Python command, libraries, and headers (#3367)

## Motivation

Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically. 

I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers.

Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends.

## Prefix

For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`.

Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things.

To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable.

## Command

In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking:

If the spec is for Python 3, try searching for the `python3` command.
If the spec is for Python 2, try searching for the `python2` command.
If neither are found, try searching for the `python` command.

## Libraries

Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work.

The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing:
```
lib/libpython2.7.dylib
```
For Python 3.6 on CentOS 6, I'm seeing:
```
lib/libpython3.so
lib/libpython3.6m.so.1.0
lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0
```
Notice the `m` after the version number. Yeah, that's a thing.

## Headers

In Python 2.7, I'm seeing:
```
include/python2.7/pyconfig.h
```
In Python 3.6, I'm seeing:
```
include/python3.6m/pyconfig.h
```
It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6

Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.

38 files changed, 262 insertions, 182 deletions

diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py
index fe1c7ec778..d73b89ea69 100644
--- a/var/spack/repos/builtin/packages/abinit/package.py
+++ b/var/spack/repos/builtin/packages/abinit/package.py
@@ -33,9 +33,9 @@ class Abinit(AutotoolsPackage):
     energy, charge density and electronic structure of systems made of
     electrons and nuclei (molecules and periodic solids) within
     Density Functional Theory (DFT), using pseudopotentials and a planewave
-    or wavelet basis. 
-    
-    ABINIT also includes options to optimize the geometry according to the 
+    or wavelet basis.
+
+    ABINIT also includes options to optimize the geometry according to the
     DFT forces and stresses, or to perform molecular dynamics
     simulations using these forces, or to generate dynamical matrices,
     Born effective charges, and dielectric tensors, based on Density-Functional
@@ -149,7 +149,7 @@ class Abinit(AutotoolsPackage):
         # LibXC library
         libxc = spec['libxc:fortran']
         options.extend([
-            'with_libxc_incs={0}'.format(libxc.cppflags),
+            'with_libxc_incs={0}'.format(libxc.headers.cpp_flags),
             'with_libxc_libs={0}'.format(libxc.libs.ld_flags + ' -lm')
         ])
 
@@ -161,7 +161,7 @@ class Abinit(AutotoolsPackage):
             hdf5 = spec['hdf5:hl']
             netcdff = spec['netcdf-fortran:shared']
             options.extend([
-                '--with-netcdf-incs={0}'.format(netcdff.cppflags),
+                '--with-netcdf-incs={0}'.format(netcdff.headers.cpp_flags),
                 '--with-netcdf-libs={0}'.format(
                     netcdff.libs.ld_flags + ' ' + hdf5.libs.ld_flags
                 ),
@@ -175,7 +175,7 @@ class Abinit(AutotoolsPackage):
 
     def check(self):
         """This method is called after the build phase if tests have been
-        explicitly activated by user. 
+        explicitly activated by user.
         """
         make('check')
         make('tests_in')
diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py
index dd6685a829..b377c30fe9 100644
--- a/var/spack/repos/builtin/packages/ack/package.py
+++ b/var/spack/repos/builtin/packages/ack/package.py
@@ -45,7 +45,7 @@ class Ack(Package):
         ack = 'ack-{0}-single-file'.format(self.version)
 
         # rewrite the script's #! line to call the perl dependency
-        shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl')
+        shbang = '#!' + spec['perl'].command.path
         filter_file(r'^#!/usr/bin/env perl', shbang, ack)
 
         install(ack, join_path(prefix.bin, "ack"))
diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py
index 7cab51b0be..3faf852739 100644
--- a/var/spack/repos/builtin/packages/blast-plus/package.py
+++ b/var/spack/repos/builtin/packages/blast-plus/package.py
@@ -206,7 +206,7 @@ class BlastPlus(AutotoolsPackage):
 
         if '+python' in spec:
             config_args.append(
-                '--with-python={0}'.format(self.spec['python'].prefix)
+                '--with-python={0}'.format(self.spec['python'].home)
             )
         else:
             config_args.append('--without-python')
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 487445ab10..d4c772ed03 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -25,7 +25,6 @@
 from spack import *
 import sys
 import os
-from glob import glob
 
 
 class Boost(Package):
@@ -173,23 +172,11 @@ class Boost(Package):
         return 'gcc'
 
     def bjam_python_line(self, spec):
-        from os.path import dirname, splitext
-        pydir = 'python%s.%s*' % spec['python'].version.version[:2]
-        incs = join_path(spec['python'].prefix.include, pydir, "pyconfig.h")
-        incs = glob(incs)
-        incs = " ".join([dirname(u) for u in incs])
-
-        pylib = 'libpython%s.%s*' % spec['python'].version.version[:2]
-        all_libs = join_path(spec['python'].prefix.lib, pylib)
-        libs = [u for u in all_libs if splitext(u)[1] == dso_suffix]
-        if len(libs) == 0:
-            libs = [u for u in all_libs if splitext(u)[1] == '.a']
-
-        libs = " ".join(libs)
-        return 'using python : %s : %s : %s : %s ;\n' % (
+        return 'using python : {0} : {1} : {2} : {3} ;\n'.format(
             spec['python'].version.up_to(2),
-            join_path(spec['python'].prefix.bin, 'python'),
-            incs, libs
+            spec['python'].command.path,
+            spec['python'].headers.directories[0],
+            spec['python'].libs[0]
         )
 
