Compiler flag handlers (#6415)

This adds the ability for packages to apply compiler flags in one of
three ways: by injecting them into the compiler wrapper calls (the
default in this PR and previously the only automated choice);
exporting environment variable definitions for variables with
corresponding names (e.g. CPPFLAGS=...); providing them as arguments
to the build system (e.g. configure).

When applying compiler flags using build system arguments, a package
must implement the 'flags_to_build_system_args" function. This is
provided for CMake and autotools packages, so for packages which
subclass those build systems, they need only update their flag
handler method specify which compiler flags should be specified as
arguments to the build system.

Convenience methods are provided to specify that all flags be applied
in one of the 3 available ways, so a custom implementation is only
required if more than one method of applying compiler flags is
needed.

This also removes redundant build system definitions from tutorial
examples

12 files changed, 372 insertions, 1320 deletions

diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index ac89f9724a..a066aa96df 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -2564,98 +2564,104 @@ build system.
 Compiler flags
 ^^^^^^^^^^^^^^
 
-Compiler flags set by the user through the Spec object can be passed to
-the build in one of two ways. For packages inheriting from the
-``CmakePackage`` or ``AutotoolsPackage`` classes, the build environment
-passes those flags to the relevant environment variables (``CFLAGS``,
-``CXXFLAGS``, etc) that are respected by the build system. For all other
-packages, the default behavior is to inject the flags directly into the
-compiler commands using Spack's compiler wrappers.
+Compiler flags set by the user through the Spec object can be passed
+to the build in one of three ways. By default, the build environment
+injects these flags directly into the compiler commands using Spack's
+compiler wrappers. In cases where the build system requires knowledge
+of the compiler flags, they can be registered with the build system by
+alternatively passing them through environment variables or as build
+system arguments. The flag_handler method can be used to change this
+behavior.
+
+Packages can override the flag_handler method with one of three
+built-in flag_handlers. The built-in flag_handlers are named
+``inject_flags``, ``env_flags``, and ``build_system_flags``. The
+``inject_flags`` method is the default. The ``env_flags`` method puts
+all of the flags into the environment variables that ``make`` uses as
+implicit variables ('CFLAGS', 'CXXFLAGS', etc.). The
+``build_system_flags`` method adds the flags as
+arguments to the invocation of ``configure`` or ``cmake``,
+respectively.
 
 .. warning::
 
-   The flag handling methods described in this section are in beta.
-   The exact semantics are liable to change to improve usability.
+   Passing compiler flags using build system arguments is only
+   supported for CMake and Autotools packages. Individual packages may
+   also differ in whether they properly respect these arguments.
 
-Individual packages can override the default behavior for the flag
-handling.  Packages can define a ``default_flag_handler`` method that
-applies to all sets of flags handled by Spack, or may define
-individual methods ``cflags_handler``, ``cxxflags_handler``,
-etc. Spack will apply the individual method for a flag set if it
-exists, otherwise the ``default_flag_handler`` method if it exists,
-and fall back on the default for that package class if neither exists.
+Individual packages may also define their own ``flag_handler``
+methods. The ``flag_handler`` method takes the package instance
+(``self``), the name of the flag, and a list of the values of the
+flag. It will be called on each of the six compiler flags supported in
+Spack. It should return a triple of ``(injf, envf, bsf)`` where
+``injf`` is a list of flags to inject via the Spack compiler wrappers,
+``envf`` is a list of flags to set in the appropriate environment
+variables, and ``bsf`` is a list of flags to pass to the build system
+as arguments.
 
-These methods are defined on the package class, and take two
-parameters in addition to the packages itself. The ``env`` parameter
-is an ``EnvironmentModifications`` object that can be used to change
-the build environment. The ``flag_val`` parameter is a tuple. Its
-first entry is the name of the flag (``cflags``, ``cxxflags``, etc.)
-and its second entry is a list of the values for that flag.
+.. warning::
 
-There are three primary idioms that can be combined to create whatever
-behavior the package requires.
+   Passing a non-empty list of flags to ``bsf`` for a build system
+   that does not support build system arguments will result in an
+   error.
 
-1. The default behavior for packages inheriting from
-``AutotoolsPackage`` or ``CmakePackage``.
+Here are the definitions of the three built-in flag handlers:
 
 .. code-block:: python
 
-    def default_flag_handler(self, env, flag_val):
-        env.append_flags(flag_val[0].upper(), ' '.join(flag_val[1]))
-        return []
+   def inject_flags(self, name, flags):
+       return (flags, None, None)
 
-2. The default behavior for other packages
+   def env_flags(self, name, flags):
+       return (None, flags, None)
 
-.. code-block:: python
+   def build_system_flags(self, name, flags):
+       return (None, None, flags)
 
-    def default_flag_handler(self, env, flag_val):
-        return flag_val[1]
+.. note::
 
+   Returning ``[]`` and ``None`` are equivalent in a ``flag_handler``
+   method.
 
-3. Packages may have additional flags to add to the build. These flags
-can be added to either idiom above. For example:
+Packages can override the default behavior either by specifying one of
+the built-in flag handlers,
 
 .. code-block:: python
 
-    def default_flag_handler(self, env, flag_val):
-        flags = flag_val[1]
-        flags.append('-flag')
-        return flags
-
-or
-
-.. code-block:: python
+   flag_handler = <PackageClass>.env_flags
 
-    def default_flag_handler(self, env, flag_val):
-        env.append_flags(flag_val[0].upper(), ' '.join(flag_val[1]))
-        env.append_flags(flag_val[0].upper(), '-flag')
-        return []
+where ``<PackageClass>`` can be any of the subclasses of PackageBase
+discussed in :ref:`installation_procedure`,
 
-Packages may also opt for methods that include aspects of any of the
-idioms above. E.g.
+or by implementing the flag_handler method. Suppose for a package
+``Foo`` we need to pass ``cflags``, ``cxxflags``, and ``cppflags``
+through the environment, the rest of the flags through compiler
+wrapper injection, and we need to add ``-lbar`` to ``ldlibs``. The
+following flag handler method accomplishes that.
 
 .. code-block:: python
 
-    def default_flag_handler(self, env, flag_val):
-        flags = []
-        if len(flag_val[1]) > 3:
-            env.append_flags(flag_val[0].upper(), ' '.join(flag_val[1][3:]))
-            flags = flag_val[1][:3]
-        else:
-            flags = flag_val[1]
-        flags.append('-flag')
-        return flags
+   def flag_handler(self, name, flags):
+       if name in ['cflags', 'cxxflags', 'cppflags']:
+           return (None, flags, None)
+       elif name == 'ldlibs':
+           flags.append('-lbar')
+       return (flags, None, None)
 
 Because these methods can pass values through environment variables,
-it is important not to override these variables unnecessarily in other
-package methods. In the ``setup_environment`` and
+it is important not to override these variables unnecessarily
+(E.g. setting ``env['CFLAGS']``) in other package methods when using
+non-default flag handlers. In the ``setup_environment`` and
 ``setup_dependent_environment`` methods, use the ``append_flags``
 method of the ``EnvironmentModifications`` class to append values to a
-list of flags whenever there is no good reason to override the
-existing value. In the ``install`` method and other methods that can
-operate on the build environment directly through the ``env``
-variable, test for environment variable existance before overriding
-values to add compiler flags.
+list of flags whenever the flag handler is ``env_flags``. If the
+package passes flags through the environment or the build system
+manually (in the install method, for example), we recommend using the
+default flag handler, or removind manual references and implementing a
+custom flag handler method that adds the desired flags to export as
+environment variables or pass to the build system. Manual flag passing
+is likely to interfere with the ``env_flags`` and
+``build_system_flags`` methods.
 
