flake8 : fixed all issues?

6 files changed, 330 insertions, 254 deletions

diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index f996f4eb84..cfe59c8d98 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -32,18 +32,21 @@ from llnl.util.filesystem import mkdirp
 from spack.modules import module_types
 from spack.util.string import *
 
-description ="Manipulate modules and dotkits."
+description = "Manipulate modules and dotkits."
 
 
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='module_command')
 
-    refresh_parser = sp.add_parser('refresh', help='Regenerate all module files.')
+    sp.add_parser('refresh', help='Regenerate all module files.')
 
     find_parser = sp.add_parser('find', help='Find module files for packages.')
-    find_parser.add_argument(
-        'module_type', help="Type of module to find file for. [" + '|'.join(module_types) + "]")
-    find_parser.add_argument('spec', nargs='+', help='spec to find a module file for.')
+    find_parser.add_argument('module_type',
+                             help="Type of module to find file for. [" +
+                             '|'.join(module_types) + "]")
+    find_parser.add_argument('spec',
+                             nargs='+',
+                             help='spec to find a module file for.')
 
 
 def module_find(mtype, spec_array):
@@ -53,7 +56,8 @@ def module_find(mtype, spec_array):
        should type to use that package's module.
     """
     if mtype not in module_types:
-        tty.die("Invalid module type: '%s'.  Options are %s" % (mtype, comma_or(module_types)))
+        tty.die("Invalid module type: '%s'.  Options are %s" %
+                (mtype, comma_or(module_types)))
 
     specs = spack.cmd.parse_specs(spec_array)
     if len(specs) > 1:
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 6ddf07776b..684a420b3b 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -134,8 +134,6 @@ from yaml.error import MarkedYAMLError
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
-
-
 """Dict from section names -> schema for that section."""
 section_schemas = {
     'compilers': {
@@ -149,25 +147,31 @@ section_schemas = {
                 'default': {},
                 'additionalProperties': False,
                 'patternProperties': {
-                    r'\w[\w-]*': {           # architecture
+                    r'\w[\w-]*': {  # architecture
                         'type': 'object',
                         'additionalProperties': False,
                         'patternProperties': {
-                            r'\w[\w-]*@\w[\w-]*': {   # compiler spec
+                            r'\w[\w-]*@\w[\w-]*': {  # compiler spec
                                 'type': 'object',
                                 'additionalProperties': False,
                                 'required': ['cc', 'cxx', 'f77', 'fc'],
                                 'properties': {
-                                    'cc':  { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'cxx': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'f77': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'fc':  { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                },},},},},},},},
-
+                                    'cc': {'anyOf': [{'type': 'string'},
+                                                     {'type': 'null'}]},
+                                    'cxx': {'anyOf': [{'type': 'string'},
+                                                      {'type': 'null'}]},
+                                    'f77': {'anyOf': [{'type': 'string'},
+                                                      {'type': 'null'}]},
+                                    'fc': {'anyOf': [{'type': 'string'},
+                                                     {'type': 'null'}]},
+                                },
+                            },
+                        },
+                    },
+                },
+            },
+        },
+    },
     'mirrors': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack mirror configuration file schema',
@@ -180,8 +184,12 @@ section_schemas = {
                 'additionalProperties': False,
                 'patternProperties': {
                     r'\w[\w-]*': {
-                        'type': 'string'},},},},},
-
+                        'type': 'string'
+                    },
+                },
+            },
+        },
+    },
     'repos': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack repository configuration file schema',
@@ -192,8 +200,11 @@ section_schemas = {
                 'type': 'array',
                 'default': [],
                 'items': {
-                    'type': 'string'},},},},
-
+                    'type': 'string'
+                },
+            },
+        },
+    },
     'packages': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack package configuration file schema',
@@ -205,39 +216,48 @@ section_schemas = {
                 'default': {},
                 'additionalProperties': False,
                 'patternProperties': {
-                    r'\w[\w-]*': { # package name
+                    r'\w[\w-]*': {  # package name
                         'type': 'object',
                         'default': {},
                         'additionalProperties': False,
                         'properties': {
                             'version': {
-                                'type' : 'array',
-                                'default' : [],
-                                'items' : { 'anyOf' : [ { 'type' : 'string' },
-                                                        { 'type' : 'number'}]}}, #version strings
+                                'type': 'array',
+                                'default': [],
+                                'items': {'anyOf': [{'type': 'string'},
+                                                    {'type': 'number'}]}
+                            },  # version strings
                             'compiler': {
-                                'type' : 'array',
-                                'default' : [],
-                                'items' : { 'type' : 'string' } }, #compiler specs
+                                'type': 'array',
+                                'default': [],
+                                'items': {'type': 'string'}
+                            },  # compiler specs
                             'buildable': {
-                                'type':  'boolean',
+                                'type': 'boolean',
                                 'default': True,
-                             },
+                            },
                             'providers': {
-                                'type':  'object',
+                                'type': 'object',
                                 'default': {},
                                 'additionalProperties': False,
                                 'patternProperties': {
                                     r'\w[\w-]*': {
-                                        'type' : 'array',
-                                        'default' : [],
-                                        'items' : { 'type' : 'string' },},},},
+                                        'type': 'array',
+                                        'default': [],
+                                        'items': {'type': 'string'},
+                                    },
+                                },
+                            },
                             'paths': {
-                                'type' : 'object',
-                                'default' : {},
+                                'type': 'object',
+                                'default': {},
                             }
-                        },},},},},},
-
+                        },
+                    },
+                },
+            },
+        },
+    },
     'modules': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack module file configuration file schema',
@@ -283,17 +303,22 @@ section_schemas = {
                         }
                     },
                     'autoload': {'$ref': '#/definitions/dependency_selection'},
-                    'prerequisites': {'$ref': '#/definitions/dependency_selection'},
+                    'prerequisites':
+                    {'$ref': '#/definitions/dependency_selection'},
                     'conflict': {'$ref': '#/definitions/array_of_strings'},
                     'environment': {
                         'type': 'object',
                         'default': {},
                         'additionalProperties': False,
                         'properties': {
-                            'set': {'$ref': '#/definitions/dictionary_of_strings'},
-                            'unset': {'$ref': '#/definitions/array_of_strings'},
-                            'prepend_path': {'$ref': '#/definitions/dictionary_of_strings'},
-                            'append_path': {'$ref': '#/definitions/dictionary_of_strings'}
+                            'set':
+                            {'$ref': '#/definitions/dictionary_of_strings'},
+                            'unset':
+                            {'$ref': '#/definitions/array_of_strings'},
+                            'prepend_path':
+                            {'$ref': '#/definitions/dictionary_of_strings'},
+                            'append_path':
+                            {'$ref': '#/definitions/dictionary_of_strings'}
                         }
                     }
                 }
@@ -304,15 +329,20 @@ section_schemas = {
                 'anyOf': [
                     {
                         'properties': {
-                            'whitelist': {'$ref': '#/definitions/array_of_strings'},
-                            'blacklist': {'$ref': '#/definitions/array_of_strings'},
+                            'whitelist':
+                            {'$ref': '#/definitions/array_of_strings'},
+                            'blacklist':
+                            {'$ref': '#/definitions/array_of_strings'},
                             'naming_scheme': {
-                                'type': 'string'  # Can we be more specific here?
+                                'type':
+                                'string'  # Can we be more specific here?
                             }
                         }
                     },
                     {
-                        'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}}
+                        'patternProperties':
+                        {r'\w[\w-]*':
+                         {'$ref': '#/definitions/module_file_configuration'}}
                     }
                 ]
             }
@@ -326,7 +356,8 @@ section_schemas = {
                     'prefix_inspections': {
                         'type': 'object',
                         'patternProperties': {
-                            r'\w[\w-]*': {  # path to be inspected for existence (relative to prefix)
+                            r'\w[\w-]*':
+                            {  # path to be inspected (relative to prefix)
                                 '$ref': '#/definitions/array_of_strings'
                             }
                         }
@@ -341,13 +372,15 @@ section_schemas = {
                     },
                     'tcl': {
                         'allOf': [
-                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {'$ref': '#/definitions/module_type_configuration'
+                             },  # Base configuration
                             {}  # Specific tcl extensions
                         ]
                     },
                     'dotkit': {
                         'allOf': [
-                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {'$ref': '#/definitions/module_type_configuration'
+                             },  # Base configuration
                             {}  # Specific dotkit extensions
                         ]
                     },
@@ -356,7 +389,6 @@ section_schemas = {
         },
     },
 }
-
 """OrderedDict of config scopes keyed by name.
    Later scopes will override earlier scopes.
 """
@@ -366,12 +398,13 @@ config_scopes = OrderedDict()
 def validate_section_name(section):
     """Raise a ValueError if the section is not a valid section."""
     if section not in section_schemas:
-        raise ValueError("Invalid config section: '%s'.  Options are %s"
-                         % (section, section_schemas))
+        raise ValueError("Invalid config section: '%s'.  Options are %s" %
+                         (section, section_schemas))
 
