diff options
69 files changed, 346 insertions, 337 deletions
diff --git a/lib/spack/spack/build_systems/python.py b/lib/spack/spack/build_systems/python.py index 91718f0cae..6dee28e4ed 100644 --- a/lib/spack/spack/build_systems/python.py +++ b/lib/spack/spack/build_systems/python.py @@ -231,7 +231,7 @@ class PythonPackage(PackageBase): if ('py-setuptools' == spec.name or # this is setuptools, or 'py-setuptools' in spec._dependencies and # it's an immediate dep 'build' in spec._dependencies['py-setuptools'].deptypes): - args += ['--single-version-externally-managed', '--root=/'] + args += ['--single-version-externally-managed', '--root=/'] return args diff --git a/lib/spack/spack/cmd/upload_s3.py b/lib/spack/spack/cmd/upload_s3.py index 9894341efe..9013d612f8 100644 --- a/lib/spack/spack/cmd/upload_s3.py +++ b/lib/spack/spack/cmd/upload_s3.py @@ -57,7 +57,7 @@ def setup_parser(subparser): index = subparsers.add_parser('index', help=update_index.__doc__) index.add_argument('-e', '--endpoint-url', - default='https://s3.spack.io', help='URL of mirror') + default='https://s3.spack.io', help='URL of mirror') index.set_defaults(func=update_index) diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py index de47076fe6..69f430b5d5 100644 --- a/lib/spack/spack/main.py +++ b/lib/spack/spack/main.py @@ -247,8 +247,8 @@ class SpackArgumentParser(argparse.ArgumentParser): spack help --all list all commands and options spack help <command> help on a specific command spack help --spec help on the package specification syntax - spack docs open http://spack.rtfd.io/ in a browser""" -.format(help=section_descriptions['help'])) + spack docs open http://spack.rtfd.io/ in a browser +""".format(help=section_descriptions['help'])) # determine help from format above return formatter.format_help() diff --git a/lib/spack/spack/schema/env.py b/lib/spack/spack/schema/env.py index 5e5b9ed64f..2a3afb0aef 100644 --- a/lib/spack/spack/schema/env.py +++ b/lib/spack/spack/schema/env.py @@ -78,7 +78,7 @@ schema = { } }, 'patternProperties': { - r'^(?!when$)\w*': spec_list_schema + r'^(?!when$)\w*': spec_list_schema } } }, @@ -87,35 +87,36 @@ schema = { 'anyOf': [ {'type': 'boolean'}, {'type': 'string'}, - {'type': 'object', - 'patternProperties': { - r'\w+': { - 'required': ['root'], - 'additionalProperties': False, - 'properties': { - 'root': { - 'type': 'string' - }, - 'link': { - 'type': 'string', - 'pattern': '(roots|all)', - }, - 'select': { - 'type': 'array', - 'items': { - 'type': 'string' - } - }, - 'exclude': { - 'type': 'array', - 'items': { - 'type': 'string' - } - }, - 'projections': projections_scheme - } - } - } + { + 'type': 'object', + 'patternProperties': { + r'\w+': { + 'required': ['root'], + 'additionalProperties': False, + 'properties': { + 'root': { + 'type': 'string' + }, + 'link': { + 'type': 'string', + 'pattern': '(roots|all)', + }, + 'select': { + 'type': 'array', + 'items': { + 'type': 'string' + } + }, + 'exclude': { + 'type': 'array', + 'items': { + 'type': 'string' + } + }, + 'projections': projections_scheme + } + } + } } ] } diff --git a/lib/spack/spack/schema/spec_set.py b/lib/spack/spack/schema/spec_set.py index 70ba8de71f..94ff6eec20 100644 --- a/lib/spack/spack/schema/spec_set.py +++ b/lib/spack/spack/schema/spec_set.py @@ -83,8 +83,9 @@ schema = { 'cdash': { 'oneOf': [ {'type': 'string'}, - {'type': 'array', - 'items': {'type': 'string'} + { + 'type': 'array', + 'items': {'type': 'string'} }, ], }, diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py index b89dbc5fe5..cf0de70856 100644 --- a/lib/spack/spack/test/config.py +++ b/lib/spack/spack/test/config.py @@ -616,7 +616,7 @@ def test_bad_command_line_scopes(tmpdir, mock_config): def test_add_command_line_scopes(tmpdir, mutable_config): config_yaml = str(tmpdir.join('config.yaml')) with open(config_yaml, 'w') as f: - f.write("""\ + f.write("""\ config: verify_ssl: False dirty: False diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py index 406915bdf0..5481bfc0ea 100644 --- a/lib/spack/spack/test/pattern.py +++ b/lib/spack/spack/test/pattern.py @@ -27,15 +27,14 @@ def interface(): def implementation(interface): """Returns an implementation of the interface""" class Implementation(interface): + def __init__(self, value): + self.value = value - def __init__(self, value): - self.value = value - - def add(self): - interface.counter += self.value + def add(self): + interface.counter += self.value - def subtract(self): - interface.counter -= self.value + def subtract(self): + interface.counter -= self.value return Implementation diff --git a/lib/spack/spack/test/variant.py b/lib/spack/spack/test/variant.py index 2a937422d3..4a76b4824e 100644 --- a/lib/spack/spack/test/variant.py +++ b/lib/spack/spack/test/variant.py @@ -714,7 +714,7 @@ def test_disjoint_set_initialization(): # Test that no error is thrown when the sets are disjoint d = disjoint_sets(('a',), ('b', 'c'), ('e', 'f')) - assert d.default is 'none' + assert d.default == 'none' assert d.multi is True assert set(x for x in d) == set(['none', 'a', 'b', 'c', 'e', 'f']) diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index e298196568..e5cadb5d61 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -25,7 +25,7 @@ class CmakeClient(CMakePackage): flipped = False run_this = True - check_this_is_None = None + check_this_is_none = None did_something = False @run_after('cmake') @@ -34,7 +34,7 @@ class CmakeClient(CMakePackage): self.callback_counter += 1 @run_after('cmake') - @on_package_attributes(run_this=True, check_this_is_None=None) + @on_package_attributes(run_this=True, check_this_is_none=None) def flip(self): self.flipped = True diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py index 973370d071..cd9ed98476 100644 --- a/var/spack/repos/builtin/packages/abyss/package.py +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -18,7 +18,7 @@ class Abyss(AutotoolsPackage): version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798') version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c') - variant('maxk', values=int, default=0, + variant('maxk', values=int, default=0, description='''set the maximum k-mer length. This value must be a multiple of 32''') @@ -44,7 +44,7 @@ class Abyss(AutotoolsPackage): '--with-sqlite=%s' % self.spec['sqlite'].prefix, '--with-mpi=%s' % self.spec['mpi'].prefix] if maxk: - args.append('--enable-maxk=%s' % maxk) + args.append('--enable-maxk=%s' % maxk) if self.spec['mpi'].name == 'mpich': - args.append('--enable-mpich') + args.append('--enable-mpich') return args diff --git a/var/spack/repos/builtin/packages/athena/package.py b/var/spack/repos/builtin/packages/athena/package.py index c543eb8c1e..504bd5b767 100644 --- a/var/spack/repos/builtin/packages/athena/package.py +++ b/var/spack/repos/builtin/packages/athena/package.py @@ -21,17 +21,60 @@ class Athena(AutotoolsPackage): # PHYSICS "packages": variant('problem', default='linear_wave', description='Problem generator', values=[ - 'blast', 'carbuncle', 'collapse3d', 'cpaw', 'cshock1d', - 'current_sheet', 'cyladvect', 'cylblast', 'cylbphi', 'cylbr', - 'cylcvmri', 'cyldiff', 'cylfieldloop', 'cylnewtmri', 'cylrayleigh', - 'cylspiral', 'cylwind', 'cylwindrot', 'cylwindrotb', 'dmr', 'fft_test', - 'field_loop', 'firehose', 'hall_drift', 'hb3', 'hgb', 'hkdisk', - 'jeans', 'jet', 'kh', 'linear_wave', 'lw_implode', 'msa', 'noh', - 'orszag-tang', 'par_collision', 'par_epicycle', 'par_strat2d', - 'par_strat3d', 'pgflow', 'rotor', 'rt', 'shk_cloud', 'shkset1d', - 'shkset2d', 'shkset3d', 'shu-osher', 'strat', 'streaming2d_multi', - 'streaming2d_single', 'streaming3d_multi', 'streaming3d_single', - 'twoibw']) + 'blast', + 'carbuncle', + 'collapse3d', + 'cpaw', + 'cshock1d', + 'current_sheet', + 'cyladvect', + 'cylblast', + 'cylbphi', + 'cylbr', + 'cylcvmri', + 'cyldiff', + 'cylfieldloop', + 'cylnewtmri', + 'cylrayleigh', + 'cylspiral', + 'cylwind', + 'cylwindrot', + 'cylwindrotb', + 'dmr', + 'fft_test', + 