Consistent docs and usage of env mod methods (#3351)

26 files changed, 124 insertions, 144 deletions

diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 211e72158c..b794bb2581 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1523,23 +1523,23 @@ properties to be used by dependents.
 
 The function declaration should look like this:
 
-.. code-block:: python
-
-   class Qt(Package):
-       ...
-       def setup_dependent_environment(self, module, spec, dep_spec):
-           """Dependencies of Qt find it using the QTDIR environment variable."""
-           os.environ['QTDIR'] = self.prefix
+.. literalinclude:: ../../../var/spack/repos/builtin/packages/qt/package.py
+   :pyobject: Qt.setup_dependent_environment
+   :linenos:
 
 Here, the Qt package sets the ``QTDIR`` environment variable so that
 packages that depend on a particular Qt installation will find it.
 
 The arguments to this function are:
 
-* **module**: the module of the dependent package, where global
-  properties can be assigned.
-* **spec**: the spec of the *dependency package* (the one the function is called on).
-* **dep_spec**: the spec of the dependent package (i.e. dep_spec depends on spec).
+* **spack_env**: List of environment modifications to be applied when
+  the dependent package is built within Spack.
+* **run_env**: List of environment modifications to be applied when
+  the dependent package is run outside of Spack. These are added to the
+  resulting module file.
+* **dependent_spec**: The spec of the dependent package about to be
+  built. This allows the extendee (self) to query the dependent's state.
+  Note that *this* package's spec is available as ``self.spec``.
 
 A good example of using these is in the Python package:
 
@@ -2805,11 +2805,8 @@ the one passed to install, only the MPI implementations all set some
 additional properties on it to help you out.  E.g., in mvapich2, you'll
 find this:
 
-.. code-block:: python
-
-    def setup_dependent_package(self, module, dep_spec):
-        self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
-        # … etc …
+.. literalinclude:: ../../../var/spack/repos/builtin/packages/mvapich2/package.py
+   :pyobject: Mvapich2.setup_dependent_package
 
 That code allows the mvapich2 package to associate an ``mpicc`` property
 with the ``mvapich2`` node in the DAG, so that dependents can access it.
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 8889de7576..80d65bd739 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -1393,32 +1393,29 @@ class PackageBase(object):
     def setup_environment(self, spack_env, run_env):
         """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
+        ``spack_env`` and ``run_env`` are ``EnvironmentModifications``
+        objects. Package authors can call methods on them to alter
         the environment within Spack and at runtime.
 
-        Both `spack_env` and `run_env` are applied within the build
-        process, before this package's `install()` method is called.
+        Both ``spack_env`` and ``run_env`` are applied within the build
+        process, before this package's ``install()`` method is called.
 
-        Modifications in `run_env` will *also* be added to the
+        Modifications in ``run_env`` will *also* be added to the
         generated environment modules for this package.
 
         Default implementation does nothing, but this can be
         overridden if the package needs a particular environment.
 
-        Examples:
-
-            1. Qt extensions need `QTDIR` set.
-
-        Args:
-            spack_env (EnvironmentModifications): list of
-                modifications to be applied when this package is built
-                within Spack.
+        Example:
 
-            run_env (EnvironmentModifications): list of environment
-                changes to be applied when this package is run outside
-                of Spack.
+        1. Qt extensions need ``QTDIR`` set.
 
+        :param EnvironmentModifications spack_env: List of environment
+            modifications to be applied when this package is built
+            within Spack.
+        :param EnvironmentModifications run_env: List of environment
+            modifications to be applied when this package is run outside
+            of Spack. These are added to the resulting module file.
         """
         pass
 
@@ -1431,32 +1428,26 @@ class PackageBase(object):
         others that follow the extension model a way to implement
         common environment or compile-time settings for dependencies.
 
-        By default, this delegates to ``self.setup_environment()``
+        This is useful if there are some common steps to installing
+        all extensions for a certain package.
 
