC
(Weighted Cross Correlation). Both warping of peak profiles and of peak
lists are supported. A vignette for the latter is contained in the inst/doc
directory of the source package - the vignette source can be found on the
package github site."""
cran = "ptw"
version('1.9-16', sha256='7e87c34b9eeaeabe3bfb937162e6cda4dd48d6bd6a97b9db8bb8303d131caa66')
version('1.9-15', sha256='22fa003f280bc000f46bca88d69bf332b29bc68435115ba8044533b70bfb7b46')
version('1.9-13', sha256='7855e74a167db3d3eba9df9d9c3daa25d7cf487cbcfe8b095f16d96eba862f46')
version('1.9-12', sha256='cdb1752e04e661e379f11867b0a17e2177e9ee647c54bbcc37d39d6b8c062b84')
depends_on('r-nloptr', type=('build', 'run'))
depends_on('r-rcppde', type=('build', 'run'), when='@1.9-16:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-mock/package.py
|
<filename>var/spack/repos/builtin/packages/py-mock/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 PyMock(PythonPackage):
"""mock is a library for testing in Python. It allows you to replace parts
of your system under test with mock objects and make assertions about how
they have been used."""
homepage = "https://github.com/testing-cabal/mock"
pypi = "mock/mock-4.0.3.tar.gz"
version('4.0.3', sha256='7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc')
version('3.0.5', sha256='83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3')
version('2.0.0', sha256='b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba')
version('1.3.0', sha256='1e247dbecc6ce057299eb7ee019ad68314bb93152e81d9a6110d35f4d5eca0f6')
depends_on('python@3.6:', type=('build', 'run'), when='@3')
depends_on('python@2.7:2.8,3.4:', type=('build', 'run'), when='@:2')
depends_on('py-setuptools@17.1:', type='build')
depends_on('py-pbr@1.3:', type=('build'), when='@:2')
depends_on('py-six@1.9:', type=('build', 'run'), when='@:2')
depends_on('py-funcsigs@1:', type=('build', 'run'), when='^python@:3.2')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-pythonsollya/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 PyPythonsollya(PythonPackage):
"""Python wrapper for the Sollya library"""
homepage = "Python wrapper for the Sollya library"
url = "https://gitlab.com/metalibm-dev/pythonsollya/-/archive/release-0.4.0-alpha0/pythonsollya-release-0.4.0-alpha0.tar.gz"
version('0.4.0-alpha0', sha256='faac899744c92b1d20980cadef309cd5610d79722322e97940ff142c207c41b5')
version('0.3.0', url='https://gitlab.com/metalibm-dev/pythonsollya/-/archive/0.3/pythonsollya-0.3.tar.gz',
sha256='cdccd0c5549247ad7498546095544d8d01e78bcb4a3e55c32d6daea6b845b6b9', preferred=True)
depends_on('py-cython', type='build')
depends_on('py-six', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('libffi', type='build')
depends_on('sollya', type=('build', 'link'))
depends_on('py-bigfloat', type=('build', 'run'))
depends_on('mpfi', type=('build', 'link'))
@run_before('install')
def patch(self):
filter_file('PYTHON ?= python2',
'PYTHON ?= ' + self.spec['python'].command.path,
'GNUmakefile',
string=True)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-symengine/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 PySymengine(PythonPackage):
"""Python wrappers for SymEngine, a symbolic manipulation library."""
homepage = "https://github.com/symengine/symengine.py"
pypi = "symengine/symengine-0.2.0.tar.gz"
git = "https://github.com/symengine/symengine.py.git"
version('master', branch='master')
# pypi source doesn't have necessary files in cmake directory
version('0.8.1',
url='https://github.com/symengine/symengine.py/archive/refs/tags/v0.8.1.tar.gz',
sha256='02fe79e6d5e9b39a1d4e6fee05a2c1d1b10fd032157c7738ed97e32406ffb087')
version('0.2.0', sha256='78a14aea7aad5e7cbfb5cabe141581f9bba30e3c319690e5db8ad99fdf2d8885')
# Build dependencies
depends_on('python@2.7:2.8,3.3:', type=('build', 'run'), when='@0.2.0')
depends_on('python@3.6:3', type=('build', 'run'), when='@0.8.1:')
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.19.1:', type='build', when='@0.2.0')
depends_on('py-cython@0.29.24:', type='build', when='@0.8.1:')
depends_on('cmake@2.8.12:', type='build')
depends_on('symengine@0.2.0', when='@0.2.0')
depends_on('symengine@0.8.1', when='@0.8.1')
def install_options(self, spec, prefix):
return ['--symengine-dir={0}'.format(spec['symengine'].prefix)]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-promises/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 RPromises(RPackage):
"""Abstractions for Promise-Based Asynchronous Programming.
Provides fundamental abstractions for doing asynchronous programming in R
using promises. Asynchronous programming is useful for allowing a single R
process to orchestrate multiple tasks in the background while also
attending to something else. Semantics are similar to 'JavaScript'
promises, but with a syntax that is idiomatic R."""
cran = "promises"
version('1.2.0.1', sha256='8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7')
version('1.1.1', sha256='3718c6eb2c3362cbe89389e613118f783f9977dbf24757f85026e661199c5800')
version('1.0.1', sha256='c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558')
depends_on('r-r6', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-later', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ray/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 Ray(CMakePackage, SourceforgePackage):
"""Parallel genome assemblies for parallel DNA sequencing"""
homepage = "http://denovoassembler.sourceforge.net/"
sourceforge_mirror_path = "denovoassembler/Ray-2.3.1.tar.bz2"
version('2.3.1', sha256='3122edcdf97272af3014f959eab9a0f0e5a02c8ffc897d842b06b06ccd748036')
depends_on('mpi')
@run_after('build')
def make(self):
mkdirp(prefix.bin)
make('PREFIX=%s' % prefix.bin)
def install(self, spec, prefix):
make('install')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/snptest/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 Snptest(Package):
"""SNPTEST is a program for the analysis of single SNP association in
genome-wide studies."""
homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html"
url = "https://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.2_linux_x86_64_dynamic.tgz"
version('2.5.2', sha256='1ffa3ebafa2c5db4866a38e01bb09f43df7973d053423ce67221cb3f8acb30f6')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('snptest_v{0}'.format(self.version), prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gmtsar/package.py
|
<filename>var/spack/repos/builtin/packages/gmtsar/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 Gmtsar(CMakePackage):
"""GMTSAR is an open source (GNU General Public License) InSAR processing
system designed for users familiar with Generic Mapping Tools (GMT).
"""
homepage = "https://topex.ucsd.edu/gmtsar/"
url = "https://elenacreinisch.com/gmtsar/GMTSAR-5.6.tar.gz"
version('5.6', sha256='0f7326f46aedf1e8e4dc80dd03f1ae8681f52a8253dc4a00a943aec14562994b')
depends_on('gmt')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gtrellis/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 RGtrellis(RPackage):
"""Genome Level Trellis Layout.
Genome level Trellis graph visualizes genomic data conditioned by
genomic categories (e.g. chromosomes). For each genomic category,
multiple dimensional data which are represented as tracks describe
different features from different aspects. This package provides high
flexibility to arrange genomic categories and to add self-defined
graphics in the plot."""
bioc = "gtrellis"
version('1.26.0', commit='f2c3121b31ad1b422e2cf503435d0590e903ff3f')
version('1.22.0', commit='<PASSWORD>')
version('1.16.1', commit='a9003<PASSWORD>c8f2a48c78d4545e2f214023c13a7da')
version('1.14.0', commit='93935fb34211d12b250e22291712e18a31b0208d')
version('1.12.1', commit='<KEY>')
version('1.11.1', commit='<KEY>')
version('1.8.0', commit='<PASSWORD>472')
depends_on('r@3.1.2:', type=('build', 'run'))
depends_on('r-iranges', type=('build', 'run'))
depends_on('r-genomicranges', type=('build', 'run'))
depends_on('r-circlize@0.3.3:', type=('build', 'run'))
depends_on('r-circlize@0.4.8:', type=('build', 'run'), when='@1.16.1')
depends_on('r-getoptlong', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-hpccm/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 PyHpccm(PythonPackage):
"""HPC Container Maker (HPCCM - pronounced H-P-see-M) is an open source
tool to make it easier to generate container specification files."""
homepage = "https://github.com/NVIDIA/hpc-container-maker"
pypi = "hpccm/hpccm-19.2.0.tar.gz"
version('19.2.0', sha256='c60eec914a802b0a76596cfd5fdf7122d3f8665fcef06ef928323f5dfb5219a6')
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-enum34', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-a4classif/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 RA4classif(RPackage):
"""Automated Affymetrix Array Analysis Classification Package.