'field_loop', + 'firehose', + 'hall_drift', + 'hb3', + 'hgb', + 'hkdisk', + 'jeans', + 'jet', + 'kh', + 'linear_wave', + 'lw_implode', + 'msa', + 'noh', + 'orszag-tang', + 'par_collision', + 'par_epicycle', + 'par_strat2d', + 'par_strat3d', + 'pgflow', + 'rotor', + 'rt', + 'shk_cloud', + 'shkset1d', + 'shkset2d', + 'shkset3d', + 'shu-osher', + 'strat', + 'streaming2d_multi', + 'streaming2d_single', + 'streaming3d_multi', + 'streaming3d_single', + 'twoibw' + ]) variant('gas', default='mhd', description='Gas properties', values=['mhd', 'hydro']) variant('eos', default='adiabatic', description='Equation of state', @@ -55,9 +98,9 @@ class Athena(AutotoolsPackage): variant('order', default='2', description='Order and type of spatial reconstruction', values=['1', '2', '3', '2p', '3p']) - variant('flux', default='roe', description='Flux function', - values=['roe', 'hllc', 'hlld', 'hlle', 'force', 'exact', - 'two-shock']) + variant('flux', default='roe', description='Flux function', values=[ + 'roe', 'hllc', 'hlld', 'hlle', 'force', 'exact', 'two-shock' + ]) variant('integrator', default='ctu', description='Unsplit integration algorithm', values=['ctu', 'vl']) diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index 5e69b8f9a8..528f26ac82 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -44,11 +44,9 @@ class Atlas(Package): multi=False ) - variant('tune_cpu', default=-1, - multi=False, - description="Number of threads to tune to,\ - -1 for autodetect, 0 for no threading" - ) + variant('tune_cpu', default=-1, multi=False, + description="Number of threads to tune to, " + "-1 for autodetect, 0 for no threading") provides('blas') provides('lapack') diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py index d3f5b1ff07..9979d95985 100644 --- a/var/spack/repos/builtin/packages/blasr/package.py +++ b/var/spack/repos/builtin/packages/blasr/package.py @@ -13,7 +13,7 @@ class Blasr(Package): homepage = "https://github.com/PacificBiosciences/blasr/wiki" url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz" - version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') + version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') depends_on('ncurses') depends_on('hdf5+cxx@1.8.12:1.8.99') diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py index 5a01b87bb8..c3e8e86e82 100644 --- a/var/spack/repos/builtin/packages/boxlib/package.py +++ b/var/spack/repos/builtin/packages/boxlib/package.py @@ -17,12 +17,8 @@ class Boxlib(CMakePackage): depends_on('mpi') - variant('dims', - default='3', - values=('1', '2', '3'), - multi=False, - description='Number of spatial dimensions' - ) + variant('dims', default='3', values=('1', '2', '3'), multi=False, + description='Number of spatial dimensions') def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 0a4d8fbf5a..4b24c3961b 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -21,7 +21,7 @@ class Breakdancer(CMakePackage): url = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz" version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6') - version('master', submodules='true', + version('master', submodules='true', git='https://github.com/genome/breakdancer.git', preferred=True) phases = ['edit', 'cmake', 'build', 'install'] diff --git a/var/spack/repos/builtin/packages/c-blosc2/package.py b/var/spack/repos/builtin/packages/c-blosc2/package.py index 2dbad3f69e..d9bcdde290 100644 --- a/var/spack/repos/builtin/packages/c-blosc2/package.py +++ b/var/spack/repos/builtin/packages/c-blosc2/package.py @@ -32,7 +32,7 @@ class CBlosc2(CMakePackage): description='support for ZSTD') depends_on('cmake@2.8.10:', type='build') - # TODO https://github.com/inikep/lizard/issues/21 + # TODO https://github.com/inikep/lizard/issues/21 # depends_on('lizard') depends_on('lz4') depends_on('snappy') diff --git a/var/spack/repos/builtin/packages/cardioid/package.py b/var/spack/repos/builtin/packages/cardioid/package.py index 5506cc6fce..54d9b2e54f 100644 --- a/var/spack/repos/builtin/packages/cardioid/package.py +++ b/var/spack/repos/builtin/packages/cardioid/package.py @@ -18,7 +18,7 @@ class Cardioid(CMakePackage): version('develop', branch='master') version('elecfem', branch='elec-fem') - variant('cuda', default=False, + variant('cuda', default=False, description='Build with cuda support') variant('mfem', default=False, description='Build with mfem support') diff --git a/var/spack/repos/builtin/packages/ccs-qcd/package.py b/var/spack/repos/builtin/packages/ccs-qcd/package.py index 5233609c94..27d89b7543 100644 --- a/var/spack/repos/builtin/packages/ccs-qcd/package.py +++ b/var/spack/repos/builtin/packages/ccs-qcd/package.py @@ -33,14 +33,12 @@ class CcsQcd(MakefilePackage): version('master', branch='master') version('1.2.1', commit='d7c6b6923f35a824e997ba8db5bd12dc20dda45c') - variant( - 'class', values=int, default=1, - description='This miniapp has five problem classes, for which the' + - ' first three are relatively small problems just for testing' + - ' this miniapp itself. The remaining two are the target problem' + + variant('class', values=int, default=1, + description='This miniapp has five problem classes, for which the' + ' first three are relatively small problems just for testing' + ' this miniapp itself. The remaining two are the target problem' ' sizes for the HPCI FS evaluation.', - multi=False, validator=class_validator - ) + multi=False, validator=class_validator) depends_on('mpi') diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py index 0f857a16f8..baa8e25bbc 100644 --- a/var/spack/repos/builtin/packages/cgm/package.py +++ b/var/spack/repos/builtin/packages/cgm/package.py @@ -10,7 +10,7 @@ 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 = "http://sigma.mcs.anl.gov/cgm-library" + homepage = "http://sigma.mcs.anl.gov/cgm-library" url = "http://ftp.mcs.anl.gov/pub/fathom/cgm-16.0.tar.gz" version('16.0', 'a68aa5954d82502ff75d5eb91a29a01c') diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py index 332dae343f..e3cf622e3c 100644 --- a/var/spack/repos/builtin/packages/chombo/package.py +++ b/var/spack/repos/builtin/packages/chombo/package.py @@ -24,12 +24,8 @@ class Chombo(MakefilePackage): variant('mpi', default=True, description='Enable MPI parallel support') variant('hdf5', default=True, description='Enable HDF5 support') - variant('dims', - default='3', - values=('1', '2', '3', '4', '5', '6'), - multi=False, - description='Number of PDE dimensions [1-6]' - ) + variant('dims', default='3', values=('1', '2', '3', '4', '5', '6'), + multi=False, description='Number of PDE dimensions [1-6]') patch('hdf5-16api.patch', when='@3.2', level=0) patch('Make.defs.local.template.patch', when='@3.2', level=0) diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py index ea41f8e1ac..9fa03e7e77 100644 --- a/var/spack/repos/builtin/packages/dataspaces/package.py +++ b/var/spack/repos/builtin/packages/dataspaces/package.py @@ -26,22 +26,22 @@ class Dataspaces(AutotoolsPackage): version('1.6.2', '73caa4920b6f2c0c6d6cb87640ff04be') variant('dimes', - default=False, - description='enabled DIMES transport mode') + default=False, + description='enabled DIMES transport mode') variant('cray-drc', - default=False, - description='using Cray Dynamic Credentials library') + default=False, + description='using Cray Dynamic Credentials library') variant('gni-cookie', - default='0x5420000', - description='Cray UGNI communication token', - values=is_string) + default='0x5420000', + description='Cray UGNI communication token', + values=is_string) variant('ptag', - default='250', - description='Cray UGNI protection tag', - values=is_string) + default='250', + description='Cray UGNI protection tag', + values=is_string) variant('mpi', - default=True, - description='Use MPI for collective communication') + default=True, + description='Use MPI for collective communication') depends_on('m4', type='build') depends_on('automake', type='build') diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py