         Example:
 
-            1. Installing python modules generally requires
-               `PYTHONPATH` to point to the lib/pythonX.Y/site-packages
-               directory in the module's install prefix.  This could
-               set that variable.
-
-        Args:
-
-            spack_env (EnvironmentModifications): list of
-                modifications to be applied when the dependent package
-                is bulit within Spack.
-
-            run_env (EnvironmentModifications): list of environment
-                changes to be applied when the dependent package is
-                run outside of Spack.
-
-            dependent_spec (Spec): The spec of the dependent package
-                about to be built. This allows the extendee (self) to
-                query the dependent's state. Note that *this*
-                package's spec is available as `self.spec`.
-
-        This is useful if there are some common steps to installing
-        all extensions for a certain package.
+        1. Installing python modules generally requires ``PYTHONPATH`` to point
+           to the ``lib/pythonX.Y/site-packages`` directory in the module's
+           install prefix. This method could be used to set that variable.
+
+        :param EnvironmentModifications spack_env: List of environment
+            modifications to be applied when the dependent package is
+            built within Spack.
+        :param EnvironmentModifications run_env: List of environment
+            modifications to be applied when the dependent package is
+            run outside of Spack. These are added to the resulting
+            module file.
+        :param Spec dependent_spec: The spec of the dependent package
+            about to be built. This allows the extendee (self) to query
+            the dependent's state. Note that *this* package's spec is
+            available as ``self.spec``.
         """
         pass
 
@@ -1470,37 +1461,29 @@ class PackageBase(object):
         its extensions. This is useful if there are some common steps
         to installing all extensions for a certain package.
 
-        Example :
-
-            1. Extensions often need to invoke the `python`
-               interpreter from the Python installation being
-               extended.  This routine can put a 'python' Executable
-               object in the module scope for the extension package to
-               simplify extension installs.
-
-            2. MPI compilers could set some variables in the
-               dependent's scope that point to `mpicc`, `mpicxx`,
-               etc., allowing them to be called by common names
-               regardless of which MPI is used.
-
-            3. BLAS/LAPACK implementations can set some variables
-               indicating the path to their libraries, since these
-               paths differ by BLAS/LAPACK implementation.
+        Examples:
 
-        Args:
+        1. Extensions often need to invoke the ``python`` interpreter
+           from the Python installation being extended. This routine
+           can put a ``python()`` Executable object in the module scope
+           for the extension package to simplify extension installs.
 
-            module (module): The Python `module` object of the
-                dependent package. Packages can use this to set
-                module-scope variables for the dependent to use.
+        2. MPI compilers could set some variables in the dependent's
+           scope that point to ``mpicc``, ``mpicxx``, etc., allowing
+           them to be called by common name regardless of which MPI is used.
 
-            dependent_spec (Spec): The spec of the dependent package
-                about to be built. This allows the extendee (self) to
-                query the dependent's state.  Note that *this*
-                package's spec is available as `self.spec`.
+        3. BLAS/LAPACK implementations can set some variables
+           indicating the path to their libraries, since these
+           paths differ by BLAS/LAPACK implementation.
 
-        This is useful if there are some common steps to installing
-        all extensions for a certain package.
+        :param spack.package.PackageBase.module module: The Python ``module``
+            object of the dependent package. Packages can use this to set
+            module-scope variables for the dependent to use.
 
+        :param Spec dependent_spec: The spec of the dependent package
+            about to be built. This allows the extendee (self) to
+            query the dependent's state.  Note that *this*
+            package's spec is available as ``self.spec``.
         """
         pass
 
diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index 95af1e4cc0..d2e3ee8f8a 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -53,7 +53,7 @@ class Bazel(Package):
         mkdir(prefix.bin)
         install('output/bazel', prefix.bin)
 
