def install(self, spec, prefix):
# edit cns_solve_environment to allow a build
shutil.copy('cns_solve_env', 'cns_solve_env.back')
filter_file(r"setenv CNS_SOLVE '_CNSsolve_location_'",
f"setenv CNS_SOLVE '{self.stage.source_path}'",
'cns_solve_env')
# copy over an almost right machine make file we could have got it from v1.3 but this is simpler
src_file = 'instlib/machine/supported/intel-x86_64bit-linux/Makefile.header.2.gfortran'
dest_file = 'instlib/machine/supported/mac-intel-darwin/Makefile.header.5.gfortran'
shutil.move(src_file, dest_file)
if not self.spec.satisfies('%fortran@:10.0.0'):
# patch the machine make file, can't be done with a patch statement it doesn't exists till we copy it
# tried just copying the file from the package directory but it caused a lockup
patch = which('patch')
patch_file = join_path(
package_root, 'nmrpack/packages/cns',
'gfortran_10_allow_argument_mismatch.patch')
patch('-p1', '-i', patch_file)
if '+aria' in self.spec:
from_path = pathlib.Path('aria2.3/cns/src')
to_path = 'source'
for target_file in from_path.iterdir():
if target_file.is_file() and target_file.suffix in ('.f',
'.inc'):
print(f'copying {target_file} to {to_path}')
shutil.copy(target_file, to_path)
if target_file.is_dir():
print(f'copying {target_file} to {to_path}')
shutil.copytree(target_file,
join_path(to_path, target_file.name))
shutil.copytree(from_path, 'aria2.3_patches_applied')
shutil.rmtree('aria2.3')
make('install')
install_tree('.', prefix)
with working_dir(prefix):
shutil.move('cns_solve_env.back', 'cns_solve_env')
replacement_env = f" setenv CNS_SOLVE '{prefix}'"
filter_file(r"setenv CNS_SOLVE '_CNSsolve_location_'",
replacement_env, 'cns_solve_env')
# remove a leftover from our previous edits
os.remove(pathlib.Path(prefix) / pathlib.Path('cns_solve_env' + '~'))
class Genie(Package): # Genie doesn"t use Autotools
"""Genie is a neutrino Monte Carlo Generator."""
homepage = "https://www.genie-mc.org"
url = "https://github.com/GENIE-MC/Generator/archive/R-3_00_06.tar.gz"
git = "https://github.com/GENIE-MC/Generator.git"
tags = ["neutrino", "hep"]
maintainers = [
# maintainer of this recipe, not affliated with the GENIE collaboration
"davehadley",
]
version("master", branch="master")
version("3.0.6",
sha256=
"ab56ea85d0c1d09029254365bfe75a1427effa717389753b9e0c1b6c2eaa5eaf")
version("3.0.4",
sha256=
"53f034618fef9f7f0e17d1c4ed72743e4bba590e824b795177a1a8a8486c861e")
version("3.0.2",
sha256=
"34d6c37017b2387c781aea7bc727a0aac0ef45d6b3f3982cc6f3fc82493f65c3")
version("3.0.0",
sha256=
"3953c7d9f1f832dd32dfbc0b9260be59431206c204aec6ab0aa68c01176f2ae6")
version("2.12.10",
sha256=
"c8762db3dcc490f80f8a61268f5b964d4d35b80134b622e89fe2307a836f2a0b")
version("2.12.8",
sha256=
"7ca169a8d9eda7267d28b76b2f3110552852f8eeae263a03cd5139caacebb4ea")
version("2.12.6",
sha256=
"3b450c609875459798ec98e12cf671cc971cbb13345af6d75bd6278d422f3309")
version("2.12.4",
sha256=
"19a4a1633b0847a9f16a44e0c74b9c224ca3bb93975aecf108603c22e807517b")
version("2.12.2",
sha256=
"cbdc45a739878940dadcaaed575b5cad6b5e7035f29605045b1ca557e6faa6d1")
version("2.12.0",
sha256=
"d2b01c80f38d269cb0296b3f2932798ef3f1d51bd130e81274fbfeeb381fac6b")
version("2.11.2",
sha256=
"0f4c25d8ceb7513553671643c9cdac5aa98c40fc8594a5ecb25c077c6b36166e")
version("2.11.0",
sha256=
"1ebe0eb65d797595413632f1cec1cb2621cb8e8d0384a2843799724a79b1d80c")
version("2.10.10",
sha256=
"1dfaadcf1bbaf6e164b612f410c4399301e63497ad6a4891706b1787ac11a7a1")
version("2.10.8",
sha256=
"4f6f5af2062e7c505b76e70547ac2ae304a9790c3e9b9592818d8aebeebc8398")
version("2.10.6",
sha256=
"d00b4288c886f81459fb2967e539f30315d4385f82d1d3f4330298d313f9a176")
version("2.10.4",
sha256=
"df909bf7e1a789ca01794995687da2af803769f0823273a4a3a31678d6d5b0f1")
version("2.10.2",
sha256=
"6abe4e0cdb5e8f5beddf0ccdbebc94c175a9f72592b1cbbffe01b88ee3972bf9")
version("2.10.0",
sha256=
"17bda900c996b6f4f10a7f6a3be94e56c3b8dcdeb2ef8865ca7f20c5fe725291")
version("2.9.0",
sha256=
"8229beb73f65f5af86a77bf141acfbe4a8b68cba9d797aae083a929906f6f2a2")
version("2.8.6",
sha256=
"310dc8e0d17a65e6b9773e398250703a3a6f94ceafe94f599ae0f7b3fecf7e6c")
depends_on("root+pythia6")
depends_on("pythia6")
depends_on("lhapdf", when="@3:")
depends_on("lhapdf5", when="@:2")
depends_on("log4cpp")
depends_on("libxml2")
depends_on("gsl")