index 8a4ce3c420..1a0a23263e 100644 --- a/var/spack/repos/builtin/packages/font-util/package.py +++ b/var/spack/repos/builtin/packages/font-util/package.py @@ -74,16 +74,14 @@ class FontUtil(AutotoolsPackage): for f_r in fonts_resource: f = f_r[0] resource(name=f, url=font_baseurl + f + '-' + f_r[1] + '.tar.gz', - md5=f_r[2], destination=f, when='fonts=' + f) + md5=f_r[2], destination=f, when='fonts=' + f) fonts.append(f) - variant( - 'fonts', - description='Installs fonts', - values=fonts, - default=','.join(fonts), - multi=True - ) + variant('fonts', + description='Installs fonts', + values=fonts, + default=','.join(fonts), + multi=True) def setup_environment(self, spack_env, run_env): spack_env.prepend_path('PATH', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py index d9f06ba71b..6605ec12b8 100644 --- a/var/spack/repos/builtin/packages/gapfiller/package.py +++ b/var/spack/repos/builtin/packages/gapfiller/package.py @@ -24,7 +24,9 @@ class Gapfiller(Package): def url_for_version(self, version): return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format( - os.getcwd(), version.dashed) + os.getcwd(), + version.dashed + ) depends_on('perl+threads', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py index b37d355170..43520c747b 100644 --- a/var/spack/repos/builtin/packages/gasnet/package.py +++ b/var/spack/repos/builtin/packages/gasnet/package.py @@ -27,7 +27,7 @@ class Gasnet(AutotoolsPackage): variant('mpi', default=True, description="Support MPI") variant('aligned-segments', default=False, description="Requirement to achieve aligned VM segments") - variant('pshm', default=True, + variant('pshm', default=True, description="Support inter-process shared memory support") variant('segment-mmap-max', default='16GB', description="Upper bound for mmap-based GASNet segments") diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 7976636f24..15acc438c3 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -115,12 +115,10 @@ class Gcc(AutotoolsPackage): # nvptx-tools does not seem to work as a dependency, # but does fine when the source is inside the gcc build directory # nvptx-tools doesn't have any releases, so grabbing the last commit - resource( - name='nvptx-tools', + resource(name='nvptx-tools', git='https://github.com/MentorEmbedded/nvptx-tools', commit='5f6f343a302d620b0868edab376c00b15741e39e', - when='+nvptx' - ) + when='+nvptx') # TODO: integrate these libraries. # depends_on('ppl') diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py index 2517cce6eb..a7b1ce5e65 100644 --- a/var/spack/repos/builtin/packages/gdl/package.py +++ b/var/spack/repos/builtin/packages/gdl/package.py @@ -19,11 +19,10 @@ class Gdl(CMakePackage): version('0.9.9', sha256='ad5de3fec095a5c58b46338dcc7367d2565c093794ab1bbcf180bba1a712cf14') version('0.9.8', '447b0362e1df5ea8af814a969e89d3ec') - variant( - 'graphicsmagick', + variant('graphicsmagick', default=False, - description='Enable GraphicsMagick' - ) + description='Enable GraphicsMagick') + variant('hdf4', default=False, description='Enable HDF4') variant('hdf5', default=True, description='Enable HDF5') variant('openmp', default=True, description='Enable OpenMP') diff --git a/var/spack/repos/builtin/packages/globalarrays/package.py b/var/spack/repos/builtin/packages/globalarrays/package.py index fcfb9e00e1..d088140edb 100644 --- a/var/spack/repos/builtin/packages/globalarrays/package.py +++ b/var/spack/repos/builtin/packages/globalarrays/package.py @@ -28,8 +28,8 @@ class Globalarrays(AutotoolsPackage): variant('blas', default=False, description='Enable BLAS') variant('lapack', default=False, description='Enable LAPACK') variant('scalapack', default=False, description='Enable SCALAPACK') - variant('armci', values=('mpi-ts', 'mpi-pr', 'mpi3', 'openib', 'ofi'), - default='mpi-ts', description='ARMCI runtime') + variant('armci', values=('mpi-ts', 'mpi-pr', 'mpi3', 'openib', 'ofi'), + default='mpi-ts', description='ARMCI runtime') depends_on('mpi') depends_on('blas', when='+blas') diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index eb08c0393b..37a8a02ee2 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -61,8 +61,8 @@ class Gromacs(CMakePackage): 'ARM_NEON', 'ARM_NEON_ASIMD')) variant('rdtscp', default=True, description='Enable RDTSCP instruction usage') variant('mdrun_only', default=False, - description='Enables the build of a cut-down version' + - ' of libgromacs and/or the mdrun program') + description='Enables the build of a cut-down version' + ' of libgromacs and/or the mdrun program') variant('openmp', default=True, description='Enables OpenMP at configure time') variant('double_precision', default=False, description='Enables a double-precision configuration') diff --git a/var/spack/repos/builtin/packages/idba/package.py b/var/spack/repos/builtin/packages/idba/package.py index ccd71621d0..2ec54b8256 100644 --- a/var/spack/repos/builtin/packages/idba/package.py +++ b/var/spack/repos/builtin/packages/idba/package.py @@ -18,4 +18,4 @@ class Idba(AutotoolsPackage): depends_on('m4', type='build') depends_on('autoconf', type='build') depends_on('automake', type='build') - depends_on('libtool', type='build') + depends_on('libtool', type='build') diff --git a/var/spack/repos/builtin/packages/intel-xed/package.py b/var/spack/repos/builtin/packages/intel-xed/package.py index 61030326da..066631a48e 100644 --- a/var/spack/repos/builtin/packages/intel-xed/package.py +++ b/var/spack/repos/builtin/packages/intel-xed/package.py @@ -20,16 +20,12 @@ class IntelXed(Package): # the mbuild resource. Xed doesn't have official releases, only # git commits. - version_list = [ - ('2019.03.01', - 'b7231de4c808db821d64f4018d15412640c34113', - '176544e1fb54b6bfb40f596111368981d287e951', - ), - ('2018.02.14', - '44d06033b69aef2c20ab01bfb518c52cd71bb537', - 'bb9123152a330c7fa1ff1a502950dc199c83e177', - ) - ] + version_list = [('2019.03.01', + 'b7231de4c808db821d64f4018d15412640c34113', + '176544e1fb54b6bfb40f596111368981d287e951'), + ('2018.02.14', + '44d06033b69aef2c20ab01bfb518c52cd71bb537', + 'bb9123152a330c7fa1ff1a502950dc199c83e177')] version('develop', branch='master') resource(name='mbuild', diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py index bfd835bc78..f532a3cd3c 100644 --- a/var/spack/repos/builtin/packages/kokkos/package.py +++ b/var/spack/repos/builtin/packages/kokkos/package.py @@ -105,18 +105,18 @@ class Kokkos(Package): # without specifying CUDA for p in gpu_values: conflicts('gpu_arch={0}'.format(p), when='~cuda', - msg='Must specify CUDA backend to use a GPU architecture.') + msg='Must specify CUDA backend to use a GPU architecture.') # Check that we haven't specified a Kokkos CUDA option # without specifying CUDA conflicts('+force_uvm', when='~cuda', - msg='Must enable CUDA to use force_uvm.') + msg='Must enable CUDA to use force_uvm.') conflicts('+use_ldg', when='~cuda', - msg='Must enable CUDA to use use_ldg.') + msg='Must enable CUDA to use use_ldg.') conflicts('+rdc', when='~cuda', - msg='Must enable CUDA to use rdc.') + msg='Must enable CUDA to use rdc.') conflicts('+enable_lambda', when='~cuda', - msg='Must enable CUDA to use enable_lambda.') + msg='Must enable CUDA to use enable_lambda.') # Check that we haven't asked for a GPU architecture that # the revision of kokkos does not support @@ -127,8 +127,8 @@ class Kokkos(Package): # see kokkos issue #1296 # https://github.com/kokkos/kokkos/issues/1296 conflicts('+cuda', when='@2.5.00:2.7.00', - msg='Kokkos build system has issue (#1296) when CUDA enabled' - ' in version 2.5.00 through 2.7.00.') + msg='Kokkos build system has issue (#1296) when CUDA enabled' + ' in version 2.5.00 through 2.7.00.') # Specify that v1.x is required as v2.x has API changes depends_on('hwloc@:1') diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py index a131a85477..eed13ad7b4 100644 --- a/var/spack/repos/builtin/packages/lbann/package.py +++ b/var/spack/repos/builtin/packages/lbann/package.py @@ -41,8 +41,8 @@ class Lbann(CMakePackage): description='The build type to build', values=('Debug', 'Release')) variant('al', default=True, description='Builds with support for Aluminum Library') - variant('conduit', default=True, - description='Builds with support for Conduit Library ' + + variant('conduit', default=True, + description='Builds with support for Conduit Library ' '(note that for v0.99 conduit is required)') variant('vtune', default=False, description='Builds with support for Intel VTune') variant('docs', default=False, description='Builds with support for building documentation') diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index 363e383f58..d26b80f622 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -40,13 +40,11 @@ class Libfabric(AutotoolsPackage): 'tcp', 'efa') - variant( - 'fabrics', - default='sockets', - description='A list of enabled fabrics', - values=fabrics, - multi=True - ) + variant('fabrics', + default='sockets', + description='A list of enabled fabrics', + values=fabrics, + multi=True) # NOTE: the 'kdreg' variant enables use of the special /dev/kdreg file to # assist in memory registration caching in the GNI provider. This diff --git a/var/spack/repos/builtin/packages/liggghts/package.py b/var/spack/repos/builtin/packages/liggghts/package.py index 9fdf5d097b..936252f268 100644 --- a/var/spack/repos/builtin/packages/liggghts/package.py +++ b/var/spack/repos/builtin/packages/liggghts/package.py @@ -22,9 +22,9 @@ class Liggghts(MakefilePackage): variant('jpeg', default=True, description='Enable JPEG support') variant('gzip', default=True, description='Enable GZIP for some input and output files') - variant('debug', default=False, + variant('debug', default=False, description='Builds a debug version of the executable') - variant('profile', default=False, + variant('profile', default=False, description='Generate profiling code') depends_on('vtk') diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py index a462ee7f25..c6e7e3d7a6 100644 --- a/var/spack/repos/builtin/packages/lulesh/package.py +++ b/var/spack/repos/builtin/packages/lulesh/package.py @@ -20,7 +20,7 @@ class Lulesh(MakefilePackage): variant('mpi', default=True, description='Build with MPI support') variant('openmp', default=True, description='Build with OpenMP support') variant('visual', default=False, - description='Build with Visualization support (Silo, hdf5)') + description='Build with Visualization support (Silo, hdf5)') depends_on('mpi', when='+mpi') depends_on('silo', when='+visual') diff --git a/var/spack/repos/builtin/packages/matlab/package.py b/var/spack/repos/builtin/packages/matlab/package.py index 639ec65890..177dad1358 100644 --- a/var/spack/repos/builtin/packages/matlab/package.py +++ b/var/spack/repos/builtin/packages/matlab/package.py @@ -22,7 +22,7 @@ class Matlab(Package): mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html""" - homepage = "https://www.mathworks.com/products/matlab.html" + homepage = "https://www.mathworks.com/products/matlab.html" version('R2018b', sha256='8cfcddd3878d3a69371c4e838773bcabf12aaf0362cc2e1ae7e8820845635cac') version('R2016b', 'b0e0b688894282139fa787b5a86a5cf7') diff --git a/var/spack/repos/builtin/packages/maverick/package.py b/var/spack/repos/builtin/packages/maverick/package.py index 8052503c65..ce1989b2e4 100644 --- a/var/spack/repos/builtin/packages/maverick/package.py +++ b/var/spack/repos/builtin/packages/maverick/package.py @@ -22,7 +22,7 @@ class Maverick(MakefilePackage): conflicts('%nag') conflicts('%pgi') conflicts('%xl') - conflicts('%xl_r') + conflicts('%xl_r') def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index 16a977d48c..7ec3fae7e0 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -73,62 +73,62 @@ class Mfem(Package): url='http://goo.gl/xrScXn', extension='.tar.gz') variant('static', default=True, - description='Build static library') + description='Build static library') variant('shared', default=False, - description='Build shared library') + description='Build shared library') variant('mpi', default=True, - description='Enable MPI parallelism') + description='Enable MPI parallelism') # Can we make the default value for 'metis' to depend on the 'mpi' value? variant('metis', default=True, - description='Enable METIS support') + description='Enable METIS support') # TODO: The 'hypre' variant is the same as 'mpi', we may want to remove it. # For now, keep the 'hypre' variant while ignoring its setting. This # is done to preserve compatibility with other packages that refer to # it, e.g. xSDK. variant('hypre', default=True, - description='Required for MPI parallelism') + description='Required for MPI parallelism') variant('openmp', default=False, - description='Enable OpenMP parallelism') + description='Enable OpenMP parallelism') variant('threadsafe', default=False, - description=('Enable thread safe features.' - ' Required for OpenMP.' - ' May cause minor performance issues.')) + description=('Enable thread safe features.' + ' Required for OpenMP.' + ' May cause minor performance issues.')) variant('superlu-dist', default=False, - description='Enable MPI parallel, sparse direct solvers') + description='Enable MPI parallel, sparse direct solvers') # Placeholder for STRUMPACK, support added in mfem v3.3.2: # variant('strumpack', default=False, - # description='Enable support for STRUMPACK') + # description='Enable support for STRUMPACK') variant('suite-sparse', default=False, - description='Enable serial, sparse direct solvers') + description='Enable serial, sparse direct solvers') variant('petsc', default=False, - description='Enable PETSc solvers, preconditioners, etc.') + description='Enable PETSc solvers, preconditioners, etc.') variant('sundials', default=False, - description='Enable Sundials time integrators') + description='Enable Sundials time integrators') variant('pumi', default=False, - description='Enable functionality based on PUMI') + description='Enable functionality based on PUMI') variant('mpfr', default=False, - description='Enable precise, 1D quadrature rules') + description='Enable precise, 1D quadrature rules') variant('lapack', default=False, - description='Use external blas/lapack routines') + description='Use external blas/lapack routines') variant('debug', default=False, - description='Build debug instead of optimized version') + description='Build debug instead of optimized version') variant('netcdf', default=False, - description='Enable Cubit/Genesis reader') + description='Enable Cubit/Genesis reader') variant('conduit', default=False, - description='Enable binary data I/O using Conduit') + description='Enable binary data I/O using Conduit') variant('gzstream', default=True, - description='Support zip\'d streams for I/O') + description='Support zip\'d streams for I/O') variant('gnutls', default=False, - description='Enable secure sockets using GnuTLS') + description='Enable secure sockets using GnuTLS') variant('libunwind', default=False, - description='Enable backtrace on error support using Libunwind') + description='Enable backtrace on error support using Libunwind') variant('timer', default='auto', - values=('auto', 'std', 'posix', 'mac', 'mpi'), - description='Timing functions to use in mfem::StopWatch') + values=('auto', 'std', 'posix', 'mac', 'mpi'), + description='Timing functions to use in mfem::StopWatch') variant('examples', default=False, - description='Build and install examples') + description='Build and install examples') variant('miniapps', default=False, - description='Build and install miniapps') + description='Build and install miniapps') conflicts('+shared', when='@:3.3.2') conflicts('~static~shared') diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py index 1d5e2326cd..034f70e292 100644 --- a/var/spack/repos/builtin/packages/mofem-cephas/package.py +++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py @@ -30,7 +30,8 @@ class MofemCephas(CMakePackage): # This