Merge branch 'custom_modulefiles_from_config' of https://github.com/epfl-scitas/spack into epfl-scitas-custom_modulefiles_from_config

8 files changed, 1138 insertions, 394 deletions

diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index f08a2bb675..15db2f7a16 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -788,7 +788,7 @@ versions are now filtered out.
 
 .. _shell-support:
 
-Environment modules
+Integration with module systems
 -------------------------------
 
 .. note::
@@ -798,42 +798,50 @@ Environment modules
    interface and/or generated module names may change in future
    versions.
 
-Spack provides some limited integration with environment module
-systems to make it easier to use the packages it provides.
+Spack provides some integration with
+`Environment Modules <http://modules.sourceforge.net/>`_
+and `Dotkit <https://computing.llnl.gov/?set=jobs&page=dotkit>`_ to make
+it easier to use the packages it installed.
+
 
 
 Installing Environment Modules
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In order to use Spack's generated environment modules, you must have
 installed the *Environment Modules* package.  On many Linux
-distributions, this can be installed from the vendor's repository.
-For example: ```yum install environment-modules``
-(Fedora/RHEL/CentOS).  If your Linux distribution does not have
-Environment Modules, you can get it with Spack:
+distributions, this can be installed from the vendor's repository:
+
+.. code-block:: sh
 
-1. Install with::
+    yum install environment-modules # (Fedora/RHEL/CentOS)
+    apt-get install environment-modules # (Ubuntu/Debian)
+
+If your Linux distribution does not have
+Environment Modules, you can get it with Spack:
 
 .. code-block:: sh
 
     spack install environment-modules
 
-2. Activate with::
 
-Add the following two lines to your ``.bashrc`` profile (or similar):
+In this case to activate it automatically you need to add the following two
+lines to your ``.bashrc`` profile (or similar):
 
 .. code-block:: sh
 
    MODULES_HOME=`spack location -i environment-modules`
    source ${MODULES_HOME}/Modules/init/bash
 
-In case you use a Unix shell other than bash, substitute ``bash`` by
-the appropriate file in ``${MODULES_HOME}/Modules/init/``.
+If you use a Unix shell other than ``bash``, modify the commands above
+accordingly and source the appropriate file in
+``${MODULES_HOME}/Modules/init/``.
 
 
-Spack and Environment Modules
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. TODO : Add a similar section on how to install dotkit ?
 
+Spack and module systems
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 You can enable shell support by sourcing some files in the
 ``/share/spack`` directory.
 
@@ -841,7 +849,7 @@ For ``bash`` or ``ksh``, run:
 
 .. code-block:: sh
 
-   . $SPACK_ROOT/share/spack/setup-env.sh
+   . ${SPACK_ROOT}/share/spack/setup-env.sh
 
 For ``csh`` and ``tcsh`` run:
 
@@ -853,17 +861,19 @@ For ``csh`` and ``tcsh`` run:
 You can put the above code in your ``.bashrc`` or ``.cshrc``, and
 Spack's shell support will be available on the command line.
 
-When you install a package with Spack, it automatically generates an
-environment module that lets you add the package to your environment.
+When you install a package with Spack, it automatically generates a module file
+that lets you add the package to your environment.
 
-Currently, Spack supports the generation of `TCL Modules
+Currently, Spack supports the generation of `Environment Modules
 <http://wiki.tcl.tk/12999>`_ and `Dotkit
 <https://computing.llnl.gov/?set=jobs&page=dotkit>`_.  Generated
 module files for each of these systems can be found in these
 directories:
 
-  * ``$SPACK_ROOT/share/spack/modules``
-  * ``$SPACK_ROOT/share/spack/dotkit``
+.. code-block:: sh
+
+  ${SPACK_ROOT}/share/spack/modules
+  ${SPACK_ROOT}/share/spack/dotkit
 
 The directories are automatically added to your ``MODULEPATH`` and
 ``DK_NODE`` environment variables when you enable Spack's `shell
@@ -919,8 +929,7 @@ of installed packages.
 
 The names here should look familiar, they're the same ones from
 ``spack find``.  You *can* use the names here directly.  For example,
-you could type either of these commands to load the callpath module
-(assuming dotkit and modules are installed):
+you could type either of these commands to load the callpath module:
 
 .. code-block:: sh
 
@@ -935,7 +944,7 @@ easy to type.  Luckily, Spack has its own interface for using modules
 and dotkits.  You can use the same spec syntax you're used to:
 
   =========================  ==========================
-  Modules                    Dotkit
+  Environment Modules        Dotkit
   =========================  ==========================
   ``spack load <spec>``      ``spack use <spec>``
   ``spack unload <spec>``    ``spack unuse <spec>``
@@ -1002,15 +1011,216 @@ used ``gcc``.  You could therefore just type:
 
 To identify just the one built with the Intel compiler.
 
+Module files generation and customization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Environment Modules and Dotkit files are generated when packages are installed,
+and are placed in the following directories under the Spack root:
+
+.. code-block:: sh
+
+  ${SPACK_ROOT}/share/spack/modules
+  ${SPACK_ROOT}/share/spack/dotkit
+
+The content that gets written in each module file can be customized in two ways:
+
+  1. overriding part of the ``spack.Package`` API within a ``package.py``
+  2. writing dedicated configuration files
+
+Override ``Package`` API
+^^^^^^^^^^^^^^^^^^^^^^^^
+There are currently two methods in ``spack.Package`` that may affect the content
+of module files:
+
+.. code-block:: python
+
+  def setup_environment(self, spack_env, run_env):
+      """Set up the compile and runtime environments for a package."""
+      pass
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+      """Set up the environment of packages that depend on this one"""
+      pass
+
+As briefly stated in the comments, the first method lets you customize the
+module file content for the package you are currently writing, the second
+allows for modifications to your dependees module file. In both cases one
+needs to fill ``run_env`` with the desired list of environment modifications.
+
+Example : ``builtin/packages/python/package.py``
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+The ``python`` package that comes with the ``builtin`` Spack repository
+overrides ``setup_dependent_environment`` in the following way:
+
+.. code-block:: python
+
+  def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+        # ...
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('PYTHONPATH', os.path.join(extension_spec.prefix, self.site_packages_dir))
+
+to insert the appropriate ``PYTHONPATH`` modifications in the module
+files of python packages.
+
+Configuration files
+^^^^^^^^^^^^^^^^^^^
+
+Another way of modifying the content of module files is writing a
+``modules.yaml`` configuration file. Following usual Spack conventions, this
+file can be placed either at *site* or *user* scope.
+
+The default site configuration reads:
+
+ .. literalinclude:: ../../../etc/spack/modules.yaml
+    :language: yaml
+
+It basically inspects the installation prefixes for the
+existence of a few folders and, if they exist, it prepends a path to a given
+list of environment variables.
+
+For each module system that can be enabled a finer configuration is possible:
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     # contains environment modules specific customizations
+   dotkit:
+     # contains dotkit specific customizations
 
-Regenerating Module files
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The structure under the ``tcl`` and ``dotkit`` keys is almost equal, and will
+be showcased in the following by some examples.
 
-Module and dotkit files are generated when packages are installed, and
-are placed in the following directories under the Spack root:
+Select module files by spec constraints
+"""""""""""""""""""""""""""""""""""""""
+Using spec syntax it's possible to have different customizations for different
+groups of module files.
 