     def determine_bootstrap_options(self, spec, withLibs, options):
@@ -198,7 +185,7 @@ class Boost(Package):
         options.append("--with-libraries=%s" % ','.join(withLibs))
 
         if '+python' in spec:
-            options.append('--with-python=%s' % python_exe)
+            options.append('--with-python=%s' % spec['python'].command.path)
 
         with open('user-config.jam', 'w') as f:
             # Boost may end up using gcc even though clang+gfortran is set in
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 0685772f82..aa7c7dc98c 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -117,15 +117,13 @@ class Cantera(Package):
         if '+python' in spec:
             options.extend([
                 'python_package=full',
-                'python_cmd={0}'.format(
-                    join_path(spec['python'].prefix.bin, 'python')),
+                'python_cmd={0}'.format(spec['python'].command.path),
                 'python_array_home={0}'.format(spec['py-numpy'].prefix)
             ])
             if spec['python'].satisfies('@3'):
                 options.extend([
                     'python3_package=y',
-                    'python3_cmd={0}'.format(
-                        join_path(spec['python'].prefix.bin, 'python')),
+                    'python3_cmd={0}'.format(spec['python'].command.path),
                     'python3_array_home={0}'.format(spec['py-numpy'].prefix)
                 ])
             else:
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index ddefde4fb7..d97c6534e4 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -174,13 +174,13 @@ class Conduit(Package):
         ##############################################
 
         if "+cmake" in spec:
-            cmake_exe = join_path(spec['cmake'].prefix.bin, "cmake")
+            cmake_exe = spec['cmake'].command.path
         else:
             cmake_exe = which("cmake")
             if cmake_exe is None:
                 msg = 'failed to find CMake (and cmake variant is off)'
                 raise RuntimeError(msg)
-            cmake_exe = cmake_exe.command
+            cmake_exe = cmake_exe.path
 
         host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
                                              sys_type,
@@ -224,21 +224,15 @@ class Conduit(Package):
         cfg.write("# Python Support\n")
 
         if "+python" in spec:
-            python_exe = join_path(spec['python'].prefix.bin, "python")
             cfg.write("# Enable python module builds\n")
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "ON"))
             cfg.write("# python from spack \n")
-            cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE", python_exe))
+            cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
+                      spec['python'].command.path))
             # install module to standard style site packages dir
             # so we can support spack activate
-            py_ver_short = "python{0}".format(spec["python"].version.up_to(2))
-            pym_prefix = join_path("${CMAKE_INSTALL_PREFIX}",
-                                   "lib",
-                                   py_ver_short,
-                                   "site-packages")
-            # use pym_prefix as the install path
             cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        pym_prefix))
+                                        site_packages_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -251,7 +245,7 @@ class Conduit(Package):
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
 
             cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = join_path(spec['doxygen'].prefix.bin, "doxygen")
+            doxygen_exe = spec['doxygen'].command.path
             cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py
index 1e83e02d65..6c41002079 100644
--- a/var/spack/repos/builtin/packages/cosmomc/package.py
+++ b/var/spack/repos/builtin/packages/cosmomc/package.py
@@ -178,7 +178,7 @@ class Cosmomc(Package):
         os.environ.pop('CLIKPATH', '')
         os.environ.pop('PLANCKLIKE', '')
 
-        exe = join_path(prefix.bin, 'cosmomc')
+        exe = spec['cosmomc'].command.path
         args = []
         if '+mpi' in spec:
             # Add mpirun prefix
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 9bc1026ba9..06e4697904 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -93,10 +93,10 @@ class Cp2k(Package):
             cppflags = [
                 '-D__FFTW3',
                 '-D__LIBINT',
-                spec['fftw'].cppflags
+                spec['fftw'].headers.cpp_flags
             ]
             fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
-            fcflags.append(spec['fftw'].cppflags)
+            fcflags.append(spec['fftw'].headers.cpp_flags)
             fftw = find_libraries('libfftw3', root=spec['fftw'].prefix.lib)
             ldflags = [fftw.search_flags]
             if 'superlu-dist@4.3' in spec:
@@ -161,14 +161,14 @@ class Cp2k(Package):
                     cppflags.append('-D__WANNIER90')
 
                 fcflags.extend([
-                    # spec['elpa:fortran'].cppflags
+                    # spec['elpa:fortran'].headers.cpp_flags
                     '-I' + join_path(
                         spec['elpa'].prefix,
                         'include',
                         'elpa-{0}'.format(str(spec['elpa'].version)),
                         'modules'
                     ),
-                    # spec[pexsi:fortran].cppflags
+                    # spec[pexsi:fortran].headers.cpp_flags
                     '-I' + join_path(spec['pexsi'].prefix, 'fortran')
                 ])
                 scalapack = spec['scalapack'].libs
diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py
index 559cc45d7a..c68e570c0f 100644
--- a/var/spack/repos/builtin/packages/foam-extend/package.py
+++ b/var/spack/repos/builtin/packages/foam-extend/package.py
@@ -356,8 +356,8 @@ echo WM_PROJECT_DIR = $WM_PROJECT_DIR
                 'CMAKE_BIN_DIR': spec['cmake'].prefix.bin,
             },
             'python': {
-                'PYTHON_DIR':     spec['python'].prefix,
-                'PYTHON_BIN_DIR': spec['python'].prefix.bin,
+                'PYTHON_DIR':     spec['python'].home,
+                'PYTHON_BIN_DIR': spec['python'].home.bin,
             },
             'flex': {
                 'FLEX_SYSTEM': 1,
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 00518c8cf4..b362060e61 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -176,7 +176,7 @@ class Gcc(AutotoolsPackage):
                      self.spec.format('$_$@'))
             return
 