Functionalities for classification of Affymetrix microarray data,
integrating within the Automated Affymetrix Array Analysis set of
packages."""
bioc = "a4Classif"
version('1.42.0', commit='820854a7ca9ed0c295479a25b7e3375c6d01d0b5')
version('1.38.0', commit='<KEY>')
version('1.32.0', commit='<KEY>')
version('1.30.0', commit='<KEY>')
version('1.28.0', commit='3464011f6c3ddb41b78acc47e775539034287be7')
version('1.26.0', commit='bc4018c3c441e1840bb3e2959c07611489439a50')
version('1.24.0', commit='<KEY>')
depends_on('r-a4core', type=('build', 'run'))
depends_on('r-a4preproc', type=('build', 'run'))
depends_on('r-biobase', type=('build', 'run'), when='@1.38.0:')
depends_on('r-rocr', type=('build', 'run'))
depends_on('r-pamr', type=('build', 'run'))
depends_on('r-glmnet', type=('build', 'run'))
depends_on('r-varselrf', type=('build', 'run'))
depends_on('r-mlinterfaces', type=('build', 'run'), when='@:1.32.0')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-multiqc/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 PyMultiqc(PythonPackage):
"""MultiQC is a tool to aggregate bioinformatics results across many
samples into a single report. It is written in Python and contains modules
for a large number of common bioinformatics tools."""
homepage = "https://multiqc.info"
pypi = "multiqc/multiqc-1.0.tar.gz"
version('1.7', sha256='02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68')
version('1.5', sha256='fe0ffd2b0d1067365ba4e54ae8991f2f779c7c684b037549b617020ea883310a')
version('1.3', sha256='cde17845680131e16521ace04235bb9496c78c44cdc7b5a0fb6fd93f4ad7a13b')
version('1.0', sha256='1a49331a3d3f2e591a6e9902bc99b16e9205731f0cd2d6eaeee0da3d0f0664c9')
depends_on('python@2.7:')
depends_on('py-setuptools', type='build')
depends_on('py-click', type=('build', 'run'))
depends_on('py-jinja2@2.9:', type=('build', 'run'))
depends_on('py-lzstring', type=('build', 'run'))
depends_on('py-future@0.14.1:', type=('build', 'run'))
depends_on('py-spectra@0.0.10:', type=('build', 'run'))
depends_on('py-matplotlib@2.0.0:2.9.9', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-simplejson', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'), when='@1.5:')
depends_on('py-enum34', type=('build', 'run'), when='@1.4:1.5 ^python@:3.3')
depends_on('py-enum34', type=('build', 'run'), when='@1.3')
depends_on('py-markdown', type=('build', 'run'), when='@1.5:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/which/package.py
|
<filename>var/spack/repos/builtin/packages/which/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 Which(AutotoolsPackage):
"""GNU which - is a utility that is used to find which executable (or
alias or shell function) is executed when entered on the shell prompt."""
homepage = "https://savannah.gnu.org/projects/which/"
url = "https://ftp.gnu.org/gnu/which/which-2.21.tar.gz"
version('2.21', sha256='f4a245b94124b377d8b49646bf421f9155d36aa7614b6ebf83705d3ffc76eaad')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-pmcmrplus/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 RPmcmrplus(RPackage):
"""Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended.
For one-way layout experiments the one-way ANOVA can be performed as an
omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test,
Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally
distributed residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test,
Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for
normally distributed residuals and heterogeneous variances are provided.
Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one
tests is provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and
all-pairs tests (Nemenyi test, Dunn test, Conover test,
Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test,
Dunn test, U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra
test, Spearman test) are included. In addition, a Friedman-test for
one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack
test for unbalanced CRBD is provided with consequent all-pairs tests
(Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and
many-to-one tests (Nemenyi test, Demsar test, Exact test). A trend can be
tested with Pages's test. Durbin's test for a two-way balanced incomplete
block design (BIBD) is given in this package as well as Gore's test for
CRBD with multiple observations per cell is given. Outlier tests, Mandel's
k- and h statistic as well as functions for Type I error and Power analysis
as well as generic summary, print and plot methods are provided."""
cran = "PMCMRplus"
version('1.9.3', sha256='76baba60f57343fa5bb6f6d2ea27aab77178e02b0d2f9d5d74abde7d18994f03')
depends_on('r@3.5.0:', type=('build', 'run'))
depends_on('r-mvtnorm@1.0:', type=('build', 'run'))
depends_on('r-multcompview', type=('build', 'run'))
depends_on('r-gmp', type=('build', 'run'))
depends_on('r-rmpfr', type=('build', 'run'))
depends_on('r-suppdists', type=('build', 'run'))
depends_on('r-ksamples@1.2.7:', type=('build', 'run'))
depends_on('r-bwstest@0.2.1:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('gmp@4.2.3:')
depends_on('mpfr@3.0.0:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libqrencode/package.py
|
<filename>var/spack/repos/builtin/packages/libqrencode/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 Libqrencode(AutotoolsPackage):
"""libqrencode - a fast and compact QR Code encoding library."""
homepage = "https://fukuchi.org/works/qrencode/"
url = "https://github.com/fukuchi/libqrencode/archive/v4.1.1.tar.gz"
git = "https://github.com/fukuchi/libqrencode.git"
maintainers = ['cessenat']
version('master', branch='master')
version('4.1.1', sha256='5385bc1b8c2f20f3b91d258bf8ccc8cf62023935df2d2676b5b67049f31a049c')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
# We assume a reasonably recent libtool is necessary
depends_on('libtool@2.4.2:', type='build')
depends_on('m4', type='build')
depends_on('pkgconfig', type='build')
# https://fukuchi.org/works/qrencode/ requires libpng-dev
depends_on('libpng@1.2.0:', type='link')
def autoreconf(self, spec, prefix):
# We had to call for autoreconf as well:
# https://stackoverflow.com/questions/3096989/libtool-version-mismatch-error
# There appears $LIBTOOLIZE --force --automake --copy is not necessary
args = [
'autoreconf --force --install',
]
with open('autogen.sh', 'a') as fh:
fh.write('\n'.join(args))
# https://fukuchi.org/works/qrencode/
# If there is no "configure" script in the source code directory,
# run "autogen.sh" at first to generate it - this is mandatory if
# you downloaded the source from GitHub
Executable('./autogen.sh')()
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ggally/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 RGgally(RPackage):
"""Extension to 'ggplot2'.
The R package 'ggplot2' is a plotting system based on the grammar of
graphics. 'GGally' extends 'ggplot2' by adding several functions to reduce
the complexity of combining geometric objects with transformed data. Some
of these functions include a pairwise plot matrix, a two group pairwise
plot matrix, a parallel coordinates plot, a survival plot, and several
functions to plot networks."""
cran = "GGally"
version('2.1.2', sha256='30352f36bf061bc98bdd5fa373ea0f23d007040bd908c7c018c8e627e0fb28e5')
version('2.1.0', sha256='7ffb86b8a4e79543cf7e6bb1e3684d738ecd8e0ba89e8ef38991898b18dd6c53')
version('1.4.0', sha256='9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe')
version('1.3.2', sha256='f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
depends_on('r-ggplot2@3.3.0:', type=('build', 'run'), when='@2.1.0:')
depends_on('r-ggplot2@3.3.4:', type=('build', 'run'), when='@2.1.2:')
depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@2.1.0:')
depends_on('r-forcats', type=('build', 'run'), when='@2.1.0:')
depends_on('r-gtable@0.2.0:', type=('build', 'run'))
depends_on('r-lifecycle', type=('build', 'run'), when='@2.1.0:')
depends_on('r-plyr@1.8.3:', type=('build', 'run'))
depends_on('r-progress', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-reshape@0.8.5:', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'), when='@1.4.0:')
depends_on('r-scales@1.1.0:', type=('build', 'run'), when='@2.1.0:')
depends_on('r-tidyr', type=('build', 'run'), when='@2.1.0:')
depends_on('openssl', when='@1.4.0:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/openfdtd/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 Openfdtd(MakefilePackage):
"""OpenFDTD is general purpose FDTD simulator applicable to a wide range
of applications. The FDTD method (Finite Difference Time Domain method)
is a method for numerically calculating the Maxwell equation, which is
the basic equation of the electromagnetic field,
by the difference method."""
homepage = "http://www.e-em.co.jp/OpenFDTD/"
url = "http://www.e-em.co.jp/OpenFDTD/OpenFDTD.zip"
version('2.7.3', sha256='22171d1dd74b4e48299b0d0c69ca933aac89d4eb77c59f579af35861eaca0faa')
version('2.7.1', sha256='3fb5fbeca3dc63243a6dc116d0f3ce3d1a854b4813f3928812ae99e07575ab1a')
version('2.6.3', sha256='1551cce7f96c1c53ad5d5e676bce2b26fd1593dd5f492a801e976a8a65a42a00')
version('2.6.0', sha256='92f7b92dc55ff6d8fc8c31eda77ca10fe25a5f54b002f2523a3d67f485d77e9f')
version('2.3.0', sha256='10ac70f2ed7160da87dd9222a5a17ca7b72365ee886235359afc48c4fb7b4be4')
variant('mpi', default=False, description='Build with MPI Support')
depends_on('mpi', when='+mpi')
def url_for_version(self, version):
url = self.url
if version < Version('2.7.3'):
url = 'http://www.e-em.co.jp/OpenFDTD/old/OpenFDTD_{0}.zip'
return url.format(version.joined)
def edit(self, spec, prefix):
makefiles = [join_path('src', 'Makefile_gcc')]
if spec.satisfies('+mpi'):
makefiles.append(join_path('mpi', 'Makefile_gcc'))
for makefile in makefiles:
m = FileFilter(makefile)
m.filter('gcc', spack_cc)
m.filter('-fopenmp', self.compiler.openmp_flag)
if spec.satisfies('+mpi'):
m.filter('mpicc', spec['mpi'].mpicc)
if spec.satisfies('%fj'):
m.filter('-Ofast', '-Kfast,ocl -D_VECTOR')
m.filter('-O2', '-Kfast,ocl -D_VECTOR')
# Openfdtd has "Makefile" and "Makefile_gcc".
# "Makefile" is used only in Windows development environment.
# The build in Windows development environment is currently unsupported.
def build(self, spec, prefix):
with working_dir('src'):
make('-f', 'Makefile_gcc')
# To make an executable file for mpi needs object files
# which are made for an executable file not for mpi.
# Therefore, the build in the "src" directory is necessary
# for to make an executable file for mpi.
if '+mpi' in self.spec:
with working_dir('mpi'):
make('-f', 'Makefile_gcc')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('ofd', prefix.bin)
if '+mpi' in self.spec:
install('ofd_mpi', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-biocparallel/package.py
|
<filename>var/spack/repos/builtin/packages/r-biocparallel/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 RBiocparallel(RPackage):
"""Bioconductor facilities for parallel evaluation.