option can be only used for development of core lib variant('copy_user_modules', default=True, - description='Copy user modules directory instead linking to source') + description='Copy user modules directory ' + 'instead of linking to source') variant('adol-c', default=True, description='Compile with ADOL-C') variant('tetgen', default=True, description='Compile with Tetgen') variant('med', default=True, description='Compile with Med') diff --git a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py index df5384f6ea..00c7aad6d8 100644 --- a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py +++ b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py @@ -26,7 +26,7 @@ class MofemFractureModule(CMakePackage): version('0.9.42', tag='v0.9.42') variant('copy_user_modules', default=True, - description='Copy user modules directory instead linking') + description='Copy user modules directory instead linking') extends('mofem-cephas') depends_on('mofem-users-modules@0.8.17', when='@0.9.50') diff --git a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py index c3a4fb7d7c..38613f334d 100644 --- a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py +++ b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py @@ -20,7 +20,7 @@ class MofemMinimalSurfaceEquation(CMakePackage): version('0.3.9', tag='v0.3.9') variant('copy_user_modules', default=True, - description='Copy user modules directory instead linking') + description='Copy user modules directory instead linking') extends('mofem-cephas') depends_on("mofem-users-modules", type=('build', 'link', 'run')) diff --git a/var/spack/repos/builtin/packages/mofem-users-modules/package.py b/var/spack/repos/builtin/packages/mofem-users-modules/package.py index f09b7fe6e3..f1f4afd938 100644 --- a/var/spack/repos/builtin/packages/mofem-users-modules/package.py +++ b/var/spack/repos/builtin/packages/mofem-users-modules/package.py @@ -30,7 +30,7 @@ class MofemUsersModules(CMakePackage): maintainers = ['likask'] variant('copy_user_modules', default=True, - description='Copy user modules directory instead linking') + description='Copy user modules directory instead linking') extends('mofem-cephas') depends_on('mofem-cephas@0.8.17', when='@0.8.17') diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py index 992f679446..54f7bd9055 100644 --- a/var/spack/repos/builtin/packages/mpifileutils/package.py +++ b/var/spack/repos/builtin/packages/mpifileutils/package.py @@ -43,17 +43,17 @@ class Mpifileutils(Package): depends_on('cmake@3.1:', when='@0.9:', type='build') variant('xattr', default=True, - description="Enable code for extended attributes") + description="Enable code for extended attributes") variant('lustre', default=False, - description="Enable optimizations and features for Lustre") + description="Enable optimizations and features for Lustre") variant('experimental', default=False, - description="Install experimental tools") + description="Install experimental tools") conflicts('+experimental', when='@:0.6') variant('gpfs', default=False, - description="Enable optimizations and features for GPFS") + description="Enable optimizations and features for GPFS") conflicts('+gpfs', when='@:0.8.1') def cmake_args(self): diff --git a/var/spack/repos/builtin/packages/nalu-wind/package.py b/var/spack/repos/builtin/packages/nalu-wind/package.py index cba8d2898b..67af366156 100644 --- a/var/spack/repos/builtin/packages/nalu-wind/package.py +++ b/var/spack/repos/builtin/packages/nalu-wind/package.py @@ -21,7 +21,7 @@ class NaluWind(CMakePackage): # Options variant('shared', default=(sys.platform != 'darwin'), - description='Build dependencies as shared libraries') + description='Build dependencies as shared libraries') variant('pic', default=True, description='Position independent code') # Third party libraries diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py index 0e25c11992..0330cdf273 100644 --- a/var/spack/repos/builtin/packages/nextflow/package.py +++ b/var/spack/repos/builtin/packages/nextflow/package.py @@ -10,20 +10,14 @@ class Nextflow(Package): """Data-driven computational pipelines""" homepage = "http://www.nextflow.io" - url = "https://github.com/nextflow-io/nextflow/releases/download/v0.24.1/nextflow" + url = "https://github.com/nextflow-io/nextflow/releases/download/v0.24.1/nextflow" - version('0.25.6', '29d739b6caf8ceb5aa9997310ee8d0e7', - expand=False) - version('0.24.1', '80ec8c4fe8e766e0bdd1371a50410d1d', - expand=False) - version('0.23.3', '71fb69275b6788af1c6f1165f40d362e', - expand=False) - version('0.21.0', '38e5e335cb33f05ba358e1f883c8386c', - expand=False) - version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', - expand=False) - version('0.17.3', '5df00105fb1ce6fd0ba019ae735d9617', - expand=False) + version('0.25.6', '29d739b6caf8ceb5aa9997310ee8d0e7', expand=False) + version('0.24.1', '80ec8c4fe8e766e0bdd1371a50410d1d', expand=False) + version('0.23.3', '71fb69275b6788af1c6f1165f40d362e', expand=False) + version('0.21.0', '38e5e335cb33f05ba358e1f883c8386c', expand=False) + version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', expand=False) + version('0.17.3', '5df00105fb1ce6fd0ba019ae735d9617', expand=False) depends_on('java') diff --git a/var/spack/repos/builtin/packages/nlohmann-json/package.py b/var/spack/repos/builtin/packages/nlohmann-json/package.py index 7e157825ac..628e4395bc 100644 --- a/var/spack/repos/builtin/packages/nlohmann-json/package.py +++ b/var/spack/repos/builtin/packages/nlohmann-json/package.py @@ -22,7 +22,7 @@ class NlohmannJson(CMakePackage): version('3.1.1', sha256='9f3549824af3ca7e9707a2503959886362801fb4926b869789d6929098a79e47') variant('single_header', default=True, - description='Use amalgamated single-header') + description='Use amalgamated single-header') depends_on('cmake@3.8:', type='build') diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 3b88ff8062..cd9e618d06 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -44,8 +44,7 @@ class Openspeedshop(CMakePackage): description="build with cuda packages included.") variant('gui', default='qt3', values=('none', 'qt3', 'qt4'), - description='Build or not build a GUI of choice' - ) + description='Build or not build a GUI of choice') variant('build_type', default='None', values=('None'), description='CMake build type') diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py index 6bed409806..2974f970f7 100644 --- a/var/spack/repos/builtin/packages/perl-test-most/package.py +++ b/var/spack/repos/builtin/packages/perl-test-most/package.py @@ -18,4 +18,4 @@ class PerlTestMost(PerlPackage): depends_on('perl-test-differences', type=('build', 'run')) depends_on('perl-test-exception', type=('build', 'run')) depends_on('perl-test-warn', type=('build', 'run')) - depends_on('perl-test-deep', type=('build', 'run')) + depends_on('perl-test-deep', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/picsar/package.py b/var/spack/repos/builtin/packages/picsar/package.py index 2163243d3a..0f876d0679 100644 --- a/var/spack/repos/builtin/packages/picsar/package.py +++ b/var/spack/repos/builtin/packages/picsar/package.py @@ -23,7 +23,7 @@ class Picsar(MakefilePackage): variant('vtune', default=False, description='Vtune profiling') variant('sde', default=False, description='sde profiling') variant('map', default=False, description='Allinea Map profiling') - variant('library', default=False, + variant('library', default=False, description='Create static and dynamic library') depends_on('mpi') @@ -43,9 +43,9 @@ class Picsar(MakefilePackage): if self.spec.satisfies(key): comp = value targets.append('COMP={0}'.format(comp)) - if comp is 'user': - targets.append('FARGS={0}{1}'.format('-g -O3 ', - self.compiler.openmp_flag)) + if comp == 'user': + targets.append( + 'FARGS={0}{1}'.format('-g -O3 ', self.compiler.openmp_flag)) if '+prod' in self.spec: mode = 'prod' diff --git a/var/spack/repos/builtin/packages/picsarlite/package.py