Merge branch 'features/python-modules' into develop

var/spack/packages/R/package.py

@@ -0,0 +1,33 @@
+from spack import *
+
+class R(Package):
+    """R is 'GNU S', a freely available language and environment for
+       statistical computing and graphics which provides a wide va
+       riety of statistical and graphical techniques: linear and
+       nonlinear modelling, statistical tests, time series analysis,
+       classification, clustering, etc. Please consult the R project
+       homepage for further information."""
+    homepage = "http://www.example.com"
+    url      = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
+
+    version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
+
+    depends_on("readline")
+    depends_on("ncurses")
+    depends_on("icu")
+    depends_on("glib")
+    depends_on("zlib")
+    depends_on("libtiff")
+    depends_on("jpeg")
+    depends_on("cairo")
+    depends_on("pango")
+    depends_on("freetype")
+    depends_on("tcl")
+    depends_on("tk")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--enable-R-shlib",
+                  "--enable-BLAS-shlib")
+        make()
+        make("install")

var/spack/packages/geos/package.py

@@ -0,0 +1,31 @@
+from spack import *
+
+class Geos(Package):
+    """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
+       Topology Suite (JTS). As such, it aims to contain the complete
+       functionality of JTS in C++. This includes all the OpenGIS
+       Simple Features for SQL spatial predicate functions and spatial
+       operators, as well as specific JTS enhanced topology functions."""
+
+    homepage = "http://trac.osgeo.org/geos/"
+    url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
+
+    version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
+    version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
+    version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
+    version('3.3.9', '4794c20f07721d5011c93efc6ccb8e4e')
+    version('3.3.8', '75be476d0831a2d14958fed76ca266de')
+    version('3.3.7', '95ab996d22672b067d92c7dee2170460')
+    version('3.3.6', '6fadfb941541875f4976f75fb0bbc800')
+    version('3.3.5', '2ba61afb7fe2c5ddf642d82d7b16e75b')
+    version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
+    version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
+
+    extends('python')
+    depends_on('swig')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix,
+                  "--enable-python")
+        make()
+        make("install")

var/spack/packages/hdf5/package.py

@@ -18,12 +18,14 @@ class Hdf5(Package):
 
     # TODO: currently hard-coded to use OpenMPI
     def install(self, spec, prefix):
+
         configure(
             "--prefix=%s" % prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
             "--enable-parallel",
-            "CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
-            "CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++")
+            "--enable-shared",
+            "CC=%s" % spec['mpich'].prefix.bin + "/mpicc",
+            "CXX=%s" % spec['mpich'].prefix.bin + "/mpic++")
 
         make()
         make("install")

var/spack/packages/libgcrypt/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+class Libgcrypt(Package):
+    """Libgcrypt is a general purpose cryptographic library based on
+       the code from GnuPG. It provides functions for all cryptographic
+       building blocks: symmetric ciphers, hash algorithms, MACs, public
+       key algorithms, large integer functions, random numbers and a lot
+       of supporting functions. """
+    homepage = "http://www.gnu.org/software/libgcrypt/"
+    url      = "ftp://ftp.gnupg.org/gcrypt/libgcrypt/libgcrypt-1.6.2.tar.bz2"
+
+    version('1.6.2', 'b54395a93cb1e57619943c082da09d5f')
+
+    depends_on("libgpg-error")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

var/spack/packages/libgpg-error/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class LibgpgError(Package):
+    """Libgpg-error is a small library that defines common error
+       values for all GnuPG components. Among these are GPG, GPGSM,
+       GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry,
+       SmartCard Daemon and possibly more in the future. """
+
+    homepage = "https://www.gnupg.org/related_software/libgpg-error"
+    url      = "ftp://ftp.gnupg.org/gcrypt/libgpg-error/libgpg-error-1.18.tar.bz2"
+
+    version('1.18', '12312802d2065774b787cbfc22cc04e9')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

var/spack/packages/libxml2/package.py

@@ -9,6 +9,9 @@ class Libxml2(Package):
 