This package provides modified versions and novel implementation of
functions for parallel evaluation, tailored to use with Bioconductor
objects."""
bioc = "BiocParallel"
version('1.28.3', commit='2f9d88ad83659939e7911d49c2d24d2cd599c7cc')
version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f')
version('1.18.1', commit='<PASSWORD>')
version('1.16.6', commit='<KEY>')
version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299')
version('1.12.0', commit='<PASSWORD>')
version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.28.3:')
depends_on('r-futile-logger', type=('build', 'run'))
depends_on('r-snow', type=('build', 'run'))
depends_on('r-bh', type=('build', 'run'), when='@1.12.0:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-lavaan/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 RLavaan(RPackage):
"""Latent Variable Analysis.
Fit a variety of latent variable models, including confirmatory factor
analysis, structural equation modeling and latent growth curve models."""
cran = "lavaan"
version('0.6-10', sha256='4d6944eb6d5743e7a2a2c7b56aec5d5de78585a52789be235839fb9f5f468c37')
version('0.6-9', sha256='d404c4eb40686534f9c05f24f908cd954041f66d1072caea4a3adfa83a5f108a')
version('0.6-8', sha256='40e204909100b7338619ae23cd87e0a4058e581c286da2327f36dbb3834b84a2')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-mnormt', type=('build', 'run'))
depends_on('r-pbivnorm', type=('build', 'run'))
depends_on('r-numderiv', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-caracas/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/r-caracas/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 RCaracas(RPackage):
"""Computer Algebra.
Computer algebra via the 'SymPy' library (<https://www.sympy.org/>). This
makes it possible to solve equations symbolically, find symbolic integrals,
symbolic sums and other important quantities."""
cran = "caracas"
version('1.1.1', sha256='e14487c9492417cf5c7d7373c37dbb4fea4d91180a1a03154e51eaa7878b2769')
version('1.0.1', sha256='2482dd7b77791243b8174cb41b80b735c3ebd7db837bbf991127514f492af594')
version('1.0.0', sha256='0da6f1d94d1dacb1c11a3635bdff8f7cd8f84373deffa7126636d0876d48e42b')
depends_on('r@3.0:', type=('build', 'run'))
depends_on('r-reticulate@1.14:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'), when='@1.1.1:')
depends_on('python@3.6:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/mlhka/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 Mlhka(Package):
"""A maximum likelihood ratio test of natural selection, using polymorphism
and divergence data."""
homepage = "https://wright.eeb.utoronto.ca"
git = "https://github.com/rossibarra/MLHKA.git"
version('2.1', commit='<PASSWORD>')
def install(self, spec, prefix):
cxx = which('c++')
cxx('MLHKA_version{0}.cpp'.format(self.version), '-o', 'MLHKA')
mkdirp(prefix.bin)
install('MLHKA', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/bbcp/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 Bbcp(Package):
"""Securely and quickly copy data from source to target"""
homepage = "https://www.slac.stanford.edu/~abh/bbcp/"
git = "https://www.slac.stanford.edu/~abh/bbcp/bbcp.git"
version('master', branch='master')
depends_on('zlib')
depends_on('openssl')
depends_on('libnsl')
def install(self, spec, prefix):
cd("src")
make()
# BBCP wants to build the executable in a directory whose name depends
# on the system type
makesname = Executable("../MakeSname")
bbcp_executable_path = "../bin/%s/bbcp" % makesname(
output=str).rstrip("\n")
destination_path = "%s/bin/" % prefix
mkdirp(destination_path)
install(bbcp_executable_path, destination_path)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/sowing/package.py
|
<filename>var/spack/repos/builtin/packages/sowing/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 Sowing(AutotoolsPackage):
"""Sowing generates Fortran interfaces and documentation for PETSc
and MPICH.
"""
homepage = "https://www.mcs.anl.gov/petsc/index.html"
url = "https://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz"
version('1.1.26-p1', sha256='fa0bd07295e5d768f2c33c8ab32205cc6411d42cb40bde0700fb57f9ee31c3d9')
version('1.1.25-p1', sha256='c3a5bb170fffeeb1405ec4c3a048744a528d2bef24de29b6ac5e970cfeaddab5')
version('1.1.23-p1', sha256='3e36f59e06fccbbf7b78d185c5654edaf70cf76f1c584bcbf08c39d7f29125e8')
def build(self, spec, prefix):
make('ALL', parallel=False)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-installer/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 PyInstaller(PythonPackage):
"""A library for installing Python wheels."""
homepage = "https://github.com/pradyunsg/installer"
pypi = "installer/installer-0.4.0.tar.gz"
version('0.4.0', sha256='17d7ca174039fbd85f268e16042e3132ebb03d91e1bbe0f63b9ec6b40619414a')
depends_on('python@2.7,3.5:', type=('build', 'run'))
depends_on('py-flit-core@2', type='build')
depends_on('py-configparser@3.5:', when='^python@:2', type=('build', 'run'))
depends_on('py-importlib-resources', when='^python@:3.6', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/operating_systems/cray_backend.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
import re
import llnl.util.tty as tty
import spack.error
import spack.version
from spack.util.module_cmd import module
from .linux_distro import LinuxDistro
#: Possible locations of the Cray CLE release file,
#: which we look at to get the CNL OS version.
_cle_release_file = '/etc/opt/cray/release/cle-release'
_clerelease_file = '/etc/opt/cray/release/clerelease'
def read_cle_release_file():
"""Read the CLE release file and return a dict with its attributes.
This file is present on newer versions of Cray.
The release file looks something like this::
RELEASE=6.0.UP07
BUILD=6.0.7424
...
The dictionary we produce looks like this::
{
"RELEASE": "6.0.UP07",
"BUILD": "6.0.7424",
...
}
Returns:
dict: dictionary of release attributes
"""
with open(_cle_release_file) as release_file:
result = {}
for line in release_file:
# use partition instead of split() to ensure we only split on
# the first '=' in the line.
key, _, value = line.partition('=')
result[key] = value.strip()
return result
def read_clerelease_file():
"""Read the CLE release file and return the Cray OS version.
This file is present on older versions of Cray.
The release file looks something like this::
5.2.UP04
Returns:
str: the Cray OS version
"""
with open(_clerelease_file) as release_file:
for line in release_file:
return line.strip()
class CrayBackend(LinuxDistro):
"""Compute Node Linux (CNL) is the operating system used for the Cray XC
series super computers. It is a very stripped down version of GNU/Linux.
Any compilers found through this operating system will be used with
modules. If updated, user must make sure that version and name are
updated to indicate that OS has been upgraded (or downgraded)
"""
def __init__(self):
name = 'cnl'
version = self._detect_crayos_version()
if version:
# If we found a CrayOS version, we do not want the information
# from LinuxDistro. In order to skip the logic from
# external.distro.linux_distribution, while still calling __init__
# methods further up the MRO, we skip LinuxDistro in the MRO and
# call the OperatingSystem superclass __init__ method
super(LinuxDistro, self).__init__(name, version)
else:
super(CrayBackend, self).__init__()
self.modulecmd = module
def __str__(self):
return self.name + str(self.version)
@classmethod
def _detect_crayos_version(cls):
if os.path.isfile(_cle_release_file):
release_attrs = read_cle_release_file()
if 'RELEASE' not in release_attrs:
# This Cray system uses a base OS not CLE/CNL
return None
v = spack.version.Version(release_attrs['RELEASE'])
return v[0]
elif os.path.isfile(_clerelease_file):
v = read_clerelease_file()
return spack.version.Version(v)[0]
else:
# Not all Cray systems run CNL on the backend.
# Systems running in what Cray calls "cluster" mode run other
# linux OSs under the Cray PE.
# So if we don't detect any Cray OS version on the system,
# we return None. We can't ever be sure we will get a Cray OS
# version.
# Returning None allows the calling code to test for the value
# being "True-ish" rather than requiring a try/except block.
return None
def arguments_to_detect_version_fn(self, paths):
import spack.compilers
command_arguments = []
for compiler_name in spack.compilers.supported_compilers():
cmp_cls = spack.compilers.class_for_compiler_name(compiler_name)
# If the compiler doesn't have a corresponding
# Programming Environment, skip to the next
if cmp_cls.PrgEnv is None:
continue
if cmp_cls.PrgEnv_compiler is None:
tty.die('Must supply PrgEnv_compiler with PrgEnv')
compiler_id = spack.compilers.CompilerID(self, compiler_name, None)
detect_version_args = spack.compilers.DetectVersionArgs(
id=compiler_id, variation=(None, None),
language='cc', path='cc'
)
command_arguments.append(detect_version_args)
return command_arguments
def detect_version(self, detect_version_args):
import spack.compilers
modulecmd = self.modulecmd
compiler_name = detect_version_args.id.compiler_name
compiler_cls = spack.compilers.class_for_compiler_name(compiler_name)
output = modulecmd('avail', compiler_cls.PrgEnv_compiler)
version_regex = r'({0})/([\d\.]+[\d]-?[\w]*)'.format(
compiler_cls.PrgEnv_compiler
)
matches = re.findall(version_regex, output)
version = tuple(version for _, version in matches
if 'classic' not in version)
compiler_id = detect_version_args.id
value = detect_version_args._replace(
id=compiler_id._replace(version=version)
)
return value, None
def make_compilers(self, compiler_id, paths):
import spack.spec
name = compiler_id.compiler_name
cmp_cls = spack.compilers.class_for_compiler_name(name)
compilers = []
for v in compiler_id.version:
comp = cmp_cls(
spack.spec.CompilerSpec(name + '@' + v),
self, "any",
['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name + '/' + v])
compilers.append(comp)
return compilers
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-truncnorm/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 RTruncnorm(RPackage):
"""Truncated Normal Distribution.
