Merge branch 'develop' into features/fastmath

var/spack/mock_configs/site_spackconfig

@@ -1,12 +0,0 @@
-[compiler "gcc@4.5.0"]
-    cc  = /path/to/gcc
-    cxx = /path/to/g++
-    f77 = /path/to/gfortran
-    fc  = /path/to/gfortran
-
-[compiler "clang@3.3"]
-    cc  = /path/to/clang
-    cxx = /path/to/clang++
-    f77 = None
-    fc  = None
-

var/spack/mock_configs/site_spackconfig/compilers.yaml

@@ -0,0 +1,12 @@
+compilers:
+  all:
+    clang@3.3:
+      cc: /path/to/clang
+      cxx: /path/to/clang++
+      f77: None
+      fc: None
+    gcc@4.5.0:
+      cc: /path/to/gcc
+      cxx: /path/to/g++
+      f77: /path/to/gfortran
+      fc: /path/to/gfortran

var/spack/mock_packages/a/package.py

@@ -0,0 +1,12 @@
+from spack import *
+
+class A(Package):
+    """Simple package with no dependencies"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/a-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/mock_packages/b/package.py

@@ -0,0 +1,12 @@
+from spack import *
+
+class B(Package):
+    """Simple package with no dependencies"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/b-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/mock_packages/c/package.py

@@ -0,0 +1,12 @@
+from spack import *
+
+class C(Package):
+    """Simple package with no dependencies"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/c-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/mock_packages/e/package.py

@@ -0,0 +1,12 @@
+from spack import *
+
+class E(Package):
+    """Simple package with no dependencies"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/e-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/mock_packages/mpich/package.py

@@ -30,6 +30,9 @@ class Mpich(Package):
     list_url   = "http://www.mpich.org/static/downloads/"
     list_depth = 2
 
+    variant('debug', default=False,
+            description="Compile MPICH with debug flags.")
+
     version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
     version('3.0.3', 'foobarbaz')
     version('3.0.2', 'foobarbaz')

var/spack/mock_packages/mpileaks/package.py

@@ -33,6 +33,9 @@ class Mpileaks(Package):
     version(2.2, 'foobarbaz')
     version(2.3, 'foobarbaz')
 
+    variant('debug', default=False, description='Debug variant')
+    variant('opt',   default=False, description='Optimized variant')
+
     depends_on("mpi")
     depends_on("callpath")
 

var/spack/mock_packages/optional-dep-test-2/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class OptionalDepTest2(Package):
+    """Depends on the optional-dep-test package"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/optional-dep-test-2-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    variant('odt', default=False)
+    variant('mpi', default=False)
+
+    depends_on('optional-dep-test', when='+odt')
+    depends_on('optional-dep-test+mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+        pass

var/spack/mock_packages/optional-dep-test/package.py

@@ -0,0 +1,29 @@
+from spack import *
+
+class OptionalDepTest(Package):
+    """Description"""
+
+    homepage = "http://www.example.com"
+    url      = "http://www.example.com/optional_dep_test-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('1.1', '0123456789abcdef0123456789abcdef')
+
+    variant('a',   default=False)
+    variant('f',   default=False)
+    variant('mpi', default=False)
+
+    depends_on('a', when='+a')
+    depends_on('b', when='@1.1')
+    depends_on('c', when='%intel')
+    depends_on('d', when='%intel@64.1')
+    depends_on('e', when='%clang@34:40')
+
+    depends_on('f', when='+f')
+    depends_on('g', when='^f')
+    depends_on('mpi', when='^g')
+
+    depends_on('mpi', when='+mpi')
+
+    def install(self, spec, prefix):
+        pass

var/spack/packages/Mitos/package.py

@@ -7,9 +7,10 @@ class Mitos(Package):
     homepage = "https://github.com/scalability-llnl/Mitos"
     url      = "https://github.com/scalability-llnl/Mitos"
 