 
 def extend_with_default(validator_class):
-    """Add support for the 'default' attribute for properties and patternProperties.
+    """Add support for the 'default' attribute for
+       properties and patternProperties
 
        jsonschema does not handle this out of the box -- it only
        validates.  This allows us to set default values for configs
@@ -380,13 +413,15 @@ def extend_with_default(validator_class):
 
     """
     validate_properties = validator_class.VALIDATORS["properties"]
-    validate_pattern_properties = validator_class.VALIDATORS["patternProperties"]
+    validate_pattern_properties = validator_class.VALIDATORS[
+        "patternProperties"]
 
     def set_defaults(validator, properties, instance, schema):
         for property, subschema in properties.iteritems():
             if "default" in subschema:
                 instance.setdefault(property, subschema["default"])
-        for err in validate_properties(validator, properties, instance, schema):
+        for err in validate_properties(validator, properties, instance,
+                                       schema):
             yield err
 
     def set_pp_defaults(validator, properties, instance, schema):
@@ -397,17 +432,19 @@ def extend_with_default(validator_class):
                         if re.match(property, key) and val is None:
                             instance[key] = subschema["default"]
 
-        for err in validate_pattern_properties(validator, properties, instance, schema):
+        for err in validate_pattern_properties(validator, properties, instance,
+                                               schema):
             yield err
 
     return validators.extend(validator_class, {
-        "properties" : set_defaults,
-        "patternProperties" : set_pp_defaults
+        "properties": set_defaults,
+        "patternProperties": set_pp_defaults
     })
 
 
 DefaultSettingValidator = extend_with_default(Draft4Validator)
 
+
 def validate_section(data, schema):
     """Validate data read in from a Spack YAML file.
 
@@ -429,9 +466,9 @@ class ConfigScope(object):
     """
 
     def __init__(self, name, path):
-        self.name = name           # scope name.
-        self.path = path           # path to directory containing configs.
-        self.sections = {}         # sections read from config files.
+        self.name = name  # scope name.
+        self.path = path  # path to directory containing configs.
+        self.sections = {}  # sections read from config files.
 
