Add PythonPackage base class

- Add a PythonPackage class with build system support.
  - Support build phases in PythonPackage
  - Add a custom sanity check for PythonPackages
  - Get rid of nolink dependencies in python packages

- Update spack create to use new PythonPackage class

- Port most of Python packages to new PythonPackage class

- Conducted a massive install and activate of Python packages.
  - Fixed bugs introduced by install and activate.

- Update API docs on PythonPackage

var/spack/repos/builtin/packages/py-functools32/package.py

@@ -25,17 +25,11 @@
 from spack import *
 
 
-class PyFunctools32(Package):
+class PyFunctools32(PythonPackage):
     """Backport of the functools module from Python 3.2.3 for use on 2.7 and
     PyPy."""
 
     homepage = "https://github.com/MiCHiLU/python-functools32"
-    # base https://pypi.python.org/pypi/functools32
     url      = "https://pypi.python.org/packages/source/f/functools32/functools32-3.2.3-2.tar.gz"
 
     version('3.2.3-2', '09f24ffd9af9f6cd0f63cb9f4e23d4b2')
-
-    extends('python')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-futures/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyFutures(Package):
+class PyFutures(PythonPackage):
     """Backport of the concurrent.futures package from Python 3.2"""
 
     homepage = "https://pypi.python.org/pypi/futures"
@@ -33,9 +33,4 @@ class PyFutures(Package):
 
     version('3.0.5', 'ced2c365e518242512d7a398b515ff95')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-genders/package.py

@@ -36,6 +36,9 @@ class PyGenders(Package):
             url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz')
     extends('python')
 
+    # FIXME: Missing a dependency on genders
+    # #include <genders.h>
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make(parallel=False)

var/spack/repos/builtin/packages/py-genshi/package.py

@@ -22,11 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-from spack import version, extends, depends_on
-from spack import Package
+from spack import *
 
 
-class PyGenshi(Package):
+class PyGenshi(PythonPackage):
     """Python toolkit for generation of output for the web"""
     homepage = "https://genshi.edgewall.org/"
     url      = "http://ftp.edgewall.com/pub/genshi/Genshi-0.7.tar.gz"
@@ -35,8 +34,4 @@ class PyGenshi(Package):
     version('0.6.1', '372c368c8931110b0a521fa6091742d7')
     version('0.6', '604e8b23b4697655d36a69c2d8ef7187')
 
-    extends("python")
     depends_on("py-setuptools", type='build')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-gnuplot/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyGnuplot(Package):
+class PyGnuplot(PythonPackage):
     """Gnuplot.py is a Python package that allows you to create graphs from
        within Python using the gnuplot plotting program."""
     homepage = "http://gnuplot-py.sourceforge.net/"
@@ -33,8 +33,4 @@ class PyGnuplot(Package):
 
     version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1')
 
-    extends('python')
     depends_on('py-numpy', type=('build', 'run'))
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-h5py/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyH5py(Package):
+class PyH5py(PythonPackage):
     """The h5py package provides both a high- and low-level interface to the
     HDF5 library from Python."""
 
@@ -38,8 +38,6 @@ class PyH5py(Package):
 
     variant('mpi', default=True, description='Build with MPI support')
 
-    extends('python')
-
     # Build dependencies
     depends_on('py-cython@0.19:', type='build')
     depends_on('pkg-config', type='build')
@@ -55,11 +53,11 @@ class PyH5py(Package):
     # Runtime dependencies
     depends_on('py-six', type=('build', 'run'))
 
-    def install(self, spec, prefix):
-        setup_py('configure', '--hdf5={0}'.format(spec['hdf5'].prefix))
+    phases = ['configure', 'install']
+
+    def configure(self, spec, prefix):
+        self.setup_py('configure', '--hdf5={0}'.format(spec['hdf5'].prefix))
 
         if '+mpi' in spec:
             env['CC'] = spec['mpi'].mpicc
-            setup_py('configure', '--mpi')
-
-        setup_py('install', '--prefix={0}'.format(prefix))
+            self.setup_py('configure', '--mpi')