-    version('0.7', git='https://github.com/scalability-llnl/Mitos.git', tag='v0.7')
+    version('0.9', '8a8f05b35e04e9f37fa15436b98d5b25', git='https://github.com/scalability-llnl/Mitos.git', tag='v0.9')
 
-    depends_on('dyninst')
+    depends_on('dyninst@8.2.1:')
+    depends_on('hwloc')
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

var/spack/packages/adept-utils/package.py

@@ -30,7 +30,8 @@ class AdeptUtils(Package):
     homepage = "https://github.com/scalability-llnl/adept-utils"
     url      = "https://github.com/scalability-llnl/adept-utils/archive/v1.0.tar.gz"
 
-    version('1.0', '5c6cd9badce56c945ac8551e34804397')
+    version('1.0.1', '731a310717adcb004d9d195130efee7d')
+    version('1.0',   '5c6cd9badce56c945ac8551e34804397')
 
     depends_on("boost")
     depends_on("mpi")

var/spack/packages/binutils/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Binutils(Package):
+    """GNU binutils, which contain the linker, assembler, objdump and others"""
+    homepage = "http://www.gnu.org/software/binutils/"
+    url      = "ftp://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
+
+    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
+    version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
+    version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
+    version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")

var/spack/packages/cppcheck/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+class Cppcheck(Package):
+    """A tool for static C/C++ code analysis."""
+    homepage = "http://cppcheck.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/cppcheck/cppcheck/1.68/cppcheck-1.68.tar.bz2"
+
+    version('1.68', 'c015195f5d61a542f350269030150708')
+
+    def install(self, spec, prefix):
+        # cppcheck does not have a configure script
+        make()
+        # manually install the final cppcheck binary
+        mkdirp(prefix.bin)
+        install('cppcheck', prefix.bin)

var/spack/packages/gcc/package.py

@@ -47,6 +47,7 @@ class Gcc(Package):
     depends_on("gmp")
     depends_on("mpc")     # when @4.5:
     depends_on("libelf")
+    depends_on("binutils")
 
     # Save these until we can do optional deps.
     #depends_on("isl")
@@ -73,6 +74,10 @@ def install(self, spec, prefix):
                   "--with-stage1-ldflags=%s" % self.rpath_args,
                   "--with-boot-ldflags=%s"   % self.rpath_args,
                   "--enable-lto",
+                  "--with-gnu-ld",
+                  "--with-ld=%s/bin/ld" % spec['binutils'].prefix,
+                  "--with-gnu-as",
+                  "--with-as=%s/bin/as" % spec['binutils'].prefix,
                   "--with-quad")
         make()
         make("install")

var/spack/packages/memaxes/package.py

@@ -5,12 +5,11 @@ class Memaxes(Package):
 
     homepage = "https://github.com/scalability-llnl/MemAxes"
 
-    version('0.5', 'b0f561d48aa7301e028d074bc4b5751b',
+    version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5',
             url='https://github.com/scalability-llnl/MemAxes/archive/v0.5.tar.gz')
 
     depends_on("cmake@2.8.9:")
     depends_on("qt@5:")
-    depends_on("vtk")
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

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

@@ -3,9 +3,10 @@
 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"
+    url      = "https://pypi.python.org/packages/source/C/Cython/cython-0.22.tar.gz"
 
     version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+    version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
 
     extends('python')
 

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

@@ -6,6 +6,7 @@ class PyDateutil(Package):
     url      = "https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.0.tar.gz"
 
     version('2.4.0', '75714163bb96bedd07685cdb2071b8bc')
+    version('2.4.2', '4ef68e1c485b09e9f034e10473e5add2')
 
     extends('python')
     depends_on('py-setuptools')

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

@@ -0,0 +1,15 @@
+from spack import *
+
+class PyGenders(Package):
+    """Genders is a static cluster configuration database used for cluster configuration management. It is used by a variety of tools and scripts for management of large clusters."""
+    homepage = "https://github.com/chaos/genders"
+    url      = "https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz"
+
+    version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e', url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz')
+    extends('python')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" %prefix)
+        make(parallel=False)
+        make("install")
+