-        gcc = Executable(join_path(self.prefix.bin, 'gcc'))
+        gcc = self.spec['gcc'].command
         lines = gcc('-dumpspecs', output=str).strip().split("\n")
         specs_file = join_path(self.spec_dir, 'specs')
         with closing(open(specs_file, 'w')) as out:
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index dc58cc8993..1b9a4f0818 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -72,7 +72,7 @@ class Gdal(Package):
         args.append("--prefix=%s" % prefix)
         args.append("--with-liblzma=yes")
         args.append("--with-zlib=%s" % spec['zlib'].prefix)
-        args.append("--with-python=%s" % spec['python'].prefix.bin + "/python")
+        args.append("--with-python=%s" % spec['python'].command.path)
         args.append("--without-libtool")
 
         if '+geos' in spec:
diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index 324186cfbc..2419eed038 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -60,9 +60,8 @@ class Geos(Package):
     def install(self, spec, prefix):
         args = ["--prefix=%s" % prefix]
 #        if '+python' in spec:
-#            os.environ['PYTHON'] = join_path(spec['python'].prefix, 'bin',
-#                'python' if spec['python'].version[:1][0] <= 2 else 'python3')
-#            os.environ['SWIG'] = join_path(spec['swig'].prefix, 'bin', 'swig')
+#            os.environ['PYTHON'] = spec['python'].command.path
+#            os.environ['SWIG'] = spec['swig'].command.path
 #
 #            args.append("--enable-python")
 
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index dfa4e08643..d71f49bff6 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -162,8 +162,7 @@ class Git(AutotoolsPackage):
             '--with-iconv={0}'.format(spec['libiconv'].prefix),
             '--with-libpcre={0}'.format(spec['pcre'].prefix),
             '--with-openssl={0}'.format(spec['openssl'].prefix),
-            '--with-perl={0}'.format(
-                join_path(spec['perl'].prefix.bin, 'perl')),
+            '--with-perl={0}'.format(spec['perl'].command.path),
             '--with-zlib={0}'.format(spec['zlib'].prefix),
         ]
 
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index 7f1523ca6d..05a903ea74 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -117,7 +117,7 @@ class Go(Package):
         shutil.copytree('bin', os.path.join(prefix, '/bin'))
         """
         #  Add a go command/compiler for extensions
-        module.go = Executable(join_path(self.spec.prefix.bin, 'go'))
+        module.go = self.spec['go'].command
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         if os.environ.get('GOROOT', False):
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
index 79f23d7d92..053a4d4852 100644
--- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -69,7 +69,7 @@ class Hdf5Blosc(Package):
         # if sys.platform == "darwin":
         #     fix_darwin_install_name(prefix.lib)
 
-        libtool = Executable(join_path(spec["libtool"].prefix.bin, "libtool"))
+        libtool = spec["libtool"].command
 
         # TODO: these vars are not used.
         # if "+mpi" in spec["hdf5"]:
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 4da24dd7f1..5a3f9e5657 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -257,7 +257,7 @@ HDF5 version {version} {version}
                 cc = Executable(spec['mpi'].mpicc)
             else:
                 cc = Executable(self.compiler.cc)
-            cc(*(['-c', "check.c"] + spec['hdf5'].cppflags.split()))
+            cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
             cc(*(['-o', "check", "check.o"] +
                  spec['hdf5'].libs.ld_flags.split()))
             try:
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 3d56f08dc0..0aa9574a6d 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -81,7 +81,7 @@ class HoomdBlue(CMakePackage):
         spec = self.spec
 
         cmake_args = [
-            '-DPYTHON_EXECUTABLE={0}/python'.format(spec['python'].prefix.bin),
+            '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
         ]
 
         # MPI support
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index 4e7c65f53a..007a384f10 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -185,7 +185,7 @@ class Julia(Package):
             juliarc.write('\n')
 
         # Install some commonly used packages
-        julia = Executable(join_path(prefix.bin, "julia"))
+        julia = spec['julia'].command
         julia("-e", 'Pkg.init(); Pkg.update()')
 
         # Install HDF5
@@ -216,7 +216,7 @@ class Julia(Package):
             with open(join_path(prefix, "etc", "julia", "juliarc.jl"),
                       "a") as juliarc:
                 juliarc.write('# Python\n')
-                juliarc.write('ENV["PYTHON"] = "%s"\n' % spec["python"].prefix)
+                juliarc.write('ENV["PYTHON"] = "%s"\n' % spec["python"].home)
                 juliarc.write('\n')
             # Python's OpenSSL package installer complains:
             # Error: PREFIX too long: 166 characters, but only 128 allowed
diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index 470998d882..4324b1dcd3 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -49,7 +49,7 @@ class Libxml2(AutotoolsPackage):
         spec = self.spec
         if '+python' in spec:
             python_args = [
-                '--with-python={0}'.format(spec['python'].prefix),
+                '--with-python={0}'.format(spec['python'].home),
                 '--with-python-install-dir={0}'.format(site_packages_dir)
             ]
         else:
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index d2bf06e358..868e336778 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -339,7 +339,7 @@ class Llvm(CMakePackage):
         cmake_args = [
             '-DLLVM_REQUIRES_RTTI:BOOL=ON',
             '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp',
-            '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix
+            '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path),
         ]
 