b/var/spack/repos/builtin/packages/picsarlite/package.py index 5ce6e34e88..a144fac0d8 100644 --- a/var/spack/repos/builtin/packages/picsarlite/package.py +++ b/var/spack/repos/builtin/packages/picsarlite/package.py @@ -26,7 +26,7 @@ class Picsarlite(MakefilePackage): variant('vtune', default=False, description='Vtune profiling') variant('sde', default=False, description='sde profiling') variant('map', default=False, description='Allinea Map profiling') - variant('library', default=False, + variant('library', default=False, description='Create static and dynamic library') depends_on('mpi') @@ -44,9 +44,9 @@ class Picsarlite(MakefilePackage): if self.spec.satisfies(key): comp = value targets.append('COMP={0}'.format(comp)) - if comp is 'user': - targets.append('FARGS={0}{1}'.format('-g -O3 ', - self.compiler.openmp_flag)) + if comp == 'user': + targets.append( + 'FARGS={0}{1}'.format('-g -O3 ', self.compiler.openmp_flag)) if '+prod' in self.spec: mode = 'prod' diff --git a/var/spack/repos/builtin/packages/pumi/package.py b/var/spack/repos/builtin/packages/pumi/package.py index b69ac7e6e6..827ed6187a 100644 --- a/var/spack/repos/builtin/packages/pumi/package.py +++ b/var/spack/repos/builtin/packages/pumi/package.py @@ -37,10 +37,10 @@ class Pumi(CMakePackage): variant('zoltan', default=False, description='Enable Zoltan Features') variant('fortran', default=False, description='Enable FORTRAN interface') variant('simmodsuite', default='none', - values=('none', 'base', 'kernels', 'full'), - description="Enable Simmetrix SimModSuite Support: 'base' enables " - "the minimum set of functionality, 'kernels' adds CAD kernel support " - "to 'base', and 'full' enables all functionality.") + values=('none', 'base', 'kernels', 'full'), + description="Enable Simmetrix SimModSuite Support: 'base' enables " + "the minimum set of functionality, 'kernels' adds CAD kernel " + "support to 'base', and 'full' enables all functionality.") depends_on('mpi') depends_on('cmake@3:', type='build') @@ -51,11 +51,11 @@ class Pumi(CMakePackage): simfull = simkernels + "+abstract+adv+advmodel\ +import+paralleladapt+parallelmesh" depends_on('simmetrix-simmodsuite' + simbase, - when='simmodsuite=base') + when='simmodsuite=base') depends_on('simmetrix-simmodsuite' + simkernels, - when='simmodsuite=kernels') + when='simmodsuite=kernels') depends_on('simmetrix-simmodsuite' + simfull, - when='simmodsuite=full') + when='simmodsuite=full') def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/py-bokeh/package.py b/var/spack/repos/builtin/packages/py-bokeh/package.py index 9ce72eff36..f1401598c2 100644 --- a/var/spack/repos/builtin/packages/py-bokeh/package.py +++ b/var/spack/repos/builtin/packages/py-bokeh/package.py @@ -23,4 +23,4 @@ class PyBokeh(PythonPackage): depends_on('py-numpy@1.7.1:', type=('build', 'run')) depends_on('py-tornado@4.3:', type=('build', 'run')) depends_on('py-futures@3.0.3:', type=('build', 'run'), - when='^python@2.7:2.8') + when='^python@2.7:2.8') diff --git a/var/spack/repos/builtin/packages/py-cvxopt/package.py b/var/spack/repos/builtin/packages/py-cvxopt/package.py index fdcc902cef..eda664b855 100644 --- a/var/spack/repos/builtin/packages/py-cvxopt/package.py +++ b/var/spack/repos/builtin/packages/py-cvxopt/package.py @@ -20,7 +20,7 @@ class PyCvxopt(PythonPackage): variant('gsl', default=False, description='Use GSL random number generators for constructing random matrices') variant('fftw', default=False, description='Install the cvxopt.fftw interface to FFTW') variant('glpk', default=False, description='Enable support for the linear programming solver GLPK') - # variant('mosek', default=False, description='Enable support for the linear, second-order cone, and quadratic programming solvers in MOSEK') # noqa: flake8 + # variant('mosek', default=False, description='Enable support for the linear, second-order cone, and quadratic programming solvers in MOSEK') # noqa variant('dsdp', default=False, description='Enable support for the semidefinite programming solver DSDP') # Required dependencies diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py index f98a0fb063..ee83b8b72c 100644 --- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py +++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py @@ -26,7 +26,7 @@ class PyMdanalysis(PythonPackage): version('0.16.0', sha256='c4824fa1fddd336daa39371436187ebb023366885fb250c2827ed7fce2546bd4') version('0.15.0', '19e5a8e6c2bfe85f6209d1d7a36e4f20') - variant('analysis', default=True, + variant('analysis', default=True, description='Enable analysis packages: matplotlib, scipy, seaborn') variant('amber', default=False, description='Support AMBER netcdf format.') diff --git a/var/spack/repos/builtin/packages/py-pycares/package.py b/var/spack/repos/builtin/packages/py-pycares/package.py index 6080f09c23..27ef3c4869 100644 --- a/var/spack/repos/builtin/packages/py-pycares/package.py +++ b/var/spack/repos/builtin/packages/py-pycares/package.py @@ -17,4 +17,4 @@ class PyPycares(PythonPackage): version('3.0.0', '5f938c037c5905ebc5617a157c654088') depends_on('python@2.6:') - depends_on('py-cffi') + depends_on('py-cffi') diff --git a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py index 6ead324903..ebf4b8ec4c 100644 --- a/var/spack/repos/builtin/packages/py-scikit-optimize/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-optimize/package.py @@ -19,7 +19,7 @@ class PyScikitOptimize(PythonPackage): version('0.5.2', sha256='1d7657a4b8ef9aa6d81e49b369c677c584e83269f11710557741d3b3f8fa0a75') - variant('plots', default=True, + variant('plots', default=True, description='Build with plot support from py-matplotlib') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-ytopt/package.py b/var/spack/repos/builtin/packages/py-ytopt/package.py index ef27c4e457..395cb32f87 100644 --- a/var/spack/repos/builtin/packages/py-ytopt/package.py +++ b/var/spack/repos/builtin/packages/py-ytopt/package.py @@ -16,7 +16,7 @@ class PyYtopt(PythonPackage): version('0.1.0', sha256='c7081fe3585a5b7a25bcb84733cd2326b72de3bfc4f84d6ad110341f24c3e612') depends_on('py-scikit-learn', type=('build', 'run')) - depends_on('py-scikit-optimize', type=('build', 'run')) + depends_on('py-scikit-optimize', type=('build', 'run')) def build_args(self, spec, prefix): args = [] diff --git a/var/spack/repos/builtin/packages/pythia6/package.py b/var/spack/repos/builtin/packages/pythia6/package.py index cfb9313cfc..a1a8632c2a 100644 --- a/var/spack/repos/builtin/packages/pythia6/package.py +++ b/var/spack/repos/builtin/packages/pythia6/package.py @@ -108,17 +108,14 @@ class Pythia6(CMakePackage): sha256=checksum, expand=False, destination='example', - placement={example: example} - ) + placement={example: example}) # Docs. - docs \ - = {'http://www.hepforge.org/archive/pythiasix/update_notes-6.4.28.txt': - 'a229be4ba9a4eb65a9d53600a5f388b620038d56694c6cb4671c2be224b67751', - 'http://home.thep.lu.se/~torbjorn/pythia6/lutp0613man2.pdf': - '03d637310ea80f0d7aea761492bd38452c602890d8cf913a1ec9edacd79fa43d', - 'https://pythiasix.hepforge.org/pythia6-announcement.txt': - '2a52def41f0c93e32e0db58dbcf072b987ebfbd32e42ccfc1f9382fcf65f1271'} + docs = { + 'http://www.hepforge.org/archive/pythiasix/update_notes-6.4.28.txt': 'a229be4ba9a4eb65a9d53600a5f388b620038d56694c6cb4671c2be224b67751', + 'http://home.thep.lu.se/~torbjorn/pythia6/lutp0613man2.pdf': '03d637310ea80f0d7aea761492bd38452c602890d8cf913a1ec9edacd79fa43d', + 'https://pythiasix.hepforge.org/pythia6-announcement.txt': '2a52def41f0c93e32e0db58dbcf072b987ebfbd32e42ccfc1f9382fcf65f1271' + } for docurl, checksum in iteritems(docs): doc = os.path.basename(urlparse(docurl).path) @@ -127,8 +124,7 @@ class Pythia6(CMakePackage): sha256=checksum, expand=False, destination='doc', - placement={doc: doc} - ) + placement={doc: doc}) # The included patch customizes some routines provided in dummy form # by the original source to be useful out of the box in the vast diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py