         # Register in a dict of all ConfigScopes
         # TODO: make this cleaner.  Mocking up for testing is brittle.
@@ -442,16 +479,14 @@ class ConfigScope(object):
         validate_section_name(section)
         return os.path.join(self.path, "%s.yaml" % section)
 
-
     def get_section(self, section):
-        if not section in self.sections:
-            path   = self.get_section_filename(section)
+        if section not in self.sections:
+            path = self.get_section_filename(section)
             schema = section_schemas[section]
-            data   = _read_config_file(path, schema)
+            data = _read_config_file(path, schema)
             self.sections[section] = data
         return self.sections[section]
 
-
     def write_section(self, section):
         filename = self.get_section_filename(section)
         data = self.get_section(section)
@@ -463,8 +498,8 @@ class ConfigScope(object):
         except jsonschema.ValidationError as e:
             raise ConfigSanityError(e, data)
         except (yaml.YAMLError, IOError) as e:
-            raise ConfigFileError("Error writing to config file: '%s'" % str(e))
-
+            raise ConfigFileError("Error writing to config file: '%s'" %
+                                  str(e))
 
     def clear(self):
         """Empty cached config information."""
@@ -496,8 +531,8 @@ def validate_scope(scope):
         return config_scopes[scope]
 
     else:
-        raise ValueError("Invalid config scope: '%s'.  Must be one of %s"
-                         % (scope, config_scopes.keys()))
+        raise ValueError("Invalid config scope: '%s'.  Must be one of %s" %
+                         (scope, config_scopes.keys()))
 
 
 def _read_config_file(filename, schema):
@@ -523,12 +558,12 @@ def _read_config_file(filename, schema):
         return data
 
     except MarkedYAMLError as e:
-        raise ConfigFileError(
-            "Error parsing yaml%s: %s" % (str(e.context_mark), e.problem))
+        raise ConfigFileError("Error parsing yaml%s: %s" %
+                              (str(e.context_mark), e.problem))
 
     except IOError as e:
-        raise ConfigFileError(
-            "Error reading configuration file %s: %s" % (filename, str(e)))
+        raise ConfigFileError("Error reading configuration file %s: %s" %
+                              (filename, str(e)))
 
 
 def clear_config_caches():
@@ -551,6 +586,7 @@ def _merge_yaml(dest, source):
     parent instead of merging.
 
     """
+
     def they_are(t):
         return isinstance(dest, t) and isinstance(source, t)
 
@@ -571,7 +607,7 @@ def _merge_yaml(dest, source):
     # Source dict is merged into dest.
     elif they_are(dict):
         for sk, sv in source.iteritems():
-            if not sk in dest:
+            if sk not in dest:
                 dest[sk] = copy.copy(sv)
             else:
                 dest[sk] = _merge_yaml(dest[sk], source[sk])
@@ -653,7 +689,7 @@ def print_section(section):
         data = syaml.syaml_dict()
         data[section] = get_config(section)
         syaml.dump(data, stream=sys.stdout, default_flow_style=False)
-    except (yaml.YAMLError, IOError) as e:
+    except (yaml.YAMLError, IOError):
         raise ConfigError("Error reading configuration: %s" % section)
 
 
@@ -683,15 +719,22 @@ def is_spec_buildable(spec):
     """Return true if the spec pkgspec is configured as buildable"""
     allpkgs = get_config('packages')
     name = spec.name
-    if not spec.name in allpkgs:
+    if name not in allpkgs:
         return True
-    if not 'buildable' in allpkgs[spec.name]:
+    if 'buildable' not in allpkgs[name]:
         return True
     return allpkgs[spec.name]['buildable']
 
 
-class ConfigError(SpackError): pass
-class ConfigFileError(ConfigError): pass
+class ConfigError(SpackError):
+
+    pass
+
+
+class ConfigFileError(ConfigError):
+
+    pass
+
 
 def get_path(path, data):
     if path:
@@ -699,8 +742,10 @@ def get_path(path, data):
     else:
         return data
 
+
 class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
+
     def __init__(self, validation_error, data):
         # Try to get line number from erroneous instance and its parent
         instance_mark = getattr(validation_error.instance, '_start_mark', None)
@@ -733,5 +778,6 @@ class ConfigFormatError(ConfigError):
         message = '%s: %s' % (location, validation_error.message)
         super(ConfigError, self).__init__(message)
 
+
 class ConfigSanityError(ConfigFormatError):
     """Same as ConfigFormatError, raised when config is written by Spack."""
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 92ab4e6bea..9748b4033a 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -26,7 +26,8 @@ class SetEnv(NameValueModifier):
 
 class UnsetEnv(NameModifier):
     def execute(self):
-        os.environ.pop(self.name, None)  # Avoid throwing if the variable was not set
+        # Avoid throwing if the variable was not set
+        os.environ.pop(self.name, None)
 
 
 class SetPath(NameValueModifier):
@@ -55,7 +56,9 @@ class RemovePath(NameValueModifier):
     def execute(self):
         environment_value = os.environ.get(self.name, '')
         directories = environment_value.split(':') if environment_value else []
-        directories = [os.path.normpath(x) for x in directories if x != os.path.normpath(self.value)]
+        directories = [os.path.normpath(x)
+                       for x in directories
+                       if x != os.path.normpath(self.value)]
         os.environ[self.name] = ':'.join(directories)
 
 
@@ -63,7 +66,8 @@ class EnvironmentModifications(object):
     """
     Keeps track of requests to modify the current environment.
 