var/spack/repos/builtin/packages/py-html5lib/package.py

+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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
+##############################################################################
+from spack import *
+
+
+class PyHtml5lib(PythonPackage):
+    """HTML parser based on the WHATWG HTML specification."""
+
+    homepage = "https://github.com/html5lib/html5lib-python"
+    url      = "https://pypi.python.org/packages/ae/ae/bcb60402c60932b32dfaf19bb53870b29eda2cd17551ba5639219fb5ebf9/html5lib-0.9999999.tar.gz"
+
+    version('0.9999999', 'ef43cb05e9e799f25d65d1135838a96f')
+
+    depends_on('python@2.6:2.7,3.2:3.4')
+    depends_on('py-six', type=('build', 'run'))

var/spack/repos/builtin/packages/py-imagesize/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyImagesize(Package):
+class PyImagesize(PythonPackage):
     """Parses image file headers and returns image size. Supports PNG, JPEG,
     JPEG2000, and GIF image file formats."""
 
@@ -35,9 +35,4 @@ class PyImagesize(Package):
     version('0.7.1', '976148283286a6ba5f69b0f81aef8052',
             url="https://pypi.python.org/packages/53/72/6c6f1e787d9cab2cc733cf042f125abec07209a58308831c9f292504e826/imagesize-0.7.1.tar.gz")
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-iminuit/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyIminuit(Package):
+class PyIminuit(PythonPackage):
     """Interactive IPython-Friendly Minimizer based on SEAL Minuit2."""
 
     homepage = "https://pypi.python.org/pypi/iminuit"
@@ -34,13 +34,9 @@ class PyIminuit(Package):
     version('1.2', '4701ec472cae42015e26251703e6e984')
 
     # Required dependencies
-    extends('python')
     depends_on('py-setuptools', type='build')
 
     # Optional dependencies
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('py-cython', type='build')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-ipykernel/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyIpykernel(Package):
+class PyIpykernel(PythonPackage):
     """IPython Kernel for Jupyter"""
 
     homepage = "https://pypi.python.org/pypi/ipykernel"
@@ -42,15 +42,10 @@ class PyIpykernel(Package):
     version('4.1.1', '51376850c46fb006e1f8d1cd353507c5')
     version('4.1.0', '638a43e4f8a15872f749090c3f0827b6')
 
-    extends('python')
-
     depends_on('python@2.7:2.7.999,3.3:')
     depends_on('py-setuptools', type='build')
-    depends_on('py-traitlets@4.1.0:')
-    depends_on('py-tornado@4.0:')
-    depends_on('py-ipython@4.0:')
-    depends_on('py-jupyter-client')
-    depends_on('py-pexpect')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-traitlets@4.1.0:', type=('build', 'run'))
+    depends_on('py-tornado@4.0:', type=('build', 'run'))
+    depends_on('py-ipython@4.0:', type=('build', 'run'))
+    depends_on('py-jupyter-client', type=('build', 'run'))
+    depends_on('py-pexpect', type=('build', 'run'))

var/spack/repos/builtin/packages/py-ipython-genutils/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyIpythonGenutils(Package):
+class PyIpythonGenutils(PythonPackage):
     """Vestigial utilities from IPython"""
 
     homepage = "https://pypi.python.org/pypi/ipython_genutils"
@@ -33,10 +33,5 @@ class PyIpythonGenutils(Package):
 
     version('0.1.0', '9a8afbe0978adbcbfcb3b35b2d015a56')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-ipython/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyIpython(Package):
+class PyIpython(PythonPackage):
     """IPython provides a rich toolkit to help you make the most out of using
        Python interactively."""
     homepage = "https://pypi.python.org/pypi/ipython"
@@ -35,13 +35,15 @@ class PyIpython(Package):
     version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
     version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
 
-    extends('python')
     depends_on('py-pygments', type=('build', 'run'))
     depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('py-backports-shutil-get-terminal-size', when="^python@:3.2.999")
-    depends_on('py-pathlib2', when="^python@:3.3.999")
-    depends_on('py-pickleshare')
-    depends_on('py-simplegeneric')
 
