Revert "added a bunch of packages and added submodule"

This reverts commit 79808da760.

.gitignore

@@ -8,4 +8,3 @@
 /etc/spackconfig
 /share/spack/dotkit
 /share/spack/modules
-*.ropeproject

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "/lib/spack/spack/util/python_recipe_parser"]
+[submodule "utils/python_recipe_parser"]
-	path = /lib/spack/spack/util/python_recipe_parser
+	path = utils/python_recipe_parser
 	url = https://github.com/karenyyng/spack_python_package_parser

var/spack/packages/asciidoc/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Asciidoc(Package):
+    """ A presentable text document format for writing articles, UNIX man
+    pages and other small to medium sized documents."""
+    homepage = "http://asciidoc.org"
+    url      = "http://downloads.sourceforge.net/project/asciidoc/asciidoc/8.6.9/asciidoc-8.6.9.tar.gz"
+
+    version('8.6.9', 'c59018f105be8d022714b826b0be130a')
+
+    depends_on('libxml2')
+    depends_on('libxslt')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/boost/package.py

@@ -14,6 +14,10 @@ class Boost(Package):
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 2
 
+    version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87')
+    version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546')
+    version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76')
+    version('1.56.0', 'a744cf167b05d72335f27c88115f211d')
     version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354')
     version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279')
     version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2')

var/spack/packages/bowtie2/bowtie2-2.5.patch

@@ -0,0 +1,16 @@
+--- Makefile	2015-02-26 10:50:00.000000000 -0800
++++ Makefile.new	2015-07-29 18:03:59.891357399 -0700
+@@ -22,10 +22,10 @@
+ #
+ 
+ INC =
+-GCC_PREFIX = $(shell dirname `which gcc`)
++GCC_PREFIX =
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CC = cc 
++CPP = c++
+ CXX = $(CPP)
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1

var/spack/packages/bowtie2/package.py

@@ -0,0 +1,24 @@
+from spack import *
+from glob import glob
+class Bowtie2(Package):
+    """Description"""
+    homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
+    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
+
+    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+        for bow in glob("bowtie2*"):
+            install(bow, prefix.bin)
+        # install('bowtie2',prefix.bin)
+        # install('bowtie2-align-l',prefix.bin)
+        # install('bowtie2-align-s',prefix.bin)
+        # install('bowtie2-build',prefix.bin)
+        # install('bowtie2-build-l',prefix.bin)
+        # install('bowtie2-build-s',prefix.bin)
+        # install('bowtie2-inspect',prefix.bin)
+        # install('bowtie2-inspect-l',prefix.bin)
+        # install('bowtie2-inspect-s',prefix.bin)
+

var/spack/packages/cscope/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Cscope(Package):
+    """Cscope is a developer's tool for browsing source code."""
+    homepage = "http://http://cscope.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/cscope/cscope/15.8b/cscope-15.8b.tar.gz"
+
+    version('15.8b', '8f9409a238ee313a96f9f87fe0f3b176')
+
+    # Can be configured to use flex (not necessary)
+    # ./configure --with-flex
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/czmq/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+class Czmq(Package):
+    """ A C interface to the ZMQ library """
+    homepage = "http://czmq.zeromq.org"
+    url      = "https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz"
+
+    version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
+
+    depends_on('zeromq')
+
+    def install(self, spec, prefix):
+        bash = which("bash")
+        bash("./autogen.sh")
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")
+

var/spack/packages/docbook-xml/package.py

@@ -0,0 +1,19 @@
+import os
+import glob
+from spack import *
+
+
+class DocbookXml(Package):
+    """Docbook DTD XML files."""
+    homepage = "http://www.oasis-open.org/docbook"
+    url = "http://www.oasis-open.org/docbook/xml/4.5/docbook-xml-4.5.zip"
+
+    version('4.5', '03083e288e87a7e829e437358da7ef9e')
+
+    def install(self, spec, prefix):
+        cp = which('cp')
+
+        install_args = ['-a', '-t', prefix]
+        install_args.extend(glob.glob('*'))
+
+        cp(*install_args)

var/spack/packages/doxygen/package.py

@@ -0,0 +1,25 @@
+#------------------------------------------------------------------------------
+# Author: Justin Too <justin@doubleotoo.com>
+# Date: September 11, 2015
+#------------------------------------------------------------------------------
+
+from spack import *
+
+class Doxygen(Package):
+    """Doxygen is the de facto standard tool for generating documentation
+    from annotated C++ sources, but it also supports other popular programming
+    languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba,
+    Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..
+    """
+    homepage = "http://www.stack.nl/~dimitri/doxygen/"
+    url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
+
+    version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
+
+    depends_on("cmake@2.8.12:")
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make()
+        make("install")