-    def setup_dependent_package(self, module, dep_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         class BazelExecutable(Executable):
             """Special callable executable object for bazel so the user can
                specify parallel or not on a per-invocation basis.  Using
@@ -84,8 +84,8 @@ class Bazel(Package):
                 return super(BazelExecutable, self).__call__(*args, **kwargs)
 
         jobs = cpu_count()
-        if not dep_spec.package.parallel:
+        if not dependent_spec.package.parallel:
             jobs = 1
-        elif dep_spec.package.make_jobs:
-            jobs = dep_spec.package.make_jobs
+        elif dependent_spec.package.make_jobs:
+            jobs = dependent_spec.package.make_jobs
         module.bazel = BazelExecutable('bazel', 'build', jobs)
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 61dae81a3d..de62ea213c 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -287,5 +287,5 @@ class Dealii(CMakePackage):
 
         return options
 
-    def setup_environment(self, spack_env, env):
-        env.set('DEAL_II_DIR', self.prefix)
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('DEAL_II_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py
index f1e1a08c8f..cff971f373 100644
--- a/var/spack/repos/builtin/packages/docbook-xml/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xml/package.py
@@ -42,7 +42,7 @@ class DocbookXml(Package):
             else:
                 install(src, dst)
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         catalog = os.path.join(self.spec.prefix, 'catalog.xml')
         spack_env.set('XML_CATALOG_FILES', catalog, separator=' ')
 
diff --git a/var/spack/repos/builtin/packages/docbook-xsl/package.py b/var/spack/repos/builtin/packages/docbook-xsl/package.py
index 5de9cecdbb..2554e4d7bf 100644
--- a/var/spack/repos/builtin/packages/docbook-xsl/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xsl/package.py
@@ -44,7 +44,7 @@ class DocbookXsl(Package):
             else:
                 install(src, dst)
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         catalog = os.path.join(self.spec.prefix, 'catalog.xml')
         spack_env.set('XML_CATALOG_FILES', catalog, separator=' ')
 
diff --git a/var/spack/repos/builtin/packages/everytrace-example/package.py b/var/spack/repos/builtin/packages/everytrace-example/package.py
index 76b437a38a..17a7ed8658 100644
--- a/var/spack/repos/builtin/packages/everytrace-example/package.py
+++ b/var/spack/repos/builtin/packages/everytrace-example/package.py
@@ -38,5 +38,5 @@ class EverytraceExample(CMakePackage):
     # Currently the only MPI this everytrace works with.
     depends_on('openmpi')
 
-    def setup_environment(self, spack_env, env):
-        env.prepend_path('PATH', join_path(self.prefix, 'bin'))
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', join_path(self.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py
index d884c7b165..11d2a66bf4 100644
--- a/var/spack/repos/builtin/packages/everytrace/package.py
+++ b/var/spack/repos/builtin/packages/everytrace/package.py
@@ -47,5 +47,5 @@ class Everytrace(CMakePackage):
             '-DUSE_MPI=%s' % ('YES' if '+mpi' in spec else 'NO'),
             '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO')]
 
-    def setup_environment(self, spack_env, env):
-        env.prepend_path('PATH', join_path(self.prefix, 'bin'))
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', join_path(self.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py
index e2a1b54210..a9e352e101 100644
--- a/var/spack/repos/builtin/packages/fastqc/package.py
+++ b/var/spack/repos/builtin/packages/fastqc/package.py
@@ -53,8 +53,8 @@ class Fastqc(Package):
 
     # In theory the 'run' dependency on 'jdk' above should take
     # care of this for me. In practice, it does not.
-    def setup_environment(self, spack_env, env):
+    def setup_environment(self, spack_env, run_env):
         """Add <prefix> to the path; the package has a script at the
            top level.
         """
-        env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin'))
+        run_env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py
index b497144f2f..8d54486bf5 100644
--- a/var/spack/repos/builtin/packages/go-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py
@@ -87,7 +87,7 @@ class GoBootstrap(Package):
             else:
                 shutil.copy2(f, os.path.join(prefix, f))
 
-    def setup_dependent_environment(self, spack_env, run_env, dep_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('GOROOT_BOOTSTRAP', self.spec.prefix)
 
     def setup_environment(self, spack_env, run_env):
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 3a1ca9f1e8..6559e90496 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -114,7 +114,7 @@ class Go(Package):
     def setup_environment(self, spack_env, run_env):
         spack_env.set('GOROOT_FINAL', self.spec.prefix)
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Called before go modules' install() methods.
 