 In rare circumstances such as compiling and running small unit tests, a
 package developer may need to know what are the appropriate compiler
diff --git a/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py b/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py
deleted file mode 100644
index 90ff8540bd..0000000000
--- a/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py
+++ /dev/null
@@ -1,460 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import inspect
-import os
-import os.path
-import shutil
-import stat
-from subprocess import PIPE
-from subprocess import check_call
-
-import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir, join_path, force_remove
-from spack.package import PackageBase, run_after, run_before
-from spack.util.executable import Executable
-
-
-class AutotoolsPackage(PackageBase):
-    """Specialized class for packages built using GNU Autotools.
-
-    This class provides four phases that can be overridden:
-
-        1. :py:meth:`~.AutotoolsPackage.autoreconf`
-        2. :py:meth:`~.AutotoolsPackage.configure`
-        3. :py:meth:`~.AutotoolsPackage.build`
-        4. :py:meth:`~.AutotoolsPackage.install`
-
-    They all have sensible defaults and for many packages the only thing
-    necessary will be to override the helper method
-    :py:meth:`~.AutotoolsPackage.configure_args`.
-    For a finer tuning you may also override:
-
-        +-----------------------------------------------+--------------------+
-        | **Method**                                    | **Purpose**        |
-        +===============================================+====================+
-        | :py:attr:`~.AutotoolsPackage.build_targets`   | Specify ``make``   |
-        |                                               | targets for the    |
-        |                                               | build phase        |
-        +-----------------------------------------------+--------------------+
-        | :py:attr:`~.AutotoolsPackage.install_targets` | Specify ``make``   |
-        |                                               | targets for the    |
-        |                                               | install phase      |
-        +-----------------------------------------------+--------------------+
-        | :py:meth:`~.AutotoolsPackage.check`           | Run  build time    |
-        |                                               | tests if required  |
-        +-----------------------------------------------+--------------------+
-
-    """
-    #: Phases of a GNU Autotools package
-    phases = ['autoreconf', 'configure', 'build', 'install']
-    #: This attribute is used in UI queries that need to know the build
-    #: system base class
-    build_system_class = 'AutotoolsPackage'
-    #: Whether or not to update ``config.guess`` on old architectures
-    patch_config_guess = True
-
-    #: Targets for ``make`` during the :py:meth:`~.AutotoolsPackage.build`
-    #: phase
-    build_targets = []
-    #: Targets for ``make`` during the :py:meth:`~.AutotoolsPackage.install`
-    #: phase
-    install_targets = ['install']
-
-    #: Callback names for build-time test
-    build_time_test_callbacks = ['check']
-
-    #: Callback names for install-time test
-    install_time_test_callbacks = ['installcheck']
-
-    #: Set to true to force the autoreconf step even if configure is present
-    force_autoreconf = False
-    #: Options to be passed to autoreconf when using the default implementation
-    autoreconf_extra_args = []
-
-    @run_after('autoreconf')
-    def _do_patch_config_guess(self):
-        """Some packages ship with an older config.guess and need to have
-        this updated when installed on a newer architecture. In particular,
-        config.guess fails for PPC64LE for version prior to a 2013-06-10
-        build date (automake 1.13.4)."""
-
-        if not self.patch_config_guess or not self.spec.satisfies(
-                'target=ppc64le'
-        ):
-            return
-        my_config_guess = None
-        config_guess = None
-        if os.path.exists('config.guess'):
-            # First search the top-level source directory
-            my_config_guess = 'config.guess'
-        else:
-            # Then search in all sub directories.
-            # We would like to use AC_CONFIG_AUX_DIR, but not all packages
-            # ship with their configure.in or configure.ac.
-            d = '.'
-            dirs = [os.path.join(d, o) for o in os.listdir(d)
-                    if os.path.isdir(os.path.join(d, o))]
-            for dirname in dirs:
-                path = os.path.join(dirname, 'config.guess')
-                if os.path.exists(path):
-                    my_config_guess = path
-
-        if my_config_guess is not None:
-            try:
-                check_call([my_config_guess], stdout=PIPE, stderr=PIPE)
-                # The package's config.guess already runs OK, so just use it
-                return
-            except Exception:
-                pass
-        else:
-            return
-
-        # Look for a spack-installed automake package
-        if 'automake' in self.spec:
-            automake_path = os.path.join(self.spec['automake'].prefix, 'share',
-                                         'automake-' +
-                                         str(self.spec['automake'].version))
-            path = os.path.join(automake_path, 'config.guess')
-            if os.path.exists(path):
-                config_guess = path
-        # Look for the system's config.guess
-        if config_guess is None and os.path.exists('/usr/share'):
-            automake_dir = [s for s in os.listdir('/usr/share') if
-                            "automake" in s]
-            if automake_dir:
-                automake_path = os.path.join('/usr/share', automake_dir[0])
-                path = os.path.join(automake_path, 'config.guess')
-                if os.path.exists(path):
-                    config_guess = path
-        if config_guess is not None:
-            try:
-                check_call([config_guess], stdout=PIPE, stderr=PIPE)
-                mod = os.stat(my_config_guess).st_mode & 0o777 | stat.S_IWUSR
-                os.chmod(my_config_guess, mod)
-                shutil.copyfile(config_guess, my_config_guess)
-                return
-            except Exception:
-                pass
-
-        raise RuntimeError('Failed to find suitable config.guess')
-
-    @property
-    def configure_directory(self):
-        """Returns the directory where 'configure' resides.
-
-        :return: directory where to find configure
-        """
-        return self.stage.source_path
-
-    @property
-    def configure_abs_path(self):
-        # Absolute path to configure
-        configure_abs_path = join_path(
-            os.path.abspath(self.configure_directory), 'configure'
-        )
-        return configure_abs_path
-
-    @property
-    def build_directory(self):
-        """Override to provide another place to build the package"""
-        return self.configure_directory
-
-    def default_flag_handler(self, spack_env, flag_val):
-        # Relies on being the first thing that can affect the spack_env
-        # EnvironmentModification after it is instantiated or no other
-        # method trying to affect these variables. Currently both are true
-        # flag_val is a tuple (flag, value_list).
-        spack_env.set(flag_val[0].upper(),
-                      ' '.join(flag_val[1]))
-        return []
-
-    @run_before('autoreconf')
-    def delete_configure_to_force_update(self):
-        if self.force_autoreconf:
-            force_remove(self.configure_abs_path)
-
-    def autoreconf(self, spec, prefix):
-        """Not needed usually, configure should be already there"""
-        # If configure exists nothing needs to be done
-        if os.path.exists(self.configure_abs_path):
-            return
-        # Else try to regenerate it
-        autotools = ['m4', 'autoconf', 'automake', 'libtool']
-        missing = [x for x in autotools if x not in spec]
-        if missing:
-            msg = 'Cannot generate configure: missing dependencies {0}'
-            raise RuntimeError(msg.format(missing))
-        tty.msg('Configure script not found: trying to generate it')
-        tty.warn('*********************************************************')
-        tty.warn('* If the default procedure fails, consider implementing *')
-        tty.warn('*        a custom AUTORECONF phase in the package       *')
-        tty.warn('*********************************************************')
-        with working_dir(self.configure_directory):
-            m = inspect.getmodule(self)
-            # This part should be redundant in principle, but
-            # won't hurt
-            m.libtoolize()
-            m.aclocal()
-            # This line is what is needed most of the time
-            # --install, --verbose, --force
-            autoreconf_args = ['-ivf']
-            if 'pkg-config' in spec:
-                autoreconf_args += [
-                    '-I',
-                    join_path(spec['pkg-config'].prefix, 'share', 'aclocal'),
-                ]
-            autoreconf_args += self.autoreconf_extra_args
-            m.autoreconf(*autoreconf_args)
-
-    @run_after('autoreconf')
-    def set_configure_or_die(self):
-        """Checks the presence of a ``configure`` file after the
-        autoreconf phase. If it is found sets a module attribute
-        appropriately, otherwise raises an error.
-
-        :raises RuntimeError: if a configure script is not found in
-            :py:meth:`~AutotoolsPackage.configure_directory`
-        """
-        # Check if a configure script is there. If not raise a RuntimeError.
-        if not os.path.exists(self.configure_abs_path):
-            msg = 'configure script not found in {0}'
-            raise RuntimeError(msg.format(self.configure_directory))
-
-        # Monkey-patch the configure script in the corresponding module
-        inspect.getmodule(self).configure = Executable(
-            self.configure_abs_path
-        )
-
-    def configure_args(self):
-        """Produces a list containing all the arguments that must be passed to
-        configure, except ``--prefix`` which will be pre-pended to the list.
-
-        :return: list of arguments for configure
-        """
-        return []
-
-    def configure(self, spec, prefix):
-        """Runs configure with the arguments specified in
-        :py:meth:`~.AutotoolsPackage.configure_args`
-        and an appropriately set prefix.
-        """
-        options = ['--prefix={0}'.format(prefix)] + self.configure_args()
-
-        with working_dir(self.build_directory, create=True):
-            inspect.getmodule(self).configure(*options)
-
-    def build(self, spec, prefix):
-        """Makes the build targets specified by
-        :py:attr:``~.AutotoolsPackage.build_targets``