-  * ``$SPACK_ROOT/share/spack/modules``
-  * ``$SPACK_ROOT/share/spack/dotkit``
+Considering :
+
+.. code-block:: yaml
+
+ modules:
+   tcl:
+     all: # Default addition for every package
+       environment:
+         set:
+           BAR: 'bar'
+     ^openmpi:: # A double ':' overrides previous rules
+       environment:
+         set:
+           BAR: 'baz'
+     zlib:
+       environment:
+         prepend_path:
+           LD_LIBRARY_PATH: 'foo'
+     zlib%gcc@4.8:
+       environment:
+         unset:
+         - FOOBAR
+
+what will happen is that:
+
+ - every module file will set ``BAR=bar``
+ - unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``
+ - any spec that satisfies ``zlib`` will additionally prepend ``foo`` to ``LD_LIBRARY_PATH``
+ - any spec that satisfies ``zlib%gcc@4.8`` will additionally unset ``FOOBAR``
+
+.. note::
+  Order does matter
+    The modifications associated with the ``all`` keyword are always evaluated
+    first, no matter where they appear in the configuration file. All the other
+    spec constraints are instead evaluated top to bottom.
+
+Filter modifications out of module files
+""""""""""""""""""""""""""""""""""""""""
+
+Modifications to certain environment variables in module files are generated by
+default. Suppose you would like to avoid having ``CPATH`` and ``LIBRARY_PATH``
+modified by your dotkit modules. Then :
+
+.. code-block:: yaml
+
+  modules:
+    dotkit:
+      all:
+        filter:
+          environment_blacklist: ['CPATH', 'LIBRARY_PATH']  # Exclude changes to any of these variables
+
+will generate dotkit module files that will not contain modifications to either
+``CPATH`` or ``LIBRARY_PATH`` and environment module files that instead will
+contain those modifications.
+
+Autoload dependencies
+"""""""""""""""""""""
+
+The following lines in ``modules.yaml``:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      all:
+        autoload: 'direct'
+
+will produce environment module files that will automatically load their direct
+dependencies.
+
+.. note::
+  Allowed values for ``autoload`` statements
+    Allowed values for ``autoload`` statements are either ``none``, ``direct``
+    or ``all``. In ``tcl`` configuration it is possible to use the option
+    ``prerequisites`` that accepts the same values and will add ``prereq``
+    statements instead of automatically loading other modules.
+
+Blacklist or whitelist the generation of specific module files
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Sometimes it is desirable not to generate module files, a common use case being
+not providing the users with software built using the system compiler.
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      whitelist: ['gcc', 'llvm']  # Whitelist will have precedence over blacklist
+      blacklist: ['%gcc@4.4.7']  # Assuming gcc@4.4.7 is the system compiler
+
+will skip module file generation for anything that satisfies ``%gcc@4.4.7``,
+with the exception of specs that satisfy ``gcc`` or ``llvm``.
+
+Customize the naming scheme and insert conflicts
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+A configuration file like:
+
+.. code-block:: yaml
+
+  modules:
+    tcl:
+      naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
+      all:
+        conflict: ['{name}', 'intel/14.0.1']
+
+will create module files that will conflict with ``intel/14.0.1`` and with the
+base directory of the same module, effectively preventing the possibility to
+load two or more versions of the same software at the same time.
+
+.. note::
+  Tokens available for the naming scheme
+    currently only the tokens shown in the example are available to construct
+    the naming scheme
+
+.. note::
+  The ``conflict`` option is ``tcl`` specific
+
+Regenerating module files
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Sometimes you may need to regenerate the modules files.  For example,
 if newer, fancier module support is added to Spack at some later date,
@@ -1020,7 +1230,7 @@ new features.
 .. _spack-module:
 
 ``spack module refresh``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+""""""""""""""""""""""""
 
 Running ``spack module refresh`` will remove the
 ``share/spack/modules`` and ``share/spack/dotkit`` directories, then
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index a67f5c0c13..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:
@@ -89,7 +93,6 @@ def module_refresh():
             shutil.rmtree(cls.path, ignore_errors=False)
         mkdirp(cls.path)
         for spec in specs:
-            tty.debug("   Writing file for %s" % spec)
             cls(spec).write()
 
 
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 9488e49ab9..2e2787c37c 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -118,21 +118,20 @@ Will make Spack take compilers *only* from the user configuration, and
 the site configuration will be ignored.
 
 """
+import copy
 import os
 import re
 import sys
-import copy
-import jsonschema
-from jsonschema import Draft4Validator, validators
-import yaml
-from yaml.error import MarkedYAMLError
-from ordereddict_backport import OrderedDict
 
+import jsonschema
 import llnl.util.tty as tty
-from llnl.util.filesystem import mkdirp
-
 import spack
+import yaml
+from jsonschema import Draft4Validator, validators
+from llnl.util.filesystem import mkdirp
+from ordereddict_backport import OrderedDict
 from spack.error import SpackError
+from yaml.error import MarkedYAMLError
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
@@ -146,7 +145,7 @@ section_schemas = {
         'type': 'object',
         'additionalProperties': False,
         'patternProperties': {
-            'compilers:?': { # optional colon for overriding site config.
+            'compilers:?': {  # optional colon for overriding site config.
                 'type': 'object',
                 'default': {},
                 'additionalProperties': False,
@@ -195,6 +194,7 @@ section_schemas = {
                 'default': [],
                 'items': {
                     'type': 'string'},},},},
+
     'packages': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack package configuration file schema',
@@ -238,24 +238,120 @@ section_schemas = {
                                 'default' : {},
                             }
                         },},},},},},
+
     'modules': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack module file configuration file schema',
         'type': 'object',
         'additionalProperties': False,
+        'definitions': {
+            'array_of_strings': {
+                'type': 'array',
+                'default': [],
+                'items': {
+                    'type': 'string'
+                }
+            },
+            'dictionary_of_strings': {
+                'type': 'object',
+                'patternProperties': {
+                    r'\w[\w-]*': {  # key
+                        'type': 'string'
+                    }
+                }
+            },
+            'dependency_selection': {
+                'type': 'string',
+                'enum': ['none', 'direct', 'all']
+            },
+            'module_file_configuration': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'properties': {
+                    'filter': {
+                        'type': 'object',
+                        'default': {},
+                        'additionalProperties': False,
+                        'properties': {
+                            'environment_blacklist': {
+                                'type': 'array',
+                                'default': [],
+                                'items': {
+                                    'type': 'string'
+                                }
+                            }
+                        }
+                    },
+                    'autoload': {'$ref': '#/definitions/dependency_selection'},
+                    'prerequisites': {'$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': {'$ref': '#/definitions/dictionary_of_strings'}
+                        }
+                    }
+                }
+            },
+            'module_type_configuration': {
+                'type': 'object',
+                'default': {},
+                'anyOf': [
+                    {
+                        'properties': {
+                            'whitelist': {'$ref': '#/definitions/array_of_strings'},
+                            'blacklist': {'$ref': '#/definitions/array_of_strings'},
+                            'naming_scheme': {
+                                'type': 'string'  # Can we be more specific here?
+                            }
+                        }
+                    },
+                    {
+                        'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}}
+                    }
+                ]
+            }
+        },
         'patternProperties': {
             r'modules:?': {
                 'type': 'object',
                 'default': {},
                 'additionalProperties': False,
                 'properties': {
+                    'prefix_inspections': {
+                        'type': 'object',
+                        'patternProperties': {
+                            r'\w[\w-]*': {  # path to be inspected for existence (relative to prefix)
+                                '$ref': '#/definitions/array_of_strings'
+                            }
+                        }
+                    },
                     'enable': {
                         'type': 'array',
                         'default': [],
                         'items': {
-                            'type': 'string'
+                            'type': 'string',
+                            'enum': ['tcl', 'dotkit']
                         }
-                    }
+                    },
+                    'tcl': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific tcl extensions
+                        ]
+                    },
+                    'dotkit': {
+                        'allOf': [
+                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
+                            {}  # Specific dotkit extensions
+                        ]
+                    },
                 }
             },
         },
@@ -411,7 +507,7 @@ def _read_config_file(filename, schema):
 
     elif not os.path.isfile(filename):
         raise ConfigFileError(
-            "Invlaid configuration. %s exists but is not a file." % filename)
+            "Invalid configuration. %s exists but is not a file." % filename)
 
     elif not os.access(filename, os.R_OK):
         raise ConfigFileError("Config file is not readable: %s" % filename)
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 72aafa4e2d..3fbe2531c1 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1,7 +1,7 @@
-import os
-import os.path
 import collections
 import inspect
+import os
+import os.path
 
 
 class NameModifier(object):
@@ -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 (optional)
         """
         self.env_modifications = []
         if other is not None:
@@ -93,7 +97,8 @@ class EnvironmentModifications(object):
     @staticmethod
     def _check_other(other):
         if not isinstance(other, EnvironmentModifications):
-            raise TypeError('other must be an instance of EnvironmentModifications')
+            raise TypeError(
+                'other must be an instance of EnvironmentModifications')
 
     def _get_outside_caller_attributes(self):
         stack = inspect.stack()
@@ -101,12 +106,10 @@ 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 +173,8 @@ 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 path
+        list
 