         if '+gold' in spec:
diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py
index 3a8be3f56e..10c5ec5701 100644
--- a/var/spack/repos/builtin/packages/nwchem/package.py
+++ b/var/spack/repos/builtin/packages/nwchem/package.py
@@ -88,7 +88,7 @@ class Nwchem(Package):
             'MPI_LOC=%s' % spec['mpi'].prefix,
             'USE_PYTHONCONFIG=y',
             'PYTHONVERSION=%s' % spec['python'].version.up_to(2),
-            'PYTHONHOME=%s' % spec['python'].prefix,
+            'PYTHONHOME=%s' % spec['python'].home,
             'BLASOPT=%s' % ((lapack + blas).ld_flags),
             'BLAS_LIB=%s' % blas.ld_flags,
             'LAPACK_LIB=%s' % lapack.ld_flags,
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 81f4841931..4ebb38aa7a 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -150,7 +150,7 @@ class Openblas(MakefilePackage):
         blessed_file = join_path(os.path.dirname(self.module.__file__),
                                  'test_cblas_dgemm.output')
 
-        include_flags = spec['openblas'].cppflags
+        include_flags = spec['openblas'].headers.cpp_flags
         link_flags = spec['openblas'].libs.ld_flags
         if self.compiler.name == 'intel':
             link_flags += ' -lifcore'
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index 8a721032a6..b052cfa12a 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-from glob import glob
 
 
 class Opencv(Package):
@@ -166,22 +165,11 @@ class Opencv(Package):
 
         # Python
         if '+python' in spec:
-            python = spec['python']
-
-            try:
-                python_lib = glob(join_path(
-                    python.prefix.lib, 'libpython*.{0}'.format(dso_suffix)))[0]
-            except KeyError:
-                raise InstallError('Cannot find libpython')
-
-            try:
-                python_include_dir = glob(join_path(python.prefix.include,
-                                                    'python*'))[0]
-            except KeyError:
-                raise InstallError('Cannot find python include directory')
+            python_exe = spec['python'].command.path
+            python_lib = spec['python'].libs[0]
+            python_include_dir = spec['python'].headers.directories[0]
 
             if '^python@3:' in spec:
-                python_exe = join_path(python.prefix.bin, 'python3')
                 cmake_options.extend([
                     '-DBUILD_opencv_python3=ON',
                     '-DPYTHON3_EXECUTABLE={0}'.format(python_exe),
@@ -190,7 +178,6 @@ class Opencv(Package):
                     '-DBUILD_opencv_python2=OFF',
                 ])
             elif '^python@2:3' in spec:
-                python_exe = join_path(python.prefix.bin, 'python2')
                 cmake_options.extend([
                     '-DBUILD_opencv_python2=ON',
                     '-DPYTHON2_EXECUTABLE={0}'.format(python_exe),
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index c4b150f56c..6ad28ce3b7 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -167,24 +167,18 @@ class Openspeedshop(Package):
         # Appends to cmakeOptions the options that will enable
         # the appropriate base level options to the openspeedshop
         # cmake build.
-        python_vers = format(spec['python'].version.up_to(2))
-        python_pv = '/python' + python_vers
-        python_pvs = '/libpython' + python_vers + '.' + format(dso_suffix)
+        python_exe = spec['python'].command.path
+        python_library = spec['python'].libs[0]
+        python_include = spec['python'].headers.directories[0]
 
         BaseOptions = []
 
         BaseOptions.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
         BaseOptions.append('-DLIBELF_DIR=%s' % spec['libelf'].prefix)
         BaseOptions.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
-        BaseOptions.append(
-            '-DPYTHON_EXECUTABLE=%s'
-            % join_path(spec['python'].prefix + '/bin/python'))
-        BaseOptions.append(
-            '-DPYTHON_INCLUDE_DIR=%s'
-            % join_path(spec['python'].prefix.include) + python_pv)
-        BaseOptions.append(
-            '-DPYTHON_LIBRARY=%s'
-            % join_path(spec['python'].prefix.lib) + python_pvs)
+        BaseOptions.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
+        BaseOptions.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
+        BaseOptions.append('-DPYTHON_LIBRARY=%s' % python_library)
         BaseOptions.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
         BaseOptions.append('-DBoost_NO_BOOST_CMAKE=TRUE')
         BaseOptions.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
diff --git a/var/spack/repos/builtin/packages/pagmo/package.py b/var/spack/repos/builtin/packages/pagmo/package.py
index 5a06b70e38..eeeb437db7 100644
--- a/var/spack/repos/builtin/packages/pagmo/package.py
+++ b/var/spack/repos/builtin/packages/pagmo/package.py
@@ -110,7 +110,7 @@ class Pagmo(CMakePackage):
         if '+python' in spec:
             args.extend([
                 # By default picks up the system python not the Spack build
-                '-DPYTHON_EXECUTABLE={0}'.format(python_exe),
+                '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
                 # By default installs to the python prefix not the pagmo prefix
                 '-DPYTHON_MODULES_DIR={0}'.format(site_packages_dir),
             ])
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 9b2b33625a..ea0722dab8 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -120,8 +120,7 @@ class Paraview(CMakePackage):
         if '+python' in spec:
             cmake_args.extend([
                 '-DPARAVIEW_ENABLE_PYTHON:BOOL=ON',
-                '-DPYTHON_EXECUTABLE:FILEPATH=%s/bin/python'
-                % spec['python'].prefix
+                '-DPYTHON_EXECUTABLE:FILEPATH=%s' % spec['python'].command.path
             ])
 
