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player1537-forks/spack
|
var/spack/repos/builtin/packages/py-typesentry/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 PyTypesentry(PythonPackage):
"""Python library for run-time type checking for type-annotated functions.
"""
homepage = "https://github.com/h2oai/typesentry"
git = "https://github.com/h2oai/typesentry.git"
# See the git history of __version__.py for versioning information
version('0.2.7', commit='<PASSWORD>')
depends_on('py-setuptools', type='build')
depends_on('py-colorama@0.3.0:', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/cmd/bootstrap.py
|
<filename>lib/spack/spack/cmd/bootstrap.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 __future__ import print_function
import os.path
import shutil
import llnl.util.tty
import llnl.util.tty.color
import spack
import spack.bootstrap
import spack.cmd.common.arguments
import spack.config
import spack.main
import spack.util.path
description = "manage bootstrap configuration"
section = "system"
level = "long"
def _add_scope_option(parser):
scopes = spack.config.scopes()
scopes_metavar = spack.config.scopes_metavar
parser.add_argument(
'--scope', choices=scopes, metavar=scopes_metavar,
help="configuration scope to read/modify"
)
def setup_parser(subparser):
sp = subparser.add_subparsers(dest='subcommand')
status = sp.add_parser('status', help='get the status of Spack')
status.add_argument(
'--optional', action='store_true', default=False,
help='show the status of rarely used optional dependencies'
)
status.add_argument(
'--dev', action='store_true', default=False,
help='show the status of dependencies needed to develop Spack'
)
enable = sp.add_parser('enable', help='enable bootstrapping')
_add_scope_option(enable)
disable = sp.add_parser('disable', help='disable bootstrapping')
_add_scope_option(disable)
reset = sp.add_parser(
'reset', help='reset bootstrapping configuration to Spack defaults'
)
spack.cmd.common.arguments.add_common_arguments(
reset, ['yes_to_all']
)
root = sp.add_parser(
'root', help='get/set the root bootstrap directory'
)
_add_scope_option(root)
root.add_argument(
'path', nargs='?', default=None,
help='set the bootstrap directory to this value'
)
list = sp.add_parser(
'list', help='list the methods available for bootstrapping'
)
_add_scope_option(list)
trust = sp.add_parser(
'trust', help='trust a bootstrapping method'
)
_add_scope_option(trust)
trust.add_argument(
'name', help='name of the method to be trusted'
)
untrust = sp.add_parser(
'untrust', help='untrust a bootstrapping method'
)
_add_scope_option(untrust)
untrust.add_argument(
'name', help='name of the method to be untrusted'
)
def _enable_or_disable(args):
# Set to True if we called "enable", otherwise set to false
value = args.subcommand == 'enable'
spack.config.set('bootstrap:enable', value, scope=args.scope)
def _reset(args):
if not args.yes_to_all:
msg = [
"Bootstrapping configuration is being reset to Spack's defaults. "
"Current configuration will be lost.\n",
"Do you want to continue?"
]
ok_to_continue = llnl.util.tty.get_yes_or_no(
''.join(msg), default=True
)
if not ok_to_continue:
raise RuntimeError('Aborting')
for scope in spack.config.config.file_scopes:
# The default scope should stay untouched
if scope.name == 'defaults':
continue
# If we are in an env scope we can't delete a file, but the best we
# can do is nullify the corresponding configuration
if (scope.name.startswith('env') and
spack.config.get('bootstrap', scope=scope.name)):
spack.config.set('bootstrap', {}, scope=scope.name)
continue
# If we are outside of an env scope delete the bootstrap.yaml file
bootstrap_yaml = os.path.join(scope.path, 'bootstrap.yaml')
backup_file = bootstrap_yaml + '.bkp'
if os.path.exists(bootstrap_yaml):
shutil.move(bootstrap_yaml, backup_file)
def _root(args):
if args.path:
spack.config.set('bootstrap:root', args.path, scope=args.scope)
root = spack.config.get('bootstrap:root', default=None, scope=args.scope)
if root:
root = spack.util.path.canonicalize_path(root)
print(root)
def _list(args):
sources = spack.config.get(
'bootstrap:sources', default=None, scope=args.scope
)
if not sources:
llnl.util.tty.msg(
"No method available for bootstrapping Spack's dependencies"
)
return
def _print_method(source, trusted):
color = llnl.util.tty.color
def fmt(header, content):
header_fmt = "@*b{{{0}:}} {1}"
color.cprint(header_fmt.format(header, content))
trust_str = "@*y{UNKNOWN}"
if trusted is True:
trust_str = "@*g{TRUSTED}"
elif trusted is False:
trust_str = "@*r{UNTRUSTED}"
fmt("Name", source['name'] + ' ' + trust_str)
print()
fmt(" Type", source['type'])
print()
info_lines = ['\n']
for key, value in source.get('info', {}).items():
info_lines.append(' ' * 4 + '@*{{{0}}}: {1}\n'.format(key, value))
if len(info_lines) > 1:
fmt(" Info", ''.join(info_lines))
description_lines = ['\n']
for line in source['description'].split('\n'):
description_lines.append(' ' * 4 + line + '\n')
fmt(" Description", ''.join(description_lines))
trusted = spack.config.get('bootstrap:trusted', {})
for s in sources:
_print_method(s, trusted.get(s['name'], None))
def _write_trust_state(args, value):
name = args.name
sources = spack.config.get('bootstrap:sources')
matches = [s for s in sources if s['name'] == name]
if not matches:
names = [s['name'] for s in sources]
msg = ('there is no bootstrapping method named "{0}". Valid '
'method names are: {1}'.format(name, ', '.join(names)))
raise RuntimeError(msg)
if len(matches) > 1:
msg = ('there is more than one bootstrapping method named "{0}". '
'Please delete all methods but one from bootstrap.yaml '
'before proceeding').format(name)
raise RuntimeError(msg)
# Setting the scope explicitly is needed to not copy over to a new scope
# the entire default configuration for bootstrap.yaml
scope = args.scope or spack.config.default_modify_scope('bootstrap')
spack.config.add(
'bootstrap:trusted:{0}:{1}'.format(name, str(value)), scope=scope
)
def _trust(args):
_write_trust_state(args, value=True)
msg = '"{0}" is now trusted for bootstrapping'
llnl.util.tty.msg(msg.format(args.name))
def _untrust(args):
_write_trust_state(args, value=False)
msg = '"{0}" is now untrusted and will not be used for bootstrapping'
llnl.util.tty.msg(msg.format(args.name))
def _status(args):
sections = ['core', 'buildcache']
if args.optional:
sections.append('optional')
if args.dev:
sections.append('develop')
header = "@*b{{Spack v{0} - {1}}}".format(
spack.spack_version, spack.bootstrap.spec_for_current_python()
)
print(llnl.util.tty.color.colorize(header))
print()
# Use the context manager here to avoid swapping between user and
# bootstrap config many times
missing = False
with spack.bootstrap.ensure_bootstrap_configuration():
for current_section in sections:
status_msg, fail = spack.bootstrap.status_message(section=current_section)
missing = missing or fail
if status_msg:
print(llnl.util.tty.color.colorize(status_msg))
print()
legend = ('Spack will take care of bootstrapping any missing dependency marked'
' as [@*y{B}]. Dependencies marked as [@*y{-}] are instead required'
' to be found on the system.')
if missing:
print(llnl.util.tty.color.colorize(legend))
print()
def bootstrap(parser, args):
callbacks = {
'status': _status,
'enable': _enable_or_disable,
'disable': _enable_or_disable,
'reset': _reset,
'root': _root,
'list': _list,
'trust': _trust,
'untrust': _untrust
}
callbacks[args.subcommand](args)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/yarn/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 Yarn(Package):
"""Fast, reliable, and secure dependency management."""
homepage = "https://yarnpkg.com"
url = "https://github.com/yarnpkg/yarn/releases/download/v1.22.4/yarn-v1.22.4.tar.gz"
maintainers = ['cosmicexplorer']
depends_on('node-js@4.0:', type='run')
version('1.22.4', sha256='bc5316aa110b2f564a71a3d6e235be55b98714660870c5b6b2d2d3f12587fb58')
version('1.22.2', sha256='de4cff575ae7151f8189bf1d747f026695d768d0563e2860df407ab79c70693d')
version('1.22.1', sha256='3af905904932078faa8f485d97c928416b30a86dd09dcd76e746a55c7f533b72')
version('1.22.0', sha256='de8871c4e2822cba80d58c2e72366fb78567ec56e873493c9ca0cca76c60f9a5')
version('1.21.1', sha256='d1d9f4a0f16f5ed484e814afeb98f39b82d4728c6c8beaafb5abc99c02db6674')
def install(self, spec, prefix):
install_tree('.', prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-git2r/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 RGit2r(RPackage):
"""Provides Access to Git Repositories.
Interface to the 'libgit2' library, which is a pure C implementation of the
'Git' core methods. Provides access to 'Git' repositories to extract data
and running some basic 'Git' commands."""
cran = "git2r"
version('0.29.0', sha256='f8f7a181dc0ac761f2a0c4099bfd744ded01c0e0832cab32dc5b4da32accd48e')
version('0.28.0', sha256='ce6d148d21d2c87757e98ef4474b2d09faded9b9b866f046bd26d4ca925e55f2')
version('0.27.1', sha256='099207f180aa45ddcc443cbb22487eafd14e1cd8e5979b3476214253fd773bc0')
version('0.26.1', sha256='13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435')
version('0.26.0', sha256='56671389c3a50591e1dae3be8c3b0112d06d291f897d7fe14db17aea175616cf')
version('0.18.0', sha256='91b32e49afb859c0c4f6f77988343645e9499e5046ef08d945d4d8149b6eff2d')
version('0.15.0', sha256='682ab9e7f71b2ed13a9ef95840df3c6b429eeea070edeb4d21d725cf0b72ede6')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('libgit2')
depends_on('zlib')
depends_on('openssl')
depends_on('libssh2')
|
player1537-forks/spack
|
lib/spack/spack/util/hash.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 base64
import hashlib
import sys
import spack.util.crypto
def b32_hash(content):
"""Return the b32 encoded sha1 hash of the input string as a string."""
sha = hashlib.sha1(content.encode('utf-8'))
b32_hash = base64.b32encode(sha.digest()).lower()
if sys.version_info[0] >= 3:
b32_hash = b32_hash.decode('utf-8')
return b32_hash
def base32_prefix_bits(hash_string, bits):
"""Return the first <bits> bits of a base32 string as an integer."""
if bits > len(hash_string) * 5:
raise ValueError("Too many bits! Requested %d bit prefix of '%s'."
% (bits, hash_string))
hash_bytes = base64.b32decode(hash_string, casefold=True)
return spack.util.crypto.prefix_bits(hash_bytes, bits)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-stringr/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 RStringr(RPackage):
"""Simple, Consistent Wrappers for Common String Operations.
A consistent, simple and easy to use set of wrappers around the fantastic
'stringi' package. All function and argument names (and positions) are
consistent, all functions deal with "NA"'s and zero length vectors in the
same way, and the output from one function is easy to feed into the input
of another."""
cran = "stringr"
version('1.4.0', sha256='87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd')
version('1.3.1', sha256='7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343')
version('1.2.0', sha256='61d0b30768bbfd7c0bb89310e2de5b7b457ac504538acbcca50374b46b16129a')
version('1.1.0', sha256='ccb1f0e0f3e9524786f6cbae705c42eedf3874d0e641564e5e00517d892c5a33')
version('1.0.0', sha256='f8267db85b83c0fc8904009719c93296934775b0d6890c996ec779ec5336df4a')
depends_on('r@3.1:', type=('build', 'run'))
depends_on('r-stringi@1.1.7:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-glue@1.2.0:', type=('build', 'run'), when='@1.3.0:')
|
player1537-forks/spack
|
lib/spack/spack/test/cmd/debug.py
|
<reponame>player1537-forks/spack<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)
import os
import os.path
import platform
import pytest
import spack.config
import spack.platforms
from spack.main import SpackCommand, get_version
from spack.util.executable import which
debug = SpackCommand('debug')
@pytest.mark.db
def test_create_db_tarball(tmpdir, database):
with tmpdir.as_cwd():
debug('create-db-tarball')
# get the first non-dotfile to avoid coverage files in the directory
files = os.listdir(os.getcwd())
tarball_name = next(f for f in files if not f.startswith('.'))
# debug command made an archive
assert os.path.exists(tarball_name)
# print contents of archive
tar = which('tar')
contents = tar('tzf', tarball_name, output=str)
# DB file is included
assert 'index.json' in contents
# specfiles from all installs are included
for spec in database.query():
# externals won't have a specfile
if spec.external:
continue
spec_suffix = '%s/.spack/spec.json' % spec.dag_hash()
assert spec_suffix in contents
def test_report():
out = debug('report')
host_platform = spack.platforms.host()
host_os = host_platform.operating_system('frontend')
host_target = host_platform.target('frontend')
architecture = spack.spec.ArchSpec(
(str(host_platform), str(host_os), str(host_target))
)
assert get_version() in out
assert platform.python_version() in out
assert str(architecture) in out
assert spack.config.get('config:concretizer') in out
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-restview/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 PyRestview(PythonPackage):
"""A viewer for ReStructuredText documents that renders them on the fly."""
homepage = "https://mg.pov.lt/restview/"
pypi = "restview/restview-2.6.1.tar.gz"
version('2.6.1', sha256='14d261ee0edf30e0ebc1eb320428ef4898e97422b00337863556966b851fb5af')
depends_on('python@2.7:2.8,3.3:3.5')
depends_on('py-setuptools', type='build')
depends_on('py-docutils@0.13.1:', type=('build', 'run'))
depends_on('py-readme-renderer', type=('build', 'run'))
depends_on('py-pygments', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ppopen-appl-bem/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 PpopenApplBem(MakefilePackage):
"""ppOpen-APPL/BEM is software used to support a boundary element analysis
executed on a parallel computer.
The current version includes a software framework for a parallel BEM
analysis and an H-matrix library.
If you want to use the framework based on dense matrix computations,
please move to the directory 'src/framework' and
'src/framework_with_template'.
If you want to use the H-matrix library, please
move to the directly 'src/HACApK_with_BEM-BB-framework_1.0.0'.
"""
homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
git = "https://github.com/Post-Peta-Crest/ppOpenHPC.git"
version('master', branch='APPL/BEM')
depends_on('mpi')
parallel = False
hacapk_src_dir = join_path(
'HACApK_1.0.0',
'src',
'HACApK_with_BEM-BB-framework_1.0.0'
)
src_directories = [
join_path('bem-bb-framework_dense', 'src', 'framework_with_templates'),
join_path('bem-bb-framework_dense', 'src', 'framework'),
hacapk_src_dir
]
def edit(self, spec, prefix):
flags = [self.compiler.openmp_flag]
fflags = flags[:]
if spec.satisfies('%gcc'):
fflags.append('-ffree-line-length-none')
filter_file(
'bem-bb-SCM.out',
'HACApK-bem-bb-sSCM.out',
join_path(self.hacapk_src_dir, 'Makefile')
)
for d in self.src_directories:
with working_dir(d):
with open('Makefile', 'a') as m:
m.write('ifeq ($(SYSTEM),spack)\n')
m.write(' CC = {0}\n'.format(spec['mpi'].mpicc))
m.write(' F90 = {0}\n'.format(spec['mpi'].mpifc))
m.write(' CCFLAGS = {0}\n'.format(' '.join(flags)))
m.write(' F90FLAGS = {0}\n'.format(' '.join(fflags)))
m.write(' FFLAGS = {0}\n'.format(' '.join(fflags)))
m.write(' LDFLAGS = {0}\n'.format(' '.join(flags)))
m.write('endif\n')
def build(self, spec, prefix):
for d in self.src_directories:
with working_dir(d):
make('SYSTEM=spack')
def install(self, spec, prefix):
mkdir(prefix.bin)
mkdir(prefix.src)
for d in self.src_directories:
for f in find(d, '*.out'):
copy(f, prefix.bin)
install_src = join_path(prefix.src, os.path.basename(d))
mkdir(install_src)
install_tree(d, install_src)
with working_dir(install_src):
make('clean')
|
player1537-forks/spack
|
lib/spack/spack/schema/__init__.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)
"""This module contains jsonschema files for all of Spack's YAML formats."""
import six
import llnl.util.lang
import llnl.util.tty
import spack.spec
# jsonschema is imported lazily as it is heavy to import
# and increases the start-up time
def _make_validator():
import jsonschema
def _validate_spec(validator, is_spec, instance, schema):
"""Check if the attributes on instance are valid specs."""
import jsonschema
if not validator.is_type(instance, "object"):
return
for spec_str in instance:
try:
spack.spec.parse(spec_str)
except spack.spec.SpecParseError as e:
yield jsonschema.ValidationError(
'"{0}" is an invalid spec [{1}]'.format(spec_str, str(e))
)
def _deprecated_properties(validator, deprecated, instance, schema):
if not (validator.is_type(instance, "object") or
validator.is_type(instance, "array")):
return
# Get a list of the deprecated properties, return if there is none
deprecated_properties = [
x for x in instance if x in deprecated['properties']
]
if not deprecated_properties:
return
# Retrieve the template message
msg_str_or_func = deprecated['message']
if isinstance(msg_str_or_func, six.string_types):
msg = msg_str_or_func.format(properties=deprecated_properties)
else:
msg = msg_str_or_func(instance, deprecated_properties)
is_error = deprecated['error']
if not is_error:
llnl.util.tty.warn(msg)
else:
import jsonschema
yield jsonschema.ValidationError(msg)
return jsonschema.validators.extend(
jsonschema.Draft4Validator, {
"validate_spec": _validate_spec,
"deprecatedProperties": _deprecated_properties
}
)
Validator = llnl.util.lang.Singleton(_make_validator)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-keras/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 tempfile
from spack import *
class PyKeras(PythonPackage):
"""Deep Learning library for Python. Convnets, recurrent neural networks,
and more. Runs on Theano or TensorFlow."""