var/spack/packages/eigen/package.py

@@ -1,17 +0,0 @@
-from spack import *
-
-class Eigen(Package):
-    """Eigen is a C++ template library for linear algebra: matrices, vectors,
-    numerical solvers, and related algorithms.."""
-    homepage = "http://eigen.tuxfamily.org/"
-    url      = "http://bitbucket.org/eigen/eigen/get/3.2.5.tar.gz"
-
-    version('3.2.5', '8cc513ac6ec687117acadddfcacf551b')
-
-    def install(self, spec, prefix):
-        import os 
-        os.system("mkdir ./build_dir && cd ./build_dir")
-        cmake('../', *std_cmake_args)
-
-        make()
-        make("install")

var/spack/packages/elfutils/package.py

@@ -0,0 +1,26 @@
+from spack import *
+
+class Elfutils(Package):
+    """elfutils is a collection of various binary tools such as
+    eu-objdump, eu-readelf, and other utilities that allow you to
+    inspect and manipulate ELF files. Refer to Table 5.Tools Included
+    in elfutils for Red Hat Developer for a complete list of binary
+    tools that are distributed with the Red Hat Developer Toolset
+    version of elfutils."""
+
+    homepage = "https://fedorahosted.org/elfutils/"
+
+    version('0.163',
+            git='git://git.fedorahosted.org/git/elfutils.git',
+            tag='elfutils-0.163')
+
+    provides('elf')
+
+    def install(self, spec, prefix):
+        autoreconf = which('autoreconf')
+        autoreconf('-if')
+
+        configure('--prefix=%s' % prefix, '--enable-maintainer-mode')
+        make()
+        make("install")
+

var/spack/packages/fish/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Fish(Package):
+    """fish is a smart and user-friendly command line shell for OS X, Linux, and
+    the rest of the family.
+    """
+
+    homepage = "http://fishshell.com/"
+    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
+    list_url = homepage
+
+    version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/flux/package.py

@@ -0,0 +1,36 @@
+from spack import *
+import os
+
+class Flux(Package):
+    """ A next-generation resource manager (pre-alpha) """
+
+    homepage = "https://github.com/flux-framework/flux-core"
+    url      = "https://github.com/flux-framework/flux-core"
+
+    version('master', branch='master', git='https://github.com/flux-framework/flux-core')
+
+    # Also needs autotools, but should use the system version if available
+    depends_on("zeromq@4.0.4:")
+    depends_on("czmq@2.2:")
+    depends_on("lua@5.1:5.1.99")
+    depends_on("munge")
+    depends_on("libjson-c")
+    depends_on("libxslt")
+    # TODO: This provides a catalog, hacked with environment below for now
+    depends_on("docbook-xml")
+    depends_on("asciidoc")
+    depends_on("python")
+    depends_on("py-cffi")
+
+    def install(self, spec, prefix):
+        # Bootstrap with autotools
+        bash = which('bash')
+        bash('./autogen.sh')
+
+        # Fix asciidoc dependency on xml style sheets and whatnot
+        os.environ['XML_CATALOG_FILES'] = os.path.join(spec['docbook-xml'].prefix,
+                                                       'catalog.xml')
+        # Configure, compile & install
+        configure("--prefix=" + prefix)
+        make("install", "V=1")
+

var/spack/packages/gflags/package.py

@@ -0,0 +1,21 @@
+import os
+from spack import *
+
+class Gflags(Package):
+    """The gflags package contains a C++ library that implements
+    commandline flags processing. It includes built-in support for
+    standard types such as string and the ability to define flags
+    in the source file in which they are used. Online documentation
+    available at: https://gflags.github.io/gflags/"""
+
+    homepage = "https://gflags.github.io/gflags"
+    url      = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz"
+
+    version('2.1.2', 'ac432de923f9de1e9780b5254884599f')
+
+    def install(self, spec, prefix):
+        cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
+              "-DBUILD_SHARED_LIBS=ON")
+        make()
+        make("test")
+        make("install")

var/spack/packages/ghostscript/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Ghostscript(Package):
+    """an interpreter for the PostScript language and for PDF. """
+    homepage = "http://ghostscript.com/"
+    url      = "http://downloads.ghostscript.com/public/ghostscript-9.16.tar.gz"
+
+    version('9.16', '829319325bbdb83f5c81379a8f86f38f')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" %prefix, "--enable-shared")
+
+        make()
+        make("install")
+

var/spack/packages/glog/package.py

@@ -0,0 +1,15 @@
+import os
+from spack import *
+
+class Glog(Package):
+    """C++ implementation of the Google logging module."""
+
+    homepage = "https://github.com/google/glog"
+    url      = "https://github.com/google/glog/archive/v0.3.3.tar.gz"
+
+    version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

var/spack/packages/graphviz/package.py

@@ -1,24 +1,21 @@
 from spack import *
 
 class Graphviz(Package):
-    """graph visualization software."""
+    """Graph Visualization Software"""
     homepage = "http://www.graphviz.org"
     url      = "http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.38.0.tar.gz"
 
     version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
-    version('2.36.0', '1f41664dba0c93109ac8b71216bf2b57')
 