Density, probability, quantile and random number generation functions for
the truncated normal distribution."""
cran = "truncnorm"
version('1.0-8', sha256='49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e')
depends_on('r@3.4.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/qca/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 Qca(CMakePackage):
"""Taking a hint from the similarly-named Java Cryptography Architecture,
QCA aims to provide a straightforward and cross-platform crypto API,
using Qt datatypes and conventions. QCA separates the API from the
implementation, using plugins known as Providers. The advantage of
this model is to allow applications to avoid linking to or explicitly
depending on any particular cryptographic library. This allows one to
easily change or upgrade crypto implementations without even needing
to recompile the application!
QCA should work everywhere Qt does, including Windows/Unix/MacOSX. """
homepage = "https://userbase.kde.org/QCA"
url = "https://github.com/KDE/qca/archive/v2.1.3.tar.gz"
version('2.3.0', sha256='39aa18f0985d82949f4dccce04af3eb8d4b6b64e0c71785786738d38d8183b0a')
version('2.2.90', sha256='074ac753b51a6fa15503be9418f7430effe368fd31dc41567942d832e539b17e')
version('2.2.1', sha256='c67fc0fa8ae6cb3d0ba0fbd8fca8ee8e4c5061b99f1fd685fd7d9800cef17f6b')
version('2.1.3', sha256='a5135ffb0250a40e9c361eb10cd3fe28293f0cf4e5c69d3761481eafd7968067')
depends_on('qt@4.2:')
depends_on('qt@:5.10.0', when='@2.1.3')
def cmake_args(self):
args = []
args.append('-DCMAKE_CXX_STANDARD=11')
if self.spec['qt'].version.up_to(1) == Version(4):
args.append('-DQT4_BUILD=ON')
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-tempora/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 PyTempora(PythonPackage):
"""Objects and routines pertaining to date and time (tempora) """
homepage = "https://github.com/jaraco/tempora"
pypi = "tempora/tempora-1.14.1.tar.gz"
version('1.14.1', sha256='cb60b1d2b1664104e307f8e5269d7f4acdb077c82e35cd57246ae14a3427d2d6')
depends_on('py-setuptools', type='build')
depends_on('py-setuptools-scm@1.15.0:', type='build')
depends_on('py-six', type=('build', 'run'))
depends_on('py-pytz', type=('build', 'run'))
depends_on('py-jaraco-functools@1.20:', type=('build', 'run'))
depends_on('python@2.7:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gromacs-swaxs/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.pkg.builtin.gromacs import Gromacs
class GromacsSwaxs(Gromacs):
"""Modified Gromacs for small-angle scattering calculations (SAXS/WAXS/SANS)"""
homepage = 'https://biophys.uni-saarland.de/swaxs.html'
url = 'https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2019.swaxs-0.1/gromacs-swaxs-release-2019.swaxs-0.1.tar.bz2'
git = 'https://gitlab.com/cbjh/gromacs-swaxs.git'
maintainers = ['w8jcik']
version('2021.4-0.2', sha256='ea0dbe868d20e05c8fca337e0dddc16116a83fa7a6ac3a924942e9d00952ed62',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2021.swaxs-0.2/gromacs-swaxs-release-2021.swaxs-0.2.tar.bz2')
version('2021.4-0.1', sha256='eda1c8a7aae6001ef40480addf9fff9cdccc7e2b80480e36d069f50d6f2be26e', deprecated=True,
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2021.swaxs-0.1/gromacs-swaxs-release-2021.swaxs-0.1.tar.bz2')
version('2020.6-0.2', sha256='c22a7c6a0ee54eee1b3e224530f65e6f976a7aca5dc0f5ea22b2935a5a4357e9',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2020.swaxs-0.2/gromacs-swaxs-release-2020.swaxs-0.2.tar.bz2')
version('2020.6-0.1', sha256='3d8360a3cc9144772786bddaa11e3dbc37d6a466b99f3314bf3928261c2fddcf', deprecated=True,
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2020.swaxs-0.1/gromacs-swaxs-release-2020.swaxs-0.1.tar.bz2')
version('2019.6-0.3', sha256='1cf81592813333954bb1051321543f211d81f120a821a0c9386081e4cd367e84',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2019.swaxs-0.3/gromacs-swaxs-release-2019.swaxs-0.3.tar.bz2')
version('2019.6-0.2', sha256='a45eeee3983a4443d3a40ea417770f3abd93f43eb80e021fd9d6830e414565cb', deprecated=True,
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2019.swaxs-0.2/gromacs-swaxs-release-2019.swaxs-0.2.tar.bz2')
version('2019.6-0.1', sha256='91da09eed80646d6a1c500be78891bef22623a19795a9bc89adf9f2ec4f85635',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2019.swaxs-0.1/gromacs-swaxs-release-2019.swaxs-0.1.tar.bz2')
version('2018.8-0.4', sha256='465bbd234b6805209cf39c6bfa4f482c367b947742bb2b9a3d535d362f254dcb',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2018.swaxs-0.4/gromacs-swaxs-release-2018.swaxs-0.4.tar.bz2')
version('2018.8-0.3', sha256='5e94d636fda28e81ff1f3cff2c9f6e7f458bf496f4d1ed7bc10e911bd98b303c', deprecated=True,
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2018.swaxs-0.3/gromacs-swaxs-release-2018.swaxs-0.3.tar.bz2')
version('2018.8-0.2', sha256='f8bf0d363334a9117a2a8deb690dadaa826b73b57a761949c7846a13b84b5af5',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2018.swaxs-0.2/gromacs-swaxs-release-2018.swaxs-0.2.tar.bz2')
version('2018.8-0.1', sha256='478f45286dfedb8f01c2d5bf0773a391c2de2baf85283ef683e911bc43e24675',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2018.swaxs-0.1/gromacs-swaxs-release-2018.swaxs-0.1.tar.bz2')
version('2016.6-0.1', sha256='11e8ae6b3141f356bae72b595737a1f253b878d313169703ba33a69ded01a04e',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-2016.swaxs-0.1/gromacs-swaxs-release-2016.swaxs-0.1.tar.bz2')
version('5.1.5-0.3', sha256='a9e8382eec3cc0d943e1869f13945ea4a971a95a70eb314c1f26a17fa7d03792',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-5-1.swaxs-0.3/gromacs-swaxs-release-5-1.swaxs-0.3.tar.bz2')
version('5.0.7-0.5', sha256='7f7f69726472a641a5443f1993a6e1fb8cfa9c74aeaf46e8c5d1db37005ece79',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-5-0.swaxs-0.5/gromacs-swaxs-release-5-0.swaxs-0.5.tar.bz2')
version('4.6.7-0.8', sha256='1cfa34fe9ff543b665cd556f3395a9aa67f916110ba70255c97389eafe8315a2',
url='https://gitlab.com/cbjh/gromacs-swaxs/-/archive/release-4-6.swaxs-0.8/gromacs-swaxs-release-4-6.swaxs-0.8.tar.bz2')
conflicts('+plumed')
conflicts('+opencl')
conflicts('+sycl')
def remove_parent_versions(self):
"""
By inheriting GROMACS package we also inherit versions.
They are not valid, so we are removing them.
"""
for version_key in Gromacs.versions.keys():
if version_key in self.versions:
del self.versions[version_key]
def __init__(self, spec):
super(GromacsSwaxs, self).__init__(spec)
self.remove_parent_versions()
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/coreutils/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 Coreutils(AutotoolsPackage, GNUMirrorPackage):
"""The GNU Core Utilities are the basic file, shell and text
manipulation utilities of the GNU operating system. These are
the core utilities which are expected to exist on every
operating system.
"""
homepage = 'https://www.gnu.org/software/coreutils/'
gnu_mirror_path = 'coreutils/coreutils-8.26.tar.xz'
tags = ['core-packages']
version('8.32', sha256='4458d8de7849df44ccab15e16b1548b285224dbba5f08fac070c1c0e0bcc4cfa')
version('8.31', sha256='ff7a9c918edce6b4f4b2725e3f9b37b0c4d193531cac49a48b56c4d0d3a9e9fd')
version('8.30', sha256='e831b3a86091496cdba720411f9748de81507798f6130adeaef872d206e1b057')
version('8.29', sha256='92d0fa1c311cacefa89853bdb53c62f4110cdfda3820346b59cbd098f40f955e')
version('8.26', sha256='155e94d748f8e2bc327c66e0cbebdb8d6ab265d2f37c3c928f7bf6c3beba9a8e')
version('8.23', sha256='ec43ca5bcfc62242accb46b7f121f6b684ee21ecd7d075059bf650ff9e37b82d')
variant("gprefix", default=False, description="prefix commands with 'g', to avoid conflicts with OS utilities")
patch('https://src.fedoraproject.org/rpms/coreutils/raw/6b50cb9f/f/coreutils-8.32-ls-removed-dir.patch',
when='@8.32 target=aarch64:',
sha256='5878894375a8fda98150783430b30c0b7104899dc5522034ebcaf8c961183b7e')
build_directory = 'spack-build'
def configure_args(self):
spec = self.spec
configure_args = []
if spec.satisfies('platform=darwin'):
if "+gprefix" in self.spec:
configure_args.append('--program-prefix=g')
configure_args.append('--without-gmp')
configure_args.append('gl_cv_func_ftello_works=yes')
return configure_args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-plogr/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 RPlogr(RPackage):
"""The 'plog' C++ Logging Library.