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix=%s' % prefix)
+    # These dependencies breaks concretization
+    # See https://github.com/LLNL/spack/issues/2793
+    # depends_on('py-backports-shutil-get-terminal-size', when="^python@:3.2.999")  # noqa
+    # depends_on('py-pathlib2', when="^python@:3.3.999")
+    depends_on('py-backports-shutil-get-terminal-size', type=('build', 'run'))
+    depends_on('py-pathlib2', type=('build', 'run'))
+
+    depends_on('py-pickleshare', type=('build', 'run'))
+    depends_on('py-simplegeneric', type=('build', 'run'))

var/spack/repos/builtin/packages/py-ipywidgets/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyIpywidgets(Package):
+class PyIpywidgets(PythonPackage):
     """IPython widgets for the Jupyter Notebook"""
 
     homepage = "https://github.com/ipython/ipywidgets"
@@ -33,13 +33,8 @@ class PyIpywidgets(Package):
 
     version('5.2.2', '112f3daa4aa0f42f8dda831cea3649c8')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
-    depends_on('py-ipython@4.0.0:')
-    depends_on('py-ipykernel@4.2.2:')
-    depends_on('py-traitlets@4.2.1:')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-ipython@4.0.0:', type=('build', 'run'))
+    depends_on('py-ipykernel@4.2.2:', type=('build', 'run'))
+    depends_on('py-traitlets@4.2.1:', type=('build', 'run'))

var/spack/repos/builtin/packages/py-jdcal/package.py

@@ -25,15 +25,10 @@
 from spack import *
 
 
-class PyJdcal(Package):
+class PyJdcal(PythonPackage):
     """Julian dates from proleptic Gregorian and Julian calendars"""
 
     homepage = 'http://github.com/phn/jdcal'
     url      = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz"
 
     version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9')
-
-    extends('python')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix=%s' % prefix)

var/spack/repos/builtin/packages/py-jinja2/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyJinja2(Package):
+class PyJinja2(PythonPackage):
     """Jinja2 is a template engine written in pure Python. It provides
     a Django inspired non-XML syntax but supports inline expressions
     and an optional sandboxed environment."""
@@ -39,11 +39,6 @@ class PyJinja2(Package):
     version('2.7.1', '282aed153e69f970d6e76f78ed9d027a')
     version('2.7',   'c2fb12cbbb523c57d3d15bfe4dc0e8fe')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('py-markupsafe', type=('build', 'run'))
     depends_on('py-babel@0.8:', type=('build', 'run'))  # optional, required for i18n
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))

var/spack/repos/builtin/packages/py-jsonschema/package.py

@@ -25,19 +25,18 @@
 from spack import *
 
 
-class PyJsonschema(Package):
+class PyJsonschema(PythonPackage):
     """Jsonschema: An(other) implementation of JSON Schema for Python."""
 
     homepage = "http://github.com/Julian/jsonschema"
-    # base https://pypi.python.org/pypi/jsonschema
     url      = "https://pypi.python.org/packages/source/j/jsonschema/jsonschema-2.5.1.tar.gz"
 
     version('2.5.1', '374e848fdb69a3ce8b7e778b47c30640')
 
-    extends('python')
     depends_on('py-setuptools', type='build')
-    depends_on('py-vcversioner')
-    depends_on('py-functools32', when="^python@2.7")
+    depends_on('py-vcversioner', type=('build', 'run'))
 
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    # This dependency breaks concretization
+    # See https://github.com/LLNL/spack/issues/2793
+    # depends_on('py-functools32', when="^python@2.7", type=('build', 'run'))
+    depends_on('py-functools32', type=('build', 'run'))

var/spack/repos/builtin/packages/py-jupyter-client/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyJupyterClient(Package):
+class PyJupyterClient(PythonPackage):
     """Jupyter protocol client APIs"""
 
     homepage = "https://github.com/jupyter/jupyter_client"
@@ -40,13 +40,8 @@ class PyJupyterClient(Package):
     version('4.1.0', 'cf42048b889c8434fbb5813a9eec1d34')
     version('4.0.0', '00fa63c67cb3adf359d09dc4d803aff5')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
-    depends_on('py-traitlets')
-    depends_on('py-jupyter-core')
-    depends_on('py-zmq@13:')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-traitlets', type=('build', 'run'))
+    depends_on('py-jupyter-core', type=('build', 'run'))
+    depends_on('py-zmq@13:', type=('build', 'run'))