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
 
+    depends_on('zlib')
+    depends_on('xz')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
                   "--without-python")

var/spack/packages/libxslt/package.py

@@ -0,0 +1,24 @@
+from spack import *
+
+class Libxslt(Package):
+    """Libxslt is the XSLT C library developed for the GNOME
+       project. XSLT itself is a an XML language to define
+       transformation for XML. Libxslt is based on libxml2 the XML C
+       library developed for the GNOME project. It also implements
+       most of the EXSLT set of processor-portable extensions
+       functions and some of Saxon's evaluate and expressions
+       extensions."""
+    homepage = "http://www.xmlsoft.org/XSLT/index.html"
+    url      = "http://xmlsoft.org/sources/libxslt-1.1.28.tar.gz"
+
+    version('1.1.28', '9667bf6f9310b957254fdcf6596600b7')
+
+    depends_on("libxml2")
+    depends_on("xz")
+    depends_on("zlib")
+    depends_on("libgcrypt")
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")

var/spack/packages/py-basemap/package.py

@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class PyBasemap(Package):
+    """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python."""
+    homepage = "http://matplotlib.org/basemap/"
+    url      = "https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-1.0.7/basemap-1.0.7.tar.gz"
+
+    version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8')
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-pil')
+    depends_on("geos")
+
+    def install(self, spec, prefix):
+        env['GEOS_DIR'] = spec['geos'].prefix
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-biopython/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class PyBiopython(Package):
+    """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."""
+    homepage = "http://biopython.org/wiki/Main_Page"
+    url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
+
+    version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67')
+
+    extends('python')
+    depends_on('py-mx')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-cython/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyCython(Package):
+    """The Cython compiler for writing C extensions for the Python language."""
+    homepage = "https://pypi.python.org/pypi/cython"
+    url      = "https://pypi.python.org/packages/source/C/Cython/Cython-0.21.2.tar.gz"
+
+    version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-dateutil/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyDateutil(Package):
+    """Extensions to the standard Python datetime module."""
+    homepage = "https://pypi.python.org/pypi/dateutil"
+    url      = "https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.0.tar.gz"
+
+    version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-epydoc/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyEpydoc(Package):
+    """Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings."""
+    homepage = "https://pypi.python.org/pypi/epydoc"
+    url      = "https://pypi.python.org/packages/source/e/epydoc/epydoc-3.0.1.tar.gz"
+
+    version('3.0.1', '36407974bd5da2af00bf90ca27feeb44')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyGnuplot(Package):
+    """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/"
+    url      = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz"
+
+    version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1')
+
+    extends('python')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -0,0 +1,18 @@
+from spack import *
+import re
+
+class PyH5py(Package):
+    """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+    homepage = "https://pypi.python.org/pypi/h5py"
+    url      = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
+
+    version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+
+    extends('python', ignore=lambda f: re.match(r'cy*', f))
+    depends_on('hdf5')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
+        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -0,0 +1,15 @@
+from spack import *
+
+class PyIpython(Package):
+    """IPython provides a rich toolkit to help you make the most out of using Python interactively."""
+    homepage = "https://pypi.python.org/pypi/ipython"
+    url      = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz"
+
+    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
+
+    extends('python')
+    depends_on('py-pygments')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-libxml2/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class PyLibxml2(Package):
+    """A Python wrapper around libxml2."""
+    homepage = "https://xmlsoft.org/python.html"
+    url      = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz"
+
+    version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3')
+
+    extends('python')
+    depends_on('libxml2')
+    depends_on('libxslt')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-matplotlib/package.py