A simple header-only logging library for C++. Add 'LinkingTo: plogr' to
'DESCRIPTION', and '#include <plogr.h>' in your C++ modules to use it."""
cran = "plogr"
version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29')
version('0.1-1', sha256='22755c93c76c26252841f43195df31681ea865e91aa89726010bd1b9288ef48f')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/hdf5-vol-async/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 Hdf5VolAsync(CMakePackage):
"""This package enables asynchronous IO in HDF5."""
homepage = "https://sdm.lbl.gov/"
git = "https://github.com/hpc-io/vol-async"
maintainers = ['hyoklee']
version('v1.0')
depends_on('argobots@main')
depends_on('hdf5@develop-1.13+mpi+threadsafe')
def cmake_args(self):
"""Populate cmake arguments for HDF5 VOL."""
args = [
self.define('BUILD_SHARED_LIBS:BOOL', True),
self.define('BUILD_TESTING:BOOL=ON', self.run_tests)
]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-uproot3/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 PyUproot3(PythonPackage):
"""ROOT I/O in pure Python and Numpy.
uproot is a reader and a writer of the ROOT file format using only Python
and Numpy. Unlike the standard C++ ROOT implementation, uproot is only an
I/O library, primarily intended to stream data into machine learning
libraries in Python. Unlike PyROOT and root_numpy, uproot does not depend
on C++ ROOT. Instead, it uses Numpy to cast blocks of data from the ROOT
file as Numpy arrays."""
homepage = "https://github.com/scikit-hep/uproot3"
pypi = "uproot3/uproot3-3.14.4.tar.gz"
version('3.14.4', sha256='4396746ba5ef9071bb0a9da53294e4613a7f4548218940f86496e79d682d20eb')
depends_on('python@2.7:2.9,3.5:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-pytest-runner', type='build')
depends_on('py-numpy@1.13.1:', type=('build', 'run'))
depends_on('py-awkward0', type=('build', 'run'))
depends_on('py-uproot3-methods', type=('build', 'run'))
depends_on('py-cachetools', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-datalad-container/package.py
|
<filename>var/spack/repos/builtin/packages/py-datalad-container/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 PyDataladContainer(PythonPackage):
"""DataLad extension package for working with containerized environments"""
homepage = "https://github.com/datalad/datalad-container/"
pypi = "datalad_container/datalad_container-1.1.5.tar.gz"
version('1.1.5', sha256='f6099a0124ddb2f021531d5020a583eca3cd9243e4e609b0f58e3f72e779b601')
depends_on('py-setuptools', type='build')
depends_on('py-datalad@0.13:', type='run')
depends_on('py-requests@1.2:', type='run')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-futile-options/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 RFutileOptions(RPackage):
"""Futile Options Management.
A scoped options management framework."""
cran = "futile.options"
version('1.0.1', sha256='7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570')
version('1.0.0', sha256='ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2')
depends_on('r@2.8.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-genetics/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 RGenetics(RPackage):
"""Population Genetics.
Classes and methods for handling genetic data. Includes classes to
represent genotypes and haplotypes at single markers up to multiple markers
on multiple chromosomes. Function include allele frequencies, flagging
homo/heterozygotes, flagging carriers of certain alleles, estimating and
testing for Hardy-Weinberg disequilibrium, estimating and testing for
linkage disequilibrium, ..."""
cran = "genetics"
version('1.3.8.1.3', sha256='fef2c95f6a57f32b3cf4acf003480439462bb28297c501c617de307bfeee9252')
version('1.3.8.1.2', sha256='30cb67de2e901578fd802deb7fbfea6c93024c9fb6ea66cad88430a3a2a51eec')
depends_on('r-combinat', type=('build', 'run'))
depends_on('r-gdata', type=('build', 'run'))
depends_on('r-gtools', type=('build', 'run'))
depends_on('r-mass', type=('build', 'run'))
depends_on('r-mvtnorm', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/tag.py
|
<filename>lib/spack/spack/tag.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)
"""Classes and functions to manage package tags"""
import collections
import copy
import sys
if sys.version_info >= (3, 5):
from collections.abc import Mapping # novm
else:
from collections import Mapping
import spack.error
import spack.util.spack_json as sjson
def _get_installed_package_names():
"""Returns names of packages installed in the active environment."""
specs = spack.environment.installed_specs()
return [spec.name for spec in specs]
def packages_with_tags(tags, installed, skip_empty):
"""
Returns a dict, indexed by tag, containing lists of names of packages
containing the tag or, if no tags, for all available tags.
Arguments:
tags (list or None): list of tags of interest or None for all
installed (bool): True if want names of packages that are installed;
otherwise, False if want all packages with the tag
skip_empty (bool): True if exclude tags with no associated packages;
otherwise, False if want entries for all tags even when no such
tagged packages
"""
tag_pkgs = collections.defaultdict(lambda: list)
spec_names = _get_installed_package_names() if installed else []
keys = spack.repo.path.tag_index if tags is None else tags
for tag in keys:
packages = [name for name in spack.repo.path.tag_index[tag] if
not installed or name in spec_names]
if packages or not skip_empty:
tag_pkgs[tag] = packages
return tag_pkgs
class TagIndex(Mapping):
"""Maps tags to list of packages."""
def __init__(self):
self._tag_dict = collections.defaultdict(list)
@property
def tags(self):
return self._tag_dict
def to_json(self, stream):
sjson.dump({'tags': self._tag_dict}, stream)
@staticmethod
def from_json(stream):
d = sjson.load(stream)
if not isinstance(d, dict):
raise TagIndexError("TagIndex data was not a dict.")
if 'tags' not in d:
raise TagIndexError("TagIndex data does not start with 'tags'")
r = TagIndex()
for tag, packages in d['tags'].items():
r[tag].extend(packages)
return r
def __getitem__(self, item):
return self._tag_dict[item]
def __iter__(self):
return iter(self._tag_dict)
def __len__(self):
return len(self._tag_dict)
def copy(self):
"""Return a deep copy of this index."""
clone = TagIndex()
clone._tag_dict = copy.deepcopy(self._tag_dict)
return clone
def get_packages(self, tag):
"""Returns all packages associated with the tag."""
return self.tags[tag] if tag in self.tags else []
def merge(self, other):
"""Merge another tag index into this one.
Args:
other (TagIndex): tag index to be merged
"""
other = other.copy() # defensive copy.
for tag in other.tags:
if tag not in self.tags:
self.tags[tag] = other.tags[tag]
continue
spkgs, opkgs = self.tags[tag], other.tags[tag]
self.tags[tag] = sorted(list(set(spkgs + opkgs)))
def update_package(self, pkg_name):
"""Updates a package in the tag index.
Args:
pkg_name (str): name of the package to be removed from the index
"""
package = spack.repo.path.get(pkg_name)
# Remove the package from the list of packages, if present
for pkg_list in self._tag_dict.values():
if pkg_name in pkg_list:
pkg_list.remove(pkg_name)
# Add it again under the appropriate tags
for tag in getattr(package, 'tags', []):
tag = tag.lower()
self._tag_dict[tag].append(package.name)
class TagIndexError(spack.error.SpackError):
"""Raised when there is a problem with a TagIndex."""
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gitcreds/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 RGitcreds(RPackage):
"""Query 'git' Credentials from 'R'.
Query, set, delete credentials from the 'git' credential store. Manage
'GitHub' tokens and other 'git' credentials. This package is to be used by
other packages that need to authenticate to 'GitHub' and/or other 'git'
repositories."""
cran = "gitcreds"
version('0.1.1', sha256='b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea')
depends_on('git', type='run')
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/nosource-install/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 NosourceInstall(BundlePackage):
"""Simple bundle package with one dependency and metadata 'install'."""
homepage = "http://www.example.com"
version('2.0')
version('1.0')
depends_on('dependency-install')
# The install phase must be specified.
phases = ['install']
# The install method must also be present.
def install(self, spec, prefix):
touch(join_path(self.prefix, 'install.txt'))
@run_after('install')
def post_install(self):
touch(join_path(self.prefix, 'post-install.txt'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/scorpio/package.py
|
<filename>var/spack/repos/builtin/packages/scorpio/package.py
# Copyright 2013-2021 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 Scorpio(CMakePackage):
"""SCORPIO Scalable Parallel I/O module for Environmental Management Applications
This library provides software that read/write data sets from/to parallel file
systems in an efficient and scalable manner
"""
homepage = "https://gitlab.com/truchas/tpl-forks/scorpio"
git = "https://gitlab.com/truchas/tpl-forks/scorpio.git"
maintainers = ['pbrady']
version('develop', branch='truchas')
version('2021-12-10',
commit='b802f16877a6562ccdbeca8887910d3bd3e25cbb',
preferred=True)
depends_on('cmake@3.16:', type='build')
depends_on('mpi')
depends_on('hdf5@1.10.6: +hl +mpi')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-fastmatrix/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 RFastmatrix(RPackage):
"""Fast Computation of some Matrices Useful in Statistics.