var/spack/repos/builtin/packages/py-jupyter-console/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyJupyterConsole(Package):
+class PyJupyterConsole(PythonPackage):
     """Jupyter Terminal Console"""
 
     homepage = "https://github.com/jupyter/jupyter_console"
@@ -37,15 +37,10 @@ class PyJupyterConsole(Package):
     version('4.0.3', '0e928ea261e7f8154698cf69ed4f2459')
     version('4.0.2', 'f2e174938c91136549b908bd39fa5d59')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
-    depends_on('py-jupyter-client')
-    depends_on('py-ipython')
-    depends_on('py-ipykernel')
-    depends_on('py-pygments')
-    depends_on('py-prompt-toolkit@1.0.0:1.999.999')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-jupyter-client', type=('build', 'run'))
+    depends_on('py-ipython', type=('build', 'run'))
+    depends_on('py-ipykernel', type=('build', 'run'))
+    depends_on('py-pygments', type=('build', 'run'))
+    depends_on('py-prompt-toolkit@1.0.0:1.999.999', type=('build', 'run'))

var/spack/repos/builtin/packages/py-jupyter-core/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyJupyterCore(Package):
+class PyJupyterCore(PythonPackage):
     """Core Jupyter functionality"""
 
     homepage = "http://jupyter-core.readthedocs.io/"
@@ -42,11 +42,6 @@ class PyJupyterCore(Package):
     version('4.0.1', 'f849136b2badaaba2a8a3b397bf04639')
     version('4.0',   'b6b37cb4f40bd0fcd20433cb2cc7a4c1')
 
-    extends('python')
-
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
-    depends_on('py-traitlets')
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-traitlets', type=('build', 'run'))

var/spack/repos/builtin/packages/py-jupyter-notebook/package.py

@@ -25,7 +25,7 @@
 from spack import *
 
 
-class PyJupyterNotebook(Package):
+class PyJupyterNotebook(PythonPackage):
     """Jupyter Interactive Notebook"""
 
     homepage = "https://github.com/jupyter/notebook"
@@ -44,23 +44,18 @@ class PyJupyterNotebook(Package):
 
     variant('terminal', default=False, description="Enable terminal functionality")
 
-    extends('python')
-    
     depends_on('py-setuptools', type='build')
     depends_on('python@2.7:2.7.999,3.3:')
     depends_on('npm', type='build')
-    depends_on('py-jinja2')
-    depends_on('py-tornado@4:')
-    depends_on('py-ipython-genutils')
-    depends_on('py-traitlets')
-    depends_on('py-jupyter-core')
-    depends_on('py-jupyter-client')
-    depends_on('py-jupyter-console')
-    depends_on('py-nbformat')
-    depends_on('py-nbconvert')
-    depends_on('py-ipykernel')
-    depends_on('py-terminado@0.3.3:', when="+terminal")
-    depends_on('py-ipywidgets', when="+terminal")
-
-    def install(self, spec, prefix):
-        setup_py('install', '--prefix={0}'.format(prefix))
+    depends_on('py-jinja2', type=('build', 'run'))
+    depends_on('py-tornado@4:', type=('build', 'run'))
+    depends_on('py-ipython-genutils', type=('build', 'run'))
+    depends_on('py-traitlets', type=('build', 'run'))
+    depends_on('py-jupyter-core', type=('build', 'run'))
+    depends_on('py-jupyter-client', type=('build', 'run'))
+    depends_on('py-jupyter-console', type=('build', 'run'))
+    depends_on('py-nbformat', type=('build', 'run'))
+    depends_on('py-nbconvert', type=('build', 'run'))
+    depends_on('py-ipykernel', type=('build', 'run'))
+    depends_on('py-terminado@0.3.3:', when="+terminal", type=('build', 'run'))
+    depends_on('py-ipywidgets', when="+terminal", type=('build', 'run'))