-    Each call to a method to modify the environment stores the extra information on the caller in the request:
+    Each call to a method to modify the environment stores the extra
+    information on the caller in the request:
     - 'filename' : filename of the module where the caller is defined
     - 'lineno': line number where the request occurred
     - 'context' : line of code that issued the request that failed
@@ -71,10 +75,10 @@ class EnvironmentModifications(object):
 
     def __init__(self, other=None):
         """
-        Initializes a new instance, copying commands from other if it is not None
+        Initializes a new instance, copying commands from other if not None
 
         Args:
-            other: another instance of EnvironmentModifications from which (optional)
+            other: another instance of EnvironmentModifications
         """
         self.env_modifications = []
         if other is not None:
@@ -93,7 +97,7 @@ class EnvironmentModifications(object):
     @staticmethod
     def _check_other(other):
         if not isinstance(other, EnvironmentModifications):
-            raise TypeError('other must be an instance of EnvironmentModifications')
+            raise TypeError('not an instance of EnvironmentModifications')
 
     def _get_outside_caller_attributes(self):
         stack = inspect.stack()
@@ -101,12 +105,10 @@ class EnvironmentModifications(object):
             _, filename, lineno, _, context, index = stack[2]
             context = context[index].strip()
         except Exception:
-            filename, lineno, context = 'unknown file', 'unknown line', 'unknown context'
-        args = {
-            'filename': filename,
-            'lineno': lineno,
-            'context': context
-        }
+            filename = 'unknown file'
+            lineno = 'unknown line'
+            context = 'unknown context'
+        args = {'filename': filename, 'lineno': lineno, 'context': context}
         return args
 
     def set(self, name, value, **kwargs):
@@ -170,7 +172,7 @@ class EnvironmentModifications(object):
 
     def remove_path(self, name, path, **kwargs):
         """
-        Stores in the current object a request to remove a path from a path list
+        Stores in the current object a request to remove a path from a list
 
         Args:
             name: name of the path list in the environment
@@ -185,7 +187,8 @@ class EnvironmentModifications(object):
         Returns a dict of the modifications grouped by variable name
 
         Returns:
-            dict mapping the environment variable name to the modifications to be done on it
+            dict mapping the environment variable name to the modifications
+            to be done on it
         """
         modifications = collections.defaultdict(list)
         for item in self:
@@ -203,7 +206,8 @@ class EnvironmentModifications(object):
         Applies the modifications and clears the list
         """
         modifications = self.group_by_name()
-        # Apply the modifications to the environment variables one variable at a time
+        # Apply the modifications to the environment variables one variable
+        # at a time
         for name, actions in sorted(modifications.items()):
             for x in actions:
                 x.execute()
@@ -224,13 +228,17 @@ def concatenate_paths(paths):
 
 def set_or_unset_not_first(variable, changes, errstream):
     """
-    Check if we are going to set or unset something after other modifications have already been requested
+    Check if we are going to set or unset something after other modifications
+    have already been requested
     """
-    indexes = [ii for ii, item in enumerate(changes) if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
+    indexes = [ii
+               for ii, item in enumerate(changes)
+               if ii != 0 and type(item) in [SetEnv, UnsetEnv]]
     if indexes:
         good = '\t    \t{context} at {filename}:{lineno}'
         nogood = '\t--->\t{context} at {filename}:{lineno}'
-        errstream('Suspicious requests to set or unset the variable \'{var}\' found'.format(var=variable))
+        message = 'Suspicious requests to set or unset the variable \'{var}\' found'  # NOQA: ignore=E501
+        errstream(message.format(var=variable))
         for ii, item in enumerate(changes):
             print_format = nogood if ii in indexes else good
             errstream(print_format.format(**item.args))
@@ -238,8 +246,8 @@ def set_or_unset_not_first(variable, changes, errstream):
 
 def validate(env, errstream):
     """
-    Validates the environment modifications to check for the presence of suspicious patterns. Prompts a warning for
-    everything that was found
+    Validates the environment modifications to check for the presence of
+    suspicious patterns. Prompts a warning for everything that was found
 
     Current checks:
     - set or unset variables after other changes on the same variable
@@ -254,7 +262,8 @@ def validate(env, errstream):
 
 def filter_environment_blacklist(env, variables):
     """
-    Generator that filters out any change to environment variables present in the input list
+    Generator that filters out any change to environment variables present in
+    the input list
 
     Args:
         env: list of environment modifications
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index ffed469b20..0dc6f06f55 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -23,36 +23,34 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """
-This module contains code for creating environment modules, which can include dotkits, tcl modules, lmod, and others.
+This module contains code for creating environment modules, which can include
+dotkits, tcl modules, lmod, and others.
 
-The various types of modules are installed by post-install hooks and removed after an uninstall by post-uninstall hooks.
-This class consolidates the logic for creating an abstract description of the information that module systems need.
-Currently that includes a number of directories to be appended to paths in the user's environment:
+The various types of modules are installed by post-install hooks and removed
+after an uninstall by post-uninstall hooks. This class consolidates the logic
+for creating an abstract description of the information that module systems
+need.
 
-  * /bin directories to be appended to PATH
-  * /lib* directories for LD_LIBRARY_PATH
-  * /include directories for CPATH
-  * /man* and /share/man* directories for MANPATH
-  * the package prefix for CMAKE_PREFIX_PATH
+This module also includes logic for coming up with unique names for the module
+files so that they can be found by the various shell-support files in
+$SPACK/share/spack/setup-env.*.
 