Small set of functions to fast computation of some matrices and operations
useful in statistics and econometrics. Currently, there are functions for
efficient computation of duplication, commutation and symmetrizer matrices
with minimal storage requirements. Some commonly used matrix decompositions
(LU and LDL), basic matrix operations (for instance, Hadamard, Kronecker
products and the Sherman-Morrison formula) and iterative solvers for linear
systems are also available. In addition, the package includes a number of
common statistical procedures such as the sweep operator, weighted mean and
covariance matrix using an online algorithm, linear regression (using
Cholesky, QR, SVD, sweep operator and conjugate gradients methods), ridge
regression (with optimal selection of the ridge parameter considering the
GCV procedure), functions to compute the multivariate skewness, kurtosis,
Mahalanobis distance (checking the positive defineteness) and the
Wilson-Hilferty transformation of chi squared variables. Furthermore, the
package provides interfaces to C code callable by another C code from other
R packages."""
cran = "fastmatrix"
version('0.3-8196', sha256='72fae07c627b995a091ccc3e14b2b2167474e3b1f14d723e87252538cf978fb6')
version('0.3', sha256='d92e789454a129db5f6f5b23e0d2245f3d55ff34b167427af265b9a6331e7c21')
depends_on('r@3.5.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gbrd/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/r-gbrd/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 RGbrd(RPackage):
"""Utilities for processing Rd objects and files.
Provides utilities for processing Rd objects and files. Extract argument
descriptions and other parts of the help pages of functions."""
cran = "gbRd"
version('0.4-11', sha256='0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b')
|
player1537-forks/spack
|
lib/spack/spack/util/unparse/__init__.py
|
# Copyright (c) 2014-2021, <NAME> and Spack Project Developers.
#
# SPDX-License-Identifier: Python-2.0
# coding: utf-8
from __future__ import absolute_import
from six.moves import cStringIO
from .unparser import Unparser
__version__ = '1.6.3'
def unparse(tree, py_ver_consistent=False):
v = cStringIO()
unparser = Unparser(py_ver_consistent=py_ver_consistent)
unparser.visit(tree, v)
return v.getvalue().strip() + "\n"
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-watchdog/package.py
|
<gh_stars>1-10
# 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 PyWatchdog(PythonPackage):
"""Python library and shell utilities to monitor filesystem events."""
homepage = "https://github.com/gorakhargosh/watchdog"
url = "https://github.com/gorakhargosh/watchdog/archive/v0.10.3.tar.gz"
version('0.10.3', sha256='f7e5040b483cc9a8618a4e72c11a527b42434a0766ea96dce633e8b44b1369de')
version('0.10.2', sha256='4dba861f5e6960c8063ad68137772ff35f1516ea47d64b53042dabd2d8f8dbdc')
version('0.10.1', sha256='972c6050eb5d275b582c75e6ff71ef562a6c3be6361d6d9b37110e0ba718994d')
version('0.10.0', sha256='39e2966b8c9596e45b463815668989b87c7d205e47c7e6e4a7db9a58354b99ff')
version('0.9.0', sha256='e8a32701dff43a4e671a40acf92f55a8fffd8ca74333b75436d63a94d104faef')
version('0.8.3', sha256='e9a27d0ab121fc86217ab833e778c76880aad4ecdb623796f4b7aee9925394ed')
version('0.8.2', sha256='386e882c8bc7df8a3c4c8803e6fcf2f7cf836c9a8867ff9d91b4af19d262d023')
version('0.8.1', sha256='05e5d8acd5061aff789359cd8f25a85ba4c848a8feded3fc68f9c57f0b181373')
version('0.8.0', sha256='5abac06e63ad8d5b001626a16bfdd1b918637aa8d85cf933e68de2e627b56053')
version('0.7.1', sha256='d795fa85ce9252eeb2294a5182c99013433aeb736cc7a1fc9e14e1e2a1a19690')
depends_on('python@2.7,3.4:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-pyyaml', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/intel-oneapi-inspector/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/intel-oneapi-inspector/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 platform
from spack import *
class IntelOneapiInspector(IntelOneApiPackage):
"""Intel Inspector is a memory and thread checking and debugging tool to increase
the reliability, security, and accuracy of C/C++ and Fortran applications."""
maintainers = ['rscohn2']
homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html'
if platform.system() == 'Linux':
version('2022.0.0',
url='https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/l_inspector_oneapi_p_2022.0.0.56_offline.sh',
sha256='79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741',
expand=False)
version('2021.4.0',
url='https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/l_inspector_oneapi_p_2021.4.0.266_offline.sh',
sha256='c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274',
expand=False)
version('2021.3.0',
url='https://registrationcenter-download.intel.com/akdlm/irc_nas/17946/l_inspector_oneapi_p_2021.3.0.217_offline.sh',
sha256='1371ca74be2a6d4b069cdb3f8f2d6109abbc3261a81f437f0fe5412a7b659b43',
expand=False)
@property
def component_dir(self):
return 'inspector'
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/sqoop/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 Sqoop(MavenPackage):
"""Apache Sqoop is a tool designed for efficiently transferring bulk
data between Apache Hadoop and structured datastores such as relational
databases."""
homepage = "https://sqoop.apache.org/"
url = "https://downloads.apache.org/sqoop/1.99.7/sqoop-1.99.7.tar.gz"
list_url = "https://downloads.apache.org/sqoop/"
list_depth = 1
version('1.99.7', sha256='caca533554235d9e999435be59a13b5ecae514b3c914ca3b54868fca43a3b74a')
depends_on('java@8', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-domc/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 RDomc(RPackage):
"""Foreach Parallel Adaptor for 'parallel'.
Provides a parallel backend for the %dopar% function using the multicore
functionality of the parallel package."""
cran = "doMC"
version('1.3.7', sha256='defab27adc298a6746896d83251f8355d62c01012d51ef96d491875a2e74b54d')
version('1.3.6', sha256='2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2')
version('1.3.4', sha256='76a1092fca59b441e6f89eb7e2fb3a12de807f736a217949c80339f20c958778')
depends_on('r@2.14.0:', type=('build', 'run'))
depends_on('r-foreach@1.2.0:', type=('build', 'run'))
depends_on('r-iterators@1.0.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-gffutils/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 PyGffutils(PythonPackage):
"""GFF and GTF file manipulation and interconversion
gffutils is a Python package for working with and manipulating the GFF and
GTF format files typically used for genomic annotations. Files are loaded
into a sqlite3 database, allowing much more complex manipulation of
hierarchical features (e.g., genes, transcripts, and exons) than is
possible with plain-text methods alone."""
homepage = "https://github.com/daler/gffutils"
pypi = "gffutils/gffutils-0.10.1.tar.gz"
maintainers = ['dorton21']
version('0.10.1', sha256='a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb')
depends_on('py-setuptools', type='build')
depends_on('py-pyfaidx@0.5.5.2:', type=('build', 'run'))
depends_on('py-six@1.12.0:', type=('build', 'run'))
depends_on('py-argh@0.26.2:', type=('build', 'run'))
depends_on('py-argcomplete@1.9.4:', type=('build', 'run'))
depends_on('py-simplejson', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-abadata/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 RAbadata(RPackage):
"""Averaged gene expression in human brain regions from Allen Brain Atlas.
Provides the data for the gene expression enrichment analysis conducted
in the package 'ABAEnrichment'. The package includes three datasets
which are derived from the Allen Brain Atlas: (1) Gene expression data
from Human Brain (adults) averaged across donors, (2) Gene expression
data from the Developing Human Brain pooled into five age categories and
averaged across donors and (3) a developmental effect score based on the
Developing Human Brain expression data. All datasets are restricted to
protein coding genes."""
bioc = "ABAData"
version('1.24.0', commit='<PASSWORD>')
version('1.20.0', commit='<KEY>')
version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd')
version('1.12.0', commit='<KEY>')
version('1.10.0', commit='197edb2c3fc733c9e44dde2b9b86ecedcd2c5e1a')
version('1.8.0', commit='<PASSWORD>')
version('1.6.0', commit='<PASSWORD>')
depends_on('r@3.2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-gcs-oauth2-boto-plugin/package.py
|
<filename>var/spack/repos/builtin/packages/py-gcs-oauth2-boto-plugin/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 PyGcsOauth2BotoPlugin(PythonPackage):
"""Auth plugin allowing use the use of OAuth 2.0 credentials
for Google Cloud Storage in the Boto library."""
homepage = "https://github.com/GoogleCloudPlatform/gcs-oauth2-boto-plugin"
pypi = "gcs-oauth2-boto-plugin/gcs-oauth2-boto-plugin-2.7.tar.gz"
maintainers = ['dorton21']
version('2.7', sha256='c95b011717911a6c40fbd3aa07a8faa0ab57570dee178d7148531327c4c6f93e')
depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-rsa@:4.0', when='^python@:3.4', type=('build', 'run'))
depends_on('py-boto@2.29.1:', type=('build', 'run'))
depends_on('py-google-auth@0.1.0:', type=('build', 'run'))
depends_on('py-httplib2@0.18:', type=('build', 'run'))
depends_on('py-oauth2client@2.2.0:', type=('build', 'run'))
depends_on('py-pyopenssl@0.13:', type=('build', 'run'))
depends_on('py-retry-decorator@1.0.0:', type=('build', 'run'))
depends_on('py-six@1.12.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-meshio/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 PyMeshio(PythonPackage):
"""MeshIO is a Python library to read and write many mesh formats."""
homepage = "https://github.com/nschloe/meshio"
pypi = "meshio/meshio-5.0.0.tar.gz"
version('5.0.1', sha256='e283f40b5fb68fc5c232829c33c086789661438960762b22dc2823571a089a8b')
version('5.0.0', sha256='f6327c06d6171d30e0991d3dcb048751035f9cfac1f19e2444971275fd971188')
version('4.4.6', sha256='be352a0924c9eff99768a6f402b7558dbb280bbf1e7bf43f18cef92db418684f')
depends_on('python@3.7:', when='@5.0.0:', type=('build', 'run'))
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools@42:', type='build')
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-importlib-metadata', when='^python@:3.7', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/cardioid/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 Cardioid(CMakePackage):
"""Cardiac simulation suite."""