@@ -0,0 +1,46 @@
+from spack import *
+import os
+
+class PyMatplotlib(Package):
+    """Python plotting package."""
+    homepage = "https://pypi.python.org/pypi/matplotlib"
+    url      = "https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.2.tar.gz"
+
+    version('1.4.2', '7d22efb6cce475025733c50487bd8898')
+
+    extends('python', ignore=r'bin/nosetests.*$')
+
+    depends_on('py-pyside')
+    depends_on('py-ipython')
+    depends_on('py-pyparsing')
+    depends_on('py-six')
+    depends_on('py-dateutil')
+    depends_on('py-pytz')
+    depends_on('py-nose')
+    depends_on('py-numpy')
+
+    depends_on('qt')
+    depends_on('bzip2')
+    depends_on('tcl')
+    depends_on('tk')
+    depends_on('qhull')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
+
+        if str(self.version) == '1.4.2':
+            # hack to fix configuration file
+            config_file = None
+            for p,d,f in os.walk(prefix.lib):
+                for file in f:
+                    if file.find('matplotlibrc') != -1:
+                        config_file = join_path(p, 'matplotlibrc')
+                        print config_file
+            if config_file == None:
+                raise InstallError('could not find config file')
+            filter_file(r'backend      : pyside',
+                        'backend      : Qt4Agg',
+                        config_file)
+            filter_file(r'#backend.qt4 : PyQt4',
+                        'backend.qt4 : PySide',
+                        config_file)

var/spack/packages/py-mpi4py/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyMpi4py(Package):
+    """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings."""
+    homepage = "https://pypi.python.org/pypi/mpi4py"
+    url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
+
+    version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-mx/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyMx(Package):
+    """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types."""
+    homepage = "http://www.egenix.com/products/python/mxBase/"
+    url      = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz"
+
+    version('3.2.8', '9d9d3a25f9dc051a15e97f452413423b')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-nose/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+class PyNose(Package):
+    """nose extends the test loading and running features of unittest,
+    making it easier to write, find and run tests."""
+
+    homepage = "https://pypi.python.org/pypi/nose"
+    url      = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
+
+    version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
+
+    extends('python', ignore=r'bin/nosetests.*$')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-numpy/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyNumpy(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/numpy"
+    url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
+
+    version('1.9.1', '78842b73560ec378142665e712ae4ad9')
+
+    extends('python')
+    depends_on('py-nose')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pexpect/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPexpect(Package):
+    """Pexpect allows easy control of interactive console applications."""
+    homepage = "https://pypi.python.org/pypi/pexpect"
+    url      = "https://pypi.python.org/packages/source/p/pexpect/pexpect-3.3.tar.gz"
+
+    version('3.3', '0de72541d3f1374b795472fed841dce8')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pil/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPil(Package):
+    """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities."""
+
+    homepage = "http://www.pythonware.com/products/pil/"
+    url      = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz"
+
+    version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pmw/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPmw(Package):
+    """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts."""
+    homepage = "https://pypi.python.org/pypi/Pmw"
+    url      = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz"
+
+    version('2.0.0', 'c7c3f26c4f5abaa99807edefee578fc0')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pychecker/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPychecker(Package):
+    """"""
+    homepage = "http://pychecker.sourceforge.net/"
+    url      = "http://sourceforge.net/projects/pychecker/files/pychecker/0.8.19/pychecker-0.8.19.tar.gz"
+
+    version('0.8.19', 'c37182863dfb09209d6ba4f38fce9d2b')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pygments/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPygments(Package):
+    """Pygments is a syntax highlighting package written in Python."""
+    homepage = "https://pypi.python.org/pypi/pygments"
+    url      = "https://pypi.python.org/packages/source/P/Pygments/Pygments-2.0.1.tar.gz"
+
+    version('2.0.1', 'e0daf4c14a4fe5b630da765904de4d6c')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pylint/package.py