homepage = "https://keras.io"
git = "https://github.com/keras-team/keras"
url = 'https://github.com/keras-team/keras/archive/refs/tags/v2.7.0.tar.gz'
version('2.7.0', sha256='7502746467ab15184e2e267f13fbb2c3f33ba24f8e02a097d229ba376dabaa04')
version('2.6.0', sha256='15586a3f3e1ed9182e6e0d4c0dbd052dfb7250e779ceb7e24f8839db5c63fcae')
version('2.5.0', commit='9c266106163390f173625c4e7b1ccb03ae145ffc')
version('2.4.3', sha256='fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973')
version('2.2.4', sha256='90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9')
version('2.2.3', sha256='694aee60a6f8e0d3d6d3e4967e063b4623e3ca90032f023fd6d16bb5f81d18de')
version('2.2.2', sha256='468d98da104ec5c3dbb10c2ef6bb345ab154f6ca2d722d4c250ef4d6105de17a')
version('2.2.1', sha256='0d3cb14260a3fa2f4a5c4c9efa72226ffac3b4c50135ba6edaf2b3d1d23b11ee')
version('2.2.0', sha256='5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf')
version('2.1.6', sha256='c14af1081242c25617ade7eb62121d58d01f16e1e744bae9fc4f1f95a417716e')
version('2.1.5', sha256='907ad29add1fff27342a9f4fe3e60003d450d3af41a38f22f629c7736fc8399d')
version('2.1.4', sha256='7ee1fcc79072ac904a4f008d715bcb78c60250ae3cd41d99e268c60ade8d0d3a')
version('2.1.3', sha256='7ca3a381523bad40a6922e88951a316664cb088fd01cea07e5ec8ada3327e3c7')
version('2.1.2', sha256='3ee56fc129d9d00b1916046e50056047836f97ada59df029e5661fb34442d5e8')
version('2.1.1', sha256='f0ca2458c60d9711edf4291230b31795307ad3781cb6232ff4792b53c8f55123')
version('2.1.0', sha256='67a0d66c20fff99312fc280e34c8f6dc3dbb027d4a33c13c79bec3c1173f6909')
version('2.0.9', sha256='6b8572cf1b4a22fd0120b7c23382ba4fa04a6f0397e02af1249be9a7309d1767')
version('2.0.8', sha256='899dc6aaed366f20100b9f80cf1093ea5b43eecc74afd1dc63a4e48dfa776ab9')
version('2.0.7', sha256='a6c72ee2b94be1ffefe7e77b69582b9827211f0c356b2189459711844d3634c0')
version('2.0.6', sha256='0519480abe4ad18b2c2d1bc580eab75edd82c95083d341a1157952f4b00019bb')
version('2.0.5', sha256='cbce24758530e070fe1b403d6d21391cbea78c037b70bf6afc1ca9f1f8269eff')
version('2.0.4', sha256='1cbe62af6821963321b275d5598fd94e63c11feaa1d4deaa79c9eb9ee0e1d68a')
version('2.0.3', sha256='398dbd4a95e9d3ab2b2941d3e0c19362d397a2a6c3a667ab89d3d6aad30997f4')
version('1.2.2', sha256='d2b18c4336eb9c4f0d03469870257efa7980a9b036c9d46dcf4d49e7f4487e2d')
version('1.2.1', sha256='6adce75b2050608e6683c3046ef938bfdc5bfcd4c6b6c522df5e50d18e0ac7c6')
version('1.2.0', sha256='33d5297cd0c280640dc5c075466995c05911bc1da35c83ae57b2a48188b605e2')
version('1.1.2', sha256='cfde0a424961ead4982a7ebefd77d8ca382810b5a69b566fa64c57d8f340eeb4')
version('1.1.1', sha256='be1b67f62e5119f6f24a239a865dc47e6d9aa93b97b506ba34cab7353dbc23b6')
version('1.1.0', sha256='36d83b027ba9d2c9da8e1eefc28f600ca93dc03423e033b633cbac9061af8a5d')
depends_on('python@3.6:', type=('build', 'run'), when='@2.4')
depends_on('py-numpy@1.9.1:', type=('build', 'run'), when='@2.4')
depends_on('py-scipy@0.14:', type=('build', 'run'), when='@2.4')
depends_on('py-h5py', type=('build', 'run'), when='@2.4')
depends_on('py-keras-applications', type='run', when='@2.2:2.4')
depends_on('py-keras-preprocessing', type='run', when='@2.2:2.4')
depends_on('py-setuptools', type='build')
depends_on('py-theano', type=('build', 'run'), when='@:2.2')
depends_on('py-pyyaml', type=('build', 'run'), when='@:2.4')
depends_on('py-six', type=('build', 'run'), when='@:2.2')
depends_on('py-tensorflow@2.5.0:2.5', type=('build', 'run'), when='@2.5.0:2.5')
depends_on('py-tensorflow@2.6.0:2.6', type=('build', 'run'), when='@2.6.0:2.6')
depends_on('py-tensorflow@2.7.0:2.7', type=('build', 'run'), when='@2.7.0:2.7')
depends_on('bazel', type='build', when='@2.5.0:')
depends_on('protobuf', type='build', when='@2.5.0:')
def url_for_version(self, version):
if version >= Version('2.6.0'):
return super(PyKeras, self).url_for_version(version)
else:
url = 'https://pypi.io/packages/source/K/Keras/Keras-{0}.tar.gz'
return url.format(version.dotted)
@when('@2.5.0:')
def patch(self):
infile = join_path(self.package_dir, 'protobuf_build.patch')
with open(infile, 'r') as source_file:
text = source_file.read()
with open('keras/keras.bzl', mode='a') as f:
f.write(text)
filter_file('load("@com_google_protobuf//:protobuf.bzl", "py_proto_library")',
'load("@org_keras//keras:keras.bzl", "py_proto_library")',
'keras/protobuf/BUILD',
string=True)
@when('@2.5.0:')
def install(self, spec, prefix):
self.tmp_path = tempfile.mkdtemp(dir='/tmp', prefix='spack')
env['HOME'] = self.tmp_path
args = [
# Don't allow user or system .bazelrc to override build settings
'--nohome_rc',
'--nosystem_rc',
# Bazel does not work properly on NFS, switch to /tmp
'--output_user_root=' + self.tmp_path,
'build',
# Spack logs don't handle colored output well
'--color=no',
'--jobs={0}'.format(make_jobs),
# Enable verbose output for failures
'--verbose_failures',
# Show (formatted) subcommands being executed
'--subcommands=pretty_print',
'--spawn_strategy=local',
# Ask bazel to explain what it's up to
# Needs a filename as argument
'--explain=explainlogfile.txt',
# Increase verbosity of explanation,
'--verbose_explanations',
# bazel uses system PYTHONPATH instead of spack paths
'--action_env', 'PYTHONPATH={0}'.format(env['PYTHONPATH']),
'//keras/tools/pip_package:build_pip_package',
]
bazel(*args)
build_pip_package = Executable(
'bazel-bin/keras/tools/pip_package/build_pip_package')
buildpath = join_path(self.stage.source_path, 'spack-build')
build_pip_package('--src', buildpath)
with working_dir(buildpath):
args = std_pip_args + ['--prefix=' + prefix, '.']
pip(*args)
remove_linked_tree(self.tmp_path)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/unigen/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 Unigen(MakefilePackage):
"""The United Generators project was launched by the Virtual Institute 146
VI-SIM in September 2005 following a proposal of <NAME>.
The goal was to facilitate comparison between various models (see below)
and/or various experiments (HADES, FOPI, CERES, NA49, CBM). The package
at present allows to convert output of various event generators to a
generic root format."""
homepage = "https://www.gsi.de/work/wissenschaftliche_netzwerke/helmholtz_virtuelle_institute/unigen.htm"
url = "https://github.com/FairRootGroup/UniGen/archive/v2.3.tar.gz"
tags = ['hep']
version('2.3', sha256='8783bcabbdf8c50dab6e93153cff9cfb267a9a9e61aef51bf1e17679ba42a717')
patch('unigen-2.3.patch', level=0)
depends_on('root', type=('build', 'link'))
def build(self, spec, prefix):
mkdirp(join_path(self.build_directory, 'lib'))
make('TOPDIR=' + self.build_directory, 'all')
def install(self, spec, prefix):
make('DESTDIR=' + prefix, 'TOPDIR=' + self.build_directory, 'install')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-whoosh/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 PyWhoosh(PythonPackage):
"""Fast, pure-Python full text indexing, search, and spell checking library."""
homepage = "https://whoosh.readthedocs.io"
pypi = "Whoosh/Whoosh-2.7.4.tar.gz"
version('2.7.4', sha256='7ca5633dbfa9e0e0fa400d3151a8a0c4bec53bd2ecedc0a67705b17565c31a83')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/melissa/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 Melissa(CMakePackage):
"""Melissa is a file-avoiding, adaptive, fault-tolerant and elastic
framework, to run large-scale sensitivity analysis on supercomputers.
"""
homepage = 'https://gitlab.inria.fr/melissa/melissa'
url = 'https://gitlab.inria.fr/melissa/melissa/-/archive/v1.0/melissa-v1.0.tar.bz2'
git = 'https://gitlab.inria.fr/melissa/melissa.git'
# attention: Git**Hub**.com accounts
maintainers = ['christoph-conrads', 'raffino']
version('master', branch='master')
version('develop', branch='develop')
version('0.7.1', sha256='c30584f15fecf6297712a88e4d28851bfd992f31209fd7bb8af2feebe73d539d')
version('0.7.0', sha256='a801d0b512e31a0750f98cfca80f8338985e06abf9b26e96f7645a022864e41c', deprecated=True)
variant('no_mpi_api', default=False, description="Enable the deprecated no-MPI API")
variant('shared', default=True, description="Build shared libraries")
depends_on('cmake@3.7.2:', type='build')
depends_on('libzmq@4.1.5:')
depends_on('mpi')
depends_on('pkgconfig', type='build')
depends_on('python@3.5.3:', type=('build', 'run'))
def cmake_args(self):
args = [
self.define('BUILD_TESTING', self.run_tests),
self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
self.define_from_variant('MELISSA_ENABLE_NO_MPI_API', 'no_mpi_api')
]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/cc65/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 Cc65(MakefilePackage):
"""cc65 is a complete cross development package for 65(C)02 systems,
including a powerful macro assembler, a C compiler, linker, librarian
and several other tools."""
homepage = "https://cc65.github.io/"
url = "https://github.com/cc65/cc65/archive/V2.18.tar.gz"
version('2.18', sha256='d14a22fb87c7bcbecd8a83d5362d5d317b19c6ce2433421f2512f28293a6eaab')
version('2.17', sha256='73b89634655bfc6cef9aa0b8950f19657a902ee5ef0c045886e418bb116d2eac')
version('2.16', sha256='fdbbf1efbf2324658a5774fdceef4a1b202322a04f895688d95694843df76792')
version('2.15', sha256='adeac1a4b04183dd77fba1d69e56bbf4a6d358e0b253ee43ef4cac2391ba848a')
version('2.14', sha256='128bda63490eb43ad25fd3615adee4c819c0b7da4b9b8f1801df36bd19e3bdf8')
def install(self, spec, prefix):
make('PREFIX={0}'.format(prefix), 'install')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ltrace/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 Ltrace(AutotoolsPackage):
"""Ltrace intercepts and records dynamic library calls which are called
by an executed process and the signals received by that process. It
can also intercept and print the system calls executed by the program."""
homepage = "https://www.ltrace.org"
url = "https://www.ltrace.org/ltrace_0.7.3.orig.tar.bz2"
version('0.7.3', sha256='0e6f8c077471b544c06def7192d983861ad2f8688dd5504beae62f0c5f5b9503')
conflicts('platform=darwin', msg='ltrace runs only on Linux.')
def configure_args(self):
# Disable -Werror since some functions used by ltrace
# have been deprecated in recent version of glibc
return ['--disable-werror']
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/bitlbee/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 Bitlbee(AutotoolsPackage):
"""An IRC to other chat networks gateway."""
homepage = "https://www.bitlbee.org/"
url = "https://github.com/bitlbee/bitlbee/archive/3.5.1.tar.gz"
version('3.6-1', sha256='81c6357fe08a8941221472e3790e2b351e3a8a41f9af0cf35395fdadbc8ac6cb')
version('3.6', sha256='6ec3a1054eaa98eaaabe6159cb4912cfd6286f71adcfa970419b273b38fdfe0c')
version('3.5-2', sha256='cdcf3ed829d1905b73687b6aa189bbfaf9194f886d9fc7156646827dc0384fdb')
depends_on('glib')
depends_on('gnutls')
depends_on('libgcrypt')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/coral/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/coral/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 Coral(CMakePackage):
"""CORAL is an abstraction layer with an SQL-free API to access data stored
using relational database technologies. It is used directly by
experiment-specific applications and internally by COOL."""
homepage = "https://coral-cool.docs.cern.ch/"
git = "https://gitlab.cern.ch/lcgcoral/coral.git"
tags = ['hep']
version('3.3.10', tag='CORAL_3_3_10')
version('3.3.3', tag='CORAL_3_3_3')
variant('binary_tag', default='auto')
depends_on('ninja')
depends_on('ccache')
depends_on('boost')
depends_on('cppunit')
depends_on('expat')
depends_on('frontier-client')
depends_on('libaio')
depends_on('mariadb')
depends_on('python')
# depends_on('qmtest')
depends_on('xerces-c')
depends_on('sqlite')
depends_on('gperftools')
depends_on('igprof')
depends_on('libunwind')
depends_on('valgrind')
depends_on('oracle-instant-client')
depends_on('libtirpc')
def determine_binary_tag(self):
# As far as I can tell from reading the source code, `binary_tag`
# can be almost arbitraryThe only real difference it makes is
# disabling oracle dependency for non-x86 platforms
if self.spec.variants['binary_tag'].value != 'auto':
return self.spec.variants['binary_tag'].value
binary_tag = str(self.spec.target.family) + \
'-' + self.spec.os + \
'-' + self.spec.compiler.name + str(self.spec.compiler.version.joined) + \
('-opt' if 'Rel' in self.spec.variants['build_type'].value else '-dbg')
return binary_tag
def cmake_args(self):
args = ['-DBINARY_TAG=' + self.determine_binary_tag()]
if self.spec['python'].version >= Version("3.0.0"):
args.append('-DLCG_python3=on')
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-fastai/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 PyFastai(PythonPackage):
"""You can use fastai without any installation by using
Google Colab. In fact, every page of this documentation is
also available as an interactive notebook - click "Open in
colab" at the top of any page to open it (be sure to change
the Colab runtime to "GPU" to have it run fast!) See the
fast.ai documentation on Using Colab for more
information."""
homepage = "https://github.com/fastai/fastai/tree/master/"
pypi = "fastai/fastai-2.5.3.tar.gz"
version('2.5.3', sha256='0cae50617979b052f0ed7337800e6814ee346b792203cf48305709c935e8eeb7')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools@36.2:', type='build')
depends_on('py-pip', type='build')
depends_on('py-packaging', type='build')
depends_on('py-fastdownload@0.0.5:1', type=('build', 'run'))
depends_on('py-fastcore@1.3.22:1.3', type=('build', 'run'))
depends_on('py-torchvision@0.8.2:', type=('build', 'run'))
depends_on('py-matplotlib', type=('build', 'run'))
depends_on('py-pandas', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-fastprogress@0.2.4:', type=('build', 'run'))
depends_on('pil@6.0.1:', type=('build', 'run'))
depends_on('py-scikit-learn', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-spacy@:3', type=('build', 'run'))
depends_on('py-torch@1.7.0:1.10', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-nor1mix/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 RNor1mix(RPackage):
"""Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods).
One dimensional Normal Mixture Models Classes, for, e.g., density
estimation or clustering algorithms research and teaching; providing the
widely used Marron-Wand densities. Efficient random number generation and
graphics; now fitting to data by ML (Maximum Likelihood) or EM
estimation."""
cran = "nor1mix"
version('1.3-0', sha256='9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0')
version('1.2-3', sha256='435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-markdown-it-py/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/py-markdown-it-py/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 PyMarkdownItPy(PythonPackage):
"""Markdown parser, done right.
100% CommonMark support, extensions, syntax plugins & high speed """
homepage = "https://github.com/executablebooks/markdown-it-py"
git = "https://github.com/executablebooks/markdown-it-py"
pypi = "markdown-it-py/markdown-it-py-1.1.0.tar.gz"
version('1.1.0', sha256='36be6bb3ad987bfdb839f5ba78ddf094552ca38ccbd784ae4f74a4e1419fc6e3')
depends_on('python@3.6:3', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-attrs@19:21', type=('build', 'run'))
depends_on('py-typing-extensions@3.7.4:', type=('build', 'run'), when='^python@:3.7')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-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)
class PyRay(PythonPackage):
"""A system for parallel and distributed Python that unifies the ML
ecosystem."""
homepage = "https://github.com/ray-project/ray"
url = "https://github.com/ray-project/ray/archive/ray-0.8.7.tar.gz"
version('0.8.7', sha256='2df328f1bcd3eeb4fa33119142ea0d669396f4ab2a3e78db90178757aa61534b')
build_directory = 'python'
depends_on('python@3.6:', type=('build', 'run'))
depends_on('bazel@3.2.0', type='build')
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.29.14:', type='build')
depends_on('py-wheel', type='build')
depends_on('py-aiohttp', type=('build', 'run'))
depends_on('py-aioredis', type=('build', 'run'))
depends_on('py-click@7.0:', type=('build', 'run'))
depends_on('py-colorama', type=('build', 'run'))
depends_on('py-colorful', type=('build', 'run'))
depends_on('py-filelock', type=('build', 'run'))
depends_on('py-google', type=('build', 'run'))
depends_on('py-gpustat', type=('build', 'run'))
depends_on('py-grpcio@1.28.1:', type=('build', 'run'))
depends_on('py-jsonschema', type=('build', 'run'))
depends_on('py-msgpack@1.0:1', type=('build', 'run'))
depends_on('py-numpy@1.16:', type=('build', 'run'))
depends_on('py-protobuf@3.8.0:', type=('build', 'run'))
depends_on('py-py-spy@0.2.0:', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-redis@3.3.2:3.4', type=('build', 'run'))
depends_on('py-opencensus', type=('build', 'run'))
depends_on('py-prometheus-client@0.7.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/siesta/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 Siesta(Package):
"""SIESTA performs electronic structure calculations and ab initio molecular
dynamics simulations of molecules and solids."""
homepage = "https://departments.icmab.es/leem/siesta/"
version('4.0.2', sha256='bafbda19358f0c1dd39bb1253c92ee548791a1c0f648977051d2657216874f7e')
version('4.0.1', sha256='bfb9e4335ae1d1639a749ce7e679e739fdead5ee5766b5356ea1d259a6b1e6d1',
url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz')
version('3.2-pl-5', sha256='e438bb007608e54c650e14de7fa0b5c72562abb09cbd92dcfb5275becd929a23',
url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz')
patch('configure.patch', when='@:4.0')
depends_on('mpi')
depends_on('blas')
depends_on('lapack')
depends_on('scalapack')
depends_on('netcdf-c')
depends_on('netcdf-fortran')
phases = ['configure', 'build', 'install']
def flag_handler(self, name, flags):
if '%gcc@10:' in self.spec and name == 'fflags':
flags.append('-fallow-argument-mismatch')
return (flags, None, None)
def configure(self, spec, prefix):
sh = which('sh')
configure_args = ['--enable-mpi',
'--with-blas=%s' % spec['blas'].libs,
'--with-lapack=%s' % spec['lapack'].libs,
# need to include BLAS below because Intel MKL's
# BLACS depends on BLAS, otherwise the compiler
# test fails
'--with-blacs=%s' % (spec['scalapack'].libs +
spec['blas'].libs),
'--with-scalapack=%s' % spec['scalapack'].libs,
'--with-netcdf=%s' % (spec['netcdf-fortran'].libs +
spec['netcdf-c'].libs),
# need to specify MPIFC explicitly below, otherwise
# Intel's mpiifort is not found
'MPIFC=%s' % spec['mpi'].mpifc
]
if self.spec.satisfies('%gcc'):
configure_args.append('FCFLAGS=-ffree-line-length-0')
for d in ['Obj', 'Obj_trans']:
with working_dir(d, create=True):
sh('../Src/configure', *configure_args)
if spec.satisfies('@:4.0%intel'):
with open('arch.make', 'a') as f:
f.write('\natom.o: atom.F\n')
f.write('\t$(FC) -c $(FFLAGS) -O1')
f.write('$(INCFLAGS) $(FPPFLAGS) $<')
sh('../Src/obj_setup.sh')
def build(self, spec, prefix):
with working_dir('Obj'):
make(parallel=False)
with working_dir('Obj_trans'):
make('transiesta', parallel=False)
with working_dir('Util'):
sh = which('sh')
sh('build_all.sh')
def install(self, spec, prefix):
mkdir(prefix.bin)
with working_dir('Obj'):
install('siesta', prefix.bin)
with working_dir('Obj_trans'):
install('transiesta', prefix.bin)
for root, _, files in os.walk('Util'):
for fname in files:
fname = join_path(root, fname)
if os.access(fname, os.X_OK):
install(fname, prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-scales/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 RScales(RPackage):
"""Scale Functions for Visualization.