         if '+mpi' in spec:
diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py
index ad67cae48c..dc1f7be93c 100644
--- a/var/spack/repos/builtin/packages/perl/package.py
+++ b/var/spack/repos/builtin/packages/perl/package.py
@@ -113,11 +113,10 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     @run_after('install')
     def install_cpanm(self):
         spec = self.spec
-        prefix = self.prefix
 
         if '+cpanm' in spec:
             with working_dir(join_path('cpanm', 'cpanm')):
-                perl = Executable(join_path(prefix.bin, 'perl'))
+                perl = spec['perl'].command
                 perl('Makefile.PL')
                 make()
                 make('install')
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index 60443cbcc6..3022cd7959 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -122,7 +122,7 @@ class Plumed(AutotoolsPackage):
 
     def setup_dependent_package(self, module, dependent_spec):
         # Make plumed visible from dependent packages
-        module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
+        module.plumed = self.spec['plumed'].command
 
     @run_before('autoreconf')
     def filter_gslcblas(self):
diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py
index b6baee7e07..8becd9e9f7 100644
--- a/var/spack/repos/builtin/packages/pocl/package.py
+++ b/var/spack/repos/builtin/packages/pocl/package.py
@@ -104,7 +104,7 @@ class Pocl(CMakePackage):
         with working_dir(checkdir, create=True):
             source = join_path(os.path.dirname(self.module.__file__),
                                "example1.c")
-            cflags = spec["pocl"].cppflags.split()
+            cflags = spec["pocl"].headers.cpp_flags.split()
             # ldflags = spec["pocl"].libs.ld_flags.split()
             ldflags = ["-L%s" % spec["pocl"].prefix.lib,
                        "-lOpenCL", "-lpoclu"]
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index d14aff363b..976b5d3c4e 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -115,8 +115,7 @@ class Psi4(Package):
             ' -I'.join([
                 os.path.join(spec['psi4'].prefix.include, 'psi4'),
                 os.path.join(spec['boost'].prefix.include, 'boost'),
-                os.path.join(spec['python'].prefix.include, 'python{0}'.format(
-                    spec['python'].version.up_to(2))),
+                os.path.join(spec['python'].headers.directories[0]),
                 spec['lapack'].prefix.include,
                 spec['blas'].prefix.include,
                 '/usr/include'
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index bc3de0479b..12b77813d1 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -24,7 +24,9 @@
 ##############################################################################
 import ast
 import os
+import platform
 import re
+import sys
 from contextlib import closing
 
 import spack
@@ -33,10 +35,11 @@ from llnl.util.lang import match_predicate
 from llnl.util.filesystem import force_remove
 from spack import *
 from spack.util.environment import *
+from spack.util.prefix import Prefix
 import spack.util.spack_json as sjson
 
 
-class Python(Package):
+class Python(AutotoolsPackage):
     """The Python programming language."""
 
     homepage = "http://www.python.org"
@@ -62,6 +65,10 @@ class Python(Package):
 
     extendable = True
 
+    # --enable-shared is known to cause problems for some users on macOS
+    # See http://bugs.python.org/issue29846
+    variant('shared', default=sys.platform != 'darwin',
+            description='Enable shared libraries')
     variant('tk', default=False, description='Provide support for Tkinter')
     variant('ucs4', default=False,
             description='Enable UCS4 (wide) unicode strings')
@@ -82,13 +89,14 @@ class Python(Package):
     depends_on("tk", when="+tk")
     depends_on("tcl", when="+tk")
 
-    patch('ncurses.patch')
+    # Patch does not work for Python 3.1
+    patch('ncurses.patch', when='@:2.8,3.2:')
 
     _DISTUTIL_VARS_TO_SAVE = ['LDSHARED']
     _DISTUTIL_CACHE_FILENAME = 'sysconfig.json'
     _distutil_vars = None
 
-    @when('@2.7,3.4:')
+    @when('@2.7:2.8,3.4:')
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
         # user's local configurations to change the Spack installation.  In
@@ -100,7 +108,10 @@ class Python(Package):
             r'\1setup.py\2 --no-user-cfg \3\6'
         )
 
-    def install(self, spec, prefix):
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        prefix = self.prefix
+
         # TODO: The '--no-user-cfg' option for Python installation is only in
         # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and
         # adding support for ignoring user configuration will require
@@ -110,23 +121,27 @@ class Python(Package):
                       'user configurations are present.').format(self.version))
 
         # Need this to allow python build to find the Python installation.
-        env['PYTHONHOME'], env['PYTHONPATH'] = prefix, prefix
-        env['MACOSX_DEPLOYMENT_TARGET'] = '10.6'
+        spack_env.set('PYTHONHOME', prefix)
+        spack_env.set('PYTHONPATH', prefix)
+        spack_env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0])
+
+    def configure_args(self):
+        spec = self.spec
 
-        # Rest of install is pretty standard except setup.py needs to
-        # be able to read the CPPFLAGS and LDFLAGS as it scans for the
-        # library and headers to build
+        # setup.py needs to be able to read the CPPFLAGS and LDFLAGS
+        # as it scans for the library and headers to build
         dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')]
         config_args = [
-            '--prefix={0}'.format(prefix),
             '--with-threads',
-            '--enable-shared',
             'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
             'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
         ]
-        if spec.satisfies("platform=darwin") and ('%gcc' in spec):
+        if spec.satisfies('%gcc platform=darwin'):
             config_args.append('--disable-toolbox-glue')
 