         Args:
             name: name of the path list in the environment
@@ -185,7 +189,8 @@ 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 +208,7 @@ 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 modifications one variable at a time
         for name, actions in sorted(modifications.items()):
             for x in actions:
                 x.execute()
@@ -224,13 +229,19 @@ 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 +249,8 @@ 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
@@ -250,3 +261,20 @@ def validate(env, errstream):
     modifications = env.group_by_name()
     for variable, list_of_changes in sorted(modifications.items()):
         set_or_unset_not_first(variable, list_of_changes, errstream)
+
+
+def filter_environment_blacklist(env, variables):
+    """
+    Generator that filters out any change to environment variables present in
+    the input list
+
+    Args:
+        env: list of environment modifications
+        variables: list of variable names to be filtered
+
+    Yields:
+        items in env if they are not in variables
+    """
+    for item in env:
+        if item.name not in variables:
+            yield item
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 61624fbd70..53f054094a 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -23,33 +23,35 @@
 # 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 in hooks/ implements the logic for writing its specific type of
+module file.
 """
+import copy
+import datetime
 import os
 import os.path
 import re
-import shutil
+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
+from spack.build_environment import set_module_variables_for_package
 from spack.environment import *
 
 __all__ = ['EnvModule', 'Dotkit', 'TclModule']
@@ -61,56 +63,175 @@ CONFIGURATION = spack.config.get_config('modules')
 
 
 def print_help():
-    """For use by commands to tell user how to activate shell support."""
-
-    tty.msg("This command requires spack's shell integration.",
-            "",
+    """
+    For use by commands to tell user how to activate shell support.
+    """
+    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 accordingly 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
-    prefix_inspections = {
-        'bin': ('PATH',),
-        'man': ('MANPATH',),
-        'lib': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-        'lib64': ('LIBRARY_PATH', 'LD_LIBRARY_PATH'),
-        'include': ('CPATH',)
-    }
-    for attribute, variables in prefix_inspections.items():
-        expected = getattr(prefix, attribute)
+    prefix_inspections = CONFIGURATION.get('prefix_inspections', {})
+    for relative_path, variables in prefix_inspections.items():
+        expected = join_path(prefix, relative_path)
         if os.path.isdir(expected):
             for variable in variables:
                 env.prepend_path(variable, expected)
-    # PKGCONFIG
-    for expected in (join_path(prefix.lib, 'pkgconfig'), join_path(prefix.lib64, 'pkgconfig')):
-        if os.path.isdir(expected):
-            env.prepend_path('PKG_CONFIG_PATH', expected)
-    # CMake related variables
-    env.prepend_path('CMAKE_PREFIX_PATH', prefix)
     return env
 
 
+def dependencies(spec, request='all'):
+    """
+    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'
+    """
+    if request not in ('none', 'direct', 'all'):
+        message = "Wrong value for argument 'request' : "
+        message += "should be one of ('none', 'direct', 'all')"
+        raise tty.error(message + " [current value is '%s']" % request)
+
+    if request == 'none':
+        return []
+
+    if request == 'direct':
+        return [xx for _, xx in spec.dependencies.items()]
+
+    # FIXME : during module file creation nodes seem to be visited multiple
+    # FIXME : times even if cover='nodes' is given. This work around permits
+    # FIXME : to get a unique list of spec anyhow. Do we miss a merge
+    # FIXME : 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)]
+    return [xx for ii, xx in l if not (xx in seen or seen_add(xx))]
+
+
+def update_dictionary_extending_lists(target, update):
+    for key in update:
+        value = target.get(key, None)
+        if isinstance(value, list):
+            target[key].extend(update[key])
+        elif isinstance(value, dict):
+            update_dictionary_extending_lists(target[key], update[key])
+        else:
+            target[key] = update[key]
+
+
+def parse_config_options(module_generator):
+    """
+    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
+
+    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
+    """
+    # Get the configuration for this kind of generator
+    module_configuration = copy.deepcopy(CONFIGURATION.get(
+        module_generator.name, {}))
+
+    #####
+    # Merge all the rules
+    #####
+    module_file_actions = module_configuration.pop('all', {})
+    for spec, conf in module_configuration.items():
+        override = False
+        if spec.endswith(':'):
+            spec = spec.strip(':')
+            override = True
+        if module_generator.spec.satisfies(spec):
+            if override:
+                module_file_actions = {}
+            update_dictionary_extending_lists(module_file_actions, conf)
+
+    #####
+    # Process the common rules
+    #####
+
+    # Automatic loading loads
+    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'))
+    # Environment modifications
+    environment_actions = module_file_actions.pop('environment', {})
+    env = EnvironmentModifications()
+
+    def process_arglist(arglist):
+        if method == 'unset':
+            for x in arglist:
+                yield (x, )
+        else:
+            for x in arglist.iteritems():
+                yield x
+
+    for method, arglist in environment_actions.items():
+        for args in process_arglist(arglist):
+            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.
+
+    Args:
+        specs: sequence of spec instances
+        module_name: type of module file objects
+
+    Yields:
+        non blacklisted specs
+    """
+    for x in specs:
+        if module_types[module_name](x).blacklisted:
+            tty.debug('\tFILTER : %s' % x)
+            continue
+        yield x
+
+
 class EnvModule(object):
     name = 'env_module'
     formats = {}
@@ -118,7 +239,8 @@ 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):
@@ -134,8 +256,41 @@ 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):
+        try:
+            naming_scheme = CONFIGURATION[self.name]['naming_scheme']
+        except KeyError:
+            naming_scheme = self.default_naming_format
+        return naming_scheme
+
+    @property
+    def tokens(self):
+        tokens = {
+            'name': self.spec.name,
+            'version': self.spec.version,
+            'compiler': self.spec.compiler
+        }
+        return tokens
+
+    @property
+    def use_name(self):
+        """
+        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
+        # Not everybody is working on linux...
+        parts = name.split('/')
+        name = join_path(*parts)
+        return name
 
     @property
     def category(self):
@@ -144,13 +299,51 @@ class EnvModule(object):
             return self.pkg.category
         # Extensions
         for extendee in self.pkg.extendees:
-            return '{extendee} extension'.format(extendee=extendee)
+            return '{extendee}_extension'.format(extendee=extendee)
         # Not very descriptive fallback
-        return 'spack installed package'
+        return 'spack'
 
+    @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)]
+        if whitelist_matches:
+            message = '\tWHITELIST : %s [matches : ' % self.spec.cshort_spec
+            for rule in whitelist_matches:
+                message += '%s ' % rule
+            message += ' ]'
+            tty.debug(message)
+
+        if blacklist_matches:
+            message = '\tBLACKLIST : %s [matches : ' % self.spec.cshort_spec
+            for rule in blacklist_matches:
+                message += '%s ' % rule
+            message += ' ]'
+            tty.debug(message)
+
+        if not whitelist_matches and blacklist_matches:
+            return True
+
+        return False
 
     def write(self):
-        """Write out a module file for this object."""
+        """
+        Writes out a module file for this object.
+
+        This method employs a template pattern and expects derived classes to:
+        - override the header property
+        - provide formats for autoload, prerequisites and environment changes
+        """
+        if self.blacklisted:
+            return
+        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):
             mkdirp(module_dir)
@@ -159,42 +352,73 @@ class EnvModule(object):
         # installation prefix
         env = inspect_path(self.spec.prefix)
 
-        # Let the extendee modify their extensions before asking for
-        # package-specific modifications
+        # Let the extendee/dependency modify their extensions/dependencies
+        # before asking for package-specific modifications
         spack_env = EnvironmentModifications()
-        for item in self.pkg.extendees:
-            try:
-                package = self.spec[item].package
-                package.setup_dependent_package(self.pkg.module, self.spec)
-                package.setup_dependent_environment(spack_env, env, self.spec)
-            except:
-                # The extends was conditional, so it doesn't count here
-                # eg: extends('python', when='+python')
-                pass
+        # 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__)
+            for mod in modules:
+                set_module_variables_for_package(package, mod)
+            set_module_variables_for_package(package, package.module)
+            package.setup_dependent_package(self.pkg.module, self.spec)
+            package.setup_dependent_environment(spack_env, env, self.spec)
 
         # Package-specific environment modifications
+        set_module_variables_for_package(self.pkg, self.pkg.module)
         self.spec.package.setup_environment(spack_env, env)
 