Graphical scales map data to aesthetics, and provide methods for
automatically determining breaks and labels for axes and legends."""
cran = "scales"
version('1.1.1', sha256='40b2b66522f1f314a20fd09426011b0cdc9d16b23ee2e765fe1930292dd03705')
version('1.0.0', sha256='0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c')
version('0.5.0', sha256='dbfcc0817c4ab8b8777ec7d68ebfe220177c193cfb5bd0e8ba5d365dbfe3e97d')
version('0.4.1', sha256='642b88fb1fce7bac72a0038ce532b65b8a79dffe826fec25033cf386ab630cd3')
version('0.4.0', sha256='851ef6136339b361b3f843fb73ea89f9112279b9cc126bdb38acde8d24c1c6a7')
depends_on('r@2.13:', type=('build', 'run'))
depends_on('r@3.1:', type=('build', 'run'), when='@1.0.0:')
depends_on('r@3.2:', type=('build', 'run'), when='@1.1.1:')
depends_on('r-farver@2.0.3:', type=('build', 'run'), when='@1.1.1:')
depends_on('r-labeling', type=('build', 'run'))
depends_on('r-lifecycle', type=('build', 'run'), when='@1.1.1:')
depends_on('r-munsell@0.5:', type=('build', 'run'))
depends_on('r-r6', type=('build', 'run'))
depends_on('r-rcolorbrewer', type=('build', 'run'))
depends_on('r-viridislite', type=('build', 'run'))
depends_on('r-dichromat', type=('build', 'run'), when='@:0.5.0')
depends_on('r-plyr', type=('build', 'run'), when='@:0.5.0')
depends_on('r-rcpp', type=('build', 'run'), when='@:1.0.0')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-pygobject/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 PyPygobject(PythonPackage):
"""bindings for the GLib, and GObject,
to be used in Python."""
homepage = "https://pypi.python.org/pypi/pygobject"
version('3.38.0', sha256='0372d1bb9122fc19f500a249b1f38c2bb67485000f5887497b4b205b3e7084d5')
version('3.28.3', sha256='3dd3e21015d06e00482ea665fc1733b77e754a6ab656a5db5d7f7bfaf31ad0b0')
version('2.28.6', sha256='fb8a1d4f665130a125011659bd347c7339c944232163dbb9a34fd0686577adb8')
version('2.28.3', sha256='7da88c169a56efccc516cebd9237da3fe518a343095a664607b368fe21df95b6',
url='http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.3.tar.bz2')
extends('python')
depends_on('py-setuptools', type='build')
depends_on('pkgconfig', type='build')
depends_on("libffi")
depends_on('glib')
depends_on('python@2.0:2', when='@2.0:2', type=('build', 'run'))
depends_on('py-pycairo', type=('build', 'run'), when='@3:')
depends_on('py-py2cairo', type=('build', 'run'), when='@2.0:2')
depends_on('gobject-introspection')
depends_on('gtkplus', when='@3:')
patch('pygobject-2.28.6-introspection-1.patch', when='@2.28.3:2.28.6')
# patch from https://raw.githubusercontent.com/NixOS/nixpkgs/master/pkgs/development/python-modules/pygobject/pygobject-2.28.6-gio-types-2.32.patch
# for https://bugzilla.gnome.org/show_bug.cgi?id=668522
patch('pygobject-2.28.6-gio-types-2.32.patch', when='@2.28.6')
# pygobject links directly using the compiler, not spack's wrapper.
# This causes it to fail to add the appropriate rpaths. This patch modifies
# pygobject's setup.py file to add -Wl,-rpath arguments for dependent
# libraries found with pkg-config.
patch('pygobject-3.28.3-setup-py.patch', when='@3.28.3')
def url_for_version(self, version):
url = 'http://ftp.gnome.org/pub/GNOME/sources/pygobject'
return url + '/%s/pygobject-%s.tar.xz' % (version.up_to(2), version)
# pygobject version 2 requires an autotools build
@when('@2.0:2')
def build(self, spec, prefix):
configure('--prefix=%s' % spec.prefix)
@when('@2.0:2')
def install(self, spec, prefix):
make('install', parallel=False)
@when('^python@3:')
def patch(self):
filter_file(
r'Pycairo_IMPORT',
r'//Pycairo_IMPORT',
'gi/pygi-foreign-cairo.c')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/xplor-nih/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 XplorNih(Package):
"""XPLOR-NIH is a structure determination program.
Note: A manual download is required for XPLOR-NIH.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
https://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://nmr.cit.nih.gov/xplor-nih/"
manual_download = True
version('2.45', '<PASSWORD>e046604beb0effc89a1adb7bab438')
depends_on('python', type=('build', 'run'))
def url_for_version(self, version):
return "file://{0}/xplor-nih-{1}-Linux_x86_64.tar.gz".format(os.getcwd(), version)
def install(self, spec, prefix):
install_tree(self.stage.source_path, prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/memtester/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 Memtester(MakefilePackage):
"""A userspace utility for testing the memory subsystem for faults."""
homepage = "http://pyropus.ca/software/memtester/"
url = "http://pyropus.ca/software/memtester/old-versions/memtester-4.3.0.tar.gz"
version('4.3.0', sha256='f9dfe2fd737c38fad6535bbab327da9a21f7ce4ea6f18c7b3339adef6bf5fd88')
version('4.2.2', sha256='a494569d58d642c796332a1b7f3b4b86845b52da66c15c96fbeecd74e48dae8e')
version('4.2.1', sha256='3433e1c757e56457610f5a97bf1a2d612c609290eba5183dd273e070134a21d2')
version('4.2.0', sha256='cb9d5437a0c429d18500bddef93084bb2fead0d5ccfedfd00ee28ff118e52695')
version('4.1.3', sha256='ac56f0b6d6d6e58bcf2a3fa7f2c9b29894f5177871f21115a1906c535106acf6')
def edit(self, spec, prefix):
makefile = FileFilter("Makefile")
makefile.filter("INSTALLPATH\t= /usr/local",
"INSTALLPATH\t= {0}".format(self.prefix))
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/simple-standalone-test/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 SimpleStandaloneTest(Package):
"""This package has a simple stand-alone test features."""
homepage = "http://www.example.com/simple_test"
url = "http://www.unit-test-should-replace-this-url/simple_test-1.0.tar.gz"
version('1.0', '0123456789abcdef0123456789abcdef')
def test(self):
msg = 'simple stand-alone test'
self.run_test('echo', [msg],
expected=[msg],
purpose='test: running {0}'.format(msg))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/antimony/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 Antimony(CMakePackage):
"""Human readable language for modifying sbml"""
homepage = "http://antimony.sourceforge.net/"
url = "antimony"
maintainers = ['rblake-llnl']
version('2.8', sha256='7e3e38706c074b72e241ac56ef4ce23e87ef8c718c70f29b2207f1847c43770f')
version('2.7', sha256='7ad181cac632282ae77ced09388dd92db87ea4683eed8c45f2b43861ae2acad4')
version('2.6', sha256='afc8dc5ec6bc2cd3085038f80362327456f219171b09a13f775b50550c8b1d87')
version('2.5', sha256='138d6b45df62198ca71bd3b3c8fd06920f8a78d7de7f6dbc1b89fa7ea7c7d215')
version('2.4', sha256='1597efa823f9a48f5a40373cbd40386207764807fbc0b79cf20d0f8570a7e54b')
version('2.2', sha256='795c777dd90c28fd8c3f4f8896702744b7389cff2fcf40e797b4bfafbb6f7251')
version('2.0', sha256='778146206e5f420d0e3d30dc25eabc9bad2759bfaf6b4b355bb1f72c5bc9593f')
def url_for_version(self, version):
url = "https://downloads.sourceforge.net/project/antimony/Antimony source/{0}/antimony_src_v{1}.tar.gz".format(version, version)
return url
variant("qt", default=False,
description="Build the QT editor.")
variant("python", default=False,
description="Build python bindings.")
depends_on('sbml~cpp')
depends_on('swig')
depends_on('qt', when="+qt")
depends_on('python', when="+python")
def cmake_args(self):
spec = self.spec
args = [
'-DWITH_SBML:BOOL=ON',
'-DWITH_COMP_SBML:BOOL=ON',
'-DWITH_LIBSBML_EXPAT:BOOL=OFF',
'-DWITH_LIBSBML_LIBXML:BOOL=ON',
'-DWITH_LIBSBML_XERCES:BOOL=OFF',
'-DLIBSBML_INSTALL_DIR:PATH=' + spec['sbml'].prefix,
'-DWITH_CELLML:BOOL=OFF',
'-DWITH_SBW:BOOL=OFF',
'-DWITH_SWIG:BOOL=ON',
]
args.append(self.define_from_variant('WITH_PYTHON', 'python'))
args.append(self.define_from_variant('WITH_QTANTIMONY', "qt"))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-mypy/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 PyMypy(PythonPackage):
"""Optional static typing for Python."""
homepage = "http://www.mypy-lang.org/"
pypi = "mypy/mypy-0.740.tar.gz"
version('0.931', sha256='0038b21890867793581e4cb0d810829f5fd4441aa75796b53033af3aa30430ce')
version('0.930', sha256='51426262ae4714cc7dd5439814676e0992b55bcc0f6514eccb4cf8e0678962c2')
version('0.921', sha256='eca089d7053dff45d6dcd5bf67f1cabc311591e85d378917d97363e7c13da088')
version('0.920', sha256='a55438627f5f546192f13255a994d6d1cf2659df48adcf966132b4379fd9c86b')
version('0.910', sha256='704098302473cb31a218f1775a873b376b30b4c18229421e9e9dc8916fd16150')
version('0.900', sha256='65c78570329c54fb40f956f7645e2359af5da9d8c54baa44f461cdc7f4984108')
version('0.800', sha256='e0202e37756ed09daf4b0ba64ad2c245d357659e014c3f51d8cd0681ba66940a')
version('0.790', sha256='2b21ba45ad9ef2e2eb88ce4aeadd0112d0f5026418324176fd494a6824b74975')
version('0.740', sha256='48c8bc99380575deb39f5d3400ebb6a8a1cb5cc669bbba4d3bb30f904e0a0e7d')
version('0.670', sha256='e80fd6af34614a0e898a57f14296d0dacb584648f0339c2e000ddbf0f4cc2f8d')
depends_on('python@3.6:', when='@0.920:', type=('build', 'run'))
depends_on('python@3.5:', when='@0.700:', type=("build", "run"))
depends_on('python@3.4:', type=('build', 'run'))
depends_on('py-setuptools@40.6.2:', when='@0.790:', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-wheel@0.30:', when='@0.790:', type='build')
depends_on('py-typed-ast@1.4.0:1', when='@0.920: ^python@:3.7', type=('build', 'run'))
depends_on('py-typed-ast@1.4.0:1.4', when='@0.900:0.910 ^python@:3.7', type=('build', 'run'))
depends_on('py-typed-ast@1.4.0:1.4', when='@0.700:0.899', type=('build', 'run'))
depends_on('py-typed-ast@1.3.1:1.3', when='@:0.699', type=('build', 'run'))
depends_on('py-typing-extensions@3.10:', when='@0.930:', type=('build', 'run'))
depends_on('py-typing-extensions@3.7.4:', when='@0.700:', type=('build', 'run'))
depends_on('py-typing@3.5.3:', when='@:0.699 ^python@:3.4', type=('build', 'run'))
depends_on('py-mypy-extensions@0.4.3:', when='@0.930:', type=('build', 'run'))
depends_on('py-mypy-extensions@0.4.3:0.4', when='@0.700:0.929', type=('build', 'run'))
depends_on('py-mypy-extensions@0.4.0:0.4', when='@:0.699', type=('build', 'run'))
depends_on('py-tomli@1.1:', when='@0.930:', type=('build', 'run'))
depends_on('py-tomli@1.1:2', when='@0.920:0.929', type=('build', 'run'))
depends_on('py-toml', when='@0.900:0.910', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/lhapdf/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 Lhapdf(AutotoolsPackage):
"""LHAPDF is a general purpose C++ interpolator,
used for evaluating PDFs from discretised data files. """
homepage = "https://lhapdf.hepforge.org/"
git = "https://gitlab.com/hepcedar/lhapdf"
# the tarballs from hepforge include bundled cython sources
# that may break the build when using incompatible python versions
# thus use the release tarball from gitlab that does not include lhapdf.cxx
url = "https://gitlab.com/hepcedar/lhapdf/-/archive/lhapdf-6.4.0/lhapdf-lhapdf-6.4.0.tar.gz"
tags = ['hep']
version('6.4.0', sha256='155702c36df46de30c5f7fa249193a9a0eea614191de1606301e06cd8062fc29')
version('6.3.0', sha256='864468439c7662bbceed6c61c7132682ec83381a23c9c9920502fdd7329dd816')
version('6.2.3', sha256='37200a1ab70247250a141dfed7419d178f9a83bd23a4f8a38e203d4e27b41308')
variant('python', default=True, description="Build python bindings")
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
extends('python', when='+python')
depends_on('py-cython', type='build', when='+python')
depends_on('py-setuptools', type='build', when='+python')
def configure_args(self):
args = ['FCFLAGS=-O3', 'CFLAGS=-O3', 'CXXFLAGS=-O3']
args.extend(self.enable_or_disable('python'))
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-dask-glm/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/py-dask-glm/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 PyDaskGlm(PythonPackage):
"""Dask-glm is a library for fitting Generalized Linear Models on
large datasets."""
homepage = "https://dask-glm.readthedocs.io/en/latest/"
pypi = "dask-glm/dask-glm-0.2.0.tar.gz"
version('0.2.0', sha256='58b86cebf04fe5b9e58092e1c467e32e60d01e11b71fdc628baaa9fc6d1adee5')
variant('docs', default=False, description='Build HTML documentation')
depends_on('py-setuptools', type='build')
depends_on('py-setuptools-scm', type='build')
depends_on('py-cloudpickle@0.2.2:', type=('build', 'run'))
depends_on('py-dask+array', type=('build', 'run'))
depends_on('py-multipledispatch@0.4.9:', type=('build', 'run'))
depends_on('py-scipy@0.18.1:', type=('build', 'run'))
depends_on('py-scikit-learn@0.18:', type=('build', 'run'), when='~docs')
depends_on('py-scikit-learn@0.18:0.21', type=('build', 'run'), when='+docs')
depends_on('py-jupyter', type='build', when='+docs')
depends_on('py-nbsphinx', type='build', when='+docs')
depends_on('py-notebook', type='build', when='+docs')
depends_on('py-numpydoc', type='build', when='+docs')
depends_on('py-sphinx', type='build', when='+docs')
depends_on('py-sphinx-rtd-theme', type='build', when='+docs')
depends_on('pandoc', type='build', when='+docs')
depends_on('py-pip', type='build', when='+docs')
depends_on('py-s3fs', type='build', when='+docs')
depends_on('py-matplotlib', type='build', when='+docs')
depends_on('llvm@:10.0.1~flang', type='build', when='+docs')
depends_on('cairo+X+ft+fc+pdf+gobject', type='build', when='+docs')
depends_on('harfbuzz+graphite2', type='build', when='+docs')
@run_after('install')
def install_docs(self):
if '+docs' in self.spec:
with working_dir('docs'):
make('html')
install_tree('docs', self.prefix.docs)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gtable/package.py
|
<filename>var/spack/repos/builtin/packages/r-gtable/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 RGtable(RPackage):
"""Arrange 'Grobs' in Tables.