@@ -0,0 +1,16 @@
+from spack import *
+import re
+
+class PyPylint(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/pylint"
+    url      = "https://pypi.python.org/packages/source/p/pylint/pylint-1.4.1.tar.gz"
+
+    version('1.4.1', 'df7c679bdcce5019389038847e4de622')
+
+    extends('python')
+    depends_on('py-nose')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pyparsing/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPyparsing(Package):
+    """A Python Parsing Module."""
+    homepage = "https://pypi.python.org/pypi/pyparsing"
+    url      = "https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.3.tar.gz"
+
+    version('2.0.3', '0fe479be09fc2cf005f753d3acc35939')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-pyqt/package.py

@@ -0,0 +1,24 @@
+from spack import *
+
+class PyPyqt(Package):
+    """PyQt is a set of Python v2 and v3 bindings for Digia's Qt
+       application framework and runs on all platforms supported by Qt
+       including Windows, MacOS/X and Linux."""
+    homepage = "http://www.riverbankcomputing.com/software/pyqt/intro"
+    url      = "http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz"
+
+    version('4.11.3', '997c3e443165a89a559e0d96b061bf70')
+
+    extends('python')
+    depends_on('py-sip')
+
+    # TODO: allow qt5 when conditional deps are supported.
+    # TODO: Fix version matching so that @4 works like @:4
+    depends_on('qt@:4')
+
+    def install(self, spec, prefix):
+        python('configure.py',
+               '--confirm-license',
+               '--destdir=%s' % site_packages_dir)
+        make()
+        make('install')

var/spack/packages/py-pyside/package.py

@@ -0,0 +1,47 @@
+from spack import *
+import os
+
+class PyPyside(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/pyside"
+    url      = "https://pypi.python.org/packages/source/P/PySide/PySide-1.2.2.tar.gz"
+
+    version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d')
+
+    # TODO: make build dependency
+    # depends_on("cmake")
+
+    extends('python')
+    depends_on('py-setuptools')
+    depends_on('qt@:4')
+
+    def patch(self):
+        """Undo PySide RPATH handling and add Spack RPATH."""
+        # Figure out the special RPATH
+        pypkg = self.spec['python'].package
+        rpath = self.rpath
+        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide'))
+
+        # Add Spack's standard CMake args to the sub-builds.
+        # They're called BY setup.py so we have to patch it.
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),
+            'setup.py')
+
+        # PySide tries to patch ELF files to remove RPATHs
+        # Disable this and go with the one we set.
+        filter_file(
+            r'^\s*rpath_cmd\(pyside_path, srcpath\)',
+            r'#rpath_cmd(pyside_path, srcpath)',
+            'pyside_postinstall.py')
+
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)
+
+

var/spack/packages/py-pytz/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPytz(Package):
+    """World timezone definitions, modern and historical."""
+    homepage = "https://pypi.python.org/pypi/pytz"
+    url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
+
+    version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-rpy2/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+class PyRpy2(Package):
+    """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions."""
+    homepage = "https://pypi.python.org/pypi/rpy2"
+    url      = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
+
+    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    depends_on('R')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-scientificpython/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class PyScientificpython(Package):
+    """ScientificPython is a collection of Python modules for
+       scientific computing. It contains support for geometry,
+       mathematical functions, statistics, physical units, IO,
+       visualization, and parallelization."""
+
+    homepage = "https://sourcesup.renater.fr/projects/scientific-py/"
+    url      = "https://sourcesup.renater.fr/frs/download.php/4411/ScientificPython-2.8.1.tar.gz"
+
+    version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-scikit-learn/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PyScikitLearn(Package):
+    """"""
+    homepage = "https://pypi.python.org/pypi/scikit-learn"
+    url      = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz"
+
+    version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-scipy/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class PyScipy(Package):
+    """Scientific Library for Python."""
+    homepage = "https://pypi.python.org/pypi/scipy"
+    url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
+
+    version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+
+    extends('python')
+    depends_on('py-nose')
+    depends_on('py-numpy')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-setuptools/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PySetuptools(Package):
+    """Easily download, build, install, upgrade, and uninstall Python packages."""
+    homepage = "https://pypi.python.org/pypi/setuptools"
+    url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
+
+    version('11.3.1', '01f69212e019a2420c1693fb43593930')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-shiboken/package.py