-This module also includes logic for coming up with unique names for the module files so that they can be found by the
-various shell-support files in $SPACK/share/spack/setup-env.*.
-
-Each hook in hooks/ implements the logic for writing its specific type of module file.
+Each hook implements the logic for writing its specific type of module.
 """
 import copy
 import datetime
 import os
 import os.path
 import re
-import textwrap
 import string
+import textwrap
 
 import llnl.util.tty as tty
 import spack
 import spack.config
 from llnl.util.filesystem import join_path, mkdirp
-from spack.build_environment import parent_class_modules, set_module_variables_for_package
+from spack.build_environment import parent_class_modules
+from spack.build_environment import set_module_variables_for_package
 from spack.environment import *
 
 __all__ = ['EnvModule', 'Dotkit', 'TclModule']
@@ -67,30 +65,26 @@ def print_help():
     """
     For use by commands to tell user how to activate shell support.
     """
-    tty.msg("This command requires spack's shell integration.",
-            "",
+    tty.msg("This command requires spack's shell integration.", "",
             "To initialize spack's shell commands, you must run one of",
             "the commands below.  Choose the right command for your shell.",
-            "",
-            "For bash and zsh:",
-            "    . %s/setup-env.sh" % spack.share_path,
-            "",
-            "For csh and tcsh:",
-            "    setenv SPACK_ROOT %s" % spack.prefix,
-            "    source %s/setup-env.csh" % spack.share_path,
-            "")
+            "", "For bash and zsh:",
+            "    . %s/setup-env.sh" % spack.share_path, "",
+            "For csh and tcsh:", "    setenv SPACK_ROOT %s" % spack.prefix,
+            "    source %s/setup-env.csh" % spack.share_path, "")
 
 
 def inspect_path(prefix):
     """
-    Inspects the prefix of an installation to search for common layouts. Issues a request to modify the environment
-    accordingly when an item is found.
+    Inspects the prefix of an installation to search for common layouts.
+    Issues a request to modify the environment when an item is found.
 
     Args:
         prefix: prefix of the installation
 
     Returns:
-        instance of EnvironmentModifications containing the requested modifications
+        instance of EnvironmentModifications containing the requested
+        modifications
     """
     env = EnvironmentModifications()
     # Inspect the prefix to check for the existence of common directories
@@ -105,18 +99,22 @@ def inspect_path(prefix):
 
 def dependencies(spec, request='all'):
     """
-    Returns the list of dependent specs for a given spec, according to the given request
+    Returns the list of dependent specs for a given spec, according to the
+    given request
 
     Args:
         spec: target spec
         request: either 'none', 'direct' or 'all'
 
     Returns:
-        empty list if 'none', direct dependency list if 'direct', all dependencies if 'all'
+        empty list if 'none', direct dependency list if 'direct', all
+        dependencies if 'all'
     """
     if request not in ('none', 'direct', 'all'):
-        raise tty.error("Wrong value for argument 'request' : should be one of ('none', 'direct', 'all') "
-                        " [current value is '%s']" % request)
+        message = "Wrong value for argument 'request' : "
+        message += "should be one of ('none', 'direct', 'all')"
+        message += " [current value is '{0}']"
+        raise tty.error(message.format(request))
 
     if request == 'none':
         return []
@@ -124,12 +122,19 @@ def dependencies(spec, request='all'):
     if request == 'direct':
         return [xx for _, xx in spec.dependencies.items()]
 
-    # FIXME : during module file creation nodes seem to be visited multiple times even if cover='nodes'
-    # FIXME : is given. This work around permits to get a unique list of spec anyhow.
-    # FIXME : Possibly we miss a merge step among nodes that refer to the same package.
+    # FIXME : during module file creation nodes seem to be visited
+    # FIXME : multiple times even if cover='nodes' is given. This work around
+    # FIXME : permits to get a unique list of spec anyhow. Maybe we miss a
+    # FIXME : merge step among nodes that refer to the same package?
     seen = set()
     seen_add = seen.add
-    l = [xx for xx in sorted(spec.traverse(order='post', depth=True, cover='nodes', root=False), reverse=True)]
+    l = [xx
+         for xx in sorted(
+             spec.traverse(order='post',
+                           depth=True,
+                           cover='nodes',
+                           root=False),
+             reverse=True)]
     return [xx for ii, xx in l if not (xx in seen or seen_add(xx))]
 
 
@@ -146,7 +151,8 @@ def update_dictionary_extending_lists(target, update):
 
 def parse_config_options(module_generator):
     """
-    Parse the configuration file and returns a bunch of items that will be needed during module file generation
+    Parse the configuration file and returns a bunch of items that will be
+    needed during module file generation
 
     Args:
         module_generator: module generator for a given spec
@@ -154,11 +160,14 @@ def parse_config_options(module_generator):
     Returns:
         autoloads: list of specs to be autoloaded
         prerequisites: list of specs to be marked as prerequisite
-        filters: list of environment variables whose modification is blacklisted in module files
-        env: list of custom environment modifications to be applied in the module file
+        filters: list of environment variables whose modification is
+        blacklisted in module files
+        env: list of custom environment modifications to be applied in the
+        module file
     """
     # Get the configuration for this kind of generator
-    module_configuration = copy.deepcopy(CONFIGURATION.get(module_generator.name, {}))
+    module_configuration = copy.deepcopy(CONFIGURATION.get(
+        module_generator.name, {}))
 
     #####
     # Merge all the rules
@@ -179,9 +188,12 @@ def parse_config_options(module_generator):
     #####
 
     # Automatic loading loads
-    module_file_actions['autoload'] = dependencies(module_generator.spec, module_file_actions.get('autoload', 'none'))
+    module_file_actions['autoload'] = dependencies(
+        module_generator.spec, module_file_actions.get('autoload', 'none'))
     # Prerequisites
-    module_file_actions['prerequisites'] = dependencies(module_generator.spec, module_file_actions.get('prerequisites', 'none'))
+    module_file_actions['prerequisites'] = dependencies(
+        module_generator.spec, module_file_actions.get('prerequisites',
+                                                       'none'))
     # Environment modifications
     environment_actions = module_file_actions.pop('environment', {})
     env = EnvironmentModifications()
@@ -189,7 +201,7 @@ def parse_config_options(module_generator):
     def process_arglist(arglist):
         if method == 'unset':
             for x in arglist:
-                yield (x,)
+                yield (x, )
         else:
             for x in arglist.iteritems():
                 yield x
@@ -198,19 +210,20 @@ def parse_config_options(module_generator):
         for args in process_arglist(arglist):
             getattr(env, method)(*args)
 