-        # TODO : implement site-specific modifications and filters
-        if not env:
-            return
-
+        # Parse configuration file
+        module_configuration, conf_env = parse_config_options(self)
+        env.extend(conf_env)
+        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):
+            module_file_content += self.autoload(x)
+        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)):
+            module_file_content += line
+        for line in self.module_specific_content(module_configuration):
+            module_file_content += line
+
+        # Dump to file
         with open(self.file_name, 'w') as f:
-            self.write_header(f)
-            for line in self.process_environment_command(env):
-                f.write(line)
+            f.write(module_file_content)
 
-    def write_header(self, stream):
+    @property
+    def header(self):
         raise NotImplementedError()
 
+    def module_specific_content(self, configuration):
+        return tuple()
+
+    def autoload(self, spec):
+        m = type(self)(spec)
+        return self.autoload_format.format(module_file=m.use_name)
+
+    def prerequisite(self, spec):
+        m = type(self)(spec)
+        return self.prerequisite_format.format(module_file=m.use_name)
+
     def process_environment_command(self, env):
         for command in env:
             try:
-                yield self.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
+                details = '{context} at {filename}:{lineno}'
+                tty.warn(message.format(command=type(command)))
+                tty.warn(details.format(**command.args))
 
     @property
     def file_name(self):
@@ -202,62 +426,65 @@ class EnvModule(object):
            where this module lives."""
         raise NotImplementedError()
 
-    @property
-    def use_name(self):
-        """Subclasses should implement this to return the name the
-           module command uses to refer to the package."""
-        raise NotImplementedError()
-
     def remove(self):
         mod_file = self.file_name
         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):
     name = 'dotkit'
     path = join_path(spack.share_path, "dotkit")
 
-    formats = {
+    environment_modifications_formats = {
         PrependPath: 'dk_alter {name} {value}\n',
         SetEnv: 'dk_setenv {name} {value}\n'
     }
 
+    autoload_format = 'dk_op {module_file}\n'
+
+    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 use_name(self):
-      return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
-                                 self.spec.compiler.name,
-                                 self.spec.compiler.version,
-                                 self.spec.dag_hash())
-
-    def write_header(self, dk_file):
+    def header(self):
         # Category
+        header = ''
         if self.category:
-            dk_file.write('#c %s\n' % self.category)
+            header += '#c %s\n' % self.category
 
         # Short description
         if self.short_description:
-            dk_file.write('#d %s\n' % self.short_description)
+            header += '#d %s\n' % self.short_description
 
         # Long description
         if self.long_description:
             for line in textwrap.wrap(self.long_description, 72):
-                dk_file.write("#h %s\n" % line)
+                header += '#h %s\n' % line
+        return header
+
+    def prerequisite(self, spec):
+        tty.warn('prerequisites:  not supported by dotkit module files')
+        tty.warn('\tYou may want to check  ~/.spack/modules.yaml')
+        return ''
 
 
 class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
 
-    formats = {
+    environment_modifications_formats = {
         PrependPath: 'prepend-path {name} \"{value}\"\n',
         AppendPath: 'append-path {name} \"{value}\"\n',
         RemovePath: 'remove-path {name} \"{value}\"\n',
@@ -265,28 +492,61 @@ class TclModule(EnvModule):
         UnsetEnv: 'unsetenv {name}\n'
     }
 
+    autoload_format = ('if ![ is-loaded {module_file} ] {{\n'
+                       '    puts stderr "Autoloading {module_file}"\n'
+                       '    module load {module_file}\n'
+                       '}}\n\n')
+
+    prerequisite_format = 'prereq {module_file}\n'
+
+    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
+
     @property
     def file_name(self):
         return join_path(TclModule.path, self.spec.architecture, self.use_name)
 
     @property
-    def use_name(self):
-      return "%s-%s-%s-%s-%s" % (self.spec.name, self.spec.version,
-                                 self.spec.compiler.name,
-                                 self.spec.compiler.version,
-                                 self.spec.dag_hash())
-
-    def write_header(self, module_file):
+    def header(self):
+        timestamp = datetime.datetime.now()
         # TCL Modulefile header
-        module_file.write('#%Module1.0\n')
+        header = '#%Module1.0\n'
+        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'
+
         # TODO : category ?
         # Short description
         if self.short_description:
-            module_file.write('module-whatis \"%s\"\n\n' % self.short_description)
+            header += 'module-whatis \"%s\"\n\n' % self.short_description
 
         # Long description
         if self.long_description:
-            module_file.write('proc ModulesHelp { } {\n')
+            header += 'proc ModulesHelp { } {\n'
             for line in textwrap.wrap(self.long_description, 72):
-                module_file.write("puts stderr \"%s\"\n" % line)
-            module_file.write('}\n\n')
+                header += 'puts stderr "%s"\n' % line
+            header += '}\n\n'
+        return header
+
+    def module_specific_content(self, configuration):
+        naming_tokens = self.tokens
+        # Conflict
+        conflict_format = configuration.get('conflict', [])
+        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 naming_dir != conflict_dir:
+                        message = 'conflict scheme does not match naming scheme [{spec}]\n\n'  # NOQA: ignore=E501
+                        message += 'naming scheme   : "{nformat}"\n'
+                        message += 'conflict scheme : "{cformat}"\n\n'
+                        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/package.py b/lib/spack/spack/package.py
index 4065553131..8e6cf32954 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -37,7 +37,6 @@ import os
 import re
 import textwrap
 import time
-import glob
 
 import llnl.util.tty as tty
 import spack
@@ -62,7 +61,6 @@ from spack.util.environment import dump_environment
 from spack.util.executable import ProcessError
 from spack.version import *
 from urlparse import urlparse
-
 """Allowed URL schemes for spack packages."""
 _ALLOWED_URL_SCHEMES = ["http", "https", "ftp", "file", "git"]
 
@@ -305,26 +303,21 @@ class Package(object):
     #
     """By default we build in parallel.  Subclasses can override this."""
     parallel = True
-
     """# jobs to use for parallel make. If set, overrides default of ncpus."""
     make_jobs = None
-
-    """Most packages are NOT extendable.  Set to True if you want extensions."""
+    """Most packages are NOT extendable. Set to True if you want extensions."""
     extendable = False
-
     """List of prefix-relative file paths (or a single path). If these do
        not exist after install, or if they exist but are not files,
        sanity checks fail.
     """
     sanity_check_is_file = []
-
     """List of prefix-relative directory paths (or a single path). If
        these do not exist after install, or if they exist but are not
        directories, sanity checks will fail.
     """
     sanity_check_is_dir = []
 
-
     def __init__(self, spec):
         # this determines how the package should be built.
         self.spec = spec
@@ -336,23 +329,24 @@ class Package(object):
             self.name = self.name[self.name.rindex('.') + 1:]
 
         # Allow custom staging paths for packages
-        self.path=None
+        self.path = None
 
         # Sanity check attributes required by Spack directives.
         spack.directives.ensure_dicts(type(self))
 
         # Check versions in the versions dict.
         for v in self.versions:
-            assert(isinstance(v, Version))
+            assert (isinstance(v, Version))
 
         # Check version descriptors
         for v in sorted(self.versions):
-            assert(isinstance(self.versions[v], dict))
+            assert (isinstance(self.versions[v], dict))
 
         # Version-ize the keys in versions dict
         try:
-            self.versions = dict((Version(v), h) for v,h in self.versions.items())
-        except ValueError, e:
+            self.versions = dict((Version(v), h)
+                                 for v, h in self.versions.items())
+        except ValueError as e:
             raise ValueError("In package %s: %s" % (self.name, e.message))
 
         # stage used to build this package.
@@ -366,9 +360,9 @@ class Package(object):
         # This makes self.url behave sanely.
         if self.spec.versions.concrete:
             # TODO: this is a really roundabout way of determining the type
-            # TODO: of fetch to do. figure out a more sane fetch strategy/package
-            # TODO: init order (right now it's conflated with stage, package, and
-            # TODO: the tests make assumptions)
+            # TODO: of fetch to do. figure out a more sane fetch
+            # TODO: strategy/package init order (right now it's conflated with
+            # TODO: stage, package, and the tests make assumptions)
             f = fs.for_package_version(self, self.version)
             if isinstance(f, fs.URLFetchStrategy):
                 self.url = self.url_for_version(self.spec.version)
@@ -387,14 +381,12 @@ class Package(object):
         if self.is_extension:
             spack.repo.get(self.extendee_spec)._check_extendable()
 
-
     @property
     def version(self):
         if not self.spec.versions.concrete:
             raise ValueError("Can only get of package with concrete version.")
         return self.spec.versions[0]
 