Tools to make it easier to work with "tables" of 'grobs'. The 'gtable'
package defines a 'gtable' grob class that specifies a grid along with a
list of grobs and their placement in the grid. Further the package makes it
easy to manipulate and combine 'gtable' objects so that complex
compositions can be build up sequentially."""
cran = "gtable"
version('0.3.0', sha256='fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3')
version('0.2.0', sha256='801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f')
depends_on('r@3.0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-tensorflow-hub/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 tempfile
class PyTensorflowHub(Package):
"""TensorFlow Hub is a library to foster the publication, discovery, and
consumption of reusable parts of machine learning models."""
homepage = "https://github.com/tensorflow/hub"
url = "https://github.com/tensorflow/hub/archive/refs/tags/v0.12.0.tar.gz"
maintainers = ['aweits']
version('0.12.0', sha256='b192ef3a9a6cbeaee46142d64b47b979828dbf41fc56d48c6587e08f6b596446')
version('0.11.0', sha256='4715a4212b45531a7c25ada7207d850467d1b5480f1940f16623f8770ad64df4')
extends('python')
depends_on('bazel', type='build')
depends_on('py-pip', type='build')
depends_on('py-wheel', type='build')
depends_on('py-setuptools', type='build')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-numpy@1.12.0:', type=('build', 'run'))
depends_on('py-protobuf@3.8.0:', type=('build', 'run'))
def install(self, spec, prefix):
tmp_path = tempfile.mkdtemp(prefix='spack')
env['TEST_TMPDIR'] = tmp_path
env['HOME'] = tmp_path
args = [
# Don't allow user or system .bazelrc to override build settings
'--nohome_rc',
'--nosystem_rc',
# Bazel does not work properly on NFS, switch to /tmp
'--output_user_root=' + tmp_path,
'build',
# Spack logs don't handle colored output well
'--color=no',
'--jobs={0}'.format(make_jobs),
# Enable verbose output for failures
'--verbose_failures',
# Show (formatted) subcommands being executed
'--subcommands=pretty_print',
'--spawn_strategy=local',
# Ask bazel to explain what it's up to
# Needs a filename as argument
'--explain=explainlogfile.txt',
# Increase verbosity of explanation,
'--verbose_explanations',
# bazel uses system PYTHONPATH instead of spack paths
'--action_env', 'PYTHONPATH={0}'.format(env['PYTHONPATH']),
'//tensorflow_hub/pip_package:build_pip_package',
]
bazel(*args)
runfiles = join_path('bazel-bin', 'tensorflow_hub', 'pip_package',
'build_pip_package.runfiles', 'org_tensorflow_hub')
insttmp_path = tempfile.mkdtemp(prefix='spack')
install(join_path('tensorflow_hub', 'pip_package', 'setup.py'), insttmp_path)
install(join_path('tensorflow_hub', 'pip_package', 'setup.cfg'), insttmp_path)
install('LICENSE', join_path(insttmp_path, 'LICENSE.txt'))
mkdirp(join_path(insttmp_path, 'tensorflow_hub'))
install_tree(join_path(runfiles, 'tensorflow_hub'),
join_path(insttmp_path, 'tensorflow_hub'))
with working_dir(insttmp_path):
args = std_pip_args + ['--prefix=' + prefix, '.']
pip(*args)
remove_linked_tree(tmp_path)
remove_linked_tree(insttmp_path)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-tidytree/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 RTidytree(RPackage):
"""A Tidy Tool for Phylogenetic Tree Data Manipulation.
Phylogenetic tree generally contains multiple components including node,
edge, branch and associated data. 'tidytree' provides an approach to
convert tree object to tidy data frame as well as provides tidy interfaces
to manipulate tree data."""
cran = "tidytree"
version('0.3.7', sha256='7816f2d48ec94ca0c1bef15ec3d536adf44a969ea3c3cfc203ceebe16808e4f2')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-ape', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
depends_on('r-lazyeval', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'))
depends_on('r-tibble', type=('build', 'run'))
depends_on('r-tidyr', type=('build', 'run'))
depends_on('r-tidyselect', type=('build', 'run'))
depends_on('r-yulab-utils@0.0.4:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-gistr/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 RGistr(RPackage):
"""Work with 'GitHub' 'Gists'.
Work with 'GitHub' 'gists' from 'R' (e.g.,
<https://en.wikipedia.org/wiki/GitHub#Gist>,
<https://docs.github.com/en/github/writing-on-github/creating-gists/>). A
'gist' is simply one or more files with code/text/images/etc. This package
allows the user to create new 'gists', update 'gists' with new files,
rename files, delete files, get and delete 'gists', star and 'un-star'
'gists', fork 'gists', open a 'gist' in your default browser, get embed
code for a 'gist', list 'gist' 'commits', and get rate limit information
when 'authenticated'. Some requests require authentication and some do not.
'Gists' website: <https://gist.github.com/>."""
cran = "gistr"
version('0.9.0', sha256='170ae025151ee688e7d31b9e49112086a8ddf4fef10155e9ee289ad7f28c8929')
version('0.4.2', sha256='43c00c7f565732125f45f6c067724771ba1b337d6dd3a6e301639fe16e11032e')
version('0.4.0', sha256='51771a257379a17552d0c88ada72ca6263954bbe896997f8a66cde3bf0b83ce0')
version('0.3.6', sha256='ab22523b79510ec03be336e1d4600ec8a3a65afe57c5843621a4cf8f966b52e5')
depends_on('r+X', type=('build', 'run'))
depends_on('r-jsonlite@1.4:', type=('build', 'run'))
depends_on('r-crul', type=('build', 'run'), when='@0.9.0:')
depends_on('r-httr@1.2.0:', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))
depends_on('r-assertthat', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))
depends_on('r-rmarkdown', type=('build', 'run'))
depends_on('r-dplyr', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/crtm/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 Crtm(CMakePackage):
"""The Community Radiative Transfer Model (CRTM) package.
The CRTM is composed of four important modules for gaseous transmittance,
surface emission and reflection, cloud and aerosol absorption and
scattering, and a solver for a radiative transfer."""
homepage = "https://www.jcsda.org/jcsda-project-community-radiative-transfer-model"
url = "https://github.com/NOAA-EMC/EMC_crtm/archive/refs/tags/v2.3.0.tar.gz"
maintainers = ['t-brown', 'edwardhartnett', 'kgerheiser', 'Hang-Lei-NOAA']
version('2.3.0', sha256='3e2c87ae5498c33dd98f9ede5c39e33ee7f298c7317b12adeb552e3a572700ce')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-gym/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 PyGym(PythonPackage):
"""OpenAI Gym is a toolkit for developing and comparing
reinforcement learning algorithms. This is the gym open-source
library, which gives you access to a standardized set of
environments."""
homepage = "https://github.com/openai/gym"
pypi = "gym/0.18.0.tar.gz"
version('0.18.0', sha256='a0dcd25c1373f3938f4cb4565f74f434fba6faefb73a42d09c9dddd0c08af53e')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-numpy@1.10.4:', type=('build', 'run'))
depends_on('py-pyglet@1.4.0:1.5.0', type=('build', 'run'), when='@0.18.0')
depends_on('py-pyglet@1.4.0:1.5.15', type=('build', 'run'), when='@0.18.1')
depends_on('pil@:8.2.0', type=('build', 'run'), when='@0.18.1')
depends_on('pil@:7.2.0', type=('build', 'run'), when='@0.18.0')
depends_on('py-cloudpickle@1.2.0:1.6', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/slf4j/package.py
|
<filename>var/spack/repos/builtin/packages/slf4j/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 Slf4j(MavenPackage):
"""The Simple Logging Facade for Java (SLF4J) serves as a simple facade
or abstraction for various logging frameworks (e.g. java.util.logging,
logback,log4j) allowing the end user to plug in the desired logging
framework at deployment time."""
homepage = "http://www.slf4j.org/"
url = "https://github.com/qos-ch/slf4j/archive/v_1.7.30.tar.gz"
version('1.7.30', sha256='217519588d0dd1f85cee2357ca31afdd7c0a1a8a6963953b3bf455cf5174633e')
version('1.7.29', sha256='e584f1f380d8c64ed8a45944cec3c2fb4d6b850783fd5bc166a9246bc8b6ac56')
version('1.7.28', sha256='14063bfcbc942bda03e07759e64307163c1646d70a42c632f066812a8630eec7')
version('1.7.27', sha256='238883cab9808a5cd58cf5245f9f13ac645c9fca878b60d959e00fc4ac588231')
version('1.7.26', sha256='dc422820f92e581241c4cfe796d01531d12bad3dc04225bdb315761871156942')
depends_on('java@8', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/log4cpp/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 Log4cpp(AutotoolsPackage):
"""Log4cpp is library of C++ classes for flexible logging to
files, syslog, IDSA and other destinations. It is modeled after
the Log4j Java library, staying as close to their API as is
reasonable."""
homepage = "http://log4cpp.sourceforge.net/"
url = "http://sourceforge.net/projects/log4cpp/files/log4cpp-1.1.3.tar.gz"
version('1.1.3', sha256='2cbbea55a5d6895c9f0116a9a9ce3afb86df383cd05c9d6c1a4238e5e5c8f51d')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/bamutil/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 Bamutil(MakefilePackage):
"""bamUtil is a repository that contains several programs
that perform operations on SAM/BAM files. All of these programs
are built into a single executable, bam.
"""
homepage = "https://genome.sph.umich.edu/wiki/BamUtil"
url = "https://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
version('1.0.13', sha256='16c1d01c37d1f98b98c144f3dd0fda6068c1902f06bd0989f36ce425eb0c592b')
depends_on('zlib', type=('build', 'link'))
# Looks like this will be fixed in 1.0.14.
# https://github.com/statgen/libStatGen/issues/9
patch('libstatgen-issue-9.patch', when='@1.0.13:')
# These are fixed in the standalone libStatGen,
# but bamutil@1.0.13 embeds its own copy, so fix 'em here.
patch('libstatgen-issue-19.patch', when='@1.0.13')
patch('libstatgen-issue-17.patch', when='@1.0.13')
patch('libstatgen-issue-7.patch', when='@1.0.13')
patch('verifybamid-issue-8.patch', when='@1.0.13')
parallel = False
@property
def install_targets(self):
return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rsvd/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 RRsvd(RPackage):
"""Randomized Singular Value Decomposition.
Low-rank matrix decompositions are fundamental tools and widely used for
data analysis, dimension reduction, and data compression. Classically,
highly accurate deterministic matrix algorithms are used for this task.
However, the emergence of large-scale data has severely challenged our
computational ability to analyze big data. The concept of randomness has
been demonstrated as an effective strategy to quickly produce approximate
answers to familiar problems such as the singular value decomposition
(SVD). The rsvd package provides several randomized matrix algorithms such
as the randomized singular value decomposition (rsvd), randomized principal
component analysis (rpca), randomized robust principal component analysis
(rrpca), randomized interpolative decomposition (rid), and the randomized
CUR decomposition (rcur). In addition several plot functions are provided.
The methods are discussed in detail by Erichson et al. (2016)
<arXiv:1608.02148>."""
cran = "rsvd"
version('1.0.5', sha256='e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e')
version('1.0.3', sha256='13560e0fc3ae6927c4cc4d5ad816b1f640a2a445b712a5a612ab17ea0ce179bb')
version('1.0.2', sha256='c8fe5c18bf7bcfe32604a897e3a7caae39b49e47e93edad9e4d07657fc392a3a')
depends_on('r@3.2.2:', type=('build', 'run'))
depends_on('r@4.0.0:', type=('build', 'run'), when='@1.0.5:')
depends_on('r-matrix', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/genesis/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 Genesis(AutotoolsPackage, CudaPackage):
"""GENESIS is a Molecular dynamics and modeling software
for bimolecular systems such as proteins, lipids, glycans,
and their complexes.
"""
homepage = "https://www.r-ccs.riken.jp/labs/cbrt/"
url = "https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2"
git = "https://github.com/genesis-release-r-ccs/genesis-2.0.git"
version("master", branch="master")
version(
"1.6.0",
sha256="d0185a5464ed4231f6ee81f6dcaa15935a99fa30b96658d2b7c25d7fbc5b38e9",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/12/genesis-1.6.0.tar.bz2",
)
version(
"1.5.1",
sha256="62a453a573c36779484b4ffed2dfa56ea03dfe1308d631b33ef03f733259b3ac",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2",
)
resource(
when="@1.6.0",
name="user_guide",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/12/GENESIS-1.6.0.pdf",
sha256="4a6d54eb8f66edde57a4099cdac40cc8e0e2fd6bdb84946da6bf2b3ed84a4ba1",
expand=False,
placement="doc",
)
resource(
when="@1.5.1",
name="user_guide",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2019/10/GENESIS-1.4.0.pdf",
sha256="da2c3f8bfa1e93adb992d3cfce09fb45d8d447a94f9a4f884ac834ea7279b9c7",
expand=False,
placement="doc",
)
variant("openmp", default=True, description="Enable OpenMP.")
variant("single", default=False, description="Enable single precision.")
variant("hmdisk", default=False, description="Enable huge molecule on hard disk.")
conflicts("%apple-clang", when="+openmp")
depends_on("autoconf", type="build", when="@1.5.1 %fj")
depends_on("autoconf", type="build", when="@master")
depends_on("automake", type="build", when="@1.5.1 %fj")
depends_on("automake", type="build", when="@master")
depends_on("libtool", type="build", when="@1.5.1 %fj")
depends_on("libtool", type="build", when="@master")
depends_on("m4", type="build", when="@1.5.1 %fj")
depends_on("m4", type="build", when="@master")
depends_on("mpi", type=("build", "run"))
depends_on("lapack")
depends_on("python@2.6.9:2.8.0", type=("build", "run"), when="@master")
patch("fj_compiler.patch", when="@master %fj")
patch("fj_compiler_1.5.1.patch", when="@1.5.1 %fj")
parallel = False
@property
def force_autoreconf(self):
# Run autoreconf due to build system patch
return self.spec.satisfies("@1.5.1 %fj")
def configure_args(self):
spec = self.spec
options = []
options.extend(self.enable_or_disable("openmp"))
options.extend(self.enable_or_disable("single"))
options.extend(self.enable_or_disable("hmdisk"))
if "+cuda" in spec:
options.append("--enable-gpu")
options.append("--with-cuda=%s" % spec["cuda"].prefix)
else:
options.append("--disable-gpu")
if spec.target == "a64fx" and self.spec.satisfies("@master %fj"):
options.append("--host=Fugaku")
return options
def setup_build_environment(self, env):
env.set("FC", self.spec["mpi"].mpifc, force=True)
env.set("F77", self.spec["mpi"].mpif77, force=True)
env.set("CC", self.spec["mpi"].mpicc, force=True)
env.set("CXX", self.spec["mpi"].mpicxx, force=True)
env.set("LAPACK_LIBS", self.spec["lapack"].libs.ld_flags)
if "+cuda" in self.spec:
cuda_arch = self.spec.variants["cuda_arch"].value
cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
env.set("NVCCFLAGS", cuda_gencode)
def install(self, spec, prefix):
make("install")
install_tree("doc", prefix.share.doc)
@property
def cached_tests_work_dir(self):
"""The working directory for cached test sources."""
return join_path(self.test_suite.current_test_cache_dir,
"tests")
@run_after("install")
def cache_test_sources(self):
"""Copy test files after the package is installed for test()."""
if self.spec.satisfies("@master"):
self.cache_extra_test_sources(["tests"])
def test(self):
"""Perform stand-alone/smoke tests using installed package."""
if not self.spec.satisfies("@master"):
print('Skipping: Tests are only available for the master branch')
return
test_name = join_path(
self.cached_tests_work_dir, "regression_test", "test.py"
)
bin_name = join_path(self.prefix.bin, "spdyn")
opts = [
test_name,
self.spec["mpi"].prefix.bin.mpirun + " -np 8 " + bin_name,
]
env["OMP_NUM_THREADS"] = "1"
self.run_test(
self.spec["python"].command.path,
options=opts,
expected="Passed 53 / 53",
purpose="test: running regression test",
work_dir=self.cached_tests_work_dir
)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-ipython/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 PyIpython(PythonPackage):
"""IPython provides a rich toolkit to help you make the most out of using
Python interactively."""
homepage = "https://ipython.readthedocs.org/"
pypi = "ipython/ipython-7.18.1.tar.gz"
version('8.0.1', sha256='ab564d4521ea8ceaac26c3a2c6e5ddbca15c8848fd5a5cc325f960da88d42974')
version('7.28.0', sha256='2097be5c814d1b974aea57673176a924c4c8c9583890e7a5f082f547b9975b11')
version('7.27.0', sha256='58b55ebfdfa260dad10d509702dc2857cb25ad82609506b070cf2d7b7df5af13')
version('7.26.0', sha256='0cff04bb042800129348701f7bd68a430a844e8fb193979c08f6c99f28bb735e')
version('7.21.0', sha256='04323f72d5b85b606330b6d7e2dc8d2683ad46c3905e955aa96ecc7a99388e70')
version('7.18.1', sha256='a331e78086001931de9424940699691ad49dfb457cea31f5471eae7b78222d5e')
version('7.5.0', sha256='e840810029224b56cd0d9e7719dc3b39cf84d577f8ac686547c8ba7a06eeab26')
version('7.3.0', sha256='06de667a9e406924f97781bda22d5d76bfb39762b678762d86a466e63f65dc39')
version('5.8.0', sha256='4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906')
version('5.1.0', sha256='7ef4694e1345913182126b219aaa4a0047e191af414256da6772cf249571b961')
version('3.1.0', sha256='532092d3f06f82b1d8d1e5c37097eae19fcf025f8f6a4b670dd49c3c338d5624')
version('2.3.1', sha256='3e98466aa2fe54540bcba9aa6e01a39f40110d67668c297340c4b9514b7cc49c')
depends_on('python@3.8:', when='@8:', type=('build', 'run'))
depends_on('python@3.7:', when='@7.17:', type=('build', 'run'))
depends_on('python@3.6:', when='@7.10:', type=('build', 'run'))
depends_on('python@3.5:', when='@7:', type=('build', 'run'))
depends_on('python@3.3:', when='@6:', type=('build', 'run'))
depends_on('python@2.7:2.8,3.3:', type=('build', 'run'))
depends_on('py-setuptools@51:', when='@8:', type='build')
depends_on('py-setuptools@18.5:', when='@4.1:', type='run')
depends_on('py-jedi@0.16:', when='@7.18,7.20:', type=('build', 'run'))
depends_on('py-jedi@0.10:', when='@7.5:7.17,7.19', type=('build', 'run'))
depends_on('py-black', when='@8:', type=('build', 'run'))
depends_on('py-decorator', type=('build', 'run'))
depends_on('py-pickleshare', type=('build', 'run'))
depends_on('py-traitlets@5:', when='@8:', type=('build', 'run'))
depends_on('py-traitlets@4.2:', type=('build', 'run'))
depends_on('py-prompt-toolkit@2.0.0:2,3.0.2:3.0', when='@7.26:', type=('build', 'run'))
depends_on('py-prompt-toolkit@3.0.2:3.0', when='@7.18:7.25', type=('build', 'run'))
depends_on('py-prompt-toolkit@2.0.0:2.0', when='@7.5.0', type=('build', 'run'))
depends_on('py-prompt-toolkit@2.0.0:2', when='@7.0.0:7.5.0', type=('build', 'run'))
depends_on('py-prompt-toolkit@1.0.4:1', when='@:7.0.0', type=('build', 'run'))
depends_on('py-pygments', type=('build', 'run'))
depends_on('py-backcall', when='@7.3.0:', type=('build', 'run'))
depends_on('py-stack-data', when='@8:', type=('build', 'run'))
depends_on('py-matplotlib-inline', when='@7.23:', type=('build', 'run'))
depends_on('py-pexpect@4.4:', when='@7.18: platform=linux', type=('build', 'run'))
depends_on('py-pexpect@4.4:', when='@7.18: platform=darwin', type=('build', 'run'))
depends_on('py-pexpect@4.4:', when='@7.18: platform=cray', type=('build', 'run'))
depends_on('py-pexpect', type=('build', 'run'))
depends_on('py-appnope', when='platform=darwin', type=('build', 'run'))
depends_on('py-colorama', when='platform=windows', type=('build', 'run'))
depends_on('py-backports-shutil-get-terminal-size', when="^python@:3.2", type=('build', 'run'))
depends_on('py-pathlib2', when="^python@:3.3", type=('build', 'run'))
depends_on('py-simplegeneric@0.8:', when='@:7.0.0', type=('build', 'run'))
@property
def import_modules(self):
modules = super(__class__, self).import_modules
if self.spec.satisfies('@8:'):
return modules
# 'IPython.kernel' is deprecated and fails to import, leave out of
# 'import_modules' to ensure that import tests pass.
ignored_imports = ["IPython.kernel"]
return [i for i in modules
if not any(map(i.startswith, ignored_imports))]
|
player1537-forks/spack
|
var/spack/repos/builtin.mock/packages/unsat-virtual-dependency/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 UnsatVirtualDependency(Package):
"""This package has a dependency on a virtual that cannot be provided"""
homepage = "http://www.example.com"
url = "http://www.example.com/v1.0.tgz"
version('1.0', sha256='0123456789abcdef0123456789abcdef')
depends_on('unsatvdep')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/gmp/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 Gmp(AutotoolsPackage, GNUMirrorPackage):
"""GMP is a free library for arbitrary precision arithmetic, operating
on signed integers, rational numbers, and floating-point numbers."""