-        # for item in arglist:
-        #     if method == 'unset':
-        #         args = [item]
-        #     else:
-        #         args = item.split(',')
-        #     getattr(env, method)(*args)
+            # for item in arglist:
+            #     if method == 'unset':
+            #         args = [item]
+            #     else:
+            #         args = item.split(',')
+            #     getattr(env, method)(*args)
 
     return module_file_actions, env
 
 
 def filter_blacklisted(specs, module_name):
     """
-    Given a sequence of specs, filters the ones that are blacklisted in the module configuration file.
+    Given a sequence of specs, filters the ones that are blacklisted in the
+    module configuration file.
 
     Args:
         specs: sequence of spec instances
@@ -233,7 +246,8 @@ class EnvModule(object):
     class __metaclass__(type):
         def __init__(cls, name, bases, dict):
             type.__init__(cls, name, bases, dict)
-            if cls.name != 'env_module' and cls.name in CONFIGURATION['enable']:
+            if cls.name != 'env_module' and cls.name in CONFIGURATION[
+                    'enable']:
                 module_types[cls.name] = cls
 
     def __init__(self, spec=None):
@@ -249,7 +263,8 @@ class EnvModule(object):
         # long description is the docstring with reduced whitespace.
         self.long_description = None
         if self.spec.package.__doc__:
-            self.long_description = re.sub(r'\s+', ' ', self.spec.package.__doc__)
+            self.long_description = re.sub(r'\s+', ' ',
+                                           self.spec.package.__doc__)
 
     @property
     def naming_scheme(self):
@@ -271,12 +286,14 @@ class EnvModule(object):
     @property
     def use_name(self):
         """
-        Subclasses should implement this to return the name the module command uses to refer to the package.
+        Subclasses should implement this to return the name the module command
+        uses to refer to the package.
         """
         naming_tokens = self.tokens
         naming_scheme = self.naming_scheme
         name = naming_scheme.format(**naming_tokens)
-        name += '-' + self.spec.dag_hash()  # Always append the hash to make the module file unique
+        name += '-' + self.spec.dag_hash(
+        )  # Always append the hash to make the module file unique
         # Not everybody is working on linux...
         parts = name.split('/')
         name = join_path(*parts)
@@ -296,8 +313,12 @@ class EnvModule(object):
     @property
     def blacklisted(self):
         configuration = CONFIGURATION.get(self.name, {})
-        whitelist_matches = [x for x in configuration.get('whitelist', []) if self.spec.satisfies(x)]
-        blacklist_matches = [x for x in configuration.get('blacklist', []) if self.spec.satisfies(x)]
+        whitelist_matches = [x
+                             for x in configuration.get('whitelist', [])
+                             if self.spec.satisfies(x)]
+        blacklist_matches = [x
+                             for x in configuration.get('blacklist', [])
+                             if self.spec.satisfies(x)]
         if whitelist_matches:
             message = '\tWHITELIST : %s [matches : ' % self.spec.cshort_spec
             for rule in whitelist_matches:
@@ -327,7 +348,8 @@ class EnvModule(object):
         """
         if self.blacklisted:
             return
-        tty.debug("\tWRITE : %s [%s]" % (self.spec.cshort_spec, self.file_name))
+        tty.debug("\tWRITE : %s [%s]" %
+                  (self.spec.cshort_spec, self.file_name))
 
         module_dir = os.path.dirname(self.file_name)
         if not os.path.exists(module_dir):
@@ -337,11 +359,12 @@ class EnvModule(object):
         # installation prefix
         env = inspect_path(self.spec.prefix)
 
-        # Let the extendee/dependency modify their extensions/dependencies before asking for
-        # package-specific modifications
+        # Let the extendee/dependency modify their extensions/dependencies
+        # before asking for package-specific modifications
         spack_env = EnvironmentModifications()
-        # TODO : the code down below is quite similar to build_environment.setup_package and needs to be
-        # TODO : factored out to a single place
+        # TODO : the code down below is quite similar to
+        # TODO : build_environment.setup_package and needs to be factored out
+        # TODO : to a single place
         for item in dependencies(self.spec, 'all'):
             package = self.spec[item.name].package
             modules = parent_class_modules(package.__class__)
@@ -358,14 +381,18 @@ class EnvModule(object):
         # Parse configuration file
         module_configuration, conf_env = parse_config_options(self)
         env.extend(conf_env)
-        filters = module_configuration.get('filter', {}).get('environment_blacklist',{})
+        filters = module_configuration.get('filter', {}).get(
+            'environment_blacklist', {})
         # Build up the module file content
         module_file_content = self.header
-        for x in filter_blacklisted(module_configuration.pop('autoload', []), self.name):
+        for x in filter_blacklisted(
+                module_configuration.pop('autoload', []), self.name):
             module_file_content += self.autoload(x)
-        for x in filter_blacklisted(module_configuration.pop('prerequisites', []), self.name):
+        for x in filter_blacklisted(
+                module_configuration.pop('prerequisites', []), self.name):
             module_file_content += self.prerequisite(x)
-        for line in self.process_environment_command(filter_environment_blacklist(env, filters)):
+        for line in self.process_environment_command(
+                filter_environment_blacklist(env, filters)):
             module_file_content += line
         for line in self.module_specific_content(module_configuration):
             module_file_content += line
@@ -392,10 +419,13 @@ class EnvModule(object):
     def process_environment_command(self, env):
         for command in env:
             try:
-                yield self.environment_modifications_formats[type(command)].format(**command.args)
+                yield self.environment_modifications_formats[type(
+                    command)].format(**command.args)
             except KeyError:
-                tty.warn('Cannot handle command of type {command} : skipping request'.format(command=type(command)))
-                tty.warn('{context} at {filename}:{lineno}'.format(**command.args))
+                message = 'Cannot handle command of type {command} : skipping request'  # NOQA: ignore=E501
+                tty.warn(message.format(command=type(command)))
+                context = '{context} at {filename}:{lineno}'
+                tty.warn(context.format(**command.args))
 