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

@@ -7,8 +7,9 @@ class PyH5py(Package):
     url      = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
 
     version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+    version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
 
-    extends('python', ignore=lambda f: re.match(r'cy*', f))
+    extends('python', ignore=lambda f: re.match(r'bin/cy*', f))
     depends_on('hdf5')
     depends_on('py-numpy')
     depends_on('py-cython')

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

@@ -6,6 +6,7 @@ class PyIpython(Package):
     url      = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz"
 
     version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
+    version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
 
     extends('python')
     depends_on('py-pygments')

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

@@ -7,6 +7,7 @@ class PyMatplotlib(Package):
     url      = "https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.2.tar.gz"
 
     version('1.4.2', '7d22efb6cce475025733c50487bd8898')
+    version('1.4.3', '86af2e3e3c61849ac7576a6f5ca44267')
 
     extends('python', ignore=r'bin/nosetests.*$')
 
@@ -28,7 +29,7 @@ class PyMatplotlib(Package):
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
 
-        if str(self.version) == '1.4.2':
+        if str(self.version) in ['1.4.2', '1.4.3']:
             # hack to fix configuration file
             config_file = None
             for p,d,f in os.walk(prefix.lib):

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

@@ -8,6 +8,7 @@ class PyNose(Package):
     url      = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
 
     version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
+    version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
 
     extends('python', ignore=r'bin/nosetests.*$')
     depends_on('py-setuptools')

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

@@ -6,6 +6,7 @@ class PyNumpy(Package):
     url      = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
     version('1.9.1', '78842b73560ec378142665e712ae4ad9')
+    version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
 
     extends('python')
     depends_on('py-nose')

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

@@ -0,0 +1,21 @@
+from spack import *
+import os
+
+class PyPandas(Package):
+    """pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language."""
+    homepage = "http://pandas.pydata.org/"
+    url      = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73"
+
+    version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
+    version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
+
+    extends('python')
+    depends_on('py-dateutil')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-scipy')
+    depends_on('py-setuptools')
+    depends_on('py-pytz')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -6,6 +6,7 @@ class PyPygments(Package):
     url      = "https://pypi.python.org/packages/source/P/Pygments/Pygments-2.0.1.tar.gz"
 
     version('2.0.1', 'e0daf4c14a4fe5b630da765904de4d6c')
+    version('2.0.2', '238587a1370d62405edabd0794b3ec4a')
 
     extends('python')
     depends_on('py-setuptools')

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

@@ -7,6 +7,7 @@ class PyPylint(Package):
     url      = "https://pypi.python.org/packages/source/p/pylint/pylint-1.4.1.tar.gz"
 
     version('1.4.1', 'df7c679bdcce5019389038847e4de622')
+    version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44')
 
     extends('python')
     depends_on('py-nose')

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

@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPypar(Package):
+    """Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel on multiple processors and communicate using MPI."""
+    homepage = "http://code.google.com/p/pypar/"
+    url      = "https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz"
+
+    version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8', url='https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz')
+    extends('python')
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        with working_dir('source'):
+            python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -6,6 +6,7 @@ class PyPytz(Package):
     url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
 
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
+    version('2015.4', '417a47b1c432d90333e42084a605d3d8')
 
     extends('python')
 

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

@@ -6,6 +6,7 @@ class PyRpy2(Package):
     url      = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
 
     version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+    version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f')
 
     extends('python')
     depends_on('py-setuptools')

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

@@ -7,8 +7,7 @@ class PyScientificpython(Package):
        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"
-
+    url      = "https://sourcesup.renater.fr/frs/download.php/file/4411/ScientificPython-2.8.1.tar.gz"
     version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77')
 
     extends('python')

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

@@ -6,6 +6,7 @@ class PyScikitLearn(Package):
     url      = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz"
 
     version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
+    version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
 
     extends('python')
 