-
     @memoized
     def version_urls(self):
         """Return a list of URLs for different versions of this
@@ -407,7 +399,6 @@ class Package(object):
                 version_urls[v] = args['url']
         return version_urls
 
-
     def nearest_url(self, version):
         """Finds the URL for the next lowest version with a URL.
            If there is no lower version with a URL, uses the
@@ -424,10 +415,11 @@ class Package(object):
                 url = version_urls[v]
         return url
 
-
     # TODO: move this out of here and into some URL extrapolation module?
     def url_for_version(self, version):
-        """Returns a URL that you can download a new version of this package from."""
+        """
+        Returns a URL that you can download a new version of this package from.
+        """
         if not isinstance(version, Version):
             version = Version(version)
 
@@ -441,14 +433,17 @@ class Package(object):
             return version_urls[version]
 
         # If we have no idea, try to substitute the version.
-        return spack.url.substitute_version(self.nearest_url(version),
-                                            self.url_version(version))
+        return spack.url.substitute_version(
+            self.nearest_url(version), self.url_version(version))
 
     def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
-        stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
-                              name=resource_stage_folder, mirror_path=resource_mirror,
+        stage = ResourceStage(resource.fetcher,
+                              root=root_stage,
+                              resource=resource,
+                              name=resource_stage_folder,
+                              mirror_path=resource_mirror,
                               path=self.path)
         return stage
 
@@ -474,7 +469,8 @@ class Package(object):
             else:
                 # Construct resource stage
                 resource = resources[ii - 1]  # ii == 0 is root!
-                stage = self._make_resource_stage(composite_stage[0], fetcher, resource)
+                stage = self._make_resource_stage(composite_stage[0], fetcher,
+                                                  resource)
             # Append the item to the composite
             composite_stage.append(stage)
 
@@ -492,13 +488,11 @@ class Package(object):
             self._stage = self._make_stage()
         return self._stage
 
-
     @stage.setter
     def stage(self, stage):
         """Allow a stage object to be set to override the default."""
         self._stage = stage
 
-
     def _make_fetcher(self):
         # Construct a composite fetcher that always contains at least
         # one element (the root package). In case there are resources
@@ -515,7 +509,8 @@ class Package(object):
     @property
     def fetcher(self):
         if not self.spec.versions.concrete:
-            raise ValueError("Can only get a fetcher for a package with concrete versions.")
+            raise ValueError(
+                "Can only get a fetcher for a package with concrete versions.")
         if not self._fetcher:
             self._fetcher = self._make_fetcher()
         return self._fetcher
@@ -524,10 +519,11 @@ class Package(object):
     def fetcher(self, f):
         self._fetcher = f
 
-
     @property
     def extendee_spec(self):
-        """Spec of the extendee of this package, or None if it is not an extension."""
+        """
+        Spec of the extendee of this package, or None if it is not an extension
+        """
         if not self.extendees:
             return None
 
@@ -549,10 +545,11 @@ class Package(object):
             spec, kwargs = self.extendees[name]
             return spec
 
-
     @property
     def extendee_args(self):
-        """Spec of the extendee of this package, or None if it is not an extension."""
+        """
+        Spec of the extendee of this package, or None if it is not an extension
+        """
         if not self.extendees:
             return None
 
@@ -560,7 +557,6 @@ class Package(object):
         name = next(iter(self.extendees))
         return self.extendees[name][1]
 
-
     @property
     def is_extension(self):
         # if it is concrete, it's only an extension if it actually
@@ -571,22 +567,20 @@ class Package(object):
             # If not, then it's an extension if it *could* be an extension
             return bool(self.extendees)
 
-
     def extends(self, spec):
-        if not spec.name in self.extendees:
+        if spec.name not in self.extendees:
             return False
         s = self.extendee_spec
         return s and s.satisfies(spec)
 
-
     @property
     def activated(self):
         if not self.is_extension:
-            raise ValueError("is_extension called on package that is not an extension.")
+            raise ValueError(
+                "is_extension called on package that is not an extension.")
         exts = spack.install_layout.extension_map(self.extendee_spec)
         return (self.name in exts) and (exts[self.name] == self.spec)
 
-
     def preorder_traversal(self, visited=None, **kwargs):
         """This does a preorder traversal of the package's dependence DAG."""
         virtual = kwargs.get("virtual", False)
@@ -605,36 +599,35 @@ class Package(object):
             spec = self.dependencies[name]
 
             # currently, we do not descend into virtual dependencies, as this
-            # makes doing a sensible traversal much harder.  We just assume that
-            # ANY of the virtual deps will work, which might not be true (due to
-            # conflicts or unsatisfiable specs).  For now this is ok but we might
-            # want to reinvestigate if we start using a lot of complicated virtual
-            # dependencies
+            # makes doing a sensible traversal much harder.  We just assume
+            # that ANY of the virtual deps will work, which might not be true
+            # (due to conflicts or unsatisfiable specs).  For now this is ok
+            # but we might want to reinvestigate if we start using a lot of
+            # complicated virtual dependencies
             # TODO: reinvestigate this.
             if spec.virtual:
                 if virtual:
                     yield spec
                 continue
 
-            for pkg in spack.repo.get(name).preorder_traversal(visited, **kwargs):
+            for pkg in spack.repo.get(name).preorder_traversal(visited,
+                                                               **kwargs):
                 yield pkg
 
-
     def provides(self, vpkg_name):
-        """True if this package provides a virtual package with the specified name."""
+        """
+        True if this package provides a virtual package with the specified name
+        """
         return any(s.name == vpkg_name for s in self.provided)
 
-
     def virtual_dependencies(self, visited=None):
         for spec in sorted(set(self.preorder_traversal(virtual=True))):
             yield spec
 
-
     @property
     def installed(self):
         return os.path.isdir(self.prefix)
 
-
     @property
     def installed_dependents(self):
         """Return a list of the specs of all installed packages that depend
@@ -651,60 +644,62 @@ class Package(object):
                     dependents.append(spec)
         return dependents
 
-
     @property
     def prefix(self):
         """Get the prefix into which this package should be installed."""
         return self.spec.prefix
 
-
     @property
     def compiler(self):
-        """Get the spack.compiler.Compiler object used to build this package."""
+        """Get the spack.compiler.Compiler object used to build this package"""
         if not self.spec.concrete:
             raise ValueError("Can only get a compiler for a concrete package.")
         return spack.compilers.compiler_for_spec(self.spec.compiler)
 
-
     def url_version(self, version):
-        """Given a version, this returns a string that should be substituted into the
-           package's URL to download that version.
-           By default, this just returns the version string. Subclasses may need to
-           override this, e.g. for boost versions where you need to ensure that there
-           are _'s in the download URL.
         """
-        return str(version)
+        Given a version, this returns a string that should be substituted
+        into the package's URL to download that version.
 
+        By default, this just returns the version string. Subclasses may need
+        to override this, e.g. for boost versions where you need to ensure that
+        there are _'s in the download URL.
+        """
+        return str(version)
 
     def remove_prefix(self):
-        """Removes the prefix for a package along with any empty parent directories."""
+        """
+        Removes the prefix for a package along with any empty parent
+        directories
+        """
         spack.install_layout.remove_install_directory(self.spec)
 
-
     def do_fetch(self, mirror_only=False):
-        """Creates a stage directory and downloads the tarball for this package.
-           Working directory will be set to the stage directory.
+        """
+        Creates a stage directory and downloads the tarball for this package.
+        Working directory will be set to the stage directory.
         """
         if not self.spec.concrete:
             raise ValueError("Can only fetch concrete packages.")
 
         start_time = time.time()
-        if spack.do_checksum and not self.version in self.versions:
-            tty.warn("There is no checksum on file to fetch %s safely."
-                     % self.spec.format('$_$@'))
+        if spack.do_checksum and self.version not in self.versions:
+            tty.warn("There is no checksum on file to fetch %s safely." %
+                     self.spec.format('$_$@'))
 