-        """
-        with working_dir(self.build_directory):
-            inspect.getmodule(self).make(*self.build_targets)
-
-    def install(self, spec, prefix):
-        """Makes the install targets specified by
-        :py:attr:``~.AutotoolsPackage.install_targets``
-        """
-        with working_dir(self.build_directory):
-            inspect.getmodule(self).make(*self.install_targets)
-
-    run_after('build')(PackageBase._run_default_build_time_test_callbacks)
-
-    def check(self):
-        """Searches the Makefile for targets ``test`` and ``check``
-        and runs them if found.
-        """
-        with working_dir(self.build_directory):
-            self._if_make_target_execute('test')
-            self._if_make_target_execute('check')
-
-    def _activate_or_not(
-            self,
-            name,
-            activation_word,
-            deactivation_word,
-            activation_value=None
-    ):
-        """This function contains the current implementation details of
-        :py:meth:`~.AutotoolsPackage.with_or_without` and
-        :py:meth:`~.AutotoolsPackage.enable_or_disable`.
-
-        Args:
-            name (str): name of the variant that is being processed
-            activation_word (str): the default activation word ('with' in the
-                case of ``with_or_without``)
-            deactivation_word (str): the default deactivation word ('without'
-                in the case of ``with_or_without``)
-            activation_value (callable): callable that accepts a single
-                value. This value is either one of the allowed values for a
-                multi-valued variant or the name of a bool-valued variant.
-                Returns the parameter to be used when the value is activated.
-
-                The special value 'prefix' can also be assigned and will return
-                ``spec[name].prefix`` as activation parameter.
-
-        Examples:
-
-            Given a package with:
-
-            .. code-block:: python
-
-                variant('foo', values=('x', 'y'), description='')
-                variant('bar', default=True, description='')
-
-            calling this function like:
-
-            .. code-block:: python
-
-                _activate_or_not(
-                    'foo', 'with', 'without', activation_value='prefix'
-                )
-                _activate_or_not('bar', 'with', 'without')
-
-            will generate the following configuration options:
-
-            .. code-block:: console
-
-                --with-x=<prefix-to-x> --without-y --with-bar
-
-            for ``<spec-name> foo=x +bar``
-
-        Returns:
-            list of strings that corresponds to the activation/deactivation
-            of the variant that has been processed
-
-        Raises:
-            KeyError: if name is not among known variants
-        """
-        spec = self.spec
-        args = []
-
-        if activation_value == 'prefix':
-            activation_value = lambda x: spec[x].prefix
-
-        # Defensively look that the name passed as argument is among
-        # variants
-        if name not in self.variants:
-            msg = '"{0}" is not a variant of "{1}"'
-            raise KeyError(msg.format(name, self.name))
-
-        # Create a list of pairs. Each pair includes a configuration
-        # option and whether or not that option is activated
-        if set(self.variants[name].values) == set((True, False)):
-            # BoolValuedVariant carry information about a single option.
-            # Nonetheless, for uniformity of treatment we'll package them
-            # in an iterable of one element.
-            condition = '+{name}'.format(name=name)
-            options = [(name, condition in spec)]
-        else:
-            condition = '{name}={value}'
-            options = [
-                (value, condition.format(name=name, value=value) in spec)
-                for value in self.variants[name].values
-            ]
-
-        # For each allowed value in the list of values
-        for option_value, activated in options:
-            # Search for an override in the package for this value
-            override_name = '{0}_or_{1}_{2}'.format(
-                activation_word, deactivation_word, option_value
-            )
-            line_generator = getattr(self, override_name, None)
-            # If not available use a sensible default
-            if line_generator is None:
-                def _default_generator(is_activated):
-                    if is_activated:
-                        line = '--{0}-{1}'.format(
-                            activation_word, option_value
-                        )
-                        if activation_value is not None and activation_value(option_value):  # NOQA=ignore=E501
-                            line += '={0}'.format(
-                                activation_value(option_value)
-                            )
-                        return line
-                    return '--{0}-{1}'.format(deactivation_word, option_value)
-                line_generator = _default_generator
-            args.append(line_generator(activated))
-        return args
-
-    def with_or_without(self, name, activation_value=None):
-        """Inspects a variant and returns the arguments that activate
-        or deactivate the selected feature(s) for the configure options.
-
-        This function works on all type of variants. For bool-valued variants
-        it will return by default ``--with-{name}`` or ``--without-{name}``.
-        For other kinds of variants it will cycle over the allowed values and
-        return either ``--with-{value}`` or ``--without-{value}``.
-
-        If activation_value is given, then for each possible value of the
-        variant, the option ``--with-{value}=activation_value(value)`` or
-        ``--without-{value}`` will be added depending on whether or not
-        ``variant=value`` is in the spec.
-
-        Args:
-            name (str): name of a valid multi-valued variant
-            activation_value (callable): callable that accepts a single
-                value and returns the parameter to be used leading to an entry
-                of the type ``--with-{name}={parameter}``.
-
-                The special value 'prefix' can also be assigned and will return
-                ``spec[name].prefix`` as activation parameter.
-
-        Returns:
-            list of arguments to configure
-        """
-        return self._activate_or_not(name, 'with', 'without', activation_value)
-
-    def enable_or_disable(self, name, activation_value=None):
-        """Same as :py:meth:`~.AutotoolsPackage.with_or_without` but substitute
-        ``with`` with ``enable`` and ``without`` with ``disable``.
-
-        Args:
-            name (str): name of a valid multi-valued variant
-            activation_value (callable): if present accepts a single value
-                and returns the parameter to be used leading to an entry of the
-                type ``--enable-{name}={parameter}``
-
-                The special value 'prefix' can also be assigned and will return
-                ``spec[name].prefix`` as activation parameter.
-
-        Returns:
-            list of arguments to configure
-        """
-        return self._activate_or_not(
-            name, 'enable', 'disable', activation_value
-        )
-
-    run_after('install')(PackageBase._run_default_install_time_test_callbacks)
-
-    def installcheck(self):
-        """Searches the Makefile for an ``installcheck`` target
-        and runs it if found.
-        """
-        with working_dir(self.build_directory):
-            self._if_make_target_execute('installcheck')
-
-    # Check that self.prefix is there after installation
-    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py b/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py
deleted file mode 100644
index 5b0f5526c9..0000000000
--- a/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py
+++ /dev/null
@@ -1,224 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import inspect
-import os
-import platform
-
-import spack.build_environment
-from llnl.util.filesystem import working_dir, join_path
-from spack.util.environment import filter_system_paths
-from spack.directives import depends_on, variant
-from spack.package import PackageBase, InstallError, run_after
-
-
-class CMakePackage(PackageBase):
-    """Specialized class for packages built using CMake
-
-    For more information on the CMake build system, see:
-    https://cmake.org/cmake/help/latest/
-
-    This class provides three phases that can be overridden:
-
-        1. :py:meth:`~.CMakePackage.cmake`
-        2. :py:meth:`~.CMakePackage.build`
-        3. :py:meth:`~.CMakePackage.install`
-
-    They all have sensible defaults and for many packages the only thing
-    necessary will be to override :py:meth:`~.CMakePackage.cmake_args`.
-    For a finer tuning you may also override:
-
-        +-----------------------------------------------+--------------------+
-        | **Method**                                    | **Purpose**        |
-        +===============================================+====================+
-        | :py:meth:`~.CMakePackage.root_cmakelists_dir` | Location of the    |
-        |                                               | root CMakeLists.txt|
-        +-----------------------------------------------+--------------------+
-        | :py:meth:`~.CMakePackage.build_directory`     | Directory where to |
-        |                                               | build the package  |
-        +-----------------------------------------------+--------------------+
-
-
-    """
-    #: Phases of a CMake package
-    phases = ['cmake', 'build', 'install']
-    #: This attribute is used in UI queries that need to know the build
-    #: system base class
-    build_system_class = 'CMakePackage'
-
-    build_targets = []
-    install_targets = ['install']
-
-    build_time_test_callbacks = ['check']
-
-    #: The build system generator to use.
-    #:
-    #: See ``cmake --help`` for a list of valid generators.
-    #: Currently, "Unix Makefiles" and "Ninja" are the only generators
-    #: that Spack supports. Defaults to "Unix Makefiles".
-    #:
-    #: See https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html
-    #: for more information.
-    generator = 'Unix Makefiles'
-
-    # https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html
-    variant('build_type', default='RelWithDebInfo',
-            description='CMake build type',
-            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
-
-    depends_on('cmake', type='build')
-
-    @property
-    def root_cmakelists_dir(self):
-        """The relative path to the directory containing CMakeLists.txt
-
-        This path is relative to the root of the extracted tarball,