index 586d8964a1..771c01d8c2 100644 --- a/var/spack/repos/builtin/packages/qmcpack/package.py +++ b/var/spack/repos/builtin/packages/qmcpack/package.py @@ -62,22 +62,18 @@ class Qmcpack(CMakePackage, CudaPackage): conflicts( '+phdf5', when='~mpi', - msg='Parallel collective I/O requires MPI-enabled QMCPACK. ' \ - 'Please add "~phdf5" to the Spack install line for serial QMCPACK.' - ) - conflicts( - '+soa', - when='+cuda', - msg='QMCPACK SOA variant does not exist for CUDA' - ) - conflicts( - '^openblas+ilp64', - msg='QMCPACK does not support OpenBLAS 64-bit integer variant' - ) - conflicts( - '^intel-mkl+ilp64', - msg='QMCPACK does not support MKL 64-bit integer variant' - ) + msg='Parallel collective I/O requires MPI-enabled QMCPACK. ' + 'Please add "~phdf5" to the Spack install line for serial QMCPACK.') + + conflicts('+soa', + when='+cuda', + msg='QMCPACK SOA variant does not exist for CUDA') + + conflicts('^openblas+ilp64', + msg='QMCPACK does not support OpenBLAS 64-bit integer variant') + + conflicts('^intel-mkl+ilp64', + msg='QMCPACK does not support MKL 64-bit integer variant') # QMCPACK 3.6.0 or later requires support for C++14 compiler_warning = 'QMCPACK 3.6.0 or later requires a ' \ @@ -140,11 +136,11 @@ class Qmcpack(CMakePackage, CudaPackage): patch_checksum = '57cb1b06ee2653a87c3acc0dd4f09032fcf6ce6b8cbb9677ae9ceeb6a78f85e2' depends_on('quantum-espresso@6.4.1+mpi hdf5=parallel', patches=patch(patch_url, sha256=patch_checksum), - when='+qe+mpi', type='run') + when='+qe+mpi', type='run') depends_on('quantum-espresso@6.4.1~scalapack~mpi hdf5=serial', patches=patch(patch_url, sha256=patch_checksum), - when='+qe~mpi', type='run') + when='+qe~mpi', type='run') # Backport several patches from recent versions of QMCPACK # The test_numerics unit test is broken prior to QMCPACK 3.3.0 diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 20e453a31b..cd5012b711 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -158,7 +158,7 @@ class Qt(Package): msg="QT cannot be built as a framework except on macOS.") else: conflicts('platform=darwin', when='@4.8.6', - msg="QT 4 for macOS is only patched for 4.8.7") + msg="QT 4 for macOS is only patched for 4.8.7") use_xcode = True diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index b9d1b5eecb..16cf5627e8 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -113,7 +113,7 @@ class QuantumEspresso(Package): # as per http://epw.org.uk/Main/DownloadAndInstall . # Complain if trying to install a version older than this. conflicts('+epw', when='@:5', - msg='EPW only available from version 6.0.0 and on') + msg='EPW only available from version 6.0.0 and on') # Below goes some constraints as shown in the link above. # Constraints may be relaxed as successful reports @@ -124,11 +124,11 @@ class QuantumEspresso(Package): # EPW doesn't gets along well with OpenMPI 2.x.x conflicts('+epw', when='^openmpi@2.0.0:2.999.999', - msg='OpenMPI version incompatible with EPW') + msg='OpenMPI version incompatible with EPW') # EPW also doesn't gets along well with PGI 17.x + OpenMPI 1.10.7 conflicts('+epw', when='^openmpi@1.10.7%pgi@17.0:17.12', - msg='PGI+OpenMPI version combo incompatible with EPW') + msg='PGI+OpenMPI version combo incompatible with EPW') # Spurious problems running in parallel the Makefile # generated by the configure diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py index 2225c7051e..bc2abfdabd 100644 --- a/var/spack/repos/builtin/packages/r-geiger/package.py +++ b/var/spack/repos/builtin/packages/r-geiger/package.py @@ -25,6 +25,6 @@ class RGeiger(RPackage): depends_on('r-digest', type=('build', 'run')) depends_on('r-rcpp@0.11.0:', type=('build', 'run')) depends_on('r-coda', type=('build', 'run')) - depends_on('r-ncbit', type=('build', 'run')) + depends_on('r-ncbit', type=('build', 'run')) depends_on('r-colorspace', type=('build', 'run')) depends_on('r-mass', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py index 9f1dba7371..fc80deb4d0 100644 --- a/var/spack/repos/builtin/packages/regcm/package.py +++ b/var/spack/repos/builtin/packages/regcm/package.py @@ -37,10 +37,9 @@ class Regcm(AutotoolsPackage): # See also discussions: #974, #9934, #10797. extensions = ('knl', 'skl', 'bdw', 'nhl') variant('extension', values=any_combination_of(*extensions), - description=('Build extensions for a specific architecture. Only ' - 'available for GCC and Intel compilers; moreover, ' - 'GCC builds only one architecture optimization.') - ) + description='Build extensions for a specific architecture. Only ' + 'available for GCC and Intel compilers; moreover, ' + 'GCC builds only one architecture optimization.') variant('pnetcdf', default=False, description='Build NetCDF using the high performance parallel ' diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py index cd5f7500a2..7087572191 100644 --- a/var/spack/repos/builtin/packages/root/package.py +++ b/var/spack/repos/builtin/packages/root/package.py @@ -18,7 +18,7 @@ class Root(CMakePackage): # Master branch version('master', git="https://github.com/root-project/root.git", - branch='master') + branch='master') # Development version (when more recent than production). @@ -68,108 +68,108 @@ class Root(CMakePackage): # ###################### Variants ########################## variant('avahi', default=False, - description='Compile with avahi') + description='Compile with avahi') variant('aqua', default=False, - description='Enable Aqua interface') + description='Enable Aqua interface') # No need for a specific variant: libafterimage is not provided by spack # By default always true, we get the builtin included in the source # variant('asimage', default=True, - # description='Enable image processing support') + # description='Enable image processing support') variant('davix', default=True, - description='Compile with external Davix') + description='Compile with external Davix') variant('emacs', default=False, - description='Enable Emacs support') + description='Enable Emacs support') variant('examples', default=True, - description='Install examples') + description='Install examples') variant('fftw', default=False, - description='Enable Fast Fourier Transform support') + description='Enable Fast Fourier Transform support') variant('fits', default=False, - description='Enable support for images and data from FITS files') + description='Enable support for images and data from FITS files') variant('fortran', default=False, - description='Enable the Fortran components of ROOT') + description='Enable the Fortran components of ROOT') variant('graphviz', default=False, - description='Enable graphviz support') + description='Enable graphviz support') variant('gdml', default=True, - description='Enable GDML writer and reader') + description='Enable GDML writer and reader') variant('gminimal', default=True, - description='Ignore most of Root\'s feature defaults except for ' - 'basic graphic options') + description='Ignore most of Root\'s feature defaults except for ' + 'basic graphic options') variant('gsl', default=True, - description='Enable linking against shared libraries for GSL') + description='Enable linking against shared libraries for GSL') variant('http', default=False, - description='Enable HTTP server support') + description='Enable HTTP server support') variant('jemalloc', default=False, - description='Enable using the jemalloc allocator') + description='Enable using the jemalloc allocator') variant('kerberos', default=False, - description='Enable Kerberos support') + description='Enable Kerberos support') variant('ldap', default=False, - description='Enable LDAP support') + description='Enable LDAP support') variant('libcxx', default=False, - description='Build using libc++') + description='Build using libc++') variant('math', default=True, - description='Build the new libMathMore extended math library') + description='Build the new libMathMore extended math library') variant('memstat', default=False, - description='Enable