+        if '+shared' in spec:
+            config_args.append('--enable-shared')
+
         if '+ucs4' in spec:
             if spec.satisfies('@:2.7'):
                 config_args.append('--enable-unicode=ucs4')
@@ -140,18 +155,18 @@ class Python(Package):
         if spec.satisfies('@3:'):
             config_args.append('--without-ensurepip')
 
-        configure(*config_args)
-        make()
-        make('install')
+        return config_args
+
+    @run_after('install')
+    def post_install(self):
+        spec = self.spec
+        prefix = self.prefix
 
         self.sysconfigfilename = '_sysconfigdata.py'
         if spec.satisfies('@3.6:'):
             # Python 3.6.0 renamed the sys config file
-            python3 = os.path.join(prefix.bin,
-                                   'python{0}'.format(self.version.up_to(1)))
-            python = Executable(python3)
             sc = 'import sysconfig; print(sysconfig._get_sysconfigdata_name())'
-            cf = python('-c', sc, output=str).strip('\n')
+            cf = self.command('-c', sc, output=str).strip()
             self.sysconfigfilename = '{0}.py'.format(cf)
 
         self._save_distutil_vars(prefix)
@@ -205,7 +220,7 @@ class Python(Package):
         Spack partially covers this by setting environment variables that
         are also accounted for by distutils. Currently there is one more known
         variable that must be set, which is LDSHARED, so the method saves its
-        autogenerated value to pass it to the dependant package's setup script.
+        autogenerated value to pass it to the dependent package's setup script.
         """
 
         self._distutil_vars = {}
@@ -234,20 +249,20 @@ class Python(Package):
             pass
 
         if not input_dict:
-            tty.warn('Failed to find \'build_time_vars\' dictionary in file '
-                     '\'%s\'. This might cause the extensions that are '
-                     'installed with distutils to call compilers directly '
-                     'avoiding Spack\'s wrappers.' % input_filename)
+            tty.warn("Failed to find 'build_time_vars' dictionary in file "
+                     "'%s'. This might cause the extensions that are "
+                     "installed with distutils to call compilers directly "
+                     "avoiding Spack's wrappers." % input_filename)
             return
 
         for var_name in Python._DISTUTIL_VARS_TO_SAVE:
             if var_name in input_dict:
                 self._distutil_vars[var_name] = input_dict[var_name]
             else:
-                tty.warn('Failed to find key \'%s\' in \'build_time_vars\' '
-                         'dictionary in file \'%s\'. This might cause the '
-                         'extensions that are installed with distutils to '
-                         'call compilers directly avoiding Spack\'s wrappers.'
+                tty.warn("Failed to find key '%s' in 'build_time_vars' "
+                         "dictionary in file '%s'. This might cause the "
+                         "extensions that are installed with distutils to "
+                         "call compilers directly avoiding Spack's wrappers."
                          % (var_name, input_filename))
 
         if len(self._distutil_vars) > 0:
@@ -259,10 +274,10 @@ class Python(Package):
                 with open(output_filename, 'w') as output_file:
                     sjson.dump(self._distutil_vars, output_file)
             except:
-                tty.warn('Failed to save metadata for distutils. This might '
-                         'cause the extensions that are installed with '
-                         'distutils to call compilers directly avoiding '
-                         'Spack\'s wrappers.')
+                tty.warn("Failed to save metadata for distutils. This might "
+                         "cause the extensions that are installed with "
+                         "distutils to call compilers directly avoiding "
+                         "Spack's wrappers.")
                 # We make the cache empty if we failed to save it to file
                 # to provide the same behaviour as in the case when the cache
                 # is initialized by the method load_distutils_data().
@@ -320,6 +335,144 @@ class Python(Package):
     # ========================================================================
 