-        not to the ``build_directory``. Defaults to the current directory.
-
-        :return: directory containing CMakeLists.txt
-        """
-        return self.stage.source_path
-
-    @property
-    def std_cmake_args(self):
-        """Standard cmake arguments provided as a property for
-        convenience of package writers
-
-        :return: standard cmake arguments
-        """
-        # standard CMake arguments
-        return CMakePackage._std_args(self)
-
-    @staticmethod
-    def _std_args(pkg):
-        """Computes the standard cmake arguments for a generic package"""
-        try:
-            generator = pkg.generator
-        except AttributeError:
-            generator = 'Unix Makefiles'
-
-        # Make sure a valid generator was chosen
-        valid_generators = ['Unix Makefiles', 'Ninja']
-        if generator not in valid_generators:
-            msg  = "Invalid CMake generator: '{0}'\n".format(generator)
-            msg += "CMakePackage currently supports the following "
-            msg += "generators: '{0}'".format("', '".join(valid_generators))
-            raise InstallError(msg)
-
-        try:
-            build_type = pkg.spec.variants['build_type'].value
-        except KeyError:
-            build_type = 'RelWithDebInfo'
-
-        args = [
-            '-G', generator,
-            '-DCMAKE_INSTALL_PREFIX:PATH={0}'.format(pkg.prefix),
-            '-DCMAKE_BUILD_TYPE:STRING={0}'.format(build_type),
-            '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON'
-        ]
-
-        if platform.mac_ver()[0]:
-            args.append('-DCMAKE_FIND_FRAMEWORK:STRING=LAST')
-
-        # Set up CMake rpath
-        args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE')
-        rpaths = ':'.join(spack.build_environment.get_rpaths(pkg))
-        args.append('-DCMAKE_INSTALL_RPATH:STRING={0}'.format(rpaths))
-        # CMake's find_package() looks in CMAKE_PREFIX_PATH first, help CMake
-        # to find immediate link dependencies in right places:
-        deps = [d.prefix for d in
-                pkg.spec.dependencies(deptype=('build', 'link'))]
-        deps = filter_system_paths(deps)
-        args.append('-DCMAKE_PREFIX_PATH:STRING={0}'.format(';'.join(deps)))
-        return args
-
-    @property
-    def build_directory(self):
-        """Returns the directory to use when building the package
-
-        :return: directory where to build the package
-        """
-        return join_path(self.stage.source_path, 'spack-build')
-
-    def default_flag_handler(self, spack_env, flag_val):
-        # Relies on being the first thing that can affect the spack_env
-        # EnvironmentModification after it is instantiated or no other
-        # method trying to affect these variables. Currently both are true
-        # flag_val is a tuple (flag, value_list)
-        spack_env.set(flag_val[0].upper(),
-                      ' '.join(flag_val[1]))
-        return []
-
-    def cmake_args(self):
-        """Produces a list containing all the arguments that must be passed to
-        cmake, except:
-
-            * CMAKE_INSTALL_PREFIX
-            * CMAKE_BUILD_TYPE
-
-        which will be set automatically.
-
-        :return: list of arguments for cmake
-        """
-        return []
-
-    def cmake(self, spec, prefix):
-        """Runs ``cmake`` in the build directory"""
-        options = [os.path.abspath(self.root_cmakelists_dir)]
-        options += self.std_cmake_args
-        options += self.cmake_args()
-        with working_dir(self.build_directory, create=True):
-            inspect.getmodule(self).cmake(*options)
-
-    def build(self, spec, prefix):
-        """Make the build targets"""
-        with working_dir(self.build_directory):
-            if self.generator == 'Unix Makefiles':
-                inspect.getmodule(self).make(*self.build_targets)
-            elif self.generator == 'Ninja':
-                inspect.getmodule(self).ninja(*self.build_targets)
-
-    def install(self, spec, prefix):
-        """Make the install targets"""
-        with working_dir(self.build_directory):
-            if self.generator == 'Unix Makefiles':
-                inspect.getmodule(self).make(*self.install_targets)
-            elif self.generator == 'Ninja':
-                inspect.getmodule(self).ninja(*self.install_targets)
-
-    run_after('build')(PackageBase._run_default_build_time_test_callbacks)
-
-    def check(self):
-        """Searches the CMake-generated Makefile for the target ``test``
-        and runs it if found.
-        """
-        with working_dir(self.build_directory):
-            if self.generator == 'Unix Makefiles':
-                self._if_make_target_execute('test')
-            elif self.generator == 'Ninja':
-                self._if_ninja_target_execute('test')
-
-    # Check that self.prefix is there after installation
-    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py b/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py
deleted file mode 100644
index 5ffb88f43d..0000000000
--- a/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py
+++ /dev/null
@@ -1,129 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import inspect
-
-import llnl.util.tty as tty
-from llnl.util.filesystem import working_dir
-from spack.package import PackageBase, run_after
-
-
-class MakefilePackage(PackageBase):
-    """Specialized class for packages that are built using editable Makefiles
-
-    This class provides three phases that can be overridden:
-
-        1. :py:meth:`~.MakefilePackage.edit`
-        2. :py:meth:`~.MakefilePackage.build`
-        3. :py:meth:`~.MakefilePackage.install`
-
-    It is usually necessary to override the :py:meth:`~.MakefilePackage.edit`
-    phase, while :py:meth:`~.MakefilePackage.build` and
-    :py:meth:`~.MakefilePackage.install` have sensible defaults.
-    For a finer tuning you may override:
-
-        +-----------------------------------------------+--------------------+
-        | **Method**                                    | **Purpose**        |
-        +===============================================+====================+
-        | :py:attr:`~.MakefilePackage.build_targets`    | Specify ``make``   |
-        |                                               | targets for the    |
-        |                                               | build phase        |
-        +-----------------------------------------------+--------------------+
-        | :py:attr:`~.MakefilePackage.install_targets`  | Specify ``make``   |
-        |                                               | targets for the    |
-        |                                               | install phase      |
-        +-----------------------------------------------+--------------------+
-        | :py:meth:`~.MakefilePackage.build_directory`  | Directory where the|
-        |                                               | Makefile is located|
-        +-----------------------------------------------+--------------------+
-    """
-    #: Phases of a package that is built with an hand-written Makefile
-    phases = ['edit', 'build', 'install']
-    #: This attribute is used in UI queries that need to know the build
-    #: system base class
-    build_system_class = 'MakefilePackage'
-
-    #: Targets for ``make`` during the :py:meth:`~.MakefilePackage.build`
-    #: phase
-    build_targets = []
-    #: Targets for ``make`` during the :py:meth:`~.MakefilePackage.install`
-    #: phase
-    install_targets = ['install']
-
-    #: Callback names for build-time test
-    build_time_test_callbacks = ['check']
-
-    #: Callback names for install-time test
-    install_time_test_callbacks = ['installcheck']
-
-    @property
-    def build_directory(self):
-        """Returns the directory containing the main Makefile
-
-        :return: build directory
-        """
-        return self.stage.source_path
-
-    def edit(self, spec, prefix):
-        """Edits the Makefile before calling make. This phase cannot
-        be defaulted.
-        """
-        tty.msg('Using default implementation: skipping edit phase.')
-
-    def build(self, spec, prefix):
-        """Calls make, passing :py:attr:`~.MakefilePackage.build_targets`
-        as targets.
-        """
-        with working_dir(self.build_directory):
-            inspect.getmodule(self).make(*self.build_targets)
-
-    def install(self, spec, prefix):
-        """Calls make, passing :py:attr:`~.MakefilePackage.install_targets`
-        as targets.
-        """
-        with working_dir(self.build_directory):
-            inspect.getmodule(self).make(*self.install_targets)
-
-    run_after('build')(PackageBase._run_default_build_time_test_callbacks)
-
-    def check(self):
-        """Searches the Makefile for targets ``test`` and ``check``
-        and runs them if found.
-        """
-        with working_dir(self.build_directory):
-            self._if_make_target_execute('test')
-            self._if_make_target_execute('check')
-
-    run_after('install')(PackageBase._run_default_install_time_test_callbacks)
-
-    def installcheck(self):
-        """Searches the Makefile for an ``installcheck`` target
-        and runs it if found.
-        """
-        with working_dir(self.build_directory):
-            self._if_make_target_execute('installcheck')
-
-    # Check that self.prefix is there after installation
-    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py b/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py
deleted file mode 100644
index 190620d7a2..0000000000
--- a/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py
+++ /dev/null
@@ -1,399 +0,0 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU Lesser General Public License (as
-# published by the Free Software Foundation) version 2.1, February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-import inspect
-import os
-
-from spack.directives import depends_on, extends
-from spack.package import PackageBase, run_after
-
-from llnl.util.filesystem import working_dir
-
-
-class PythonPackage(PackageBase):
-    """Specialized class for packages that are built using Python
-    setup.py files
-
-    This class provides the following phases that can be overridden:
-
-    * build
-    * build_py
-    * build_ext
-    * build_clib
-    * build_scripts
-    * clean
-    * install
-    * install_lib
-    * install_headers
-    * install_scripts
-    * install_data
-    * sdist
-    * register
-    * bdist
-    * bdist_dumb
-    * bdist_rpm
-    * bdist_wininst
-    * upload
-    * check
-
-    These are all standard setup.py commands and can be found by running:
-
-    .. code-block:: console
-
-       $ python setup.py --help-commands
-
-    By default, only the 'build' and 'install' phases are run, but if you
-    need to run more phases, simply modify your ``phases`` list like so:
-
-    .. code-block:: python
-
-       phases = ['build_ext', 'install', 'bdist']