# GENIE does not actually require cmake, but root does.
# Spack's concretizer fails with "unsatisfiable constraint" if we don't add this.
depends_on("cmake@3:")
# GENIE Makefile's think that the spack compiler is invalid.
# Disables this check.
patch("genie_disable_gopt_with_compiler_check.patch",
level=0,
when="@2.11:")
# Flags for GENIE"s optional but disabled by default features
variant(
"atmo",
default=False,
description="Enable GENIE Atmospheric neutrino event generation app")
variant(
"fnal",
default=False,
description="Enables FNAL experiment-specific event generation app")
variant("nucleondecay",
default=False,
description="Enable GENIE Nucleon decay event generation app")
variant("masterclass",
default=False,
description="Enable GENIE neutrino masterclass app")
variant("t2k",
default=False,
description="Enable T2K-specific generation app")
variant(
"vleextension",
default=False,
description="Enable GENIE very low energy (1 MeV - 100 MeV) extension")
phases = ["configure", "build", "install"]
def url_for_version(self, version):
url = "https://github.com/GENIE-MC/Generator/archive/R-{0}.tar.gz"
if version >= Version(3):
return url.format("{0}_{1:02d}_{2:02d}".format(*version))
else:
return url.format(version.underscored)
def setup_build_environment(self, env):
env.set("GENIE", self.stage.source_path)
return super(Genie, self).setup_build_environment(env)
def setup_run_environment(self, env):
env.set("GENIE", self.prefix)
return super(Genie, self).setup_run_environment(env)
def configure(self, spec, prefix):
configure = Executable("./configure")
args = self._configure_args(spec, prefix)
configure(*args)
def build(self, spec, prefix):
# parallel build is not supported on GENIE 2
self._make(parallel=spec.satisfies("@3:"))
def install(self, spec, prefix):
# GENIE make install does not support parallel jobs
self._make("install", parallel=False)
# GENIE requires these files to be present at runtime, but doesn"t install them
# so we must install them ourselves
# install_tree function is injected into scope by spack build_environment.py
install_tree("config", os.sep.join((prefix, "config")))
install_tree("data", os.sep.join((prefix, "data")))
def _configure_args(self, spec, prefix):
args = [
"--prefix=" + prefix,
"--with-compiler=" + os.environ["CC"],
"--with-libxml2-inc={0}{1}libxml2".format(
spec["libxml2"].prefix.include, os.sep),
"--with-libxml2-lib=" + spec["libxml2"].prefix.lib,
"--with-log4cpp-inc=" + spec["log4cpp"].prefix.include,
"--with-log4cpp-lib=" + spec["log4cpp"].prefix.lib,
"--with-pythia6-lib=" + spec["pythia6"].prefix.lib,
]
if self.spec.satisfies("@:2"):
args += [
"--enable-lhapdf",
"--with-lhapdf-inc=" + spec["lhapdf5"].prefix.include,
"--with-lhapdf-lib=" + spec["lhapdf5"].prefix.lib,
# must be enabled or some GENIE 2 versions fail to link
# this option was removed in GENIE 3
"--enable-rwght",
]
else:
args += [
"--enable-lhapdf6",
"--with-lhapdf6-inc=" + spec["lhapdf"].prefix.include,
"--with-lhapdf6-lib=" + spec["lhapdf"].prefix.lib,
]
if "+vleextension" in self.spec:
args += ["--enable-vle-extension"]
if "+t2k" in self.spec:
args += ["--enable-t2k"]
if "+fnal" in self.spec:
args += ["--enable-fnal"]
if "+atmo" in self.spec:
args += ["--enable-atmo"]
if "+nucleondecay" in self.spec:
args += ["--enable-nucleon-decay"]
if "+masterclass" in self.spec:
args += ["--enable-masterclass"]
return args
def _make(self, *args, **kwargs):
parallel = kwargs.get("parallel", False)
args = list(self._make_args) + list(args)
# make function is injected into scope by spack build_environment.py
make(*args, parallel=parallel)
@property
def _make_args(self):
return [
"CC=c++",
"CXX=c++",
"LD=c++",
]
class Cns(Package):
"""CNS The Crystallography & NMR System for structure calculation (1.2 for ARIA + aria patches)"""