     @property
     def file_name(self):
@@ -408,9 +438,12 @@ class EnvModule(object):
         if os.path.exists(mod_file):
             try:
                 os.remove(mod_file)  # Remove the module file
-                os.removedirs(os.path.dirname(mod_file))  # Remove all the empty directories from the leaf up
+                os.removedirs(
+                    os.path.dirname(mod_file)
+                )  # Remove all the empty directories from the leaf up
             except OSError:
-                pass  # removedirs throws OSError on first non-empty directory found
+                # removedirs throws OSError on first non-empty directory found
+                pass
 
 
 class Dotkit(EnvModule):
@@ -424,13 +457,12 @@ class Dotkit(EnvModule):
 
     autoload_format = 'dk_op {module_file}\n'
 
-    prerequisite_format = None  # TODO : does something like prerequisite exist for dotkit?
-
-    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'
+    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
 
     @property
     def file_name(self):
-        return join_path(Dotkit.path, self.spec.architecture, '%s.dk' % self.use_name)
+        return join_path(Dotkit.path, self.spec.architecture,
+                         '%s.dk' % self.use_name)
 
     @property
     def header(self):
@@ -474,7 +506,7 @@ class TclModule(EnvModule):
 
     prerequisite_format = 'prereq {module_file}\n'
 
-    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'
+    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
 
     @property
     def file_name(self):
@@ -482,9 +514,10 @@ class TclModule(EnvModule):
 
     @property
     def header(self):
+        timestamp = datetime.datetime.now()
         # TCL Modulefile header
         header = '#%Module1.0\n'
-        header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % datetime.datetime.now()
+        header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp  # NOQA: ignore=E501
         header += '##\n'
         header += '## %s\n' % self.spec.short_spec
         header += '##\n'
@@ -509,16 +542,19 @@ class TclModule(EnvModule):
         f = string.Formatter()
         for item in conflict_format:
             line = 'conflict ' + item + '\n'
-            if len([x for x in f.parse(line)]) > 1:  # We do have placeholder to substitute
-                for naming_dir, conflict_dir in zip(self.naming_scheme.split('/'), item.split('/')):
+            if len([x for x in f.parse(line)
+                    ]) > 1:  # We do have placeholder to substitute
+                for naming_dir, conflict_dir in zip(
+                        self.naming_scheme.split('/'), item.split('/')):
                     if naming_dir != conflict_dir:
-                        message = 'conflict scheme does not match naming scheme [{spec}]\n\n'
+                        message = 'conflict scheme does not match naming'
+                        message += ' [{spec}]\n\n'
                         message += 'naming scheme   : "{nformat}"\n'
                         message += 'conflict scheme : "{cformat}"\n\n'
-                        message += '** You may want to check your `modules.yaml` configuration file **\n'
-                        tty.error(
-                            message.format(spec=self.spec, nformat=self.naming_scheme, cformat=item)
-                        )
+                        message += '** You may want to check your `modules.yaml` configuration file **\n'  # NOQA: ignore=E501
+                        tty.error(message.format(spec=self.spec,
+                                                 nformat=self.naming_scheme,
+                                                 cformat=item))
                         raise SystemExit('Module generation aborted.')
                 line = line.format(**naming_tokens)
             yield line
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 05f58ab7b1..395ca0c87a 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -23,53 +23,23 @@
 # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-import unittest
-import nose
 
-from spack.test.tally_plugin import Tally
-from llnl.util.filesystem import join_path
 import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-
+import nose
 import spack
-
+from llnl.util.filesystem import join_path
+from llnl.util.tty.colify import colify
+from spack.test.tally_plugin import Tally
 """Names of tests to be included in Spack's test suite"""
-test_names = ['versions',
-              'url_parse',
-              'url_substitution',
-              'packages',
-              'stage',
-              'spec_syntax',
-              'spec_semantics',
-              'spec_dag',
-              'concretize',
-              'multimethod',
-              'install',
-              'package_sanity',
-              'config',
-              'directory_layout',
-              'pattern',
-              'python_version',
-              'git_fetch',
-              'svn_fetch',
-              'hg_fetch',
-              'mirror',
-              'modules',
-              'url_extrapolate',
-              'cc',
-              'link_tree',
-              'spec_yaml',
-              'optional_deps',
-              'make_executable',
-              'configure_guess',
-              'lock',
-              'database',
-              'namespace_trie',
-              'yaml',
-              'sbang',
-              'environment',
-              'cmd.uninstall',
-              'cmd.test_install']
+test_names = ['versions', 'url_parse', 'url_substitution', 'packages', 'stage',
+              'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
+              'multimethod', 'install', 'package_sanity', 'config',
+              'directory_layout', 'pattern', 'python_version', 'git_fetch',
+              'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate',
+              'cc', 'link_tree', 'spec_yaml', 'optional_deps',
+              'make_executable', 'configure_guess', 'lock', 'database',
+              'namespace_trie', 'yaml', 'sbang', 'environment',
+              'cmd.uninstall', 'cmd.test_install']
 
 
 def list_tests():
@@ -80,7 +50,6 @@ def list_tests():
 def run(names, outputDir, verbose=False):
     """Run tests with the supplied names.  Names should be a list.  If
        it's empty, run ALL of Spack's tests."""
-    verbosity = 1 if not verbose else 2
 
     if not names:
         names = test_names
@@ -95,7 +64,7 @@ def run(names, outputDir, verbose=False):
     tally = Tally()
     for test in names:
         module = 'spack.test.' + test
-        print module
+        print(module)
 
         tty.msg("Running test: %s" % test)
 