-
-    Each phase provides a function <phase> that runs:
-
-    .. code-block:: console
-
-       $ python setup.py --no-user-cfg <phase>
-
-    Each phase also has a <phase_args> function that can pass arguments to
-    this call. All of these functions are empty except for the ``install_args``
-    function, which passes ``--prefix=/path/to/installation/directory``.
-
-    If you need to run a phase which is not a standard setup.py command,
-    you'll need to define a function for it like so:
-
-    .. code-block:: python
-
-       def configure(self, spec, prefix):
-           self.setup_py('configure')
-    """
-    # Default phases
-    phases = ['build', 'install']
-
-    # Name of modules that the Python package provides
-    # This is used to test whether or not the installation succeeded
-    # These names generally come from running:
-    #
-    # >>> import setuptools
-    # >>> setuptools.find_packages()
-    #
-    # in the source tarball directory
-    import_modules = []
-
-    # To be used in UI queries that require to know which
-    # build-system class we are using
-    build_system_class = 'PythonPackage'
-
-    #: Callback names for build-time test
-    build_time_test_callbacks = ['test']
-
-    #: Callback names for install-time test
-    install_time_test_callbacks = ['import_module_test']
-
-    extends('python')
-
-    depends_on('python', type=('build', 'run'))
-
-    def setup_file(self):
-        """Returns the name of the setup file to use."""
-        return 'setup.py'
-
-    @property
-    def build_directory(self):
-        """The directory containing the ``setup.py`` file."""
-        return self.stage.source_path
-
-    def python(self, *args, **kwargs):
-        inspect.getmodule(self).python(*args, **kwargs)
-
-    def setup_py(self, *args, **kwargs):
-        setup = self.setup_file()
-
-        with working_dir(self.build_directory):
-            self.python(setup, '--no-user-cfg', *args, **kwargs)
-
-    def _setup_command_available(self, command):
-        """Determines whether or not a setup.py command exists.
-
-        Args:
-            command (str): The command to look for
-
-        Returns:
-            bool: True if the command is found, else False
-        """
-        kwargs = {
-            'output': os.devnull,
-            'error':  os.devnull,
-            'fail_on_error': False
-        }
-
-        python = inspect.getmodule(self).python
-        setup = self.setup_file()
-
-        python(setup, '--no-user-cfg', command, '--help', **kwargs)
-        return python.returncode == 0
-
-    # The following phases and their descriptions come from:
-    #   $ python setup.py --help-commands
-
-    # Standard commands
-
-    def build(self, spec, prefix):
-        """Build everything needed to install."""
-        args = self.build_args(spec, prefix)
-
-        self.setup_py('build', *args)
-
-    def build_args(self, spec, prefix):
-        """Arguments to pass to build."""
-        return []
-
-    def build_py(self, spec, prefix):
-        '''"Build" pure Python modules (copy to build directory).'''
-        args = self.build_py_args(spec, prefix)
-
-        self.setup_py('build_py', *args)
-
-    def build_py_args(self, spec, prefix):
-        """Arguments to pass to build_py."""
-        return []
-
-    def build_ext(self, spec, prefix):
-        """Build C/C++ extensions (compile/link to build directory)."""
-        args = self.build_ext_args(spec, prefix)
-
-        self.setup_py('build_ext', *args)
-
-    def build_ext_args(self, spec, prefix):
-        """Arguments to pass to build_ext."""
-        return []
-
-    def build_clib(self, spec, prefix):
-        """Build C/C++ libraries used by Python extensions."""
-        args = self.build_clib_args(spec, prefix)
-
-        self.setup_py('build_clib', *args)
-
-    def build_clib_args(self, spec, prefix):
-        """Arguments to pass to build_clib."""
-        return []
-
-    def build_scripts(self, spec, prefix):
-        '''"Build" scripts (copy and fixup #! line).'''
-        args = self.build_scripts_args(spec, prefix)
-
-        self.setup_py('build_scripts', *args)
-
-    def clean(self, spec, prefix):
-        """Clean up temporary files from 'build' command."""
-        args = self.clean_args(spec, prefix)
-
-        self.setup_py('clean', *args)
-
-    def clean_args(self, spec, prefix):
-        """Arguments to pass to clean."""
-        return []
-
-    def install(self, spec, prefix):
-        """Install everything from build directory."""
-        args = self.install_args(spec, prefix)
-
-        self.setup_py('install', *args)
-
-    def install_args(self, spec, prefix):
-        """Arguments to pass to install."""
-        args = ['--prefix={0}'.format(prefix)]
-
-        # This option causes python packages (including setuptools) NOT
-        # to create eggs or easy-install.pth files.  Instead, they
-        # install naturally into $prefix/pythonX.Y/site-packages.
-        #
-        # Eggs add an extra level of indirection to sys.path, slowing
-        # down large HPC runs.  They are also deprecated in favor of
-        # wheels, which use a normal layout when installed.
-        #
-        # Spack manages the package directory on its own by symlinking
-        # extensions into the site-packages directory, so we don't really
-        # need the .pth files or egg directories, anyway.
-        if ('py-setuptools' == spec.name or          # this is setuptools, or
-            'py-setuptools' in spec._dependencies):  # it's an immediate dep
-            args += ['--single-version-externally-managed', '--root=/']
-
-        return args
-
-    def install_lib(self, spec, prefix):
-        """Install all Python modules (extensions and pure Python)."""
-        args = self.install_lib_args(spec, prefix)
-
-        self.setup_py('install_lib', *args)
-
-    def install_lib_args(self, spec, prefix):
-        """Arguments to pass to install_lib."""
-        return []
-
-    def install_headers(self, spec, prefix):
-        """Install C/C++ header files."""
-        args = self.install_headers_args(spec, prefix)
-
-        self.setup_py('install_headers', *args)
-
-    def install_headers_args(self, spec, prefix):
-        """Arguments to pass to install_headers."""
-        return []
-
-    def install_scripts(self, spec, prefix):
-        """Install scripts (Python or otherwise)."""
-        args = self.install_scripts_args(spec, prefix)
-
-        self.setup_py('install_scripts', *args)
-
-    def install_scripts_args(self, spec, prefix):
-        """Arguments to pass to install_scripts."""
-        return []
-
-    def install_data(self, spec, prefix):
-        """Install data files."""
-        args = self.install_data_args(spec, prefix)
-
-        self.setup_py('install_data', *args)
-
-    def install_data_args(self, spec, prefix):
-        """Arguments to pass to install_data."""
-        return []
-
-    def sdist(self, spec, prefix):
-        """Create a source distribution (tarball, zip file, etc.)."""
-        args = self.sdist_args(spec, prefix)
-
-        self.setup_py('sdist', *args)
-
-    def sdist_args(self, spec, prefix):
-        """Arguments to pass to sdist."""
-        return []
-
-    def register(self, spec, prefix):
-        """Register the distribution with the Python package index."""
-        args = self.register_args(spec, prefix)
-
-        self.setup_py('register', *args)
-
-    def register_args(self, spec, prefix):
-        """Arguments to pass to register."""
-        return []
-
-    def bdist(self, spec, prefix):
-        """Create a built (binary) distribution."""
-        args = self.bdist_args(spec, prefix)
-
-        self.setup_py('bdist', *args)
-
-    def bdist_args(self, spec, prefix):
-        """Arguments to pass to bdist."""
-        return []
-
-    def bdist_dumb(self, spec, prefix):
-        '''Create a "dumb" built distribution.'''
-        args = self.bdist_dumb_args(spec, prefix)
-
-        self.setup_py('bdist_dumb', *args)
-
-    def bdist_dumb_args(self, spec, prefix):
-        """Arguments to pass to bdist_dumb."""
-        return []
-
-    def bdist_rpm(self, spec, prefix):
-        """Create an RPM distribution."""
-        args = self.bdist_rpm(spec, prefix)
-
-        self.setup_py('bdist_rpm', *args)
-
-    def bdist_rpm_args(self, spec, prefix):
-        """Arguments to pass to bdist_rpm."""
-        return []
-
-    def bdist_wininst(self, spec, prefix):
-        """Create an executable installer for MS Windows."""
-        args = self.bdist_wininst_args(spec, prefix)
-
-        self.setup_py('bdist_wininst', *args)
-
-    def bdist_wininst_args(self, spec, prefix):
-        """Arguments to pass to bdist_wininst."""
-        return []
-
-    def upload(self, spec, prefix):
-        """Upload binary package to PyPI."""
-        args = self.upload_args(spec, prefix)
-
-        self.setup_py('upload', *args)
-
-    def upload_args(self, spec, prefix):
-        """Arguments to pass to upload."""
-        return []
-
-    def check(self, spec, prefix):
-        """Perform some checks on the package."""
-        args = self.check_args(spec, prefix)
-
-        self.setup_py('check', *args)
-
-    def check_args(self, spec, prefix):
-        """Arguments to pass to check."""
-        return []
-
-    # Testing
-
-    def test(self):
-        """Run unit tests after in-place build.
-
-        These tests are only run if the package actually has a 'test' command.
-        """
-        if self._setup_command_available('test'):
-            args = self.test_args(self.spec, self.prefix)
-
-            self.setup_py('test', *args)
-
-    def test_args(self, spec, prefix):
-        """Arguments to pass to test."""
-        return []
-
-    run_after('build')(PackageBase._run_default_build_time_test_callbacks)
-
-    def import_module_test(self):
-        """Attempts to import the module that was just installed.
-
-        This test is only run if the package overrides
-        :py:attr:`import_modules` with a list of module names."""
-
-        # Make sure we are importing the installed modules,
-        # not the ones in the current directory
-        with working_dir('..'):
-            for module in self.import_modules:
-                self.python('-c', 'import {0}'.format(module))
-
-    run_after('install')(PackageBase._run_default_install_time_test_callbacks)
-
-    # Check that self.prefix is there after installation
-    run_after('install')(PackageBase.sanity_check_prefix)
diff --git a/lib/spack/docs/tutorial_buildsystems.rst b/lib/spack/docs/tutorial_buildsystems.rst
index 8f5dce0892..d92db13062 100644
--- a/lib/spack/docs/tutorial_buildsystems.rst
+++ b/lib/spack/docs/tutorial_buildsystems.rst
@@ -103,7 +103,7 @@ This will open the :code:`AutotoolsPackage` file in your text editor.
     long examples. We only show what is relevant to the packager.
 