     @property
+    def command(self):
+        """Returns the Python command, which may vary depending
+        on the version of Python and how it was installed.
+
+        In general, Python 2 comes with ``python`` and ``python2`` commands,
+        while Python 3 only comes with a ``python3`` command.
+
+        :returns: The Python command
+        :rtype: Executable
+        """
+        # We need to be careful here. If the user is using an externally
+        # installed python, all 3 commands could be in the same directory.
+
+        # Search for `python2` iff using Python 2
+        if (self.spec.satisfies('@:2') and
+                os.path.exists(os.path.join(self.prefix.bin, 'python2'))):
+            command = 'python2'
+        # Search for `python3` iff using Python 3
+        elif (self.spec.satisfies('@3:') and
+                os.path.exists(os.path.join(self.prefix.bin, 'python3'))):
+            command = 'python3'
+        # If neither were found, try `python`
+        elif os.path.exists(os.path.join(self.prefix.bin, 'python')):
+            command = 'python'
+        else:
+            msg = 'Unable to locate {0} command in {1}'
+            raise RuntimeError(msg.format(self.name, self.prefix.bin))
+
+        # The python command may be a symlink if it was installed
+        # with Homebrew. Since some packages try to determine the
+        # location of libraries and headers based on the path,
+        # return the realpath
+        path = os.path.realpath(os.path.join(self.prefix.bin, command))
+
+        return Executable(path)
+
+    def print_string(self, string):
+        """Returns the appropriate print string depending on the
+        version of Python.
+
+        Examples:
+
+        * Python 2
+
+          .. code-block:: python
+
+             >>> self.print_string('sys.prefix')
+             'print sys.prefix'
+
+        * Python 3
+
+          .. code-block:: python
+
+             >>> self.print_string('sys.prefix')
+             'print(sys.prefix)'
+        """
+        if self.spec.satisfies('@:2'):
+            return 'print {0}'.format(string)
+        else:
+            return 'print({0})'.format(string)
+
+    def get_config_var(self, key):
+        """Returns the value of a single variable. Wrapper around
+        ``distutils.sysconfig.get_config_var()``."""
+
+        cmd = 'from distutils.sysconfig import get_config_var; '
+        cmd += self.print_string("get_config_var('{0}')".format(key))
+
+        return self.command('-c', cmd, output=str).strip()
+
+    def get_config_h_filename(self):
+        """Returns the full path name of the configuration header.
+        Wrapper around ``distutils.sysconfig.get_config_h_filename()``."""
+
+        cmd = 'from distutils.sysconfig import get_config_h_filename; '
+        cmd += self.print_string('get_config_h_filename()')
+
+        return self.command('-c', cmd, output=str).strip()
+
+    @property
+    def home(self):
+        """Most of the time, ``PYTHONHOME`` is simply
+        ``spec['python'].prefix``. However, if the user is using an
+        externally installed python, it may be symlinked. For example,
+        Homebrew installs python in ``/usr/local/Cellar/python/2.7.12_2``
+        and symlinks it to ``/usr/local``. Users may not know the actual
+        installation directory and add ``/usr/local`` to their
+        ``packages.yaml`` unknowingly. Query the python executable to
+        determine exactly where it is installed."""
+
+        prefix = self.get_config_var('prefix')
+        return Prefix(prefix)
+
+    @property
+    def libs(self):
+        # Spack installs libraries into lib, except on openSUSE where it
+        # installs them into lib64. If the user is using an externally
+        # installed package, it may be in either lib or lib64, so we need
+        # to ask Python where its LIBDIR is.
+        libdir = self.get_config_var('LIBDIR')
+
+        # The system Python installation on macOS and Homebrew installations
+        # install libraries into a Frameworks directory
+        frameworkprefix = self.get_config_var('PYTHONFRAMEWORKPREFIX')
+
+        if '+shared' in self.spec:
+            ldlibrary = self.get_config_var('LDLIBRARY')
+
+            if os.path.exists(os.path.join(libdir, ldlibrary)):
+                return LibraryList(os.path.join(libdir, ldlibrary))
+            elif os.path.exists(os.path.join(frameworkprefix, ldlibrary)):
+                return LibraryList(os.path.join(frameworkprefix, ldlibrary))
+            else:
+                msg = 'Unable to locate {0} libraries in {1}'
+                raise RuntimeError(msg.format(self.name, libdir))
+        else:
+            library = self.get_config_var('LIBRARY')
+
+            if os.path.exists(os.path.join(libdir, library)):
+                return LibraryList(os.path.join(libdir, library))
+            elif os.path.exists(os.path.join(frameworkprefix, library)):
+                return LibraryList(os.path.join(frameworkprefix, library))
+            else:
+                msg = 'Unable to locate {0} libraries in {1}'
+                raise RuntimeError(msg.format(self.name, libdir))
+
+    @property
+    def headers(self):
+        config_h = self.get_config_h_filename()
+
+        if os.path.exists(config_h):
+            return HeaderList(config_h)
+        else:
+            includepy = self.get_config_var('INCLUDEPY')
+            msg = 'Unable to locate {0} headers in {1}'
+            raise RuntimeError(msg.format(self.name, includepy))
+
+    @property
     def python_lib_dir(self):
         return join_path('lib', 'python{0}'.format(self.version.up_to(2)))
 
@@ -332,29 +485,10 @@ class Python(Package):
         return join_path(self.python_lib_dir, 'site-packages')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Set PYTHONPATH to include site-packages dir for the
+        """Set PYTHONPATH to include the site-packages directory for the
         extension and any other python extensions it depends on."""
-        # The python executable for version 3 may be python3 or python
-        # See https://github.com/LLNL/spack/pull/2173#issuecomment-257170199
-        pythonex = 'python{0}'.format('3' if self.spec.satisfies('@3') else '')
-        if os.path.isdir(self.prefix.bin):
-            base = self.prefix.bin
-        else:
-            base = self.prefix
-        if not os.path.isfile(os.path.join(base, pythonex)):
-            if self.spec.satisfies('@3'):
-                python = Executable(os.path.join(base, 'python'))
-                version = python('-c', 'import sys; print(sys.version)',
-                                 output=str)
-                if version.startswith('3'):
-                    pythonex = 'python'
-                else:
-                    raise RuntimeError('Cannot locate python executable')
-            else:
-                raise RuntimeError('Cannot locate python executable')
-        python = Executable(os.path.join(base, pythonex))
-        prefix = python('-c', 'import sys; print(sys.prefix)', output=str)
-        spack_env.set('PYTHONHOME', prefix.strip('\n'))
+
+        spack_env.set('PYTHONHOME', self.home)
 
         python_paths = []
         for d in dependent_spec.traverse(
@@ -378,19 +512,15 @@ class Python(Package):
         In most cases, extensions will only need to have one line::
 
         setup_py('install', '--prefix={0}'.format(prefix))"""
-        python_path = join_path(
-            self.spec.prefix.bin,
-            'python{0}'.format('3' if self.spec.satisfies('@3') else '')
-        )
 