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

@@ -6,6 +6,7 @@ class PyScipy(Package):
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
+    version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
 
     extends('python')
     depends_on('py-nose')

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

@@ -6,6 +6,7 @@ class PySetuptools(Package):
     url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
 
     version('11.3.1', '01f69212e019a2420c1693fb43593930')
+    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
 
     extends('python')
 

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

@@ -7,6 +7,7 @@ class PySip(Package):
     url      = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz"
 
     version('4.16.5', '6d01ea966a53e4c7ae5c5e48c40e49e5')
+    version('4.16.7', '32abc003980599d33ffd789734de4c36')
 
     extends('python')
 

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

@@ -7,6 +7,7 @@ class PyVirtualenv(Package):
     url      = "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz"
 
     version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49')
+    version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
 
     extends('python')
     depends_on('py-setuptools')

var/spack/packages/python/package.py

@@ -15,6 +15,7 @@ class Python(Package):
     extendable = True
 
     version('2.7.8', 'd235bdfa75b8396942e360a70487ee00')
+    version('2.7.10', 'c685ef0b8e9f27b5e3db5db12b268ac6')
 
     depends_on("openssl")
     depends_on("bzip2")
@@ -139,7 +140,9 @@ def write_easy_install_pth(self, exts):
 
 
     def activate(self, ext_pkg, **args):
-        args.update(ignore=self.python_ignore(ext_pkg, args))
+        ignore=self.python_ignore(ext_pkg, args)
+        args.update(ignore=ignore)
+
         super(Python, self).activate(ext_pkg, **args)
 
         exts = spack.install_layout.extension_map(self.spec)

var/spack/packages/qt/package.py

@@ -50,9 +50,11 @@ def setup_dependent_environment(self, module, spec, dep_spec):
 
     def patch(self):
         if self.spec.satisfies('@4'):
-            qmake_conf = 'mkspecs/common/g++-base.conf'
+            qmake_conf      = 'mkspecs/common/g++-base.conf'
+            qmake_unix_conf = 'mkspecs/common/g++-unix.conf'
         elif self.spec.satisfies('@5'):
-            qmake_conf = 'qtbase/mkspecs/common/g++-base.conf'
+            qmake_conf      = 'qtbase/mkspecs/common/g++-base.conf'
+            qmake_unix_conf = 'qtbase/mkspecs/common/g++-unix.conf'
         else:
             return
 
@@ -60,7 +62,7 @@ def patch(self):
         filter_file(r'^QMAKE_COMPILER *=.*$',  'QMAKE_COMPILER = cc', qmake_conf)
         filter_file(r'^QMAKE_CC *=.*$',        'QMAKE_CC = cc',       qmake_conf)
         filter_file(r'^QMAKE_CXX *=.*$',       'QMAKE_CXX = c++',     qmake_conf)
-
+        filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$',  'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf)
 
 
     @property

var/spack/packages/stat/package.py

@@ -5,16 +5,18 @@ class Stat(Package):
     homepage = "http://paradyn.org/STAT/STAT.html"
     url      = "https://github.com/lee218llnl/stat/archive/v2.0.0.tar.gz"
 
+    version('2.2.0', '26bd69dd57a15afdd5d0ebdb0b7fb6fc')
     version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
     version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
 
+    depends_on('libelf')
     depends_on('libdwarf')
     depends_on('dyninst')
     depends_on('graphlib')
     depends_on('launchmon')
     depends_on('mrnet')
 
-    patch('configure_mpicxx.patch', when='@2.1.0:')
+    patch('configure_mpicxx.patch', when='@2.1.0')
 
     def install(self, spec, prefix):
         configure(

var/spack/packages/uncrustify/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class Uncrustify(Package):
+    """Source Code Beautifier for C, C++, C#, ObjectiveC, D, Java, Pawn and VALA"""
+
+    homepage = "http://uncrustify.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz"
+
+    version('0.61', 'b6140106e74c64e831d0b1c4b6cf7727')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")