 
-.. literalinclude:: tutorial/examples/Autotools/autotools_class.py
+.. literalinclude:: ../../../lib/spack/spack/build_systems/autotools.py
     :language: python
     :emphasize-lines: 42,45,62
     :lines: 40-95,259-267
@@ -202,7 +202,7 @@ Let's also take a look inside the :code:`MakefilePackage` class:
 Take note of the following:
 
 
-.. literalinclude:: tutorial/examples/Makefile/makefile_class.py
+.. literalinclude:: ../../../lib/spack/spack/build_systems/makefile.py
    :language: python
    :lines: 33-79,89-107
    :emphasize-lines: 48,54,61
@@ -480,7 +480,7 @@ Let's look at these defaults in the :code:`CMakePackage` class:
 And go into a bit of detail on the highlighted sections:
 
 
-.. literalinclude:: tutorial/examples/Cmake/cmake_class.py
+.. literalinclude:: ../../../lib/spack/spack/build_systems/cmake.py
    :language: python
    :lines: 37-92, 94-155, 174-211
    :emphasize-lines: 57,68,86,94,96,99,100,101,102,111,117,135,136
@@ -675,7 +675,7 @@ at the :code:`PythonPackage` class:
 We see the following:
 
 
-.. literalinclude:: tutorial/examples/PyPackage/python_package_class.py
+.. literalinclude:: ../../../lib/spack/spack/build_systems/python.py
    :language: python
    :lines: 35, 161-364
    :linenos:
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index f1cf0d5049..cab455695e 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -128,7 +128,6 @@ class MakeExecutable(Executable):
 def set_compiler_environment_variables(pkg, env):
     assert(pkg.spec.concrete)
     compiler = pkg.compiler
-    flags = pkg.spec.compiler_flags
 