homepage = 'https://baasic.llnl.gov/comp-bio/cardioid-code.php'
git = "https://github.com/LLNL/cardioid.git"
maintainers = ['rblake-llnl']
version('develop', branch='master')
version('elecfem', branch='elec-fem')
variant('cuda', default=False,
description='Build with cuda support')
variant('mfem', default=False,
description='Build with mfem support')
depends_on('blas')
depends_on('lapack')
depends_on('mpi')
depends_on('cuda', when="+cuda")
depends_on('mfem+mpi+superlu-dist+lapack', when="+mfem")
depends_on('hypre+cuda', when="+mfem+cuda")
depends_on('cmake@3.1:', type='build')
depends_on('perl', type='build')
def cmake_args(self):
spec = self.spec
args = [
"-DLAPACK_LIB:PATH=" + ";".join(spec['lapack'].libs.libraries),
"-DBLAS_LIB:PATH=" + ";".join(spec['blas'].libs.libraries),
"-DENABLE_OPENMP:BOOL=ON",
"-DENABLE_MPI:BOOL=ON",
"-DENABLE_FIND_MPI:BOOL=OFF",
"-DMPI_C_COMPILER:STRING=" + spec['mpi'].mpicc,
"-DMPI_CXX_COMPILER:STRING=" + spec['mpi'].mpicxx,
"-DCMAKE_C_COMPILER:STRING=" + spec['mpi'].mpicc,
"-DCMAKE_CXX_COMPILER:STRING=" + spec['mpi'].mpicxx,
]
if "+cuda" in self.spec:
args.append("-DENABLE_CUDA:BOOL=ON")
args.append("-DCUDA_TOOLKIT_ROOT:PATH=" + spec['cuda'].prefix)
else:
args.append("-DENABLE_CUDA:BOOL=OFF")
if "+mfem" in self.spec:
args.append("-DMFEM_DIR:PATH=" + spec['mfem'].prefix)
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-broom/package.py
|
<filename>var/spack/repos/builtin/packages/r-broom/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 RBroom(RPackage):
"""Convert Statistical Objects into Tidy Tibbles.
Summarizes key information about statistical objects in tidy tibbles. This
makes it easy to report results, create plots and consistently work with
large numbers of models at once. Broom provides three verbs that each
provide different types of information about a model. tidy() summarizes
information about model components such as coefficients of a regression.
glance() reports information about an entire model, such as goodness of fit
measures like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence measures."""
cran = "broom"
version('0.7.12', sha256='04fac12b2546689603a474fb92a0572f4241ae87b51b21b0808814a489227bd9')
version('0.7.11', sha256='9e3999d2635ac72e8f4c3a81decd50ee5d464c001c155375b5a970a629ba2e19')
version('0.7.10', sha256='129fd5a53abef7f42b7efac6c64ebd71269b136aa648846d640562357927464f')
version('0.7.9', sha256='1d5695f97b378b2b77fb8f64a4a54b72b278913d4adf9d61a7ca4f38a1c7c5fc')
version('0.7.3', sha256='de5650e46ca6884876b63bc401d22bef9eace671147774466406d43324aebc2f')
version('0.5.2', sha256='16af7b446b24bc14461efbda9bea1521cf738c778c5e48fcc7bad45660a4ac62')
version('0.5.1', sha256='da9e6bf7cb8f960b83309cf107743976cc32b54524675f6471982abe3d1aae2e')
version('0.4.2', sha256='9f409413623cf25e7110452e6215353af5114f7044d73af182bd6c10971c5a44')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-backports', type=('build', 'run'), when='@0.5.0:')
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-dplyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-ellipsis', type=('build', 'run'), when='@0.7.3:')
depends_on('r-generics@0.0.2:', type=('build', 'run'), when='@0.5.1:')
depends_on('r-glue', type=('build', 'run'), when='@0.7.3:')
depends_on('r-purrr', type=('build', 'run'), when='@0.5.0:')
depends_on('r-rlang', type=('build', 'run'), when='@0.7.3:')
depends_on('r-stringr', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'), when='@0.5.0:')
depends_on('r-tibble@3.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-tidyr@1.0.0:', type=('build', 'run'), when='@0.7.3:')
depends_on('r-ggplot2', type=('build', 'run'), when='@0.7.10:')
depends_on('r-plyr', type=('build', 'run'), when='@:0.4.2')
depends_on('r-psych', type=('build', 'run'), when='@:0.4.2')
depends_on('r-reshape2', type=('build', 'run'), when='@:0.5.2')
depends_on('r-nlme', type=('build', 'run'), when='@:0.5.2')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-catools/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 RCatools(RPackage):
"""Moving Window Statistics, GIF, Base64, ROC AUC, etc.
Contains several basic utility functions including: moving (rolling,
running) window statistic functions, read/write for GIF and ENVI binary
files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc."""
cran = "caTools"
version('1.18.2', sha256='75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293')
version('1.18.1', sha256='ffeba4ffbeed5d491bf79b1fde3477f413341e412f77316af20439f54447c9f9')
version('1.17.1.2', sha256='69cc542fab5677462b1a768709d0c4a0a0790f5db53e1fe9ae7123787c18726b')
version('1.17.1.1', sha256='d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06')
version('1.17.1', sha256='d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4')
depends_on('r@2.2.0:', type=('build', 'run'))
depends_on('r@3.6.0:', type=('build', 'run'), when='@1.18.1:')
depends_on('r-bitops', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-cdsapi/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 PyCdsapi(PythonPackage):
"""The Climate Data Store Application Program Interface is a service providing programmatic access to CDS data. Get your UID and API key from the CDS portal at the address https://cds.climate.copernicus.eu/user and write it into the configuration file. Look at https://pypi.org/project/cdsapi/ for an example"""
homepage = "https://cds.climate.copernicus.eu"
pypi = "cdsapi/cdsapi-0.2.3.tar.gz"
version('0.2.3', sha256='333b31ec263224399635db9b21a2e1a50cd73451f5179f8d967437e7c9161d9b')
depends_on('py-setuptools', type='build')
depends_on('py-requests@2.5.0:', type=('build', 'run'))
depends_on('py-tqdm', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-azure-cli/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 PyAzureCli(PythonPackage):
"""Microsoft Azure Command-Line Tools."""
homepage = "https://github.com/Azure/azure-cli"
pypi = "azure-cli/azure-cli-2.9.1.tar.gz"
version('2.9.1', sha256='749d850f73ea8956ab510288c1061dd7066180a8583081a6d560fdc7ac8314d6')
depends_on('py-setuptools', type='build')
depends_on('py-antlr4-python3-runtime@4.7.2:4.7', type=('build', 'run'))
depends_on('py-azure-batch@9.0:9', type=('build', 'run'))
depends_on('py-azure-cli-command-modules-nspkg@2.0:2', type=('build', 'run'))
depends_on('py-azure-cli-core@2.9.1', type=('build', 'run'))
depends_on('py-azure-cli-nspkg@3.0.3:3', type=('build', 'run'))
depends_on('py-azure-cosmos@3.0.2:3', type=('build', 'run'))
depends_on('py-azure-datalake-store@0.0.48:0.0', type=('build', 'run'))
depends_on('py-azure-functions-devops-build@0.0.22:0.0', type=('build', 'run'))
depends_on('py-azure-graphrbac@0.60.0:0.60', type=('build', 'run'))
depends_on('py-azure-keyvault@1.1:1', type=('build', 'run'))
depends_on('py-azure-mgmt-advisor@2.0.1:2', type=('build', 'run'))
depends_on('py-azure-mgmt-apimanagement@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-applicationinsights@0.1.1:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-appconfiguration@0.4.0:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-authorization@0.52.0:0.52', type=('build', 'run'))
depends_on('py-azure-mgmt-batch@9.0.0:9.0', type=('build', 'run'))
depends_on('py-azure-mgmt-batchai@2.0:2', type=('build', 'run'))
depends_on('py-azure-mgmt-billing@0.2:0', type=('build', 'run'))
depends_on('py-azure-mgmt-botservice@0.2.0:0.2', type=('build', 'run'))
depends_on('py-azure-mgmt-cdn@4.1.0rc1', type=('build', 'run'))
depends_on('py-azure-mgmt-cognitiveservices@6.2.0:6.2', type=('build', 'run'))
depends_on('py-azure-mgmt-compute@13.0:13', type=('build', 'run'))
depends_on('py-azure-mgmt-consumption@2.0:2', type=('build', 'run'))
depends_on('py-azure-mgmt-containerinstance@1.4:1', type=('build', 'run'))
depends_on('py-azure-mgmt-containerregistry@3.0.0rc14', type=('build', 'run'))
depends_on('py-azure-mgmt-containerservice@9.0.1:9.0', type=('build', 'run'))
depends_on('py-azure-mgmt-cosmosdb@0.15.0:0.15', type=('build', 'run'))
depends_on('py-azure-mgmt-datalake-analytics@0.2.1:0.2', type=('build', 'run'))
depends_on('py-azure-mgmt-datalake-store@0.5.0:0.5', type=('build', 'run'))
depends_on('py-azure-mgmt-datamigration@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-deploymentmanager@0.2.0:0.2', type=('build', 'run'))
depends_on('py-azure-mgmt-devtestlabs@4.0:4', type=('build', 'run'))
depends_on('py-azure-mgmt-dns@2.1:2', type=('build', 'run'))
depends_on('py-azure-mgmt-eventgrid@3.0.0rc7', type=('build', 'run'))
depends_on('py-azure-mgmt-eventhub@4.0.0:4', type=('build', 'run'))