homepage = "https://gmplib.org"
gnu_mirror_path = "gmp/gmp-6.1.2.tar.bz2"
version('6.2.1', sha256='eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c')
version('6.2.0', sha256='f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea')
version('6.1.2', sha256='5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2')
version('6.1.1', sha256='a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6')
version('6.1.0', sha256='498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8')
version('6.0.0a', sha256='7f8e9a804b9c6d07164cf754207be838ece1219425d64e28cfa3e70d5c759aaf')
version('5.1.3', sha256='752079520b4690531171d0f4532e40f08600215feefede70b24fabdc6f1ab160')
# Old version needed for a binary package in ghc-bootstrap
version('4.3.2', sha256='936162c0312886c21581002b79932829aa048cfaf9937c6265aeaa14f1cd1775')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
# gmp's configure script seems to be broken; it sometimes misdetects
# shared library support. Regenerating it fixes the issue.
force_autoreconf = True
def flag_handler(self, name, flags):
# Work around macOS Catalina / Xcode 11 code generation bug
# (test failure t-toom53, due to wrong code in mpn/toom53_mul.o)
if self.spec.satisfies('os=catalina') and name == 'cflags':
flags.append('-fno-stack-check')
# This flag is necessary for the Intel build to pass `make check`
elif self.spec.satisfies('%intel') and name == 'cxxflags':
flags.append('-no-ftz')
return (flags, None, None)
def configure_args(self):
return ['--enable-cxx']
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/atf/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 Atf(AutotoolsPackage):
"""ATF, or Automated Testing Framework, is a collection of libraries
to write test programs in C, C++ and POSIX shell."""
homepage = "https://github.com/jmmv/atf"
url = "https://github.com/jmmv/atf/archive/atf-0.21.tar.gz"
version('0.21', sha256='da6b02d6e7242f768a7aaa7b7e52378680456e4bd9a913b6636187079c98f3cd')
version('0.20', sha256='3677cf957d7f574835b8bdd385984ba928d5695b3ff28f958e4227f810483ab7')
version('0.19', sha256='f9b1d76dad7c34ae61a75638edc517fc05b10fa4c8f97b1d13d739bffee79b16')
depends_on('m4', type='build')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libxstream/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 Libxstream(Package):
"""LIBXSTREAM is a library to work with streams, events, and code regions
that are able to run asynchronous while preserving the usual stream
conditions."""
homepage = 'https://github.com/hfp/libxstream'
url = 'https://github.com/hfp/libxstream/archive/0.9.0.tar.gz'
version('0.9.0', sha256='03365f23b337533b8e5a049a24bc5a91c0f1539dd042ca5312abccc8f713b473')
def patch(self):
kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
makefile = FileFilter('Makefile.inc')
makefile.filter('CC =', 'CC ?=', **kwargs)
makefile.filter('CXX =', 'CXX ?=', **kwargs)
makefile.filter('FC =', 'FC ?=', **kwargs)
def install(self, spec, prefix):
make()
install_tree('lib', prefix.lib)
install_tree('include', prefix.include)
install_tree('documentation', prefix.share + '/libxstream/doc/')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-epydoc/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 PyEpydoc(PythonPackage):
"""Epydoc is a tool for generating API documentation documentation for
Python modules, based on their docstrings."""
pypi = "epydoc/epydoc-3.0.1.tar.gz"
version('3.0.1', sha256='c81469b853fab06ec42b39e35dd7cccbe9938dfddef324683d89c1e5176e48f2')
# pip silently replaces distutils with setuptools
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-proc/package.py
|
<filename>var/spack/repos/builtin/packages/r-proc/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 RProc(RPackage):
"""Display and Analyze ROC Curves.
Tools for visualizing, smoothing and comparing receiver operating
characteristic (ROC curves). (Partial) area under the curve (AUC) can be
compared with statistical tests based on U-statistics or bootstrap.
Confidence intervals can be computed for (p)AUC or ROC curves."""
cran = "pROC"
version('1.18.0', sha256='d5ef54b384176ece6d6448014ba40570a98181b58fee742f315604addb5f7ba9')
version('1.17.0.1', sha256='221c726ffb81b04b999905effccfd3a223cd73cae70d7d86688e2dd30e51a6bd')
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r-plyr', type=('build', 'run'))
depends_on('r-rcpp@0.11.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-biom-utils/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/r-biom-utils/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 RBiomUtils(RPackage):
"""Utilities for the BIOM (Biological Observation Matrix) Format.
Provides utilities to facilitate import, export and computation with the
BIOM (Biological Observation Matrix) format (https://biom-format.org/)."""
cran = "BIOM.utils"
version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')
depends_on('r@3:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/fxdiv/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 Fxdiv(CMakePackage):
"""Header-only library for division via fixed-point multiplication by inverse."""
homepage = "https://github.com/Maratyszcza/FXdiv"
git = "https://github.com/Maratyszcza/FXdiv.git"
version('master', branch='master')
version('2020-04-17', commit='<PASSWORD>') # py-torch@1.6:1.9
version('2018-11-16', commit='<PASSWORD>') # py-torch@1.0:1.5
version('2018-02-24', commit='<KEY>') # py-torch@0.4
depends_on('cmake@3.5:', type='build')
depends_on('ninja', type='build')
depends_on('python', type='build')
generator = 'Ninja'
def cmake_args(self):
return [
self.define('FXDIV_BUILD_TESTS', False),
self.define('FXDIV_BUILD_BENCHMARKS', False)
]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/miniapp-ascent/package.py
|
<filename>var/spack/repos/builtin/packages/miniapp-ascent/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 MiniappAscent(Package):
"""Pantheon/E4S/Ascent in-situ miniapp example workflow"""
homepage = "https://github.com/cinemascienceworkflows/2021-04_Miniapp-Ascent"
git = "https://github.com/cinemascienceworkflows/2021-04_Miniapp-Ascent.git"
url = "https://github.com/cinemascienceworkflows/2021-04_Miniapp-Ascent/archive/refs/heads/master.zip"
version('master',
branch='master')
depends_on("ascent", type=('run'))
def install(self, spec, prefix):
install_tree(self.stage.source_path, prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-sqlalchemy-stubs/package.py
|
<filename>var/spack/repos/builtin/packages/py-sqlalchemy-stubs/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 PySqlalchemyStubs(PythonPackage):
"""
Mypy plugin and stubs for SQLAlchemy
"""
homepage = "https://github.com/dropbox/sqlalchemy-stubs"
pypi = "sqlalchemy-stubs/sqlalchemy-stubs-0.4.tar.gz"
version('0.4', sha256='c665d6dd4482ef642f01027fa06c3d5e91befabb219dc71fc2a09e7d7695f7ae')
depends_on('python@3.5:', type=('build', 'run'))
depends_on('py-mypy@0.790:', type=('build', 'run'))
depends_on('py-typing-extensions@3.7.4:', type=('build', 'run'))
depends_on('py-setuptools', type=('build'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-keyboard/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 PyKeyboard(PythonPackage):
"""Take full control of your keyboard with this small
Python library. Hook global events, register hotkeys,
simulate key presses and much more."""
homepage = "https://github.com/boppreh/keyboard"
pypi = "keyboard/keyboard-0.13.5.zip"
version('0.13.5', sha256='63ed83305955939ca5c9a73755e5cc43e8242263f5ad5fd3bb7e0b032f3d308b')
depends_on('py-setuptools', type='build')
# depends_on('py-pyobjc', when='platform=darwin', type=('build', 'run'))
# Until py-pyobjc can be created, specifying conflict with platform=darwin
conflicts('platform=darwin')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-jsonpath-ng/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 PyJsonpathNg(PythonPackage):
"""A final implementation of JSONPath for Python that aims to be
standard compliant, including arithmetic and binary comparison
operators."""
homepage = "https://github.com/h2non/jsonpath-ng"
pypi = "jsonpath-ng/jsonpath-ng-1.5.2.tar.gz"
version('1.5.2', sha256='144d91379be14d9019f51973bd647719c877bfc07dc6f3f5068895765950c69d')
depends_on('py-setuptools', type='build')
depends_on('py-ply', type=('build', 'run'))
depends_on('py-decorator', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-cowplot/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 RCowplot(RPackage):
"""Streamlined Plot Theme and Plot Annotations for 'ggplot2'.
Provides various features that help with creating publication-quality
figures with 'ggplot2', such as a set of themes, functions to align plots
and arrange them into complex compound figures, and functions that make it
easy to annotate plots and or mix plots with images. The package was
originally written for internal use in the Wilke lab, hence the name (Claus
<NAME>'s plot package). It has also been used extensively in the book
Fundamentals of Data Visualization."""
cran = "cowplot"
version('1.1.1', sha256='c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48')
version('1.0.0', sha256='70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5')
version('0.9.3', sha256='3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb')
version('0.9.2', sha256='8b92ce7f92937fde06b0cfb86c7634a39b3b2101e362cc55c4bec6b3fde1d28f')
version('0.9.1', sha256='953fd9d6ff370472b9f5a9ee867a423bea3e26e406d08a2192ec1872a2e60047')
version('0.9.0', sha256='d5632f78294c3678c08d3eb090abe1eec5cc9cd15cb5d96f9c43794ead098cb5')
version('0.8.0', sha256='a617fde25030fe764f20967fb753a953d73b47745a2146c97c2565eb4d06700d')
depends_on('r@3.3.0:', type=('build', 'run'))
depends_on('r@3.5.0:', type=('build', 'run'), when='@1.0.0:')
depends_on('r-ggplot2@2.1.1:', type=('build', 'run'))
depends_on('r-ggplot2@2.2.1:', type=('build', 'run'), when='@1.1.1:')
depends_on('r-gtable', type=('build', 'run'))
depends_on('r-rlang', type=('build', 'run'), when='@1.0.0:')
depends_on('r-scales', type=('build', 'run'))
depends_on('r-plyr@1.8.2:', type=('build', 'run'), when='@:0.9.9')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-qiskit-terra/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 PyQiskitTerra(PythonPackage):
"""Qiskit is an open-source SDK for working with quantum computers
at the level of extended quantum circuits, operators, and
algorithms."""
homepage = "https://github.com/Qiskit/qiskit-terra"
pypi = "qiskit-terra/qiskit-terra-0.18.3.tar.gz"
version('0.18.3', sha256='8737c8f1f4c6f29ec2fb02d73023f4854a396c33f78f4629a861a3e48fc789cc')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-cython@0.27.1:', type='build')
depends_on('py-contextvars@2.4:', when='^python@:3.6', type=('build', 'run'))
depends_on('py-jsonschema@2.6:', type=('build', 'run'))
depends_on('py-retworkx@0.9.0:', type=('build', 'run'))
depends_on('py-numpy@1.17:', type=('build', 'run'))
depends_on('py-scipy@1.4:', type=('build', 'run'))
depends_on('py-ply@3.10:', type=('build', 'run'))
depends_on('py-psutil@5:', type=('build', 'run'))
depends_on('py-sympy@1.3:', type=('build', 'run'))
depends_on('py-dill@0.3:', type=('build', 'run'))
depends_on('py-fastjsonschema@2.10:', type=('build', 'run'))
depends_on('py-python-constraint@1.4:', type=('build', 'run'))
depends_on('py-python-dateutil@2.8.0:', type=('build', 'run'))
depends_on('py-symengine@0.7:', type=('build', 'run'))
depends_on('py-tweedledum@1.1:1', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/hipsycl/package.py
|
<filename>var/spack/repos/builtin/packages/hipsycl/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 json
from os import path
from llnl.util import filesystem
from spack import *
class Hipsycl(CMakePackage):
"""hipSYCL is an implementation of the SYCL standard programming model
over NVIDIA CUDA/AMD HIP"""
homepage = "https://github.com/illuhad/hipSYCL"
url = "https://github.com/illuhad/hipSYCL/archive/v0.8.0.tar.gz"
git = "https://github.com/illuhad/hipSYCL.git"
maintainers = ["nazavode"]
provides("sycl")
version("stable", branch="stable", submodules=True)
version(
"0.9.1",
commit="<PASSWORD>",
submodules=True)
version(
"0.8.0",
commit="<PASSWORD>",
submodules=True,
)
variant(
"cuda",
default=False,
description="Enable CUDA backend for SYCL kernels",
)
depends_on("cmake@3.5:", type="build")
depends_on("boost +filesystem", when="@:0.8")
depends_on("boost@1.67.0:1.69.0 +filesystem +fiber +context cxxstd=17", when='@0.9.1:')
depends_on("python@3:")
depends_on("llvm@8: +clang", when="~cuda")
depends_on("llvm@9: +clang", when="+cuda")
# LLVM PTX backend requires cuda7:10.1 (https://tinyurl.com/v82k5qq)
depends_on("cuda@9:10.1", when="@0.8.1: +cuda")
# hipSYCL@:0.8.0 requires cuda@9:10.0 due to a known bug
depends_on("cuda@9:10.0", when="@:0.8.0 +cuda")
conflicts(
"%gcc@:4",
when='@:0.9.0',
msg="hipSYCL needs proper C++14 support to be built, %gcc is too old",
)
conflicts(
"%gcc@:8",
when='@0.9.1:',
msg="hipSYCL needs proper C++17 support to be built, %gcc is too old")
conflicts(
"^llvm build_type=Debug",
when="+cuda",
msg="LLVM debug builds don't work with hipSYCL CUDA backend; for "
"further info please refer to: "
"https://github.com/illuhad/hipSYCL/blob/master/doc/install-cuda.md",
)
def cmake_args(self):
spec = self.spec
args = [
"-DWITH_CPU_BACKEND:Bool=TRUE",
# TODO: no ROCm stuff available in spack yet
"-DWITH_ROCM_BACKEND:Bool=FALSE",
"-DWITH_CUDA_BACKEND:Bool={0}".format(
"TRUE" if "+cuda" in spec else "FALSE"
),
# prevent hipSYCL's cmake to look for other LLVM installations
# if the specified one isn't compatible
"-DDISABLE_LLVM_VERSION_CHECK:Bool=TRUE",
]
# LLVM directory containing all installed CMake files
# (e.g.: configs consumed by client projects)
llvm_cmake_dirs = filesystem.find(
spec["llvm"].prefix, "LLVMExports.cmake"
)
if len(llvm_cmake_dirs) != 1:
raise InstallError(
"concretized llvm dependency must provide "
"a unique directory containing CMake client "
"files, found: {0}".format(llvm_cmake_dirs)
)
args.append(
"-DLLVM_DIR:String={0}".format(path.dirname(llvm_cmake_dirs[0]))
)
# clang internal headers directory
llvm_clang_include_dirs = filesystem.find(
spec["llvm"].prefix, "__clang_cuda_runtime_wrapper.h"
)
if len(llvm_clang_include_dirs) != 1:
raise InstallError(
"concretized llvm dependency must provide a "
"unique directory containing clang internal "
"headers, found: {0}".format(llvm_clang_include_dirs)
)
args.append(
"-DCLANG_INCLUDE_PATH:String={0}".format(
path.dirname(llvm_clang_include_dirs[0])
)
)
# target clang++ executable
llvm_clang_bin = path.join(spec["llvm"].prefix.bin, "clang++")
if not filesystem.is_exe(llvm_clang_bin):
raise InstallError(
"concretized llvm dependency must provide a "
"valid clang++ executable, found invalid: "
"{0}".format(llvm_clang_bin)
)
args.append(
"-DCLANG_EXECUTABLE_PATH:String={0}".format(llvm_clang_bin)
)
# explicit CUDA toolkit
if "+cuda" in spec:
args.append(
"-DCUDA_TOOLKIT_ROOT_DIR:String={0}".format(
spec["cuda"].prefix
)
)
return args
@run_after("install")
def filter_config_file(self):
config_file_paths = filesystem.find(self.prefix, "syclcc.json")
if len(config_file_paths) != 1:
raise InstallError(
"installed hipSYCL must provide a unique compiler driver "
"configuration file, found: {0}".format(config_file_paths)
)
config_file_path = config_file_paths[0]
with open(config_file_path) as f:
config = json.load(f)
# 1. Fix compiler: use the real one in place of the Spack wrapper
config["default-cpu-cxx"] = self.compiler.cxx
# 2. Fix stdlib: we need to make sure cuda-enabled binaries find
# the libc++.so and libc++abi.so dyn linked to the sycl
# ptx backend
rpaths = set()
so_paths = filesystem.find(self.spec["llvm"].prefix, "libc++.so")
if len(so_paths) != 1:
raise InstallError(
"concretized llvm dependency must provide a "
"unique directory containing libc++.so, "
"found: {0}".format(so_paths)
)
rpaths.add(path.dirname(so_paths[0]))
so_paths = filesystem.find(self.spec["llvm"].prefix, "libc++abi.so")
if len(so_paths) != 1:
raise InstallError(
"concretized llvm dependency must provide a "
"unique directory containing libc++abi.so, "
"found: {0}".format(so_paths)
)
rpaths.add(path.dirname(so_paths[0]))
config["default-cuda-link-line"] += " " + " ".join(
"-rpath {0}".format(p) for p in rpaths
)
# Replace the installed config file
with open(config_file_path, "w") as f:
json.dump(config, f, indent=2)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-bitops/package.py
|
<reponame>player1537-forks/spack<filename>var/spack/repos/builtin/packages/r-bitops/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 RBitops(RPackage):
"""Bitwise Operations.