     # Set compiler variables used by CMake and autotools
     assert all(key in compiler.link_paths for key in (
@@ -160,11 +159,28 @@ def set_compiler_environment_variables(pkg, env):
     env.set('SPACK_F77_RPATH_ARG', compiler.f77_rpath_arg)
     env.set('SPACK_FC_RPATH_ARG',  compiler.fc_rpath_arg)
 
-    # Add every valid compiler flag to the environment, prefixed with "SPACK_"
+    # Trap spack-tracked compiler flags as appropriate.
+    # env_flags are easy to accidentally override.
+    inject_flags = {}
+    env_flags = {}
+    build_system_flags = {}
+    for flag in spack.spec.FlagMap.valid_compiler_flags():
+        injf, envf, bsf = pkg.flag_handler(flag, pkg.spec.compiler_flags[flag])
+        inject_flags[flag] = injf or []
+        env_flags[flag] = envf or []
+        build_system_flags[flag] = bsf or []
+
+    # Place compiler flags as specified by flag_handler
     for flag in spack.spec.FlagMap.valid_compiler_flags():
         # Concreteness guarantees key safety here
-        if flags[flag] != []:
-            env.set('SPACK_' + flag.upper(), ' '.join(f for f in flags[flag]))
+        if inject_flags[flag]:
+            # variables SPACK_<FLAG> inject flags through wrapper
+            var_name = 'SPACK_{0}'.format(flag.upper())
+            env.set(var_name, ' '.join(f for f in inject_flags[flag]))
+        if env_flags[flag]:
+            # implicit variables
+            env.set(flag.upper(), ' '.join(f for f in env_flags[flag]))
+    pkg.flags_to_build_system_args(build_system_flags)
 
     env.set('SPACK_COMPILER_SPEC', str(pkg.spec.compiler))
 
@@ -559,19 +575,6 @@ def setup_package(pkg, dirty):
     for s in pkg.spec.traverse():
         assert s.package.spec is s
 
-    # Trap spack-tracked compiler flags as appropriate.
-    # Must be before set_compiler_environment_variables
-    # Current implementation of default flag handler relies on this being
-    # the first thing to affect the spack_env (so there is no appending), or
-    # on no other build_environment methods trying to affect these variables
-    # (CFLAGS, CXXFLAGS, etc). Currently both are true, either is sufficient.
-    for flag in spack.spec.FlagMap.valid_compiler_flags():
-        trap_func = getattr(pkg, flag + '_handler',
-                            getattr(pkg, 'default_flag_handler',
-                                    lambda x, y: y[1]))
-        flag_val = pkg.spec.compiler_flags[flag]
-        pkg.spec.compiler_flags[flag] = trap_func(spack_env, (flag, flag_val))
-
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env, dirty)
     pkg.architecture.platform.setup_platform_environment(pkg, spack_env)
diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index 8f2af3e21e..01a59feeba 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -182,15 +182,6 @@ class AutotoolsPackage(PackageBase):
         """Override to provide another place to build the package"""
         return self.configure_directory
 
-    def default_flag_handler(self, spack_env, flag_val):
-        # Relies on being the first thing that can affect the spack_env
-        # EnvironmentModification after it is instantiated or no other
-        # method trying to affect these variables. Currently both are true
-        # flag_val is a tuple (flag, value_list).
-        spack_env.set(flag_val[0].upper(),
-                      ' '.join(flag_val[1]))
-        return []
-
     @run_before('autoreconf')
     def delete_configure_to_force_update(self):
         if self.force_autoreconf:
@@ -256,12 +247,24 @@ class AutotoolsPackage(PackageBase):
         """
         return []
 
+    def flags_to_build_system_args(self, flags):
+        """Produces a list of all command line arguments to pass specified
+        compiler flags to configure."""
+        # Has to be dynamic attribute due to caching.
+        setattr(self, 'configure_flag_args', [])
+        for flag, values in flags.items():
+            if values:
+                values_str = '{0}={1}'.format(flag.upper(), ' '.join(values))
+                self.configure_flag_args.append(values_str)
+
     def configure(self, spec, prefix):
         """Runs configure with the arguments specified in
         :py:meth:`~.AutotoolsPackage.configure_args`
         and an appropriately set prefix.
         """
-        options = ['--prefix={0}'.format(prefix)] + self.configure_args()
+        options = getattr(self, 'configure_flag_args', [])
+        options += ['--prefix={0}'.format(prefix)]
+        options += self.configure_args()
 
         with working_dir(self.build_directory, create=True):
             inspect.getmodule(self).configure(*options)
diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py
index ca9ec6f803..13c752eb2e 100644
--- a/lib/spack/spack/build_systems/cmake.py
+++ b/lib/spack/spack/build_systems/cmake.py
@@ -109,7 +109,9 @@ class CMakePackage(PackageBase):
         :return: standard cmake arguments
         """
         # standard CMake arguments
-        return CMakePackage._std_args(self)
+        std_cmake_args = CMakePackage._std_args(self)
+        std_cmake_args += getattr(self, 'cmake_flag_args', [])
+        return std_cmake_args
 
     @staticmethod
     def _std_args(pkg):
@@ -154,6 +156,44 @@ class CMakePackage(PackageBase):
         args.append('-DCMAKE_PREFIX_PATH:STRING={0}'.format(';'.join(deps)))
         return args
 
+    def flags_to_build_system_args(self, flags):
+        """Produces a list of all command line arguments to pass the specified
+        compiler flags to cmake. Note CMAKE does not have a cppflags option,
+        so cppflags will be added to cflags, cxxflags, and fflags to mimic the
+        behavior in other tools."""
+        # Has to be dynamic attribute due to caching
+        setattr(self, 'cmake_flag_args', [])
+
+        flag_string = '-DCMAKE_{0}_FLAGS={1}'
+        langs = {'C': 'c', 'CXX': 'cxx', 'Fortran': 'f'}
+
+        # Handle language compiler flags
+        for lang, pre in langs.items():
+            flag = pre + 'flags'
+            # cmake has no explicit cppflags support -> add it to all langs
+            lang_flags = ' '.join(flags.get(flag, []) + flags.get('cppflags',
+                                                                  []))
+            if lang_flags:
+                self.cmake_flag_args.append(flag_string.format(lang,
+                                                               lang_flags))
+
+        # Cmake has different linker arguments for different build types.
+        # We specify for each of them.
+        if flags['ldflags']:
+            ldflags = ' '.join(flags['ldflags'])
+            ld_string = '-DCMAKE_{0}_LINKER_FLAGS={1}'
+            # cmake has separate linker arguments for types of builds.
+            for type in ['EXE', 'MODULE', 'SHARED', 'STATIC']:
+                self.cmake_flag_args.append(ld_string.format(type, ldflags))
+
+        # CMake has libs options separated by language. Apply ours to each.
+        if flags['ldlibs']:
+            libs_flags = ' '.join(flags['ldlibs'])
+            libs_string = '-DCMAKE_{0}_STANDARD_LIBRARIES={1}'
+            for lang in langs:
+                self.cmake_flag_args.append(libs_string.format(lang,
+                                                               libs_flags))
+
     @property
     def build_directory(self):
         """Returns the directory to use when building the package
@@ -162,15 +202,6 @@ class CMakePackage(PackageBase):
         """
         return join_path(self.stage.source_path, 'spack-build')
 
-    def default_flag_handler(self, spack_env, flag_val):
-        # Relies on being the first thing that can affect the spack_env
-        # EnvironmentModification after it is instantiated or no other
-        # method trying to affect these variables. Currently both are true
-        # flag_val is a tuple (flag, value_list)
-        spack_env.set(flag_val[0].upper(),
-                      ' '.join(flag_val[1]))
-        return []
-
     def cmake_args(self):
         """Produces a list containing all the arguments that must be passed to
         cmake, except:
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 712f252494..18091f2e69 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1707,6 +1707,47 @@ class PackageBase(with_metaclass(PackageMeta, object)):
         """
         pass
 