a memory stats utility to detect memory leaks') + description='Enable a memory stats utility to detect memory leaks') # Minuit must not be installed as a dependency of root # otherwise it crashes with the internal minuit library variant('minuit', default=True, - description='Automatically search for support libraries') + description='Automatically search for support libraries') variant('mysql', default=False) variant('odbc', default=False, - description='Enable ODBC support') + description='Enable ODBC support') variant('opengl', default=True, - description='Enable OpenGL support') + description='Enable OpenGL support') # variant('oracle', default=False) - not supported by spack variant('postgres', default=False, - description='Enable postgres support') + description='Enable postgres support') variant('pythia6', default=False, - description='Enable pythia6 support') + description='Enable pythia6 support') # variant('pythia8', default=False, - not suported by spack - # description='Enable pythia8 support') + # description='Enable pythia8 support') variant('python', default=True, - description='Enable Python ROOT bindings') + description='Enable Python ROOT bindings') variant('qt4', default=False, - description='Enable Qt graphics backend') + description='Enable Qt graphics backend') variant('r', default=False, - description='Enable R ROOT bindings') + description='Enable R ROOT bindings') variant('rpath', default=True, - description='Enable RPATH') + description='Enable RPATH') variant('rootfit', default=True, - description='Build the libRooFit advanced fitting package') + description='Build the libRooFit advanced fitting package') variant('root7', default=False, - description='Enable ROOT 7 support') + description='Enable ROOT 7 support') variant('shadow', default=False, - description='Enable shadow password support') + description='Enable shadow password support') variant('sqlite', default=False, - description='Enable SQLite support') + description='Enable SQLite support') variant('ssl', default=False, - description='Enable SSL encryption support') + description='Enable SSL encryption support') variant('table', default=False, - description='Build libTable contrib library') + description='Build libTable contrib library') variant('tbb', default=True, - description='TBB multi-threading support') + description='TBB multi-threading support') variant('test', default=False, - description='Enable test suit of ROOT with CTest') + description='Enable test suit of ROOT with CTest') variant('threads', default=True, - description='Enable using thread library') + description='Enable using thread library') variant('tiff', default=True, - description='Include Tiff support in image processing') + description='Include Tiff support in image processing') variant('tmva', default=True, - description='Build TMVA multi variate analysis library') + description='Build TMVA multi variate analysis library') variant('unuran', default=True, - description='Use UNURAN for random number generation') + description='Use UNURAN for random number generation') variant('vc', default=False, - description='Enable Vc for adding new types for SIMD programming') + description='Enable Vc for adding new types for SIMD programming') variant('vdt', default=True, - description='Enable set of fast and vectorisable math functions') + description='Enable set of fast and vectorisable math functions') variant('x', default=True, - description='Enable set of graphical options') + description='Enable set of graphical options') # variant('xinetd', default=False, - not supported by spack - # description='Enable a daemon process manager') + # description='Enable a daemon process manager') variant('xml', default=True, - description='Enable XML parser interface') + description='Enable XML parser interface') variant('xrootd', default=False, - description='Build xrootd file server and its client') + description='Build xrootd file server and its client') # ###################### Compiler variants ######################## @@ -444,7 +444,7 @@ class Root(CMakePackage): '-Dvc:BOOL=%s' % ( 'ON' if '+vc' in spec else 'OFF'), '-Dveccore:BOOL=%s' % ( - 'ON' if '+veccore' in spec else 'OFF'), # not supported + 'ON' if '+veccore' in spec else 'OFF'), # not supported '-Dvdt:BOOL=%s' % ( 'ON' if '+vdt' in spec else 'OFF'), '-Dxml:BOOL=%s' % ( diff --git a/var/spack/repos/builtin/packages/sspace-longread/package.py b/var/spack/repos/builtin/packages/sspace-longread/package.py index 882ca531ba..d8882b63ba 100644 --- a/var/spack/repos/builtin/packages/sspace-longread/package.py +++ b/var/spack/repos/builtin/packages/sspace-longread/package.py @@ -25,7 +25,7 @@ class SspaceLongread(Package): def url_for_version(self, version): return "file://{0}/40SSPACE-LongRead_v{1}.tar.gz".format( - os.getcwd(), version.dashed) + os.getcwd(), version.dashed) def install(self, spec, prefix): mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/unuran/package.py b/var/spack/repos/builtin/packages/unuran/package.py index e4832e4dec..d1c126d7a5 100644 --- a/var/spack/repos/builtin/packages/unuran/package.py +++ b/var/spack/repos/builtin/packages/unuran/package.py @@ -15,10 +15,11 @@ class Unuran(AutotoolsPackage): version('1.8.1', 'a5885baab53a2608c1d85517bf5d06a5') variant('shared', default=True, - description="Enable the build of shared libraries") + description="Enable the build of shared libraries") variant('rngstreams', default=True, - description="Use RNGSTREAM library for uniform random generation") - variant('gsl', default=False, + description="Use RNGSTREAM library for uniform random generation") + variant( + 'gsl', default=False, description="Use random number generators from GNU Scientific Library") depends_on('gsl', when="+gsl") diff --git a/var/spack/repos/builtin/packages/upcxx/package.py b/var/spack/repos/builtin/packages/upcxx/package.py index 9a02e3274f..fa0874ed7e 100644 --- a/var/spack/repos/builtin/packages/upcxx/package.py +++ b/var/spack/repos/builtin/packages/upcxx/package.py @@ -42,13 +42,13 @@ class Upcxx(Package): version('2019.3.2', '844722cb0e8c0bc649017fce86469457') - variant('cuda', default=False, + variant('cuda', default=False, description='Builds a CUDA-enabled version of UPC++') - variant('scheduler', values=('slurm', 'alps', 'user', 'none'), + variant('scheduler', values=('slurm', 'alps', 'user', 'none'), default=detect_scheduler(), description="Resource manager to use") - conflicts('scheduler=none', when='platform=cray', + conflicts('scheduler=none', when='platform=cray', msg='None is unacceptable on Cray.') depends_on('cuda', when='+cuda') diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py index 15b4e25155..1bf0bbbdd2 100644 --- a/var/spack/repos/builtin/packages/vecgeom/package.py +++ b/var/spack/repos/builtin/packages/vecgeom/package.py @@ -25,10 +25,10 @@ class Vecgeom(CMakePackage): multi=False, description='Use the specified C++ standard when building.') variant('vector', - default='native', - values=('sse3', 'sse4.2', 'native'), - multi=False, - description='Specify the instruction set for vectorization.') + default='native', + values=('sse3', 'sse4.2', 'native'), + multi=False, + description='Specify the instruction set for vectorization.') depends_on('cmake@3.5:', type='build') diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py index 7739ee8d6d..c7cf5b1038 100644 --- a/var/spack/repos/builtin/packages/zfp/package.py +++ b/var/spack/repos/builtin/packages/zfp/package.py @@ -21,10 +21,10 @@ class Zfp(MakefilePackage): version('0.5.0', '2ab29a852e65ad85aae38925c5003654') variant('bsws', - default='64', - values=('8', '16', '32', '64'), - multi=False, - description='Bit stream word size: use smaller for finer ' \ + default='64', + values=('8', '16', '32', '64'), + multi=False, + description='Bit stream word size: use smaller for finer ' 'rate granularity. Use 8 for H5Z-ZFP filter.') variant('shared', default=True, |