Functions for bitwise operations on integer vectors."""
cran = "bitops"
version('1.0-7', sha256='e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4')
version('1.0-6', sha256='9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/shortbred/package.py
|
<filename>var/spack/repos/builtin/packages/shortbred/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 Shortbred(Package):
"""ShortBRED is a system for profiling protein families of interest at
very high specificity in shotgun meta'omic sequencing data."""
homepage = "https://huttenhower.sph.harvard.edu/shortbred"
url = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
version('0.9.4', sha256='a85e5609db79696d3f2d478408fc6abfeea7628de9f533c4e1e0ea3622b397ba')
depends_on('blast-plus@2.2.28:')
depends_on('cdhit@4.6:')
depends_on('muscle@3.8.31:')
depends_on('python@2.7.9:')
depends_on('py-biopython')
depends_on('usearch@6.0.307:')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('shortbred_identify.py', prefix.bin)
install('shortbred_quantify.py', prefix.bin)
install_tree('src', prefix.src)
def setup_run_environment(self, env):
env.prepend_path('PYTHONPATH', self.prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-libclang/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 PyLibclang(PythonPackage):
"""The repository contains code that taken from the LLVM project, to make
it easier to install clang's python bindings."""
homepage = "https://github.com/sighingnow/libclang"
url = "https://github.com/sighingnow/libclang/archive/refs/tags/llvm-11.1.0.tar.gz"
version(
"11.1.0",
sha256="0b53b3c237725e193c4d2bbbe096f1a1da0f0e5cd528f2892e4dfed3c8fe9506",
)
version(
"11.0.1",
sha256="739ae984a4a4043ae4d3b4db74597a36a8e46b6f0cbd139c7d2703faf40c5390",
)
version(
"11.0.0",
sha256="aec204414ea412e4d4e041b0bf48123881338ac723bbcfa948f2a1b92a2428b5",
)
version(
"10.0.1",
sha256="c15d8f97c4d0f3d4501e8b2625b343569fd92690afebe6260a2c64463d713995",
)
version(
"9.0.1",
sha256="fc84e7bf3b0eb4f11c496d6603f111e3d8cda97094d6c9c512361371f1b76f1c",
)
depends_on("python@2.7:2.8,3.3:", type=("build", "run"))
depends_on("py-setuptools", type="build")
for ver in ["9", "10", "11"]:
depends_on("llvm+clang@" + ver, when="@" + ver, type="build")
def patch(self):
filter_file(
"source_dir = './native/'",
"source_dir = '{0}'".format(self.spec["llvm"].libs.directories[0]),
"setup.py", string=True,
)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ethminer/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 Ethminer(CMakePackage):
"""The ethminer is an Ethereum GPU mining worker."""
homepage = "https://github.com/ethereum-mining/ethminer"
url = "https://github.com/ethereum-mining/ethminer/archive/v0.12.0.tar.gz"
version('0.12.0', sha256='71122c8aa1be2c29e46d7f07961fa760b1eb390e4d9a2a21cf900f6482a8755a')
variant('opencl', default=True, description='Enable OpenCL mining.')
variant('cuda', default=False, description='Enable CUDA mining.')
variant('stratum', default=True,
description='Build with Stratum protocol support.')
depends_on('python')
depends_on('boost')
depends_on('json-c')
depends_on('curl')
depends_on('zlib')
depends_on('cuda', when='+cuda')
depends_on('mesa', when='+opencl')
def cmake_args(self):
return [
self.define_from_variant('ETHASHCL', 'opencl'),
self.define_from_variant('ETHASHCUDA', 'cuda'),
self.define_from_variant('ETHSTRATUM', 'stratum')
]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-pls/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 RPls(RPackage):
"""Partial Least Squares and Principal Component Regression.
Multivariate regression methods Partial Least Squares Regression (PLSR),
Principal Component Regression (PCR) and Canonical Powered Partial Least
Squares (CPPLS)."""
cran = "pls"
version('2.8-0', sha256='eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf')
version('2.7-3', sha256='8f1d960ab74f05fdd11c4c7a3d30ff9e263fc658f5690b67278ca7c045d0742c')
version('2.7-1', sha256='f8fd817fc2aa046970c49a9a481489a3a2aef8b6f09293fb1f0218f00bfd834b')
version('2.7-0', sha256='5ddc1249a14d69a7a39cc4ae81595ac8c0fbb1e46c911af67907baddeac35875')
version('2.6-0', sha256='3d8708fb7f45863d3861fd231e06955e6750bcbe717e1ccfcc6d66d0cb4d4596')
depends_on('r@2.10:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rpsychi/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 RRpsychi(RPackage):
"""Statistics for psychiatric research.
The rpsychi offers a number of functions for psychiatry, psychiatric
nursing, clinical psychology. Functions are primarily for statistical
significance testing using published work. For example, you can conduct a
factorial analysis of variance (ANOVA), which requires only the mean,
standard deviation, and sample size for each cell, rather than the
individual data. This package covers fundamental statistical tests such as
t-test, chi-square test, analysis of variance, and multiple regression
analysis. With some exceptions, you can obtain effect size and its
confidence interval. These functions help you to obtain effect size from
published work, and then to conduct a priori power analysis or
meta-analysis, even if a researcher do not report effect size in a
published work."""
cran = 'rpsychi'
version('0.8', sha256='9c5465f59c92431e345418aee5bc1f5bc12f843492b20ccb9f92f3bdf19a80c0')
depends_on('r-gtools', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-mapproj/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 RMapproj(RPackage):
"""Map Projections.
Converts latitude/longitude into projected coordinates."""
cran = "mapproj"
version('1.2.8', sha256='865f108f1ee54cda38571b86cd46063a903824d9b4eabfdf75218023d08a7781')
version('1.2.7', sha256='f0081281b08bf3cc7052c4f1360d6d3c20d9063be57754448ad9b48ab0d34c5b')
version('1.2.6', sha256='62a5aa97837ae95ef9f973d95fe45fe43dbbf482dfa922e9df60f3c510e7efe5')
version('1.2-5', sha256='f3026a3a69a550c923b44c18b1ccc60d98e52670a438250d13f3c74cf2195f66')
version('1.2-4', sha256='cf8a1535f57e7cca0a71b3a551e77ad3e7a78f61a94bb19effd3de19dbe7dceb')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-maps@2.3-0:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/dalton/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 Dalton(CMakePackage):
"""Molecular electronic-structure program with extensive
functionality for calculations of molecular properties
at the HF, DFT, MCSCF, MC-srDFT, and CC levels of theory.
"""
homepage = "https://daltonprogram.org"
git = 'https://gitlab.com/dalton/dalton.git'
maintainers = ['foeroyingur']
version('master', branch='master', submodules=True)
version('2020.0', tag='2020.0', submodules=True)
version('2018.2', tag='2018.2', submodules=True)
variant('build_type', default='Release', values=('Debug', 'Release'),
description='CMake build type')
variant('ilp64', default=False, description='Use 64-bit integers')
variant('mpi', default=True, description='Use MPI')
variant('gen1int', default=True, description='Build Gen1Int library')
variant('pelib', default=True, when='~ilp64',
description='Build PE library to enable polarizable embedding calculations')
variant('pde', default=True, when='@2020.0: +pelib',
description='Enable polarizable density embedding through the PE library')
variant('qfitlib', default=True, description='Build QFIT library')
depends_on('cmake@3.1:', type='build')
depends_on('blas', type='link')
depends_on('lapack', type='link')
with when('+pde'):
depends_on('hdf5+fortran', when='+mpi', type='link')
depends_on('hdf5+fortran~mpi', when='~mpi', type='link')
depends_on('mpi', when='+mpi', type=('build', 'link', 'run'))
patch('pelib-master.patch', when='@master+mpi+pelib%gcc@10:',
working_dir='external/pelib')
patch('pelib-2020.0.patch', when='@2020.0+mpi+pelib%gcc@10:',
working_dir='external/pelib')
patch('soppa-2018.2.patch', when='@2018.2%intel')
patch('cbiexc-2018.2.patch', when='@2018.2%intel')
conflicts('%gcc@10:', when='@2018.2',
msg='Dalton 2018.2 cannot be built with GCC >= 10, please use an older'
' version or a different compiler suite.')
def setup_run_environment(self, env):
env.prepend_path('PATH', self.spec.prefix.join('dalton'))
def cmake_args(self):
math_libs = self.spec['lapack'].libs + self.spec['blas'].libs
if '+mpi' in self.spec:
env['CC'] = self.spec['mpi'].mpicc
env['CXX'] = self.spec['mpi'].mpicxx
env['F77'] = self.spec['mpi'].mpif77
env['FC'] = self.spec['mpi'].mpifc
args = ['-DEXPLICIT_LIBS:STRING={0}'.format(math_libs.ld_flags),
self.define('ENABLE_AUTO_BLAS', False),
self.define('ENABLE_AUTO_LAPACK', False),
self.define_from_variant('ENABLE_MPI', variant='mpi'),
self.define_from_variant('ENABLE_64BIT_INTEGERS', variant='ilp64'),
self.define_from_variant('ENABLE_GEN1INT', variant='gen1int'),
self.define_from_variant('ENABLE_PELIB', variant='pelib'),
self.define_from_variant('ENABLE_PDE', variant='pde'),
self.define_from_variant('ENABLE_QFITLIB', variant='qfitlib')]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/miniasm/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 Miniasm(MakefilePackage):
"""Miniasm is a very fast OLC-based de novo assembler for noisy long
reads."""
homepage = "http://www.example.co://github.com/lh3/miniasm"
git = "https://github.com/lh3/miniasm.git"
version('2018-3-30', commit='<PASSWORD>')
depends_on('zlib')
def install(self, spec, prefix):
install_tree('.', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-keras-applications/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 PyKerasApplications(PythonPackage):
"""Sample Deep Learning application in Keras.
Keras depends on this package to run properly."""
homepage = "https://keras.io"
url = "https://github.com/keras-team/keras-applications/archive/1.0.4.tar.gz"
version('1.0.8', sha256='7c37f9e9ef93efac9b4956301cb21ce46c474ce9da41fac9a46753bab6823dfc')
version('1.0.7', sha256='8580a885c8abe4bf8429cb0e551f23e79b14eda73d99138cfa1d355968dd4b0a')
version('1.0.6', sha256='2cb412c97153160ec267b238e958d281ac3532b139cab42045c2d7086a157c21')
version('1.0.4', sha256='37bd2f3ba9c0e0105c193999b1162fd99562cf43e5ef06c73932950ecc46d085')
version('1.0.3', sha256='35b663a4933ee3c826a9349d19048221c997f0dd5ea24dd598c05cf90c72879d')
version('1.0.2', sha256='6d8923876a7f7f2d459dd7efe3b10830f316f714b707f0c136e7f00c63035338')
version('1.0.1', sha256='05ad1a73fddd22ed73ae59065b554e7ea13d05c3d4c6755ac166702b88686db5')
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/wcs/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 Wcs(CMakePackage):
"""Simulates whole cell models using discrete event simulation."""
homepage = "https://github.com/LLNL/wcs.git"
git = "https://github.com/LLNL/wcs.git"
maintainers = ['rblake-llnl']
version('master', branch='master')
version('develop', branch='devel')
depends_on('boost+graph+filesystem+regex+system')
depends_on('sbml@5.18.0:+cpp')
depends_on('cmake@3.12:', type='build')
depends_on('cereal', type='build')
def cmake_args(self):
spec = self.spec
args = [
"-DBOOST_ROOT:PATH=" + spec['boost'].prefix,
"-DCEREAL_ROOT:PATH=" + spec['cereal'].prefix,
"-DSBML_ROOT:PATH=" + spec['sbml'].prefix,
"-DWCS_WITH_SBML:BOOL=ON",
"-DWCS_WITH_EXPRTK:BOOL=ON",
]
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-ncbit/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 RNcbit(RPackage):
"""Retrieve and build NBCI taxonomic data.
Making NCBI taxonomic data locally available and searchable as an R
object."""
cran = "ncbit"
version('2013.03.29', sha256='4480271f14953615c8ddc2e0666866bb1d0964398ba0fab6cc29046436820738')
depends_on('r@2.10:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/package.py
|
<filename>var/spack/repos/builtin/packages/py-sphinxcontrib-applehelp/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 PySphinxcontribApplehelp(PythonPackage):
"""sphinxcontrib-applehelp is a sphinx extension which outputs Apple
help books."""
homepage = "http://sphinx-doc.org/"
pypi = "sphinxcontrib-applehelp/sphinxcontrib-applehelp-1.0.1.tar.gz"
# 'sphinx' requires 'sphinxcontrib-applehelp' at build-time, but
# 'sphinxcontrib-applehelp' requires 'sphinx' at run-time. Don't bother trying to
# import any modules for this package.
import_modules = []
version('1.0.1', sha256='edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897')
depends_on('python@3.5:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-jpeg/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 RJpeg(RPackage):
"""Read and write JPEG images.
This package provides an easy and simple way to read, write and display
bitmap images stored in the JPEG format. It can read and write both files
and in-memory raw vectors."""
cran = "jpeg"
version('0.1-9', sha256='01a175442ec209b838a56a66a3908193aca6f040d537da7838d9368e46913072')
version('0.1-8.1', sha256='1db0a4976fd9b2ae27a37d3e856cca35bc2909323c7a40724846a5d3c18915a9')
version('0.1-8', sha256='d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16')
depends_on('r@2.9.0:', type=('build', 'run'))
depends_on('jpeg')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-cvxpy/package.py
|
<filename>var/spack/repos/builtin/packages/py-cvxpy/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 PyCvxpy(PythonPackage):
"""Convex optimization, for everyone."""
homepage = "https://www.cvxpy.org/index.html"
pypi = "cvxpy/cvxpy-1.0.25.tar.gz"
version('1.1.13', sha256='a9c781e74ad76097b47b86456cb3a943898f7ec9ac8f47bcefc922051cdc4a04')
version('1.0.25', sha256='8535529ddb807067b0d59661dce1d9a6ddb2a218398a38ea7772328ad8a6ea13')
# Dependency versions based on README.md in python packages
depends_on('python@3.4:', type=('build', 'run'), when='@1.1:')
depends_on('python@3.6:', type=('build', 'run'), when='@1.1.13:')
depends_on('py-setuptools', type='build')
depends_on('py-numpy@1.15:', type=('build', 'run'))
depends_on('py-scipy@1.1.0:', type=('build', 'run'))
depends_on('py-ecos@2:', type=('build', 'run'))
depends_on('py-scs@1.1.3:', type=('build', 'run'))
depends_on('py-scs@1.1.6:', type=('build', 'run'), when='@1.1.13:')
depends_on('py-osqp@0.4.1:', type=('build', 'run'))
depends_on('py-multiprocess', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'), when='@:1.0')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/cgm/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 Cgm(AutotoolsPackage):
"""The Common Geometry Module, Argonne (CGMA) is a code library
which provides geometry functionality used for mesh generation and
other applications."""
homepage = "https://sigma.mcs.anl.gov/cgm-library"
url = "https://ftp.mcs.anl.gov/pub/fathom/cgm-16.0.tar.gz"
version('16.0', sha256='b98afe70c64efa19decc5ff01602e8c7afc6b22ce646cad30dc92ecfdce6e23d')
version('13.1.1', sha256='ffde54f0c86055b06cad911bbd4297b88c3fb124c873b03ebee626f807b8ab87')
version('13.1.0', sha256='c81bead4b919bd0cea9dbc61b219e316718d940bd3dc70825c58efbf0a0acdc3')
version('13.1', sha256='985aa6c5db4257999af6f2bdfcb24f2bce74191cdcd98e937700db7fd9f6b549')
variant("mpi", default=True, description='enable mpi support')
variant("oce", default=False, description='enable oce geometry kernel')
variant("debug", default=False, description='enable debug symbols')
variant("shared", default=False, description='enable shared builds')
depends_on('mpi', when='+mpi')
depends_on('oce+X11', when='+oce')
def configure_args(self):
spec = self.spec
args = []
if '+mpi' in spec:
args.extend([
"--with-mpi",
"CC={0}".format(spec['mpi'].mpicc),
"CXX={0}".format(spec['mpi'].mpicxx)
])
else:
args.append("--without-mpi")
if '+oce' in spec:
args.append("--with-occ={0}".format(spec['oce'].prefix))
else:
args.append("--without-occ")
if '+debug' in spec:
args.append("--enable-debug")
if '+shared' in spec:
args.append("--enable-shared")
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/freefem/package.py
|
<filename>var/spack/repos/builtin/packages/freefem/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 Freefem(AutotoolsPackage):
"""FreeFEM is a popular 2D and 3D partial differential equations (PDE) solver.
It allows you to easily implement your own physics modules using the provided
FreeFEM language. FreeFEM offers a large list of finite elements, like the
Lagrange, Taylor-Hood, etc., usable in the continuous and discontinuous
Galerkin method framework.