         In most cases, extensions will only need to set GOPATH and use go::
@@ -127,13 +127,13 @@ class Go(Package):
         #  Add a go command/compiler for extensions
         module.go = Executable(join_path(self.spec.prefix.bin, 'go'))
 
-    def setup_dependent_environment(self, spack_env, run_env, ext_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         if os.environ.get('GOROOT', False):
             tty.warn('GOROOT is set, this is not recommended')
 
         path_components = []
         # Set GOPATH to include paths of dependencies
-        for d in ext_spec.traverse():
+        for d in dependent_spec.traverse():
             if d.package.extends(self.spec):
                 path_components.append(d.prefix)
 
@@ -142,4 +142,4 @@ class Go(Package):
 
         # Allow packages to find this when using module or dotkit
         run_env.prepend_path('GOPATH', ':'.join(
-            [ext_spec.prefix] + path_components))
+            [dependent_spec.prefix] + path_components))
diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py
index 6bd4689bc1..5e108a0867 100644
--- a/var/spack/repos/builtin/packages/intel-mkl/package.py
+++ b/var/spack/repos/builtin/packages/intel-mkl/package.py
@@ -125,5 +125,5 @@ class IntelMkl(IntelInstaller):
         # set up MKLROOT for everyone using MKL package
         spack_env.set('MKLROOT', self.prefix)
 
-    def setup_environment(self, spack_env, env):
-        env.set('MKLROOT', self.prefix)
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('MKLROOT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 357e2cc03a..a76e7c545b 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -86,9 +86,9 @@ class Lua(Package):
         paths.append(os.path.join(path, '?', 'init.lua'))
         cpaths.append(os.path.join(path, '?.so'))
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         lua_paths = []
-        for d in extension_spec.traverse(
+        for d in dependent_spec.traverse(
                 deptypes=('build', 'run'), deptype_query='run'):
             if d.package.extends(self.spec):
                 lua_paths.append(os.path.join(d.prefix, self.lua_lib_dir))
@@ -111,9 +111,9 @@ class Lua(Package):
         # Add LUA to PATH for dependent packages
         spack_env.prepend_path('PATH', self.prefix.bin)
 
-        # For run time environment set only the path for extension_spec and
+        # For run time environment set only the path for dependent_spec and
         # prepend it to LUAPATH
-        if extension_spec.package.extends(self.spec):
+        if dependent_spec.package.extends(self.spec):
             run_env.prepend_path('LUA_PATH', ';'.join(lua_patterns),
                                  separator=';')
             run_env.prepend_path('LUA_CPATH', ';'.join(lua_cpatterns),
@@ -149,7 +149,7 @@ class Lua(Package):
     def lua_share_dir(self):
         return os.path.join('share', 'lua', self.version.up_to(2))
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """
         Called before lua modules's install() methods.
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 4c34f3e3a0..09fc683874 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -69,7 +69,7 @@ class Mpich(AutotoolsPackage):
         spack_env.set('MPICH_F90', spack_fc)
         spack_env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_package(self, module, dep_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         if 'platform=cray' in self.spec:
             self.spec.mpicc = spack_cc
             self.spec.mpicxx = spack_cxx
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 18f2ebe0bb..de809c4fed 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -209,7 +209,7 @@ class Mvapich2(Package):
            self.version > Version('2.0'):
             run_env.set('SLURM_MPI_TYPE', 'pmi2')
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
         spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx'))
         spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77'))
@@ -221,7 +221,7 @@ class Mvapich2(Package):
         spack_env.set('MPICH_F90', spack_fc)
         spack_env.set('MPICH_FC', spack_fc)
 
-    def setup_dependent_package(self, module, dep_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicc  = join_path(self.prefix.bin, 'mpicc')
         self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
         self.spec.mpifc  = join_path(self.prefix.bin, 'mpif90')
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index fe6ea8ce68..33ed5c8bc3 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -88,7 +88,7 @@ class Octave(AutotoolsPackage):
     depends_on('gnuplot',      when='+gnuplot')
     depends_on('image-magick',  when='+magick')
     depends_on('hdf5',         when='+hdf5')
-    depends_on('jdk',          when='+jdk') # TODO: requires Java 6 ?
+    depends_on('jdk',          when='+jdk')        # TODO: requires Java 6 ?
     depends_on('llvm',         when='+llvm')
     # depends_on('opengl',      when='+opengl')    # TODO: add package
     depends_on('qhull',        when='+qhull')
@@ -225,7 +225,7 @@ class Octave(AutotoolsPackage):
     # Set up environment to make install easy for Octave extensions.
     # ========================================================================
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Called before Octave modules' install() methods.
 