@@ -105,15 +74,13 @@ def run(names, outputDir, verbose=False):
             xmlOutputFname = "unittests-{0}.xml".format(test)
             xmlOutputPath = join_path(outputDir, xmlOutputFname)
             runOpts += ["--with-xunit",
-                "--xunit-file={0}".format(xmlOutputPath)]
+                        "--xunit-file={0}".format(xmlOutputPath)]
         argv = [""] + runOpts + [module]
-        result = nose.run(argv=argv, addplugins=[tally])
+        nose.run(argv=argv, addplugins=[tally])
 
     succeeded = not tally.failCount and not tally.errorCount
-    tty.msg("Tests Complete.",
-            "%5d tests run" % tally.numberOfTestsRun,
-            "%5d failures" % tally.failCount,
-            "%5d errors" % tally.errorCount)
+    tty.msg("Tests Complete.", "%5d tests run" % tally.numberOfTestsRun,
+            "%5d failures" % tally.failCount, "%5d errors" % tally.errorCount)
 
     if succeeded:
         tty.info("OK", format='g')
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index b8b0d6fc6a..f0ff778a10 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -2,14 +2,18 @@ import collections
 from contextlib import contextmanager
 
 import StringIO
+import spack.modules
+from spack.test.mock_packages_test import MockPackagesTest
 
 FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
 
+
 # Monkey-patch open to write module files to a StringIO instance
 @contextmanager
 def mock_open(filename, mode):
     if not mode == 'w':
-        raise RuntimeError('test.modules : unexpected opening mode for monkey-patched open')
+        message = 'test.modules : unexpected opening mode [mock_open]'
+        raise RuntimeError(message)
 
     FILE_REGISTRY[filename] = StringIO.StringIO()
 
@@ -20,7 +24,6 @@ def mock_open(filename, mode):
         FILE_REGISTRY[filename] = handle.getvalue()
         handle.close()
 
-import spack.modules
 
 configuration_autoload_direct = {
     'enable': ['tcl'],
@@ -47,7 +50,8 @@ configuration_alter_environment = {
             'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
         },
         '=x86-linux': {
-            'environment': {'set': {'FOO': 'foo'}, 'unset': ['BAR']}
+            'environment': {'set': {'FOO': 'foo'},
+                            'unset': ['BAR']}
         }
     }
 }
@@ -72,15 +76,14 @@ configuration_conflicts = {
     }
 }
 
-from spack.test.mock_packages_test import MockPackagesTest
-
 
 class TclTests(MockPackagesTest):
     def setUp(self):
         super(TclTests, self).setUp()
         self.configuration_obj = spack.modules.CONFIGURATION
         spack.modules.open = mock_open
-        spack.modules.CONFIGURATION = None  # Make sure that a non-mocked configuration will trigger an error
+        # Make sure that a non-mocked configuration will trigger an error
+        spack.modules.CONFIGURATION = None
 
     def tearDown(self):
         del spack.modules.open
@@ -98,7 +101,7 @@ class TclTests(MockPackagesTest):
         spack.modules.CONFIGURATION = configuration_autoload_direct
         spec = spack.spec.Spec('mpich@3.0.4=x86-linux')
         content = self.get_modulefile_content(spec)
-        self.assertTrue('module-whatis "mpich @3.0.4"' in content )
+        self.assertTrue('module-whatis "mpich @3.0.4"' in content)
 
     def test_autoload(self):
         spack.modules.CONFIGURATION = configuration_autoload_direct
@@ -117,14 +120,22 @@ class TclTests(MockPackagesTest):
         spack.modules.CONFIGURATION = configuration_alter_environment
         spec = spack.spec.Spec('mpileaks=x86-linux')
         content = self.get_modulefile_content(spec)
-        self.assertEqual(len([x for x in content if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
-        self.assertEqual(len([x for x in content if 'setenv FOO "foo"' in x]), 1)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv FOO "foo"' in x]), 1)
         self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 1)
 
         spec = spack.spec.Spec('libdwarf=x64-linux')
         content = self.get_modulefile_content(spec)
-        self.assertEqual(len([x for x in content if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
-        self.assertEqual(len([x for x in content if 'setenv FOO "foo"' in x]), 0)
+        self.assertEqual(
+            len([x
+                 for x in content
+                 if x.startswith('prepend-path CMAKE_PREFIX_PATH')]), 0)
+        self.assertEqual(
+            len([x for x in content if 'setenv FOO "foo"' in x]), 0)
         self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 0)
 
     def test_blacklist(self):
@@ -138,6 +149,9 @@ class TclTests(MockPackagesTest):
         spack.modules.CONFIGURATION = configuration_conflicts
         spec = spack.spec.Spec('mpileaks=x86-linux')
         content = self.get_modulefile_content(spec)
-        self.assertEqual(len([x for x in content if x.startswith('conflict')]), 2)
-        self.assertEqual(len([x for x in content if x == 'conflict mpileaks']), 1)
-        self.assertEqual(len([x for x in content if x == 'conflict intel/14.0.1']), 1)
+        self.assertEqual(
+            len([x for x in content if x.startswith('conflict')]), 2)
+        self.assertEqual(
+            len([x for x in content if x == 'conflict mpileaks']), 1)
+        self.assertEqual(
+            len([x for x in content if x == 'conflict intel/14.0.1']), 1)