-        module.python_exe = python_path
-        module.python = Executable(python_path)
-        module.setup_py = Executable(python_path + ' setup.py --no-user-cfg')
+        module.python = self.command
+        module.setup_py = Executable(
+            self.command.path + ' setup.py --no-user-cfg')
 
         distutil_vars = self._load_distutil_vars()
 
         if distutil_vars:
-            for key, value in distutil_vars.iteritems():
+            for key, value in distutil_vars.items():
                 module.setup_py.add_default_env(key, value)
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
@@ -429,7 +559,7 @@ class Python(Package):
         if ext_pkg.name != 'py-pygments':
             patterns.append(r'bin/pygmentize$')
         if ext_pkg.name != 'py-numpy':
-            patterns.append(r'bin/f2py3?$')
+            patterns.append(r'bin/f2py[0-9.]*$')
 
         return match_predicate(ignore_arg, patterns)
 
@@ -457,7 +587,7 @@ class Python(Package):
 
                     paths.append(line)
 
-        site_packages = join_path(self.prefix, self.site_packages_dir)
+        site_packages = join_path(self.home, self.site_packages_dir)
         main_pth = join_path(site_packages, "easy-install.pth")
 
         if not paths:
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 8efb629487..89d1f8e568 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -22,7 +22,6 @@
 # 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 os
 from spack import *
 
 
@@ -165,8 +164,8 @@ class Scotch(Package):
 
         # General Features #
 
-        flex_path = os.path.join(self.spec['flex'].prefix.bin, 'flex')
-        bison_path = os.path.join(self.spec['bison'].prefix.bin, 'bison')
+        flex_path = self.spec['flex'].command.path
+        bison_path = self.spec['bison'].command.path
         makefile_inc.extend([
             'EXE       =',
             'OBJ       = .o',
diff --git a/var/spack/repos/builtin/packages/shiny-server/package.py b/var/spack/repos/builtin/packages/shiny-server/package.py
index e8a899115f..a3a2b2b160 100644
--- a/var/spack/repos/builtin/packages/shiny-server/package.py
+++ b/var/spack/repos/builtin/packages/shiny-server/package.py
@@ -54,9 +54,7 @@ class ShinyServer(CMakePackage):
         spec = self.spec
         options = []
 
-        options.extend([
-            "-DPYTHON=%s" % join_path(spec['python'].prefix.bin, 'python'),
-        ])
+        options.append("-DPYTHON=%s" % spec['python'].command.path)
 
         return options
 
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
index 24dca5571d..3bc6abd234 100644
--- a/var/spack/repos/builtin/packages/spark/package.py
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -69,8 +69,7 @@ class Spark(Package):
         env['JAVA_HOME'] = self.spec['jdk'].prefix
         # spack_env.set('JAVA_HOME', self.spec['jdk'].prefix)
 
-        hadoop_bin_path = join_path(self.spec['hadoop'].prefix.bin, 'hadoop')
-        hadoop_bin = Executable(hadoop_bin_path)
-        hadoop_classpath = hadoop_bin('classpath', return_output=True)
+        hadoop = self.spec['hadoop'].command
+        hadoop_classpath = hadoop('classpath', return_output=True)
 
         run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath)
diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index 6fe82baa2f..59d110330a 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -69,7 +69,7 @@ class Stat(AutotoolsPackage):
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
             "--with-libdwarf=%s"    % spec['libdwarf'].prefix,
-            "--with-python=%s/bin/python" % spec['python'].prefix
+            "--with-python=%s"      % spec['python'].command.path,
         ]
         if '+dysect' in spec:
             args.append('--enable-dysectapi')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index c7057a51df..628dd26d24 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -72,8 +72,7 @@ class Subversion(Package):
         if 'swig' in spec:
             options.append('--with-swig=%s' % spec['swig'].prefix)
         if 'perl' in spec:
-            options.append(
-                'PERL=%s' % join_path(spec['perl'].prefix.bin, 'perl'))
+            options.append('PERL=%s' % spec['perl'].command.path)
 
         configure(*options)
         make()
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index e19a33a900..e7d7b1587d 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -72,8 +72,8 @@ class SuperluDist(Package):
             'RANLIB       = true',
             'CC           = {0}'.format(self.spec['mpi'].mpicc),
             'CFLAGS       = -fPIC -std=c99 -O2 %s %s %s' % (
-                spec['parmetis'].cppflags,
-                spec['metis'].cppflags,
+                spec['parmetis'].headers.cpp_flags,
+                spec['metis'].headers.cpp_flags,
                 '-D_LONGINT' if '+int64' in spec else ''),
             'NOOPTS       = -fPIC -std=c99',
             'FORTRAN      = {0}'.format(self.spec['mpi'].mpif77),
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index 48a3762a2a..3c8505db97 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -52,7 +52,7 @@ class Visit(Package):
                 '-DVTK_MINOR_VERSION=1',
                 '-DVISIT_USE_GLEW=OFF',
                 '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin),
-                '-DPYTHON_DIR:PATH={0}'.format(spec['python'].prefix),
+                '-DPYTHON_DIR:PATH={0}'.format(spec['python'].home),
                 '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix),
                 '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix),
                 '-DVISIT_VTK_DIR:PATH={0}'.format(spec['vtk'].prefix),