@@ -0,0 +1,45 @@
+from spack import *
+import os
+
+class PyShiboken(Package):
+    """Shiboken generates bindings for C++ libraries using CPython source code."""
+    homepage = "https://shiboken.readthedocs.org/"
+    url      = "https://pypi.python.org/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz"
+
+    version('1.2.2', '345cfebda221f525842e079a6141e555')
+
+    # TODO: make build dependency
+    # depends_on("cmake")
+
+    extends('python')
+    depends_on("py-setuptools")
+    depends_on("libxml2")
+    depends_on("qt@:4.8")
+
+    def patch(self):
+        """Undo Shiboken RPATH handling and add Spack RPATH."""
+        # Add Spack's standard CMake args to the sub-builds.
+        # They're called BY setup.py so we have to patch it.
+        pypkg = self.spec['python'].package
+        rpath = self.rpath
+        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'Shiboken'))
+
+        filter_file(
+            r'OPTION_CMAKE,',
+            r'OPTION_CMAKE, ' + (
+                '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", '
+                '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)),
+            'setup.py')
+
+        # Shiboken tries to patch ELF files to remove RPATHs
+        # Disable this and go with the one we set.
+        filter_file(
+            r'^\s*rpath_cmd\(shiboken_path, srcpath\)',
+            r'#rpath_cmd(shiboken_path, srcpath)',
+            'shiboken_postinstall.py')
+
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install',
+               '--prefix=%s' % prefix,
+               '--jobs=%s' % make_jobs)

var/spack/packages/py-sip/package.py

@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class PySip(Package):
+    """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries."""
+    homepage = "http://www.riverbankcomputing.com/software/sip/intro"
+    url      = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz"
+
+    version('4.16.5', '6d01ea966a53e4c7ae5c5e48c40e49e5')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('configure.py',
+               '--destdir=%s' % site_packages_dir,
+               '--bindir=%s' % spec.prefix.bin,
+               '--incdir=%s' % python_include_dir,
+               '--sipdir=%s' % os.path.join(spec.prefix.share, 'sip'))
+        make()
+        make('install')

var/spack/packages/py-six/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PySix(Package):
+    """Python 2 and 3 compatibility utilities."""
+    homepage = "https://pypi.python.org/pypi/six"
+    url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
+
+    version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-sympy/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+class PySympy(Package):
+    """SymPy is a Python library for symbolic mathematics."""
+    homepage = "https://pypi.python.org/pypi/sympy"
+    url      = "https://pypi.python.org/packages/source/s/sympy/sympy-0.7.6.tar.gz"
+
+    version('0.7.6', '3d04753974306d8a13830008e17babca')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-virtualenv/package.py

@@ -0,0 +1,19 @@
+from spack import *
+import shutil
+
+class PyVirtualenv(Package):
+    """virtualenv is a tool to create isolated Python environments."""
+    homepage = "http://virtualenv.readthedocs.org/projects/virtualenv/"
+    url      = "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz"
+
+    version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def clean(self):
+        if os.path.exists('build'):
+            shutil.rmtree('build')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/python/package.py

@@ -1,10 +1,19 @@
+import os
+import re
+from contextlib import closing
+from llnl.util.lang import match_predicate
+
 from spack import *
+import spack
+
 
 class Python(Package):
     """The Python programming language."""
     homepage = "http://www.python.org"
     url      = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tar.xz"
 