             # Ask the user whether to skip the checksum if we're
             # interactive, but just fail if non-interactive.
-            checksum_msg = "Add a checksum or use --no-checksum to skip this check."
+            checksum_msg = "Add a checksum or use --no-checksum to skip this check."  # NOQA: ignore=E501
             ignore_checksum = False
             if sys.stdout.isatty():
-                ignore_checksum = tty.get_yes_or_no("  Fetch anyway?", default=False)
+                ignore_checksum = tty.get_yes_or_no("  Fetch anyway?",
+                                                    default=False)
                 if ignore_checksum:
                     tty.msg("Fetching with no checksum.", checksum_msg)
 
             if not ignore_checksum:
-                raise FetchError(
-                    "Will not fetch %s" % self.spec.format('$_$@'), checksum_msg)
+                raise FetchError("Will not fetch %s" %
+                                 self.spec.format('$_$@'), checksum_msg)
 
         self.stage.fetch(mirror_only)
 
@@ -723,7 +718,6 @@ class Package(object):
         self.stage.expand_archive()
         self.stage.chdir_to_source()
 
-
     def do_patch(self):
         """Calls do_stage(), then applied patches to the expanded tarball if they
            haven't been applied already."""
@@ -743,10 +737,10 @@ class Package(object):
 
         # Construct paths to special files in the archive dir used to
         # keep track of whether patches were successfully applied.
-        archive_dir     = self.stage.source_path
-        good_file       = join_path(archive_dir, '.spack_patched')
+        archive_dir = self.stage.source_path
+        good_file = join_path(archive_dir, '.spack_patched')
         no_patches_file = join_path(archive_dir, '.spack_no_patches')
-        bad_file        = join_path(archive_dir, '.spack_patch_failed')
+        bad_file = join_path(archive_dir, '.spack_patch_failed')
 
         # If we encounter an archive that failed to patch, restage it
         # so that we can apply all the patches again.
@@ -801,13 +795,11 @@ class Package(object):
         else:
             touch(no_patches_file)
 
-
     @property
     def namespace(self):
         namespace, dot, module = self.__module__.rpartition('.')
         return namespace
 
-
     def do_fake_install(self):
         """Make a fake install directory contaiing a 'fake' file in bin."""
         mkdirp(self.prefix.bin)
@@ -815,15 +807,15 @@ class Package(object):
         mkdirp(self.prefix.lib)
         mkdirp(self.prefix.man1)
 
-
     def _get_needed_resources(self):
         resources = []
         # Select the resources that are needed for this build
         for when_spec, resource_list in self.resources.items():
             if when_spec in self.spec:
                 resources.extend(resource_list)
-        # Sorts the resources by the length of the string representing their destination. Since any nested resource
-        # must contain another resource's name in its path, it seems that should work
+        # Sorts the resources by the length of the string representing their
+        # destination. Since any nested resource must contain another
+        # resource's name in its path, it seems that should work
         resources = sorted(resources, key=lambda res: len(res.destination))
         return resources
 
@@ -832,10 +824,14 @@ class Package(object):
         resource_stage_folder = '-'.join(pieces)
         return resource_stage_folder
 
-
     def do_install(self,
-                   keep_prefix=False,  keep_stage=False, ignore_deps=False,
-                   skip_patch=False, verbose=False, make_jobs=None, fake=False):
+                   keep_prefix=False,
+                   keep_stage=False,
+                   ignore_deps=False,
+                   skip_patch=False,
+                   verbose=False,
+                   make_jobs=None,
+                   fake=False):
         """Called by commands to install a package and its dependencies.
 
         Package implementations should override install() to describe
@@ -846,18 +842,20 @@ class Package(object):
         keep_stage  -- By default, stage is destroyed only if there are no
                        exceptions during build. Set to True to keep the stage
                        even with exceptions.
-        ignore_deps -- Do not install dependencies before installing this package.
+        ignore_deps -- Don't install dependencies before installing this
+                       package
         fake        -- Don't really build -- install fake stub files instead.
         skip_patch  -- Skip patch stage of build if True.
         verbose     -- Display verbose build output (by default, suppresses it)
-        make_jobs   -- Number of make jobs to use for install.  Default is ncpus.
+        make_jobs   -- Number of make jobs to use for install. Default is ncpus
         """
         if not self.spec.concrete:
             raise ValueError("Can only install concrete packages.")
 
         # No installation needed if package is external
         if self.spec.external:
-            tty.msg("%s is externally installed in %s" % (self.name, self.spec.external))
+            tty.msg("%s is externally installed in %s" %
+                    (self.name, self.spec.external))
             return
 
         # Ensure package is not already installed
@@ -869,9 +867,13 @@ class Package(object):
 
         # First, install dependencies recursively.
         if not ignore_deps:
-            self.do_install_dependencies(
-                keep_prefix=keep_prefix, keep_stage=keep_stage, ignore_deps=ignore_deps,
-                fake=fake, skip_patch=skip_patch, verbose=verbose, make_jobs=make_jobs)
+            self.do_install_dependencies(keep_prefix=keep_prefix,
+                                         keep_stage=keep_stage,
+                                         ignore_deps=ignore_deps,
+                                         fake=fake,
+                                         skip_patch=skip_patch,
+                                         verbose=verbose,
+                                         make_jobs=make_jobs)
 
         # Set parallelism before starting build.
         self.make_jobs = make_jobs
@@ -899,35 +901,41 @@ class Package(object):
                     self.do_fake_install()
                 else:
                     # Do the real install in the source directory.
-                     self.stage.chdir_to_source()
+                    self.stage.chdir_to_source()
 
-                     # Save the build environment in a file before building.
-                     env_path = join_path(os.getcwd(), 'spack-build.env')
+                    # Save the build environment in a file before building.
+                    env_path = join_path(os.getcwd(), 'spack-build.env')
 
-                     try:
-                        # Redirect I/O to a build log (and optionally to the terminal)
+                    try:
+                        # Redirect I/O to a build log (and optionally to
+                        # the terminal)
                         log_path = join_path(os.getcwd(), 'spack-build.out')
                         log_file = open(log_path, 'w')
-                        with log_output(log_file, verbose, sys.stdout.isatty(), True):
+                        with log_output(log_file, verbose, sys.stdout.isatty(),
+                                        True):
                             dump_environment(env_path)
                             self.install(self.spec, self.prefix)
 
-                     except ProcessError as e:
-                         # Annotate ProcessErrors with the location of the build log.
-                         e.build_log = log_path
-                         raise e
+                    except ProcessError as e:
+                        # Annotate ProcessErrors with the location of
+                        # the build log
+                        e.build_log = log_path
+                        raise e
 
-                     # Ensure that something was actually installed.
-                     self.sanity_check_prefix()
+                    # Ensure that something was actually installed.
+                    self.sanity_check_prefix()
 
-                     # Copy provenance into the install directory on success
-                     log_install_path = spack.install_layout.build_log_path(self.spec)
-                     env_install_path = spack.install_layout.build_env_path(self.spec)
-                     packages_dir = spack.install_layout.build_packages_path(self.spec)
+                    # Copy provenance into the install directory on success
+                    log_install_path = spack.install_layout.build_log_path(
+                        self.spec)
+                    env_install_path = spack.install_layout.build_env_path(
+                        self.spec)
+                    packages_dir = spack.install_layout.build_packages_path(
+                        self.spec)
 
-                     install(log_path, log_install_path)
-                     install(env_path, env_install_path)
-                     dump_packages(self.spec, packages_dir)
+                    install(log_path, log_install_path)
+                    install(env_path, env_install_path)
+                    dump_packages(self.spec, packages_dir)
 
                 # Run post install hooks before build stage is removed.
                 spack.hooks.post_install(self)
@@ -937,8 +945,9 @@ class Package(object):
             build_time = self._total_time - self._fetch_time
 
             tty.msg("Successfully installed %s" % self.name,
-                    "Fetch: %s.  Build: %s.  Total: %s."
-                    % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time)))
+                    "Fetch: %s.  Build: %s.  Total: %s." %
+                    (_hms(self._fetch_time), _hms(build_time),
+                     _hms(self._total_time)))
             print_pkg(self.prefix)
 
         try:
@@ -953,16 +962,17 @@ class Package(object):
                 tty.warn("Keeping install prefix in place despite error.",
                          "Spack will think this package is installed. " +
                          "Manually remove this directory to fix:",
-                         self.prefix, wrap=True)
+                         self.prefix,
+                         wrap=True)
             raise
 
         # note: PARENT of the build process adds the new package to
         # the database, so that we don't need to re-read from file.
         spack.installed_db.add(self.spec, self.prefix)
 