"""
homepage = "https://freefem.org"
url = "https://github.com/FreeFem/FreeFem-sources/archive/refs/tags/v4.9.tar.gz"
maintainers = ['corentin-dev']
version('4.9', sha256='299ba2b73dfff578b7890f693c1e835680bf55eba87263cabd60d81909e1e0e4')
version('4.8', sha256='499b1ca24d45088226a238412ea1492d9cc3eb6088866904145511469780180d')
version('4.7-1', sha256='60d84424d20b5f6abaee638dc423480fc76f9c389bba1a2f23fd984e39a3fb96')
version('4.7', sha256='c1797b642e9c3d543eaad4949d26ce1e986f531ee9be14fff606ea525ada9206')
version('4.6', sha256='6c09af8e189fc02214b0e664b679b49832c134e29cf1ede3cab29cf754f6078f')
version('4.5', sha256='5b2d4125c312da8fbedd49a72e742f18f35e0ae100c82fb493067dfad5d51432')
variant('mpi', default=False,
description='Activate MPI support')
variant('petsc', default=False,
description='Compile with PETSc/SLEPc')
depends_on('mpi', when='+mpi')
depends_on('slepc', when='+petsc')
# Patches to help configure find correctly MPI flags
# when using full path for compilers.
patch('acmpi.patch', when='@4.9', sha256='8157d89fc19227a555b54a4f2eb1c44da8aef3192077a6df2e88093b850f4c50')
patch('acmpi4.8.patch', when='@:4.8', sha256='be84f7b1b8182ff0151c258056a09bda70d72a611b0a4da1fa1954df2e0fe84e')
def autoreconf(self, spec, prefix):
autoreconf = which('autoreconf')
autoreconf('-i')
def configure_args(self):
spec = self.spec
options = ['--disable-mkl',
'CFLAGS=%s' % ' '.join(spec.compiler_flags['cflags']),
'FFLAGS=%s' % ' '.join(spec.compiler_flags['fflags']),
'CXXFLAGS=%s' % ' '.join(spec.compiler_flags['cxxflags'])]
if '+petsc' in spec:
options.append('--with-petsc=%s'
% spec['petsc'].prefix.lib.petsc.conf.petscvariables)
options.append('--with-slepc-ldflags=%s'
% spec['slepc'].libs.ld_flags)
options.append('--with-slepc-include=%s'
% spec['slepc'].headers.include_flags)
else:
options.append('--without-petsc')
options.append('--without-slepc')
return options
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-biocsingular/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 RBiocsingular(RPackage):
"""Singular Value Decomposition for Bioconductor Packages.
Implements exact and approximate methods for singular value
decomposition and principal components analysis, in a framework that
allows them to be easily switched within Bioconductor packages or
workflows. Where possible, parallelization is achieved using the
BiocParallel framework."""
bioc = "BiocSingular"
version('1.10.0', commit='<KEY>')
version('1.6.0', commit='<KEY>')
version('1.0.0', commit='<KEY>')
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'))
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-delayedarray', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-scaledmatrix', type=('build', 'run'), when='@1.10.0:')
depends_on('r-irlba', type=('build', 'run'))
depends_on('r-rsvd', type=('build', 'run'))
depends_on('r-rcpp', type=('build', 'run'))
depends_on('r-beachmat', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/fox/package.py
|
<filename>var/spack/repos/builtin/packages/fox/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 Fox(AutotoolsPackage):
"""FOX is a C++ based Toolkit for developing Graphical User Interfaces
easily and effectively. It offers a wide, and growing, collection of
Controls, and provides state of the art facilities such as drag and drop,
selection, as well as OpenGL widgets for 3D graphical manipulation. FOX
also implements icons, images, and user-convenience features such as status
line help, and tooltips. Tooltips may even be used for 3D objects!"""
homepage = "http://fox-toolkit.org/"
url = "http://fox-toolkit.org/ftp/fox-1.7.67.tar.gz"
version('1.7.67', sha256='7e511685119ef096fa90d334da46f0e50cfed8d414df32d80a7850442052f57d')
version('1.6.57', preferred=True, sha256='65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923')
patch('no_rexdebug.patch', when='@1.7.67')
variant('opengl', default=False, description='opengl support')
depends_on('bzip2')
depends_on('jpeg')
depends_on('libpng')
depends_on('libtiff')
depends_on('zlib')
depends_on('libx11')
depends_on('libsm')
depends_on('libxft')
depends_on('libxext')
depends_on('libxcursor')
depends_on('libxi')
depends_on('libxrandr')
depends_on('gl', when='+opengl')
depends_on('glu', when='+opengl', type='link')
def configure_args(self):
# Make the png link flags explicit or it will try to pick up libpng15
# from system
args = ['LDFLAGS={0}'.format(self.spec['libpng'].libs.search_flags)]
args += self.with_or_without('opengl')
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/nvtop/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 Nvtop(CMakePackage, CudaPackage):
"""Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA GPUs.
It can handle multiple GPUs and print information about them
in a htop familiar way."""
homepage = "https://github.com/Syllo/nvtop"
url = "https://github.com/Syllo/nvtop/archive/1.1.0.tar.gz"
version('1.1.0', sha256='00470cde8fc48d5a5ed7c96402607e474414d94b562b21189bdde1dbe6b1d1f3')
depends_on('ncurses')
def cmake_args(self):
return [self.define('NVML_RETRIEVE_HEADER_ONLINE', True)]
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/ucx/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 Ucx(AutotoolsPackage, CudaPackage):
"""a communication library implementing high-performance messaging for
MPI/PGAS frameworks"""
homepage = "http://www.openucx.org"
url = "https://github.com/openucx/ucx/releases/download/v1.3.1/ucx-1.3.1.tar.gz"
git = "https://github.com/openucx/ucx.git"
maintainers = ['hppritcha']
# Current
version('1.12.0', sha256='93e994de2d1a4df32381ea92ba4c98a249010d1720eb0f6110dc72c9a7d25db6')
version('1.11.2', sha256='deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df')
version('1.11.1', sha256='29338cad18858517f96b46ff83bdd259a5899e274792cebd269717c660aa86fd')
version('1.11.0', sha256='b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647')
version('1.10.1', sha256='ae9a108af6842ca135e7ec9b6131469adf9f1e50f899349fafcc69a215368bc9')
version('1.10.0', sha256='b885e24b1b94724c03cb213c355381e98df1e2d1fd7f633cf8055b6dd05db92d')
version('1.9-dev', branch='v1.9.x')
version('1.9.0', sha256='a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb')
version('1.8.1', sha256='a48820cb8d0761b5ccf3e7ba03a7c8c1dde6276017657178829e07ffc35b556a')
version('1.8.0', sha256='e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d')
version('1.7.0', sha256='6ab81ee187bfd554fe7e549da93a11bfac420df87d99ee61ffab7bb19bdd3371')
version('1.6.1', sha256='1425648aa03f5fa40e4bc5c4a5a83fe0292e2fe44f6054352fbebbf6d8f342a1')
version('1.6.0', sha256='360e885dd7f706a19b673035a3477397d100a02eb618371697c7f3ee4e143e2c')
version('1.5.2', sha256='1a333853069860e86ba69b8d071ccc9871209603790e2b673ec61f8086913fad')
version('1.5.1', sha256='567119cd80ad2ae6968ecaa4bd1d2a80afadd037ccc988740f668de10d2fdb7e')
version('1.5.0', sha256='84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458')
version('1.4.0', sha256='99891a98476bcadc6ac4ef9c9f083bc6ffb188a96b3c3bc89c8bbca64de2c76e')
# Still supported
version('1.3.1', sha256='e058c8ec830d2f50d9db1e3aaaee105cd2ad6c1e6df20ae58b9b4179de7a8992')
version('1.3.0', sha256='71e69e6d78a4950cc5a1edcbe59bf7a8f8e38d59c9f823109853927c4d442952')
version('1.2.2', sha256='914d10fee8f970d4fb286079dd656cf8a260ec7d724d5f751b3109ed32a6da63')
version('1.2.1', sha256='fc63760601c03ff60a2531ec3c6637e98f5b743576eb410f245839c84a0ad617')
version('1.2.0', sha256='1e1a62d6d0f89ce59e384b0b5b30b416b8fd8d7cedec4182a5319d0dfddf649c')
variant('thread_multiple', default=False,
description='Enable thread support in UCP and UCT')
variant('optimizations', default=True,
description='Enable optimizations')
variant('logging', default=False,
description='Enable logging')
variant('debug', default=False,
description='Enable debugging')
variant('assertions', default=False,
description='Enable assertions')
variant('parameter_checking', default=False,
description='Enable parameter checking')
variant('pic', default=True,
description='Builds with PIC support')
variant('java', default=False,
description='Builds with Java bindings')
variant('gdrcopy', default=False,
description='Enable gdrcopy support')
variant('knem', default=False,
description='Enable KNEM support')
variant('xpmem', default=False,
description='Enable XPMEM support')
variant('cma', default=False,
description="Enable Cross Memory Attach")
variant('rocm', default=False,
description="Enable ROCm support")
variant('rc', default=False,
description="Compile with IB Reliable Connection support")
variant('dc', default=False,
description="Compile with IB Dynamic Connection support")
variant('ud', default=False,
description="Compile with IB Unreliable Datagram support")
variant('mlx5-dv', default=False,
description="Compile with mlx5 Direct Verbs support")
variant('ib-hw-tm', default=False,
description="Compile with IB Tag Matching support")
variant('dm', default=False,
description="Compile with Device Memory support")
variant('cm', default=False,
description="Compile with IB Connection Manager support")
variant('backtrace-detail', default=False,
description="Enable using BFD support for detailed backtrace")
depends_on('numactl')
depends_on('rdma-core')
depends_on('pkgconfig', type='build')
depends_on('java@8', when='+java')
depends_on('maven', when='+java')
depends_on('gdrcopy', when='@1.7:+gdrcopy')
depends_on('gdrcopy@1.3', when='@:1.6+gdrcopy')
conflicts('+gdrcopy', when='~cuda',
msg='gdrcopy currently requires cuda support')
conflicts('+rocm', when='+gdrcopy',
msg='gdrcopy > 2.0 does not support rocm')
depends_on('xpmem', when='+xpmem')
depends_on('knem', when='+knem')
depends_on('binutils+ld', when='%aocc', type='build')
depends_on('binutils+ld', when='+backtrace-detail')
configure_abs_path = 'contrib/configure-release'
@when('@1.9-dev')
def autoreconf(self, spec, prefix):
Executable('./autogen.sh')()
def configure_args(self):
spec = self.spec
config_args = []
if '+thread_multiple' in spec:
config_args.append('--enable-mt')
else:
config_args.append('--disable-mt')
if '+cma' in spec:
config_args.append('--enable-cma')
else:
config_args.append('--disable-cma')
if '+paramter_checking' in spec:
config_args.append('--enable-params-check')
else:
config_args.append('--disable-params-check')
# Activate SIMD based on properties of the target
if 'avx' in self.spec.target:
config_args.append('--with-avx')
else:
config_args.append('--without-avx')
config_args.extend(self.enable_or_disable('optimizations'))
config_args.extend(self.enable_or_disable('assertions'))
config_args.extend(self.enable_or_disable('logging'))
config_args.extend(self.enable_or_disable('backtrace-detail'))
config_args.extend(self.with_or_without('pic'))
config_args.extend(self.with_or_without('rc'))
config_args.extend(self.with_or_without('ud'))
config_args.extend(self.with_or_without('dc'))
config_args.extend(self.with_or_without('mlx5-dv'))
config_args.extend(self.with_or_without('ib-hw-tm'))
config_args.extend(self.with_or_without('dm'))
config_args.extend(self.with_or_without('cm'))
config_args.extend(self.with_or_without('rocm'))
config_args.extend(self.with_or_without('java',
activation_value='prefix'))
config_args.extend(self.with_or_without('cuda',
activation_value='prefix'))
config_args.extend(self.with_or_without('gdrcopy',
activation_value='prefix'))
config_args.extend(self.with_or_without('knem',
activation_value='prefix'))
config_args.extend(self.with_or_without('xpmem',
activation_value='prefix'))
# lld doesn't support '-dynamic-list-data'
if '%aocc' in spec:
config_args.append('LDFLAGS=-fuse-ld=bfd')
return config_args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-fenics-dijitso/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 PyFenicsDijitso(PythonPackage):
"""A Python module for distributed just-in-time shared library building"""
homepage = "https://bitbucket.org/fenics-project/dijitso"
url = "https://bitbucket.org/fenics-project/dijitso/downloads/dijitso-2019.1.0.tar.gz"
git = "https://bitbucket.org/fenics-project/dijitso.git"
maintainers = ["js947", "chrisrichardson"]
version("master", branch="master")
version('2019.1.0', sha256='eaa45eec4457f3f865d72a926b7cba86df089410e78de04cd89b15bb405e8fd9')
version('2018.1.0', sha256='2084ada1e7bd6ecec0999b15a17db98c72e26f1ccbf3fcbe240b1a035a1a2e64')
version('2017.2.0', sha256='05a893d17f8a50067d303b232e41592dce2840d6499677ad8b457ba58a679b58')
version('2017.1.0', sha256='ef23952539d349fbd384d41302abc94413d485ca7e8c29e8a0debc2aadaf8657')
version('2016.2.0', sha256='1bfa0ac0d47dae75bbde8fabb1145d3caa2e6c28a1e4097ad5550a91a8a205e4')
depends_on("py-setuptools", type="build")
depends_on("python@3.5:", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libepoxy/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 Libepoxy(AutotoolsPackage):
"""Epoxy is a library for handling OpenGL function pointer management for
you."""
homepage = "https://github.com/anholt/libepoxy"
url = "https://github.com/anholt/libepoxy/releases/download/1.4.3/libepoxy-1.4.3.tar.xz"
list_url = "https://github.com/anholt/libepoxy/releases"
version('1.4.3', sha256='0b808a06c9685a62fca34b680abb8bc7fb2fda074478e329b063c1f872b826f6')
depends_on('pkgconfig', type='build')
depends_on('gl')
depends_on('libx11', when='+glx')
variant('glx', default=True, description='enable GLX support')
def configure_args(self):
# Disable egl, otherwise configure fails with:
# error: Package requirements (egl) were not met
# Package 'egl', required by 'virtual:world', not found
args = ['--enable-egl=no']
# --enable-glx defaults to auto and was failing on PPC64LE systems
# because libx11 was missing from the dependences. This explicitly
# enables/disables glx support.
if '+glx' in self.spec:
args.append('--enable-glx=yes')
else:
args.append('--enable-glx=no')
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/libcap-ng/package.py
|
<filename>var/spack/repos/builtin/packages/libcap-ng/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 LibcapNg(AutotoolsPackage):
"""Libcap-ng is a library that makes using posix capabilities easier"""
homepage = "https://github.com/stevegrubb/libcap-ng/"
url = "https://github.com/stevegrubb/libcap-ng/archive/v0.8.tar.gz"
version('0.8', sha256='836ea8188ae7c658cdf003e62a241509dd542f3dec5bc40c603f53a5aadaa93f')
version('0.7.11', sha256='78f32ff282b49b7b91c56d317fb6669df26da332c6fc9462870cec2573352222')
version('0.7.10', sha256='c3c156a215e5be5430b2f3b8717bbd1afdabe458b6068a8d163e71cefe98fc32')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
depends_on('attr', type='build')
depends_on('swig', type='build')
depends_on('python@2.7:', type=('build', 'link', 'run'), when='+python')
variant('python', default=True, description='Enable python')
extends('python', when='+python')
def setup_build_environment(self, env):
if self.spec.satisfies('+python'):
env.set('PYTHON', self.spec['python'].command.path)
def configure_args(self):
args = []
spec = self.spec
if spec.satisfies('+python'):
if spec.satisfies('^python@3:'):
args.extend(['--without-python', '--with-python3'])
else:
args.extend(['--with-python', '--without-python3'])
else:
args.extend(['--without-python', '--without-python3'])
return args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/scalasca/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 Scalasca(AutotoolsPackage):
"""Scalasca is a software tool that supports the performance optimization
of parallel programs by measuring and analyzing their runtime
behavior. The analysis identifies potential performance
bottlenecks - in particular those concerning communication and
synchronization - and offers guidance in exploring their causes.
"""
homepage = "https://www.scalasca.org"
url = "https://apps.fz-juelich.de/scalasca/releases/scalasca/2.1/dist/scalasca-2.1.tar.gz"
list_url = "https://scalasca.org/scalasca/front_content.php?idart=1072"
version('2.6', sha256='b3f9cb1d58f3e25090a39da777bae8ca2769fd10cbd6dfb9a4887d873ee2441e')
version('2.5', sha256='7dfa01e383bfb8a4fd3771c9ea98ff43772e415009d9f3c5f63b9e05f2dde0f6')
version('2.4', sha256='4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760')
version('2.3.1', sha256='8ff485d03ab2c02a5852d346ae041a191c60b4295f8f9b87fe58cd36977ba558')
version('2.2.2', sha256='909567ca294366119bbcb7e8122b94f43982cbb328e18c6f6ce7a722d72cd6d4')
version('2.1', sha256='fefe43f10becf7893863380546c80ac8db171a3b1ebf97d0258602667572c2fc')
depends_on("mpi")
# version 2.4+
depends_on('cubew@4.4:', when='@2.4:')
depends_on('scorep@6.0:', when='@2.4:', type=('run'))
# version 2.3+
depends_on('otf2@2:', when='@2.3:')
# version 2.3
depends_on('cube@4.3', when='@2.3:2.3.99')
# version 2.1 - 2.2
depends_on('cube@4.2', when='@2.1:2.2')
depends_on('otf2@1.4', when='@2.1:2.2')
def url_for_version(self, version):
return 'http://apps.fz-juelich.de/scalasca/releases/scalasca/{0}/dist/scalasca-{1}.tar.gz'.format(version.up_to(2), version)
def configure_args(self):
spec = self.spec
config_args = ["--enable-shared"]
if spec.satisfies('@2.4:'):
config_args.append("--with-cube=%s" % spec['cubew'].prefix.bin)
else:
config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
config_args.append("--with-otf2=%s" % spec['otf2'].prefix.bin)
if self.spec['mpi'].name == 'openmpi':
config_args.append("--with-mpi=openmpi")
elif self.spec.satisfies('^mpich@3:'):
config_args.append("--with-mpi=mpich3")
return config_args
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/jetty-project/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 JettyProject(MavenPackage):
"""Jetty is a lightweight highly scalable java based web
server and servlet engine."""
homepage = "https://www.eclipse.org/jetty"
url = "https://github.com/eclipse/jetty.project/archive/jetty-9.4.31.v20200723.tar.gz"
version('9.4.31.v20200723', sha256='3cab80ddc14763764509552d79d5f1f17b565a3eb0a1951991d4a6fcfee9b4b1')
version('9.4.30.v20200611', sha256='fac8bb95f8e8de245b284d359607b414893992ebb4e2b6e3ee40161297ea2111')
depends_on('java@8', type=('build', 'run'))
depends_on('maven@3:', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/csdp/package.py
|
<filename>var/spack/repos/builtin/packages/csdp/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 Csdp(MakefilePackage):
"""CSDP is a library of routines that implements a predictor corrector
variant of the semidefinite programming algorithm of Helmberg, Rendl,
Vanderbei, and Wolkowicz"""
homepage = "https://projects.coin-or.org/Csdp"
url = "https://www.coin-or.org/download/source/Csdp/Csdp-6.1.1.tgz"
version('6.1.1', sha256='0558a46ac534e846bf866b76a9a44e8a854d84558efa50988ffc092f99a138b9')
depends_on('atlas')
def edit(self, spec, prefix):
mkdirp(prefix.bin)
makefile = FileFilter('Makefile')
makefile.filter('/usr/local/bin', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-readbitmap/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 RReadbitmap(RPackage):
"""Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF).
Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images.
Identification defaults to the use of the magic number embedded in the file
rather than the file extension. Reading of JPEG and PNG image depends on
libjpg and libpng libraries. See file INSTALL for details if necessary."""
cran = "readbitmap"
version('0.1.5', sha256='737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291')
depends_on('r-bmp', type=('build', 'run'))
depends_on('r-jpeg', type=('build', 'run'))
depends_on('r-png', type=('build', 'run'))
depends_on('r-tiff', type=('build', 'run'))
depends_on('jpeg')
depends_on('libpng')
|
player1537-forks/spack
|
lib/spack/spack/test/cmd/concretize.py
|
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import pytest
import spack.environment as ev
from spack.main import SpackCommand
# everything here uses the mock_env_path
pytestmark = pytest.mark.usefixtures(
'mutable_mock_env_path', 'config', 'mutable_mock_repo')
env = SpackCommand('env')
add = SpackCommand('add')
concretize = SpackCommand('concretize')
@pytest.mark.parametrize('concretization', ['separately', 'together'])
def test_concretize_all_test_dependencies(concretization):
"""Check all test dependencies are concretized."""
env('create', 'test')
with ev.read('test') as e:
e.concretization = concretization
add('depb')
concretize('--test', 'all')
assert e.matching_spec('test-dependency')
@pytest.mark.parametrize('concretization', ['separately', 'together'])
def test_concretize_root_test_dependencies_not_recursive(concretization):
"""Check that test dependencies are not concretized recursively."""
env('create', 'test')
with ev.read('test') as e:
e.concretization = concretization
add('depb')
concretize('--test', 'root')
assert e.matching_spec('test-dependency') is None
@pytest.mark.parametrize('concretization', ['separately', 'together'])
def test_concretize_root_test_dependencies_are_concretized(concretization):
"""Check that root test dependencies are concretized."""
env('create', 'test')
with ev.read('test') as e:
e.concretization = concretization
add('a')
add('b')
concretize('--test', 'root')
assert e.matching_spec('test-dependency')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/flink/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 Flink(Package):
"""
Apache Flink is an open source stream processing framework with
powerful stream- and batch-processing capabilities.
"""
homepage = "https://flink.apache.org/"
url = "https://archive.apache.org/dist/flink/flink-1.9.1/flink-1.9.1-bin-scala_2.11.tgz"
version('1.9.1', sha256='f69de344cd593e92f8261e19ae8a47b3910e9a70a7cd1ccfb1ecd1ff000b93ea')
version('1.9.0', sha256='a2245f68309e94ed54d86a680232a518aed9c5ea030bcc0b298bc8f27165eeb7')
version('1.8.3', sha256='1ba90e99f70ad7e2583d48d1404d1c09e327e8fb8fa716b1823e427464cc8dc0')
version('1.8.2', sha256='1a315f4f1fab9d651702d177b1741439ac98e6d06e9e13f9d410b34441eeda1c')
version('1.8.1', sha256='4fc0d0f163174ec43e160fdf21a91674979b978793e60361e2fce5dddba4ddfa')
depends_on('java@8:', type='run')
def url_for_version(self, version):
url = "http://archive.apache.org/dist/flink/flink-{0}/flink-{0}-bin-scala_2.11.tgz"
return url.format(version)
def install(self, spec, prefix):
install_tree('.', prefix)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/codar-cheetah/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 CodarCheetah(PythonPackage):
"""CODAR Cheetah:
The CODAR Experiment Harness for Exascale science applications.
"""
maintainers = ['kshitij-v-mehta']
homepage = "https://github.com/CODARcode/cheetah"
url = "https://github.com/CODARcode/cheetah/archive/v1.1.0.tar.gz"
git = "https://github.com/CODARcode/cheetah.git"
version('develop', branch='dev')
version('1.1.0', sha256='519a47e4fc5b124b443839fde10b8b72120ab768398628df43e0b570a266434c')
version('1.0.0', sha256='1f935fbc1475a654f3b6d2140d8b2a6079a65c8701655e544ba1fab3a7c1bc19')
version('0.5', sha256='f37a554741eff4bb8407a68f799dd042dfc4df525e84896cad70fccbd6aca6ee')
depends_on('python@3.5:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-rsconnect/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 RRsconnect(RPackage):
"""Deployment Interface for R Markdown Documents and Shiny Applications.
Programmatic deployment interface for 'RPubs', 'shinyapps.io', and 'RStudio
Connect'. Supported content types include R Markdown documents, Shiny
applications, Plumber APIs, plots, and static web content."""
cran = "rsconnect"
version('0.8.25', sha256='3c055277f745f2ca37a73e2f425249307cea4dc95ecc59fbe05ee8b6cf26d9cf')
version('0.8.17', sha256='64767a4d626395b7871375956a9f0455c3d64ff6e779633b0e554921d85da231')
depends_on('r@3.0.0:', type=('build', 'run'))
depends_on('r-curl', type=('build', 'run'))
depends_on('r-digest', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-openssl', type=('build', 'run'))
depends_on('r-packrat@0.6:', type=('build', 'run'), when='@0.8.18:')
depends_on('r-packrat@0.5:', type=('build', 'run'))
depends_on('r-rstudioapi@0.5:', type=('build', 'run'))
depends_on('r-yaml@2.1.5:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-ml-collections/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 PyMlCollections(PythonPackage):
"""ML Collections is a library of Python collections designed for ML usecases."""
homepage = "https://https://github.com/google/ml_collections"
pypi = "ml_collections/ml_collections-0.1.0.tar.gz"
version('0.1.1', sha256='3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc')
depends_on('python@2.6:', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-absl-py', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
depends_on('py-contextlib2', type=('build', 'run'))
depends_on('py-dataclasses', type=('build', 'run'), when='python@:3.6')
depends_on('py-typing', type=('build', 'run'), when='python@:3.5')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-scater/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 RScater(RPackage):
"""Single-Cell Analysis Toolkit for Gene Expression Data in R.
A collection of tools for doing various analyses of single-cell RNA-seq
gene expression data, with a focus on quality control and
visualization."""
bioc = "scater"
version('1.22.0', commit='ea2c95c53adb8c6fab558c1cb869e2eab36aa9f8')
version('1.18.3', commit='<PASSWORD>a8e5c<PASSWORD>')
version('1.12.2', commit='<PASSWORD>')
version('1.10.1', commit='2<PASSWORD>29092f263c2b0830d48b3f963<PASSWORD>')
version('1.8.4', commit='d<PASSWORD>a9a<PASSWORD>41d53d17990d2aa2cd28874df3dcd')
version('1.6.3', commit='964effb4e883102d7c8cae627dbac4ba5d216a75')
version('1.4.0', commit='90a2eab66ff82ba6dd7fbb33e41cd0ded20fa218')
depends_on('r@3.3:', type=('build', 'run'), when='@1.4.0')
depends_on('r@3.4:', type=('build', 'run'), when='@1.6.3')
depends_on('r@3.5:', type=('build', 'run'), when='@1.8.4')
depends_on('r@3.6:', type=('build', 'run'), when='@1.12.2')
depends_on('r-singlecellexperiment', type=('build', 'run'), when='@1.6.3:')
depends_on('r-scuttle', type=('build', 'run'), when='@1.18.3:')
depends_on('r-ggplot2', type=('build', 'run'))
depends_on('r-gridextra', type=('build', 'run'), when='@1.18.3:')
depends_on('r-matrix', type=('build', 'run'))
depends_on('r-biocgenerics', type=('build', 'run'))
depends_on('r-s4vectors', type=('build', 'run'), when='@1.6.3:')
depends_on('r-summarizedexperiment', type=('build', 'run'), when='@1.6.3:')
depends_on('r-delayedarray', type=('build', 'run'), when='@1.8.4:')
depends_on('r-delayedmatrixstats', type=('build', 'run'), when='@1.8.4:')
depends_on('r-beachmat', type=('build', 'run'), when='@1.6.3:1.12.2,1.22.0:')
depends_on('r-biocneighbors', type=('build', 'run'), when='@1.12.2:')
depends_on('r-biocsingular', type=('build', 'run'), when='@1.12.2:')
depends_on('r-biocparallel', type=('build', 'run'), when='@1.10.1:')
depends_on('r-rlang', type=('build', 'run'), when='@1.18.3:')
depends_on('r-ggbeeswarm', type=('build', 'run'))
depends_on('r-viridis', type=('build', 'run'))
depends_on('r-rtsne', type=('build', 'run'), when='@1.22.0:')
depends_on('r-rcolorbrewer', type=('build', 'run'), when='@1.22.0:')
depends_on('r-ggrepel', type=('build', 'run'), when='@1.22.0:')
depends_on('r-biobase', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-biomart', type=('build', 'run'), when='@1.4.0:1.6.3')
depends_on('r-data-table', type=('build', 'run'), when='@1.4.0:1.6.3')
depends_on('r-dplyr', type=('build', 'run'), when='@1.4.0:1.12.2')
depends_on('r-edger', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-limma', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-matrixstats', type=('build', 'run'), when='@1.4.0:1.6.3')
depends_on('r-plyr', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-reshape2', type=('build', 'run'), when='@1.4.0:1.10.1')
depends_on('r-rhdf5', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-rjson', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-shiny', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-shinydashboard', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-tximport', type=('build', 'run'), when='@1.4.0:1.8.4')
depends_on('r-rcpp', type=('build', 'run'), when='@1.6.3:1.12.2')
depends_on('r-rcpp@0.12.14:', type=('build', 'run'), when='@1.8.4:1.12.2')
depends_on('r-rhdf5lib', type=('build', 'run'), when='@1.6.3:1.10.1')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-pathlib/package.py
|
<filename>var/spack/repos/builtin/packages/py-pathlib/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 PyPathlib(PythonPackage):
"""Object-oriented filesystem paths.
Attention: this backport module isn't maintained anymore. If you want to
report issues or contribute patches, please consider the pathlib2 project
instead."""
homepage = "https://pathlib.readthedocs.org/"
pypi = "pathlib/pathlib-1.0.1.tar.gz"
version('1.0.1', sha256='6940718dfc3eff4258203ad5021090933e5c04707d5ca8cc9e73c94a7894ea9f')
# pip silently replaces distutils with setuptools
depends_on('py-setuptools', type='build')
# This is a backport of the pathlib module from Python 3.4. Since pathlib is now
# part of the standard library, this module isn't needed in Python 3.4+. Although it
# can be installed, differences between this implementation and the standard library
# implementation can cause other packages to fail. If it is installed, it ends up
# masking the standard library and doesn't have the same features that the standard
# library has in newer versions of Python.
conflicts('^python@3.4:')
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/raft/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 Raft(CMakePackage):
"""RAFT: Reconstruct Algorithms for Tomography.
Toolbox under development at Brazilian Synchrotron Light Source."""
homepage = "https://bitbucket.org/gill_martinez/raft_aps"
url = "https://bitbucket.org/gill_martinez/raft_aps/get/1.2.3.tar.gz"
git = "https://bitbucket.org/gill_martinez/raft_aps.git"
version('develop', branch='master')
version('1.2.3', sha256='c41630e74491c8db272dcf4707e9b11cdcb226c0b7e978ca6eba8006f47bdae6')
depends_on('mpi')
depends_on('cmake', type='build')
depends_on('hdf5')
depends_on('fftw')
depends_on('cuda')
def install(self, spec, prefix):
"""RAFT lacks an install in its CMakeList"""
with working_dir(self.stage.source_path):
mkdirp(prefix)
# We only care about the binary
install_tree('bin', prefix.bin)
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-stringi/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 RStringi(RPackage):
"""Character String Processing Facilities.
A multitude of character string/text/natural language processing tools:
pattern searching (e.g., with 'Java'-like regular expressions or the
'Unicode' collation algorithm), random string generation, case mapping,
string transliteration, concatenation, sorting, padding, wrapping, Unicode
normalisation, date-time formatting and parsing, and many more. They are
fast, consistent, convenient, and - owing to the use of the 'ICU'
(International Components for Unicode) library - portable across all
locales and platforms."""
cran = "stringi"
version('1.7.6', sha256='0ea3d5afec5701977ff53de9afbaceb53b00aa34f5fb641cadc1eeb7759119ec')
version('1.6.2', sha256='3a151dd9b982696370ac8df3920afe462f8abbd4e41b479ff8b66cfd7b602dae')
version('1.5.3', sha256='224f1e8dedc962a676bc2e1f53016f6a129a0a38aa0f35daf6dece62ff714010')
version('1.4.3', sha256='13cecb396b700f81af38746e97b550a1d9fda377ca70c78f6cdfc770d33379ed')
version('1.3.1', sha256='32df663bb6e9527e1ac265eec2116d26f7b7e62ea5ae7cc5de217cbb8defc362')
version('1.1.5', sha256='651e85fc4ec6cf71ad8a4347f2bd4b00a490cf9eec20921a83bf5222740402f2')
version('1.1.3', sha256='9ef22062e4be797c1cb6c2c8822ad5c237edb08b0318a96be8bd1930191af389')
version('1.1.2', sha256='e50b7162ceb7ebae403475f6f8a76a39532a2abc82112db88661f48aa4b9218e')
version('1.1.1', sha256='243178a138fe68c86384feb85ead8eb605e8230113d638da5650bca01e24e165')
depends_on('r@2.14:', type=('build', 'run'))
depends_on('r@3.1:', type=('build', 'run'), when='@1.6.1:')
depends_on('icu4c@52:')
depends_on('icu4c@55:', when='@1.5.3:')
# since version 1.6.1 there is also a SystemRequirement on C++11
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-glmnet/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 PyGlmnet(PythonPackage):
"""
This is a Python wrapper for the fortran library used in the R package
glmnet.
"""
homepage = "https://github.com/civisanalytics/python-glmnet"
pypi = "glmnet/glmnet-2.2.1.tar.gz"
version('2.2.1', sha256='3222bca2e901b3f60c2dc22df7aeba6bb9c7b6451b44cbbe1b91084b66f14481')
depends_on('python@3.6:', type=('build', 'run'))
depends_on('py-setuptools', type=('build'))
depends_on('py-numpy@1.9.2:', type=('build', 'run'))
depends_on('py-scikit-learn@0.18.0:', type=('build', 'run'))
depends_on('py-scipy@0.14.1:', type=('build', 'run'))
depends_on('py-joblib@0.14.1:', type=('build', 'run'))
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/r-libcoin/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 RLibcoin(RPackage):
"""Linear Test Statistics for Permutation Inference.
Basic infrastructure for linear test statistics and permutation inference
in the framework of Strasser and Weber (1999) <https://epub.wu.ac.at/102/>.
This package must not be used by end-users. CRAN package 'coin' implements
all user interfaces and is ready to be used by anyone."""
cran = "libcoin"
version('1.0-9', sha256='2d7dd0b7c6dfc20472430570419ea36a714da7bbafd336da1fb53c5c6463d9eb')
version('1.0-6', sha256='48afc1415fc89b29e4f2c8b6f6db3cffef1531580e5c806ad7cacf4afe6a4e5a')
version('1.0-4', sha256='91dcbaa0ab8c2109aa54c3eda29ad0acd67c870efcda208e27acce9d641c09c5')
depends_on('r@3.4.0:', type=('build', 'run'))
depends_on('r-mvtnorm', type=('build', 'run'))
|
player1537-forks/spack
|
lib/spack/spack/cmd/modules/lmod.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 functools
import spack.cmd.common.arguments
import spack.cmd.modules
import spack.config
import spack.modules.lmod
def add_command(parser, command_dict):
lmod_parser = parser.add_parser(
'lmod', help='manipulate hierarchical module files'
)
sp = spack.cmd.modules.setup_parser(lmod_parser)
# Set default module file for a package
setdefault_parser = sp.add_parser(
'setdefault', help='set the default module file for a package'
)
spack.cmd.common.arguments.add_common_arguments(
setdefault_parser, ['constraint']
)
callbacks = dict(spack.cmd.modules.callbacks.items())
callbacks['setdefault'] = setdefault
command_dict['lmod'] = functools.partial(
spack.cmd.modules.modules_cmd, module_type='lmod', callbacks=callbacks
)
def setdefault(module_type, specs, args):
"""Set the default module file, when multiple are present"""
# For details on the underlying mechanism see:
#
# https://lmod.readthedocs.io/en/latest/060_locating.html#marking-a-version-as-default
#
spack.cmd.modules.one_spec_or_raise(specs)
spec = specs[0]
data = {
'modules': {
args.module_set_name: {
'lmod': {
'defaults': [str(spec)]
}
}
}
}
# Need to clear the cache if a SpackCommand is called during scripting
spack.modules.lmod.configuration_registry = {}
scope = spack.config.InternalConfigScope('lmod-setdefault', data)
with spack.config.override(scope):
writer = spack.modules.module_types['lmod'](spec, args.module_set_name)
writer.update_module_defaults()
|
player1537-forks/spack
|
var/spack/repos/builtin/packages/py-fonttools/package.py
|
<filename>var/spack/repos/builtin/packages/py-fonttools/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 PyFonttools(PythonPackage):
"""fontTools is a library for manipulating fonts, written in Python.
The project includes the TTX tool, that can convert TrueType and OpenType fonts to
and from an XML text format, which is also called TTX. It supports TrueType,
OpenType, AFM and to an extent Type 1 and some Mac-specific formats."""
homepage = "https://github.com/fonttools/fonttools"
pypi = "fonttools/fonttools-4.28.1.zip"
version('4.29.1', sha256='2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4')
version('4.28.1', sha256='8c8f84131bf04f3b1dcf99b9763cec35c347164ab6ad006e18d2f99fcab05529')
depends_on('python@3.7:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
@property
def import_modules(self):
modules = super(__class__, self).import_modules
ignored_imports = ["fontTools.ufoLib"]
return [i for i in modules
if not any(map(i.startswith, ignored_imports))]
|
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