+    def inject_flags(self, name, flags):
+        """
+        flag_handler that injects all flags through the compiler wrapper.
+        """
+        return (flags, None, None)
+
+    def env_flags(self, name, flags):
+        """
+        flag_handler that adds all flags to canonical environment variables.
+        """
+        return (None, flags, None)
+
+    def build_system_flags(self, name, flags):
+        """
+        flag_handler that passes flags to the build system arguments.  Any
+        package using `build_system_flags` must also implement
+        `flags_to_build_system_args`, or derive from a class that
+        implements it.  Currently, AutotoolsPackage and CMakePackage
+        implement it.
+        """
+        return (None, None, flags)
+
+    flag_handler = inject_flags
+    # The flag handler method is called for each of the allowed compiler flags.
+    # It returns a triple of inject_flags, env_flags, build_system_flags.
+    # The flags returned as inject_flags are injected through the spack
+    #  compiler wrappers.
+    # The flags returned as env_flags are passed to the build system through
+    #  the environment variables of the same name.
+    # The flags returned as build_system_flags are passed to the build system
+    #  package subclass to be turned into the appropriate part of the standard
+    #  arguments. This is implemented for build system classes where
+    #  appropriate and will otherwise raise a NotImplementedError.
+
+    def flags_to_build_system_args(self, flags):
+        # Takes flags as a dict name: list of values
+        if any(v for v in flags.values()):
+            msg = 'The {0} build system'.format(self.__class__.__name__)
+            msg += ' cannot take command line arguments for compiler flags'
+            raise NotImplementedError(msg)
+
     @staticmethod
     def uninstall_by_spec(spec, force=False):
         if not os.path.isdir(spec.prefix):
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index a50af94ac2..671379c717 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -211,8 +211,12 @@ class CompilerWrapperTest(unittest.TestCase):
                       ' '.join(test_command) + ' ' +
                       '-lfoo')
 
-        os.environ['SPACK_LDFLAGS'] = ''
-        os.environ['SPACK_LDLIBS'] = ''
+        del os.environ['SPACK_CFLAGS']
+        del os.environ['SPACK_CXXFLAGS']
+        del os.environ['SPACK_FFLAGS']
+        del os.environ['SPACK_CPPFLAGS']
+        del os.environ['SPACK_LDFLAGS']
+        del os.environ['SPACK_LDLIBS']
 
     def test_dep_rpath(self):
         """Ensure RPATHs for root package are added."""
diff --git a/lib/spack/spack/test/flag_handlers.py b/lib/spack/spack/test/flag_handlers.py
new file mode 100644
index 0000000000..0b785a948f
--- /dev/null
+++ b/lib/spack/spack/test/flag_handlers.py
@@ -0,0 +1,176 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import pytest
+import os
+
+import spack.spec
+import spack.build_environment
+
+
+@pytest.fixture()
+def temp_env():
+    old_env = os.environ.copy()
+    yield
+    os.environ = old_env
+
+
+def add_O3_to_build_system_cflags(name, flags):
+    build_system_flags = []
+    if name == 'cflags':
+        build_system_flags.append('-O3')
+    return (flags, None, build_system_flags)
+
+
+@pytest.mark.usefixtures('config')
+class TestFlagHandlers(object):
+    def test_no_build_system_flags(self, temp_env):
+        # Test that both autotools and cmake work getting no build_system flags
+        s1 = spack.spec.Spec('callpath')
+        s1.concretize()
+        pkg1 = spack.repo.get(s1)
+        spack.build_environment.setup_package(pkg1, False)
+
+        s2 = spack.spec.Spec('libelf')
+        s2.concretize()
+        pkg2 = spack.repo.get(s2)
+        spack.build_environment.setup_package(pkg2, False)
+
+        # Use cppflags as a canary
+        assert 'SPACK_CPPFLAGS' not in os.environ
+        assert 'CPPFLAGS' not in os.environ
+
+    def test_inject_flags(self, temp_env):
+        s = spack.spec.Spec('mpileaks cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.inject_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert os.environ['SPACK_CPPFLAGS'] == '-g'
+        assert 'CPPFLAGS' not in os.environ
+
+    def test_env_flags(self, temp_env):
+        s = spack.spec.Spec('mpileaks cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.env_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert os.environ['CPPFLAGS'] == '-g'
+        assert 'SPACK_CPPFLAGS' not in os.environ
+
+    def test_build_system_flags_cmake(self, temp_env):
+        s = spack.spec.Spec('callpath cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.build_system_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert 'SPACK_CPPFLAGS' not in os.environ
+        assert 'CPPFLAGS' not in os.environ
+
+        expected = set(['-DCMAKE_C_FLAGS=-g', '-DCMAKE_CXX_FLAGS=-g',
+                        '-DCMAKE_Fortran_FLAGS=-g'])
+        assert set(pkg.cmake_flag_args) == expected
+
+    def test_build_system_flags_autotools(self, temp_env):
+        s = spack.spec.Spec('libelf cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.build_system_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert 'SPACK_CPPFLAGS' not in os.environ
+        assert 'CPPFLAGS' not in os.environ
+
+        assert 'CPPFLAGS=-g' in pkg.configure_flag_args
+
+    def test_build_system_flags_not_implemented(self, temp_env):
+        s = spack.spec.Spec('mpileaks cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.build_system_flags
+
+        # Test the command line flags method raises a NotImplementedError
+        try:
+            spack.build_environment.setup_package(pkg, False)
+            assert False
+        except NotImplementedError:
+            assert True
+
+    def test_add_build_system_flags_autotools(self, temp_env):
+        s = spack.spec.Spec('libelf cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = add_O3_to_build_system_cflags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert '-g' in os.environ['SPACK_CPPFLAGS']
+        assert 'CPPFLAGS' not in os.environ
+
+        assert pkg.configure_flag_args == ['CFLAGS=-O3']
+
+    def test_add_build_system_flags_cmake(self, temp_env):
+        s = spack.spec.Spec('callpath cppflags=-g')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = add_O3_to_build_system_cflags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert '-g' in os.environ['SPACK_CPPFLAGS']
+        assert 'CPPFLAGS' not in os.environ
+
+        assert pkg.cmake_flag_args == ['-DCMAKE_C_FLAGS=-O3']
+
+    def test_ld_flags_cmake(self, temp_env):
+        s = spack.spec.Spec('callpath ldflags=-mthreads')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.build_system_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert 'SPACK_LDFLAGS' not in os.environ
+        assert 'LDFLAGS' not in os.environ
+
+        expected = set(['-DCMAKE_EXE_LINKER_FLAGS=-mthreads',
+                        '-DCMAKE_MODULE_LINKER_FLAGS=-mthreads',
+                        '-DCMAKE_SHARED_LINKER_FLAGS=-mthreads',
+                        '-DCMAKE_STATIC_LINKER_FLAGS=-mthreads'])
+        assert set(pkg.cmake_flag_args) == expected
+
+    def test_ld_libs_cmake(self, temp_env):
+        s = spack.spec.Spec('callpath ldlibs=-lfoo')
+        s.concretize()
+        pkg = spack.repo.get(s)
+        pkg.flag_handler = pkg.build_system_flags
+        spack.build_environment.setup_package(pkg, False)
+
+        assert 'SPACK_LDLIBS' not in os.environ
+        assert 'LDLIBS' not in os.environ
+
+        expected = set(['-DCMAKE_C_STANDARD_LIBRARIES=-lfoo',
+                        '-DCMAKE_CXX_STANDARD_LIBRARIES=-lfoo',
+                        '-DCMAKE_Fortran_STANDARD_LIBRARIES=-lfoo'])
+        assert set(pkg.cmake_flag_args) == expected