-
     def sanity_check_prefix(self):
         """This function checks whether install succeeded."""
+
         def check_paths(path_list, filetype, predicate):
             if isinstance(path_list, basestring):
                 path_list = [path_list]
@@ -970,8 +980,9 @@ class Package(object):
             for path in path_list:
                 abs_path = os.path.join(self.prefix, path)
                 if not predicate(abs_path):
-                    raise InstallError("Install failed for %s. No such %s in prefix: %s"
-                                       % (self.name, filetype, path))
+                    raise InstallError(
+                        "Install failed for %s. No such %s in prefix: %s" %
+                        (self.name, filetype, path))
 
         check_paths(self.sanity_check_is_file, 'file', os.path.isfile)
         check_paths(self.sanity_check_is_dir, 'directory', os.path.isdir)
@@ -982,13 +993,11 @@ class Package(object):
             raise InstallError(
                 "Install failed for %s.  Nothing was installed!" % self.name)
 
-
     def do_install_dependencies(self, **kwargs):
         # Pass along paths of dependencies here
         for dep in self.spec.dependencies.values():
             dep.package.do_install(**kwargs)
 
-
     @property
     def build_log_path(self):
         if self.installed:
@@ -996,7 +1005,6 @@ class Package(object):
         else:
             return join_path(self.stage.source_path, 'spack-build.out')
 
-
     @property
     def module(self):
         """Use this to add variables to the class's module's scope.
@@ -1006,7 +1014,7 @@ class Package(object):
                           fromlist=[self.__class__.__name__])
 
     def setup_environment(self, spack_env, run_env):
-        """Set up the compile and runtime environemnts for a package.
+        """Set up the compile and runtime environments for a package.
 
         `spack_env` and `run_env` are `EnvironmentModifications`
         objects.  Package authors can call methods on them to alter
@@ -1037,7 +1045,6 @@ class Package(object):
         """
         pass
 
-
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         """Set up the environment of packages that depend on this one.
 
@@ -1077,7 +1084,6 @@ class Package(object):
         """
         self.setup_environment(spack_env, run_env)
 
-
     def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.
 
@@ -1123,8 +1129,11 @@ class Package(object):
         pass
 
     def install(self, spec, prefix):
-        """Package implementations override this with their own build configuration."""
-        raise InstallError("Package %s provides no install method!" % self.name)
+        """
+        Package implementations override this with their own configuration
+        """
+        raise InstallError("Package %s provides no install method!" %
+                           self.name)
 
     def do_uninstall(self, force=False):
         if not self.installed:
@@ -1146,12 +1155,10 @@ class Package(object):
         # Once everything else is done, run post install hooks
         spack.hooks.post_uninstall(self)
 
-
     def _check_extendable(self):
         if not self.extendable:
             raise ValueError("Package %s is not extendable!" % self.name)
 
-
     def _sanity_check_extension(self):
         if not self.is_extension:
             raise ActivationError("This package is not an extension.")
@@ -1160,12 +1167,13 @@ class Package(object):
         extendee_package._check_extendable()
 
         if not extendee_package.installed:
-            raise ActivationError("Can only (de)activate extensions for installed packages.")
+            raise ActivationError(
+                "Can only (de)activate extensions for installed packages.")
         if not self.installed:
             raise ActivationError("Extensions must first be installed.")
-        if not self.extendee_spec.name in self.extendees:
-            raise ActivationError("%s does not extend %s!" % (self.name, self.extendee.name))
-
+        if self.extendee_spec.name not in self.extendees:
+            raise ActivationError("%s does not extend %s!" %
+                                  (self.name, self.extendee.name))
 
     def do_activate(self, force=False):
         """Called on an etension to invoke the extendee's activate method.
@@ -1175,8 +1183,8 @@ class Package(object):
         """
         self._sanity_check_extension()
 
-        spack.install_layout.check_extension_conflict(
-            self.extendee_spec, self.spec)
+        spack.install_layout.check_extension_conflict(self.extendee_spec,
+                                                      self.spec)
 
         # Activate any package dependencies that are also extensions.
         if not force:
@@ -1188,9 +1196,8 @@ class Package(object):
         self.extendee_spec.package.activate(self, **self.extendee_args)
 
         spack.install_layout.add_extension(self.extendee_spec, self.spec)
-        tty.msg("Activated extension %s for %s"
-                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
-
+        tty.msg("Activated extension %s for %s" %
+                (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
     def activate(self, extension, **kwargs):
         """Symlinks all files from the extension into extendee's install dir.
@@ -1201,6 +1208,7 @@ class Package(object):
         always executed.
 
         """
+
         def ignore(filename):
             return (filename in spack.install_layout.hidden_file_paths or
                     kwargs.get('ignore', lambda f: False)(filename))
@@ -1212,7 +1220,6 @@ class Package(object):
 
         tree.merge(self.prefix, ignore=ignore)
 
-
     def do_deactivate(self, **kwargs):
         """Called on the extension to invoke extendee's deactivate() method."""
         self._sanity_check_extension()
@@ -1230,7 +1237,7 @@ class Package(object):
                 for dep in aspec.traverse():
                     if self.spec == dep:
                         raise ActivationError(
-                            "Cannot deactivate %s beacuse %s is activated and depends on it."
+                            "Cannot deactivate %s because %s is activated and depends on it."  # NOQA: ignore=E501
                             % (self.spec.short_spec, aspec.short_spec))
 
         self.extendee_spec.package.deactivate(self, **self.extendee_args)
@@ -1238,11 +1245,11 @@ class Package(object):
         # redundant activation check -- makes SURE the spec is not
         # still activated even if something was wrong above.
         if self.activated:
-            spack.install_layout.remove_extension(self.extendee_spec, self.spec)
-
-        tty.msg("Deactivated extension %s for %s"
-                % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
+            spack.install_layout.remove_extension(self.extendee_spec,
+                                                  self.spec)
 
+        tty.msg("Deactivated extension %s for %s" %
+                (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@")))
 
     def deactivate(self, extension, **kwargs):
         """Unlinks all files from extension out of this package's install dir.
@@ -1253,6 +1260,7 @@ class Package(object):
         always executed.
 
         """
+
         def ignore(filename):
             return (filename in spack.install_layout.hidden_file_paths or
                     kwargs.get('ignore', lambda f: False)(filename))
@@ -1260,17 +1268,14 @@ class Package(object):
         tree = LinkTree(extension.prefix)
         tree.unmerge(self.prefix, ignore=ignore)
 
-
     def do_restage(self):
         """Reverts expanded/checked out source to a pristine state."""
         self.stage.restage()
 
-
     def do_clean(self):
         """Removes the package's build stage and source tarball."""
         self.stage.destroy()
 
-
     def format_doc(self, **kwargs):
         """Wrap doc string at 72 characters and format nicely"""
         indent = kwargs.get('indent', 0)
@@ -1285,7 +1290,6 @@ class Package(object):
             results.write((" " * indent) + line + "\n")
         return results.getvalue()
 
-
     @property
     def all_urls(self):
         urls = []
@@ -1297,7 +1301,6 @@ class Package(object):
                 urls.append(args['url'])
         return urls
 
-
     def fetch_remote_versions(self):
         """Try to find remote versions of this package using the
            list_url and any other URLs described in the package file."""
@@ -1306,26 +1309,30 @@ class Package(object):
 
         try:
             return spack.util.web.find_versions_of_archive(
-                *self.all_urls, list_url=self.list_url, list_depth=self.list_depth)
+                *self.all_urls,
+                list_url=self.list_url,
+                list_depth=self.list_depth)
         except spack.error.NoNetworkConnectionError as e:
-            tty.die("Package.fetch_versions couldn't connect to:",
-                    e.url, e.message)
-
+            tty.die("Package.fetch_versions couldn't connect to:", e.url,
+                    e.message)
 
     @property
     def rpath(self):
         """Get the rpath this package links with, as a list of paths."""
         rpaths = [self.prefix.lib, self.prefix.lib64]
-        rpaths.extend(d.prefix.lib for d in self.spec.traverse(root=False)
+        rpaths.extend(d.prefix.lib
+                      for d in self.spec.traverse(root=False)
                       if os.path.isdir(d.prefix.lib))
-        rpaths.extend(d.prefix.lib64 for d in self.spec.traverse(root=False)
+        rpaths.extend(d.prefix.lib64
+                      for d in self.spec.traverse(root=False)
                       if os.path.isdir(d.prefix.lib64))
         return rpaths
 