         In most cases, extensions will only need to have one line:
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 4d09676fac..27bde1d7aa 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -139,7 +139,7 @@ class Openmpi(AutotoolsPackage):
         spack_env.set('OMPI_FC', spack_fc)
         spack_env.set('OMPI_F77', spack_f77)
 
-    def setup_dependent_package(self, module, dep_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
         self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
         self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index 69949b0017..80cc1aa66a 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -99,7 +99,7 @@ class Plumed(AutotoolsPackage):
         plumed.stdin.write(choice)
         plumed.wait()
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         # Make plumed visible from dependent packages
         module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
 
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 11f6ebb1a5..3571ff1f15 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -53,7 +53,7 @@ class PyNumpy(PythonPackage):
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 
-    def setup_dependent_package(self, module, dep_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         python_version = self.spec['python'].version.up_to(2)
         arch = '{0}-{1}'.format(platform.system().lower(), platform.machine())
 
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index f3e2813ae8..15f7f4f987 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -335,7 +335,7 @@ class Python(Package):
     def site_packages_dir(self):
         return join_path(self.python_lib_dir, 'site-packages')
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         """Set PYTHONPATH to include site-packages dir for the
         extension and any other python extensions it depends on."""
         # The python executable for version 3 may be python3 or python
@@ -361,7 +361,7 @@ class Python(Package):
         spack_env.set('PYTHONHOME', prefix.strip('\n'))
 
         python_paths = []
-        for d in extension_spec.traverse(
+        for d in dependent_spec.traverse(
                 deptype=('build', 'run'), deptype_query='run'):
             if d.package.extends(self.spec):
                 python_paths.append(join_path(d.prefix,
@@ -371,12 +371,12 @@ class Python(Package):
         spack_env.set('PYTHONPATH', pythonpath)
 
         # For run time environment set only the path for
-        # extension_spec and prepend it to PYTHONPATH
-        if extension_spec.package.extends(self.spec):
+        # dependent_spec and prepend it to PYTHONPATH
+        if dependent_spec.package.extends(self.spec):
             run_env.prepend_path('PYTHONPATH', join_path(
-                extension_spec.prefix, self.site_packages_dir))
+                dependent_spec.prefix, self.site_packages_dir))
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Called before python modules' install() methods.
 
         In most cases, extensions will only need to have one line::
@@ -398,15 +398,15 @@ class Python(Package):
                 module.setup_py.add_default_env(key, value)
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
-        module.python_lib_dir = join_path(ext_spec.prefix,
+        module.python_lib_dir = join_path(dependent_spec.prefix,
                                           self.python_lib_dir)
-        module.python_include_dir = join_path(ext_spec.prefix,
+        module.python_include_dir = join_path(dependent_spec.prefix,
                                               self.python_include_dir)
-        module.site_packages_dir = join_path(ext_spec.prefix,
+        module.site_packages_dir = join_path(dependent_spec.prefix,
                                              self.site_packages_dir)
 
         # Make the site packages directory for extensions
-        if ext_spec.package.is_extension:
+        if dependent_spec.package.is_extension:
             mkdirp(module.site_packages_dir)
 
     # ========================================================================
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index dfe83888e5..b795cd17ab 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -128,10 +128,10 @@ class Qt(Package):
     def setup_environment(self, spack_env, run_env):
         run_env.set('QTDIR', self.prefix)
 