# FIXME: Add a proper url for your package's homepage here.
homepage = "http://cns-online.org"
url = "http://cns-online.org/download/v1.21/cns_solve_1.21_all-mp.tar.gz"
read_releases('cns', version, resource)
# patch to make SETFPEPS (set floating point epsilon work)
# see https://ask.bioexcel.eu/t/cns-errors-before-after-recompilation/54
# main patch courtesy of Brian Smith U of Glasgow
variant('configuration',
default='none',
description='where to find the configuration file',
validator=check_config_file)
variant('fp_epsilon',
default=True,
description='SETFPEPS required for modern compilers')
variant('aria', default=True, description='patches required to run aria')
resource(
name='aria2.3.2',
aria_url='http://aria.pasteur.fr/archives/aria2.3.2.tar.gz',
sha256=
'a06e9c256bf876f8bbab244a80b9c52bbd891f14cb956d85bb3bd0312b5cd5c6',
destination='.')
patch('getarch_darwin_x86_64.patch',
when='@1.21',
sha256=
'42a0d10d7684000d5c4cf1114e14d5549cc19c84b19df4d42419abd7187cf887')
patch('machvar_fpeps.patch',
when='@1.21+fp_epsilon',
sha256=
'a00db99086c63961abe4e19d253590421973a80a9e104ac85dbcc07d472b6485')
def install(self, spec, prefix):
# edit cns_solve_environment to allow a build
shutil.copy('cns_solve_env', 'cns_solve_env.back')
filter_file(r"setenv CNS_SOLVE '_CNSsolve_location_'",
f"setenv CNS_SOLVE '{self.stage.source_path}'",
'cns_solve_env')
# copy over an almost right machine make file we could have got it from v1.3 but this is simpler
src_file = 'instlib/machine/supported/intel-x86_64bit-linux/Makefile.header.2.gfortran'
dest_file = 'instlib/machine/supported/mac-intel-darwin/Makefile.header.5.gfortran'
shutil.move(src_file, dest_file)
if not self.spec.satisfies('%fortran@:10.0.0'):
# patch the machine make file, can't be done with a patch statement it doesn't exists till we copy it
# tried just copying the file from the package directory but it caused a lockup
patch = which('patch')
patch_file = join_path(
package_root, 'nmrpack/packages/cns',
'gfortran_10_allow_argument_mismatch.patch')
patch('-p1', '-i', patch_file)
if '+aria' in self.spec:
from_path = pathlib.Path('aria2.3/cns/src')
to_path = 'source'
for target_file in from_path.iterdir():
if target_file.is_file() and target_file.suffix in ('.f',
'.inc'):
print(f'copying {target_file} to {to_path}')
shutil.copy(target_file, to_path)
if target_file.is_dir():
print(f'copying {target_file} to {to_path}')
shutil.copytree(target_file,
join_path(to_path, target_file.name))
shutil.copytree(from_path, 'aria2.3_patches_applied')
shutil.rmtree('aria2.3')
make('install')
install_tree('.', prefix)
with working_dir(prefix):
shutil.move('cns_solve_env.back', 'cns_solve_env')
replacement_env = f" setenv CNS_SOLVE '{prefix}'"
filter_file(r"setenv CNS_SOLVE '_CNSsolve_location_'",
replacement_env, 'cns_solve_env')
# remove a leftover from our previous edits
os.remove(pathlib.Path(prefix) / pathlib.Path('cns_solve_env' + '~'))
@run_after('install')
@on_package_attributes(run_tests=True)
def test(self):
try:
import tempfile
with tempfile.TemporaryDirectory() as tmp_dir_name:
tmp_dir_name = '/tmp'
test_inp = f'''
stop
'''
with open(join_path(tmp_dir_name, 'test.inp'), 'w') as fp:
fp.write(test_inp)
test_csh = f'''
source {self.prefix}/cns_solve_env
cns_solve < {tmp_dir_name}/test.inp >& {tmp_dir_name}/test_output.txt
'''
with open(join_path(tmp_dir_name, 'test.csh'), 'w') as fp:
fp.write(test_csh)
csh(join(tmp_dir_name, 'test.csh'))
expected = '''
============================================================