-
     @property
     def rpath_args(self):
-        """Get the rpath args as a string, with -Wl,-rpath, for each element."""
+        """
+        Get the rpath args as a string, with -Wl,-rpath, for each element
+        """
         return " ".join("-Wl,-rpath,%s" % p for p in self.rpath)
 
 
@@ -1333,6 +1340,7 @@ def install_dependency_symlinks(pkg, spec, prefix):
     """Execute a dummy install and flatten dependencies"""
     flatten_dependencies(spec, prefix)
 
+
 def flatten_dependencies(spec, flat_dir):
     """Make each dependency of spec present in dir via symlink."""
     for dep in spec.traverse(root=False):
@@ -1341,13 +1349,13 @@ def flatten_dependencies(spec, flat_dir):
         dep_path = spack.install_layout.path_for_spec(dep)
         dep_files = LinkTree(dep_path)
 
-        os.mkdir(flat_dir+'/'+name)
+        os.mkdir(flat_dir + '/' + name)
 
-        conflict = dep_files.find_conflict(flat_dir+'/'+name)
+        conflict = dep_files.find_conflict(flat_dir + '/' + name)
         if conflict:
             raise DependencyConflictError(conflict)
 
-        dep_files.merge(flat_dir+'/'+name)
+        dep_files.merge(flat_dir + '/' + name)
 
 
 def validate_package_url(url_string):
@@ -1388,9 +1396,11 @@ def dump_packages(spec, path):
             # Create a source repo and get the pkg directory out of it.
             try:
                 source_repo = spack.repository.Repo(source_repo_root)
-                source_pkg_dir = source_repo.dirname_for_package_name(node.name)
-            except RepoError as e:
-                tty.warn("Warning: Couldn't copy in provenance for %s" % node.name)
+                source_pkg_dir = source_repo.dirname_for_package_name(
+                    node.name)
+            except RepoError:
+                tty.warn("Warning: Couldn't copy in provenance for %s" %
+                         node.name)
 
         # Create a destination repository
         dest_repo_root = join_path(path, node.namespace)
@@ -1410,7 +1420,7 @@ def print_pkg(message):
     """Outputs a message with a package icon."""
     from llnl.util.tty.color import cwrite
     cwrite('@*g{[+]} ')
-    print message
+    print(message)
 
 
 def _hms(seconds):
@@ -1419,20 +1429,25 @@ def _hms(seconds):
     h, m = divmod(m, 60)
 
     parts = []
-    if h: parts.append("%dh" % h)
-    if m: parts.append("%dm" % m)
-    if s: parts.append("%.2fs" % s)
+    if h:
+        parts.append("%dh" % h)
+    if m:
+        parts.append("%dm" % m)
+    if s:
+        parts.append("%.2fs" % s)
     return ' '.join(parts)
 
 
 class FetchError(spack.error.SpackError):
     """Raised when something goes wrong during fetch."""
+
     def __init__(self, message, long_msg=None):
         super(FetchError, self).__init__(message, long_msg)
 
 
 class InstallError(spack.error.SpackError):
     """Raised when something goes wrong during install or uninstall."""
+
     def __init__(self, message, long_msg=None):
         super(InstallError, self).__init__(message, long_msg)
 
@@ -1443,21 +1458,24 @@ class ExternalPackageError(InstallError):
 
 class PackageStillNeededError(InstallError):
     """Raised when package is still needed by another on uninstall."""
+
     def __init__(self, spec, dependents):
-        super(PackageStillNeededError, self).__init__(
-            "Cannot uninstall %s" % spec)
+        super(PackageStillNeededError, self).__init__("Cannot uninstall %s" %
+                                                      spec)
         self.spec = spec
         self.dependents = dependents
 
 
 class PackageError(spack.error.SpackError):
     """Raised when something is wrong with a package definition."""
+
     def __init__(self, message, long_msg=None):
         super(PackageError, self).__init__(message, long_msg)
 
 
 class PackageVersionError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
+
     def __init__(self, version):
         super(PackageVersionError, self).__init__(
             "Cannot determine a URL automatically for version %s" % version,
@@ -1466,6 +1484,7 @@ class PackageVersionError(PackageError):
 
 class VersionFetchError(PackageError):
     """Raised when a version URL cannot automatically be determined."""
+
     def __init__(self, cls):
         super(VersionFetchError, self).__init__(
             "Cannot fetch versions for package %s " % cls.__name__ +
@@ -1474,12 +1493,15 @@ class VersionFetchError(PackageError):
 
 class NoURLError(PackageError):
     """Raised when someone tries to build a URL for a package with no URLs."""
+
     def __init__(self, cls):
         super(NoURLError, self).__init__(
             "Package %s has no version with a URL." % cls.__name__)
 
 
-class ExtensionError(PackageError): pass
+class ExtensionError(PackageError):
+
+    pass
 
 
 class ExtensionConflictError(ExtensionError):
@@ -1495,7 +1517,8 @@ class ActivationError(ExtensionError):
 
 class DependencyConflictError(spack.error.SpackError):
     """Raised when the dependencies cannot be flattened as asked for."""
+
     def __init__(self, conflict):
         super(DependencyConflictError, self).__init__(
-            "%s conflicts with another file in the flattened directory." %(
+            "%s conflicts with another file in the flattened directory." % (
                 conflict))
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index 3c5edde66b..10eaac1344 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -23,52 +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',
-              '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():
@@ -79,8 +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
     else:
@@ -94,7 +63,7 @@ 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)
 
@@ -104,15 +73,13 @@ 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
new file mode 100644
index 0000000000..c65d663250
--- /dev/null
+++ b/lib/spack/spack/test/modules.py
@@ -0,0 +1,157 @@
+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')
+
+    FILE_REGISTRY[filename] = StringIO.StringIO()
+
+    try:
+        yield FILE_REGISTRY[filename]
+    finally:
+        handle = FILE_REGISTRY[filename]
+        FILE_REGISTRY[filename] = handle.getvalue()
+        handle.close()
+
+
+configuration_autoload_direct = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'autoload': 'direct'
+        }
+    }
+}
+
+configuration_autoload_all = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'autoload': 'all'
+        }
+    }
+}
+
+configuration_alter_environment = {
+    'enable': ['tcl'],
+    'tcl': {
+        'all': {
+            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
+        },
+        '=x86-linux': {
+            'environment': {'set': {'FOO': 'foo'},
+                            'unset': ['BAR']}
+        }
+    }
+}
+
+configuration_blacklist = {
+    'enable': ['tcl'],
+    'tcl': {
+        'blacklist': ['callpath'],
+        'all': {
+            'autoload': 'direct'
+        }
+    }
+}
+
+configuration_conflicts = {
+    'enable': ['tcl'],
+    'tcl': {
+        'naming_scheme': '{name}/{version}-{compiler.name}',
+        'all': {
+            'conflict': ['{name}', 'intel/14.0.1']
+        }
+    }
+}
+
+
+class TclTests(MockPackagesTest):
+    def setUp(self):
+        super(TclTests, self).setUp()
+        self.configuration_obj = spack.modules.CONFIGURATION
+        spack.modules.open = mock_open
+        # Make sure that a non-mocked configuration will trigger an error
+        spack.modules.CONFIGURATION = None
+
+    def tearDown(self):
+        del spack.modules.open
+        spack.modules.CONFIGURATION = self.configuration_obj
+        super(TclTests, self).tearDown()
+
+    def get_modulefile_content(self, spec):
+        spec.concretize()
+        generator = spack.modules.TclModule(spec)
+        generator.write()
+        content = FILE_REGISTRY[generator.file_name].split('\n')
+        return content
+
+    def test_simple_case(self):
+        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)
+
+    def test_autoload(self):
+        spack.modules.CONFIGURATION = configuration_autoload_direct
+        spec = spack.spec.Spec('mpileaks=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 2)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 2)
+
+        spack.modules.CONFIGURATION = configuration_autoload_all
+        spec = spack.spec.Spec('mpileaks=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 5)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 5)
+
+    def test_alter_environment(self):
+        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 '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 'unsetenv BAR' in x]), 0)
+
+    def test_blacklist(self):
+        spack.modules.CONFIGURATION = configuration_blacklist
+        spec = spack.spec.Spec('mpileaks=x86-linux')
+        content = self.get_modulefile_content(spec)
+        self.assertEqual(len([x for x in content if 'is-loaded' in x]), 1)
+        self.assertEqual(len([x for x in content if 'module load ' in x]), 1)
+
+    def test_conflicts(self):
+        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)