-    def setup_dependent_environment(self, spack_env, run_env, dspec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('QTDIR', self.prefix)
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         module.qmake = Executable(join_path(self.spec.prefix.bin, 'qmake'))
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py
index 842affc4cc..f6ec720eb7 100644
--- a/var/spack/repos/builtin/packages/r/package.py
+++ b/var/spack/repos/builtin/packages/r/package.py
@@ -149,11 +149,11 @@ class R(AutotoolsPackage):
     def r_lib_dir(self):
         return join_path('rlib', 'R', 'library')
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # Set R_LIBS to include the library dir for the
         # extension and any other R extensions it depends on.
         r_libs_path = []
-        for d in extension_spec.traverse(
+        for d in dependent_spec.traverse(
                 deptype=('build', 'run'), deptype_query='run'):
             if d.package.extends(self.spec):
                 r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
@@ -167,11 +167,11 @@ class R(AutotoolsPackage):
         # determine how many jobs can actually be started.
         spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
 
-        # For run time environment set only the path for extension_spec and
+        # For run time environment set only the path for dependent_spec and
         # prepend it to R_LIBS
-        if extension_spec.package.extends(self.spec):
+        if dependent_spec.package.extends(self.spec):
             run_env.prepend_path('R_LIBS', join_path(
-                extension_spec.prefix, self.r_lib_dir))
+                dependent_spec.prefix, self.r_lib_dir))
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('LIBRARY_PATH',
@@ -181,7 +181,7 @@ class R(AutotoolsPackage):
         run_env.prepend_path('CPATH',
                              join_path(self.prefix, 'rlib', 'R', 'include'))
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Called before R modules' install() methods. In most cases,
         extensions will only need to have one line:
             R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
@@ -191,9 +191,9 @@ class R(AutotoolsPackage):
         module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
 
         # Add variable for library directry
-        module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
+        module.r_lib_dir = join_path(dependent_spec.prefix, self.r_lib_dir)
 
         # Make the site packages directory for extensions, if it does not exist
         # already.
-        if ext_spec.package.is_extension:
+        if dependent_spec.package.is_extension:
             mkdirp(module.r_lib_dir)
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index 0f66dcebaa..a96d7f6bbc 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -79,7 +79,7 @@ class Root(Package):
             make()
             make("install")
 
-    def setup_dependent_environment(self, spack_env, run_env, dspec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('ROOTSYS', self.prefix)
         spack_env.set('ROOT_VERSION', 'v6')
         spack_env.prepend_path('PYTHONPATH', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 8dc314c171..728362a18c 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -52,20 +52,20 @@ class Ruby(Package):
         make()
         make("install")
 
-    def setup_dependent_environment(self, spack_env, run_env, extension_spec):
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # TODO: do this only for actual extensions.
         # Set GEM_PATH to include dependent gem directories
         ruby_paths = []
-        for d in extension_spec.traverse():
+        for d in dependent_spec.traverse():
             if d.package.extends(self.spec):
                 ruby_paths.append(d.prefix)
 
         spack_env.set_path('GEM_PATH', ruby_paths)
 
         # The actual installation path for this gem
-        spack_env.set('GEM_HOME', extension_spec.prefix)
+        spack_env.set('GEM_HOME', dependent_spec.prefix)
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """Called before ruby modules' install() methods.  Sets GEM_HOME
         and GEM_PATH to values appropriate for the package being built.
 
diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 8a92fca634..4d0e7f52cf 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -71,7 +71,7 @@ class Rust(Package):
             make()
             make("install")
 
-    def setup_dependent_package(self, module, ext_spec):
+    def setup_dependent_package(self, module, dependent_spec):
         """
         Called before python modules' install() methods.
 
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index 31678caac6..22b300408a 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -49,11 +49,11 @@ class Tcl(AutotoolsPackage):
         base_url = 'http://prdownloads.sourceforge.net/tcl'
         return '{0}/tcl{1}-src.tar.gz'.format(base_url, version)
 
-    def setup_environment(self, spack_env, env):
+    def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
-        env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
-                self.spec.version.up_to(2))))
+        run_env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
+            self.spec.version.up_to(2))))
 
     @run_after('install')
     def symlink_tclsh(self):