depends_on('py-azure-mgmt-hdinsight@1.5.1:1.5', type=('build', 'run'))
depends_on('py-azure-mgmt-imagebuilder@0.4.0:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-iotcentral@3.0.0:3.0', type=('build', 'run'))
depends_on('py-azure-mgmt-iothub@0.12.0:0.12', type=('build', 'run'))
depends_on('py-azure-mgmt-iothubprovisioningservices@0.2.0:0.2', type=('build', 'run'))
depends_on('py-azure-mgmt-keyvault@2.2.0:2.2', type=('build', 'run'))
depends_on('py-azure-mgmt-kusto@0.3.0:0.3', type=('build', 'run'))
depends_on('py-azure-mgmt-loganalytics@0.7.0:0.7', type=('build', 'run'))
depends_on('py-azure-mgmt-managedservices@1.0:1', type=('build', 'run'))
depends_on('py-azure-mgmt-managementgroups@0.1:0', type=('build', 'run'))
depends_on('py-azure-mgmt-maps@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-marketplaceordering@0.1:0', type=('build', 'run'))
depends_on('py-azure-mgmt-media@2.1:2', type=('build', 'run'))
depends_on('py-azure-mgmt-monitor@0.10.0:0.10', type=('build', 'run'))
depends_on('py-azure-mgmt-msi@0.2:0', type=('build', 'run'))
depends_on('py-azure-mgmt-netapp@0.8.0:0.8', type=('build', 'run'))
depends_on('py-azure-mgmt-network@11.0.0:11.0', type=('build', 'run'))
depends_on('py-azure-mgmt-policyinsights@0.5.0:0.5', type=('build', 'run'))
depends_on('py-azure-mgmt-privatedns@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-rdbms@2.2.0:2.2', type=('build', 'run'))
depends_on('py-azure-mgmt-recoveryservices@0.4.0:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-recoveryservicesbackup@0.6.0:0.6', type=('build', 'run'))
depends_on('py-azure-mgmt-redhatopenshift@0.1.0', type=('build', 'run'))
depends_on('py-azure-mgmt-redis@7.0.0:7.0', type=('build', 'run'))
depends_on('py-azure-mgmt-relay@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-mgmt-reservations@0.6.0', type=('build', 'run'))
depends_on('py-azure-mgmt-search@2.0:2', type=('build', 'run'))
depends_on('py-azure-mgmt-security@0.4.1:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-servicebus@0.6.0:0.6', type=('build', 'run'))
depends_on('py-azure-mgmt-servicefabric@0.4.0:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-signalr@0.4.0:0.4', type=('build', 'run'))
depends_on('py-azure-mgmt-sql@0.19.0:0.19', type=('build', 'run'))
depends_on('py-azure-mgmt-sqlvirtualmachine@0.5.0:0.5', type=('build', 'run'))
depends_on('py-azure-mgmt-storage@11.1.0:11.1', type=('build', 'run'))
depends_on('py-azure-mgmt-trafficmanager@0.51.0:0.51', type=('build', 'run'))
depends_on('py-azure-mgmt-web@0.47.0:0.47', type=('build', 'run'))
depends_on('py-azure-multiapi-storage@0.3.2:0.3', type=('build', 'run'))
depends_on('py-azure-loganalytics@0.1.0:0.1', type=('build', 'run'))
depends_on('py-azure-storage-common@1.4:1', type=('build', 'run'))
depends_on('py-cryptography@2.3.1:2', type=('build', 'run'))
depends_on('py-fabric@2.4:2', type=('build', 'run'))
depends_on('py-jsmin@2.2.2:2.2', type=('build', 'run'))
depends_on('py-pytz@2019.1', type=('build', 'run'))
depends_on('py-scp@0.13.2:0.13', type=('build', 'run'))
depends_on('py-sshtunnel@0.1.4:0.1', type=('build', 'run'))
depends_on('py-urllib3@1.18:1+secure', type=('build', 'run'))
depends_on('py-vsts-cd-manager@1.0.2:1.0', type=('build', 'run'))
depends_on('py-websocket-client@0.56.0:0.56', type=('build', 'run'))
depends_on('py-xmltodict@0.12:0', type=('build', 'run'))
depends_on('py-javaproperties@0.5.1', type=('build', 'run'))
depends_on('py-jsondiff@1.2.0', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/timedatex/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/timedatex/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 Timedatex(MakefilePackage):
"""timedatex is a D-Bus service that implements the
org.freedesktop.timedate1 interface. It can be used to
read and set the system clock, the real-time clock (RTC),
the system timezone, get a list of valid timezones, and
enable or disable an NTP client installed on the system.
It is a replacement for the systemd-timedated service."""
homepage = "https://github.com/mlichvar/timedatex"
url = "https://github.com/mlichvar/timedatex/archive/v0.6.tar.gz"
version('0.6', sha256='6e24c015769ee49a92bde3b1f167e25119068a00e377f9e4187a425c262ce964')
version('0.5', sha256='bc54960bb9554bb2b34985ba2b8a78480db568c3c6a9d26f2ab34de1bc0aab11')
version('0.4', sha256='204285eb03c6cec9ae1c7fdb99e7c996259ec5a918d72bf6bc28564a6f738d4a')
depends_on('glib')
def install(self, spec, prefix):
make('install', 'prefix={0}'.format(prefix))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/hdf5-vfd-gds/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 Hdf5VfdGds(CMakePackage, CudaPackage):
"""This package enables GPU Direct Storage Virtual File Driver in HDF5."""
# Package info
homepage = 'https://github.com/hpc-io/vfd-gds'
url = 'https://github.com/hpc-io/vfd-gds/archive/refs/tags/1.0.1.tar.gz'
git = 'https://github.com/hpc-io/vfd-gds.git'
maintainers = ['hyoklee', 'lrknox']
# Versions
version('master', branch='master')
version('1.0.1', sha256='00e125fd149561be991f41e883824de826d8add604aebccf103a4fb82d5faac2')
version('1.0.0', sha256='6b16105c7c49f13fc05784ee69b78d45fb159270c78d760689f9cd21e230ddd2')
# Dependencies
conflicts('~cuda')
depends_on('cmake@3.12:')
depends_on('hdf5@1.13.0:')
def cmake_args(self):
# CMake options
args = [
self.define('BUILD_TESTING', self.run_tests),
]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-werkzeug/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 PyWerkzeug(PythonPackage):
"""The Swiss Army knife of Python web development"""
homepage = "http://werkzeug.pocoo.org"
pypi = "Werkzeug/Werkzeug-0.16.0.tar.gz"
version('2.0.2', sha256='aa2bb6fc8dee8d6c504c0ac1e7f5f7dc5810a9903e793b6f715a9f015bdadb9a')
version('0.16.0', sha256='7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7')
version('0.15.6', sha256='0a24d43be6a7dce81bae05292356176d6c46d63e42a0dd3f9504b210a9cfaa43')
version('0.15.5', sha256='a13b74dd3c45f758d4ebdb224be8f1ab8ef58b3c0ffc1783a8c7d9f4f50227e6')
version('0.15.4', sha256='a0b915f0815982fb2a09161cb8f31708052d0951c3ba433ccc5e1aa276507ca6')
version('0.15.3', sha256='cfd1281b1748288e59762c0e174d64d8bcb2b70e7c57bc4a1203c8825af24ac3')
version('0.15.2', sha256='0a73e8bb2ff2feecfc5d56e6f458f5b99290ef34f565ffb2665801ff7de6af7a')
version('0.15.1', sha256='ca5c2dcd367d6c0df87185b9082929d255358f5391923269335782b213d52655')
version('0.15.0', sha256='590abe38f8be026d78457fe3b5200895b3543e58ac3fc1dd792c6333ea11af64')
version('0.11.15', sha256='455d7798ac263266dbd38d4841f7534dd35ca9c3da4a8df303f8488f38f3bcc0')
version('0.11.11', sha256='e72c46bc14405cba7a26bd2ce28df734471bc9016bc8b4cb69466c2c14c2f7e5')
depends_on('python@3.6:', when='@2:', type=('build', 'run'))
depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-dataclasses', when='@2: ^python@:3.6', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/volk/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 Volk(CMakePackage):
"""VOLK is the Vector-Optimized Library of Kernels. It is a
library that contains kernels of hand-written SIMD code for
different mathematical operations. Since each SIMD architecture
can be very different and no compiler has yet come along to handle
vectorization properly or highly efficiently, VOLK approaches the
problem differently.
For each architecture or platform that a developer wishes to
vectorize for, a new proto-kernel is added to VOLK. At runtime,
VOLK will select the correct proto-kernel. In this way, the users
of VOLK call a kernel for performing the operation that is
platform/architecture agnostic. This allows us to write portable
SIMD code."""
homepage = "https://github.com/gnuradio/volk"
url = "https://github.com/gnuradio/volk/archive/v2.3.0.tar.gz"
maintainers = ['aweits']
version('2.3.0', sha256='f42c928f561b128acfe4adb21227e4a62a3f6ab8103592fc3233765ff326d5fc')
depends_on('python@3.4:', type=('build', 'run'))
depends_on('py-mako@0.4.2:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/pangolin/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)
class Pangolin(CMakePackage):
"""Pangolin is a lightweight portable rapid development library for
managing OpenGL display / interaction and abstracting video input."""
homepage = "https://github.com/stevenlovegrove/Pangolin"
git = "https://github.com/stevenlovegrove/Pangolin.git"
version('master', branch='master')
# Required dependencies
depends_on('cmake@2.8.12:', type='build')
depends_on('gl')
depends_on('glew')
depends_on('glu', type='link')
# Optional dependencies
depends_on('eigen')
|
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