| |
| Crystallography & NMR System (CNS) |
| CNSsolve |
| |
============================================================
Version: 1.2 at patch level 1
Status: General release with ARIA enhancements
============================================================
'''.split("\n")
expected = [line.strip() for line in expected if len(line)]
ok = True
result = ''
with open(f"{tmp_dir_name}/test_output.txt", 'r') as file_handle:
result = file_handle.readlines()
result = [line.strip() for line in result if len(line)]
for line in expected:
if not line in result:
tty.error(f'line --{line}-- not in result')
ok = False
break
if not ok:
tty.error(f'''during testing strings
{expected}
not found in test output")
''')
tty.error("")
tty.error(f" output was")
tty.error("")
for line in result:
tty.error(line.strip())
except Exception as e:
tty.error('there was an error', e)
def setup_run_environment(self, env):
environment_changes = get_environment_change(self.prefix,
CNS_SOLVE_ENV)
# print('** environment_changes **', environment_changes)
#
for name, type, value in environment_changes:
if type == PREPEND:
env.prepend_path(name, value)
elif type == NEW:
env.set(name, value)
else:
raise Exception(f'unexpected change type {type}')
class Nuwro(MakefilePackage):
"""NuWro is a Monte Carlo neutrino event generator."""
homepage = "https://nuwro.github.io/user-guide/"
url = "https://github.com/NuWro/nuwro/archive/refs/tags/nuwro_19.02.2.tar.gz"
git = "https://github.com/NuWro/nuwro"
maintainers = [
# maintainer of this recipe, not affliated with the NuWro collaboration
"davehadley"
]
version(
"19.2.2",
sha256=
"e6edf0cd3d9ae22261193ec9ee56f6a0bee5fbeae684f92361f091bb7f1fb055",
)
version(
"19.2.1",
sha256=
"66ec5ce8be747e821edf2e784fe579226c73301a886b0805410d929b61a90371",
)
version(
"19.2.0",
sha256=
"6b5dd5419fc43c3df9fc3c976180fffe24e48478502acdb86b4af8cc0f55e94f",
)
version(
"18.2.1",
sha256=
"4d3324207e1ff7192905b80dc0d422028ac06f1681c84430d8c33f6626a09c67",
)
version(
"18.2.0",
sha256=
"f98f5073ed3b1d21604ffd3ec1e2ca907a15aacd69c8e813526e3d2fd40b2ebc",
)
version(
"17.9.0",
sha256=
"350fa6043fa39253afad30bbcb655bde7d85b641843344aa978faca32535456d",
)
version(
"17.1.1",
sha256=
"5071d9d1495b780060215729bf7c52e1db0f26a213a1c25b5f7c99d43af97f65",
)
version(
"17.1.0",
sha256=
"bbbf73bc3c7436fb2fd28c7df538b4e20ad3f2f90a6c1c72f739f14a2ab8cf64",
)
depends_on("root+pythia6")
# nuwro does not actually require cmake, but root does.
# Spack's concretizer fails with "unsatisfiable constraint" if we don't add this.
depends_on("cmake@3:")
# Missing include directive in nuwro2rootracker.cc causes compilation failure with
# some versions of ROOT
patch("nuwro2rootracker_missing_include.patch", level=0)
def url_for_version(self, version):
return ("https://github.com/NuWro/nuwro/archive/refs/tags/"
"nuwro_{0}.{1:02d}.{2}.tar.gz".format(version[0], version[1],
version[2]))
@property
def build_targets(self):
return [
"CC=c++",
"CXX=c++",
"LD=c++",
"FC=fc",
"VERSION=%s" % self.spec.version,
]
def install(self, spec, prefix):
# nuwro has no install stage,
# so we must install its binaries ourselves
# install_tree function is injected into scope by spack build_environment.py
install_tree("bin", prefix.bin) # noqa
install_tree("data", os.sep.join((prefix, "data"))) # noqa
def setup_run_environment(self, env):
# nuwro uses this environment variable to find the data directory
env.set("NUWRO", self.prefix)
return super(Nuwro, self).setup_run_environment(env)