flake8: make entire repository pass spack flake8 -a

- Fix trailing whitespace missed by the bug described in #12755. - Fix other style issues that have crept in over time (this can happen when flake8 adds new checks with new versions)
2019-09-07 19:27:51 -07:00 · 2019-09-07 19:27:51 -07:00 · a2220f3150
commit a2220f3150
parent 0ec80e8f16
69 changed files with 346 additions and 337 deletions
--- a/lib/spack/spack/build_systems/python.py
+++ b/lib/spack/spack/build_systems/python.py
@ -231,7 +231,7 @@ def install_args(self, spec, prefix):
        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

--- 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)

--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@ -247,8 +247,8 @@ def add_subcommand_group(title, commands):
  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()
--- a/lib/spack/spack/schema/env.py
+++ b/lib/spack/spack/schema/env.py
@ -78,7 +78,7 @@
                                }
                            },
                            'patternProperties': {
-                               r'^(?!when$)\w*': spec_list_schema
+                                r'^(?!when$)\w*': spec_list_schema
                            }
                        }
                    },
@ -87,35 +87,36 @@
                        '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
+                                        }
+                                    }
+                                }
                            }
                        ]
                    }
--- a/lib/spack/spack/schema/spec_set.py
+++ b/lib/spack/spack/schema/spec_set.py
@ -83,8 +83,9 @@
                'cdash': {
                    'oneOf': [
                        {'type': 'string'},
-                        {'type': 'array',
-                         'items': {'type': 'string'}
+                        {
+                            'type': 'array',
+                            'items': {'type': 'string'}
                        },
                    ],
                },
--- 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
--- a/lib/spack/spack/test/pattern.py
+++ b/lib/spack/spack/test/pattern.py
@ -27,15 +27,14 @@ def subtract(self):
 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

--- 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'])

--- 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 @@ def increment(self):
        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

--- 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 @@ def configure_args(self):
                '--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
--- 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'])
--- 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')
--- 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')
--- 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
--- 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']
--- 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')
--- 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')
--- 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')

--- 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')
--- 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)
--- 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')
--- 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)
--- 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'))

--- 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")
--- 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')
--- 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')
--- 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')
--- 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')

--- 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')
--- 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',
--- 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')
--- 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')
--- 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
--- 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')
--- 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')
--- 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')

--- 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)
--- 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')
--- 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')
--- 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')
--- 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'))
--- 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')
--- 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):
--- 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
--- 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')

--- 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')

--- 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')
--- 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'))
--- 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 @@ def build_targets(self):
            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'
--- 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 @@ def build_targets(self):
            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'
--- 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
--- 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')
--- 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
--- 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.')
--- 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')
--- 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'))
--- 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 = []
--- 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
--- 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
--- 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

--- 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
--- 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'))
--- 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 '
--- 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 @@ def cmake_args(self):
            '-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' % (
--- 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)
--- 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")
--- 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')
--- 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')

--- 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,