+    extendable = True
+
     version('2.7.8', 'd235bdfa75b8396942e360a70487ee00')
 
     depends_on("openssl")
@@ -23,3 +32,126 @@ def install(self, spec, prefix):
                   "--enable-shared")
         make()
         make("install")
+
+
+    # ========================================================================
+    # Set up environment to make install easy for python extensions.
+    # ========================================================================
+
+    @property
+    def python_lib_dir(self):
+        return os.path.join('lib', 'python%d.%d' % self.version[:2])
+
+
+    @property
+    def python_include_dir(self):
+        return os.path.join('include', 'python%d.%d' % self.version[:2])
+
+
+    @property
+    def site_packages_dir(self):
+        return os.path.join(self.python_lib_dir, 'site-packages')
+
+
+    def setup_dependent_environment(self, module, spec, ext_spec):
+        """Called before python modules' install() methods.
+
+        In most cases, extensions will only need to have one line::
+
+            python('setup.py', 'install', '--prefix=%s' % prefix)
+        """
+        # Python extension builds can have a global python executable function
+        module.python = Executable(join_path(spec.prefix.bin, 'python'))
+
+        # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
+        module.python_lib_dir     = os.path.join(ext_spec.prefix, self.python_lib_dir)
+        module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir)
+        module.site_packages_dir  = os.path.join(ext_spec.prefix, self.site_packages_dir)
+
+        # Make the site packages directory if it does not exist already.
+        mkdirp(module.site_packages_dir)
+
+        # Set PYTHONPATH to include site-packages dir for the
+        # extension and any other python extensions it depends on.
+        python_paths = []
+        for d in ext_spec.traverse():
+            if d.package.extends(self.spec):
+                python_paths.append(os.path.join(d.prefix, self.site_packages_dir))
+        os.environ['PYTHONPATH'] = ':'.join(python_paths)
+
+
+    # ========================================================================
+    # Handle specifics of activating and deactivating python modules.
+    # ========================================================================
+
+    def python_ignore(self, ext_pkg, args):
+        """Add some ignore files to activate/deactivate args."""
+        ignore_arg = args.get('ignore', lambda f: False)
+
+        # Always ignore easy-install.pth, as it needs to be merged.
+        patterns = [r'easy-install\.pth$']
+
+        # Ignore pieces of setuptools installed by other packages.
+        if ext_pkg.name != 'py-setuptools':
+            patterns.append(r'/site\.pyc?$')
+            patterns.append(r'setuptools\.pth')
+            patterns.append(r'bin/easy_install[^/]*$')
+            patterns.append(r'setuptools.*egg$')
+
+        return match_predicate(ignore_arg, patterns)
+
+
+    def write_easy_install_pth(self, exts):
+        paths = []
+        for ext in sorted(exts.values()):
+            ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir)
+            easy_pth = "%s/easy-install.pth" % ext_site_packages
+
+            if not os.path.isfile(easy_pth):
+                continue
+
+            with closing(open(easy_pth)) as f:
+                for line in f:
+                    line = line.rstrip()
+
+                    # Skip lines matching these criteria
+                    if not line: continue
+                    if re.search(r'^(import|#)', line): continue
+                    if (ext.name != 'py-setuptools' and
+                        re.search(r'setuptools.*egg$', line)): continue
+
+                    paths.append(line)
+
+        site_packages = os.path.join(self.prefix, self.site_packages_dir)
+        main_pth = "%s/easy-install.pth" % site_packages
+
+        if not paths:
+            if os.path.isfile(main_pth):
+                os.remove(main_pth)
+
+        else:
+            with closing(open(main_pth, 'w')) as f:
+                f.write("import sys; sys.__plen = len(sys.path)\n")
+                for path in paths:
+                    f.write("%s\n" % path)
+                f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; "
+                        "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n")
+
+
+    def activate(self, ext_pkg, **args):
+        args.update(ignore=self.python_ignore(ext_pkg, args))
+        super(Python, self).activate(ext_pkg, **args)
+
+        exts = spack.install_layout.extension_map(self.spec)
+        exts[ext_pkg.name] = ext_pkg.spec
+        self.write_easy_install_pth(exts)
+
+
+    def deactivate(self, ext_pkg, **args):
+        args.update(ignore=self.python_ignore(ext_pkg, args))
+        super(Python, self).deactivate(ext_pkg, **args)
+
+        exts = spack.install_layout.extension_map(self.spec)
+        if ext_pkg.name in exts:        # Make deactivate idempotent.
+            del exts[ext_pkg.name]
+            self.write_easy_install_pth(exts)

var/spack/packages/qhull/package.py

@@ -0,0 +1,27 @@
+from spack import *
+
+class Qhull(Package):
+    """Qhull computes the convex hull, Delaunay triangulation, Voronoi
+       diagram, halfspace intersection about a point, furt hest-site
+       Delaunay triangulation, and furthest-site Voronoi diagram. The
+       source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull
+       implements the Quickhull algorithm for computing the convex
+       hull. It handles roundoff errors from floating point
+       arithmetic. It computes volumes, surface areas, and
+       approximations to the convex hull.
+
+       Qhull does not support triangulation of non-convex surfaces,
+       mesh generation of non-convex objects, medium-sized inputs in
+       9-D and higher, alpha shapes, weighted Voronoi diagrams,
+       Voronoi volumes, or constrained Delaunay triangulations."""
+
+    homepage = "http://www.qhull.org"
+
+    version('1.0', 'd0f978c0d8dfb2e919caefa56ea2953c',
+            url="http://www.qhull.org/download/qhull-2012.1-src.tgz")
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make("install")

var/spack/packages/qt/package.py

@@ -1,3 +1,4 @@
+import os
 from spack import *
 
 class Qt(Package):
@@ -20,6 +21,11 @@ class Qt(Package):
     depends_on("libmng")
     depends_on("jpeg")
 
+    def setup_dependent_environment(self, module, spec, dep_spec):
+        """Dependencies of Qt find it using the QTDIR environment variable."""
+        os.environ['QTDIR'] = self.prefix
+
+
     def patch(self):
         # Fix qmake compilers in the default mkspec
         qmake_conf = 'mkspecs/common/g++-base.conf'
@@ -37,8 +43,9 @@ def install(self, spec, prefix):
                   '-fast',
                   '-optimized-qmake',
                   '-no-pch',
-                  '-no-phonon',
-                  '-no-phonon-backend',
+                  # phonon required for py-pyqt
+                  # '-no-phonon',
+                  # '-no-phonon-backend',
                   '-no-openvg')
         make()
         make("install")

var/spack/packages/tcl/package.py

@@ -0,0 +1,22 @@
+from spack import *
+
+class Tcl(Package):
+    """Tcl (Tool Command Language) is a very powerful but easy to
+       learn dynamic programming language, suitable for a very wide
+       range of uses, including web and desktop applications,
+       networking, administration, testing and many more. Open source
+       and business-friendly, Tcl is a mature yet evolving language
+       that is truly cross platform, easily deployed and highly
+       extensible."""
+    homepage = "http://www.tcl.tk"
+
+    version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f',
+            url="http://prdownloads.sourceforge.net/tcl/tcl8.6.3-src.tar.gz")
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        with working_dir('unix'):
+            configure("--prefix=%s" % prefix)
+            make()
+            make("install")

var/spack/packages/tk/package.py

@@ -0,0 +1,22 @@
+from spack import *
+
+class Tk(Package):
+    """Tk is a graphical user interface toolkit that takes developing
+       desktop applications to a higher level than conventional
+       approaches. Tk is the standard GUI not only for Tcl, but for
+       many other dynamic languages, and can produce rich, native
+       applications that run unchanged across Windows, Mac OS X, Linux
+       and more."""
+    homepage = "http://www.tcl.tk"
+    url      = "http://prdownloads.sourceforge.net/tcl/tk8.6.3-src.tar.gz"
+
+    version('src', '85ca4dbf4dcc19777fd456f6ee5d0221')
+
+    depends_on("tcl")
+
+    def install(self, spec, prefix):
+        with working_dir('unix'):
+            configure("--prefix=%s" % prefix,
+                      "--with-tcl=%s" % spec['tcl'].prefix.lib)
+            make()
+            make("install")