-    depends_on("cairo@1.1.10")
+    parallel = False
-    depends_on("freetype@2.1.10")
+
-    depends_on("fontconfig")
+    depends_on("swig")
-    depends_on("zlib@1.2.3")
+    depends_on("python")
-    # depends_on("libpng@1.2.10")
+    depends_on("ghostscript")
-    # depends_on("expat@2.0.0")
-    # depends_on("gd@2.0.34")
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
+        configure("--prefix=%s" %prefix)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")
+

var/spack/packages/leveldb/package.py

@@ -0,0 +1,29 @@
+import os
+import glob
+from spack import *
+
+class Leveldb(Package):
+    """LevelDB is a fast key-value storage library written at Google
+    that provides an ordered mapping from string keys to string values."""
+
+    homepage = "https://github.com/google/leveldb"
+    url      = "https://github.com/google/leveldb/archive/v1.18.tar.gz"
+
+    version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0')
+
+    depends_on("snappy")
+
+    def install(self, spec, prefix):
+        make()
+
+        mkdirp(prefix.include)
+        mkdirp(prefix.lib)
+
+        cp = which('cp')
+
+        # cp --preserve=links libleveldb.* prefix/lib
+        args = glob.glob('libleveldb.*')
+        args.append(prefix + '/lib')
+        cp('--preserve=links', *args)
+
+        cp('-r', 'include/leveldb', prefix + '/include')

var/spack/packages/libdrm/package.py

@@ -2,7 +2,7 @@
 
 class Libdrm(Package):
     """A userspace  library for  accessing the  DRM, direct
-    rendering  manager, on  Linux,  BSD and  other  operating
+    rendering  manager, on  Linux,  BSD and  other  operating 
     systems that support the  ioctl interface."""
 
     homepage = "http://dri.freedesktop.org/libdrm/" # no real website...
@@ -11,11 +11,8 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
-    depends_on("libpciaccess")
-
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
-        make("clean")
         make()
         make("install")

var/spack/packages/libelf/package.py

@@ -36,6 +36,8 @@ class Libelf(Package):
     version('0.8.13', '4136d7b4c04df68b686570afa26988ac')
     version('0.8.12', 'e21f8273d9f5f6d43a59878dc274fec7')
 
+    provides('elf')
+
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",

var/spack/packages/libffi/package.py

@@ -6,9 +6,9 @@ class Libffi(Package):
     to call any function specified by a call interface description at
     run time."""
     homepage = "https://sourceware.org/libffi/"
-    url      = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz"
+    
-
+    version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
-    version('3.1', 'f5898b29bbfd70502831a212d9249d10')
+    #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

var/spack/packages/libjson-c/package.py

@@ -0,0 +1,14 @@
+from spack import *
+
+class LibjsonC(Package):
+    """ A JSON implementation in C """
+    homepage = "https://github.com/json-c/json-c/wiki"
+    url      = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.11.tar.gz"
+
+    version('0.11', 'aa02367d2f7a830bf1e3376f77881e98')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")

var/spack/packages/libpciaccess/package.py

@@ -1,16 +1,21 @@
 from spack import *
 
 class Libpciaccess(Package):
-    """Generic PCI access library"""
+    """Generic PCI access library."""
-    homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
-    url      = "http://pkgs.fedoraproject.org/repo/pkgs/libpciaccess/libpciaccess-0.13.2.tar.bz2/b7c0d3afce14eedca57312a3141ec13a/libpciaccess-0.13.2.tar.bz2"
 
-    version('0.13.2', 'b7c0d3afce14eedca57312a3141ec13a')
+    homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
+    url      = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
+
+    version('0.13.4', git='http://anongit.freedesktop.org/git/xorg/lib/libpciaccess.git',
+            tag='libpciaccess-0.13.4')
+
+    depends_on('autoconf')
+    depends_on('libtool')
 
     def install(self, spec, prefix):
-        import os
+        from subprocess import call
-        os.system("autoconf")
+        call(["./autogen.sh"])
-        configure('--prefix=%s' % prefix)
+        configure("--prefix=%s" % prefix)
 
         make()
         make("install")

var/spack/packages/libsodium/package.py

@@ -0,0 +1,19 @@
+from spack import *
+
+class Libsodium(Package):
+    """Sodium is a modern, easy-to-use software library for encryption,
+    decryption, signatures, password hashing and more."""
+    homepage = "https://download.libsodium.org/doc/"
+    url      = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.3.tar.gz"
+
+    version('1.0.3', 'b3bcc98e34d3250f55ae196822307fab')
+    version('1.0.2', 'dc40eb23e293448c6fc908757738003f')
+    version('1.0.1', '9a221b49fba7281ceaaf5e278d0f4430')
+    version('1.0.0', '3093dabe4e038d09f0d150cef064b2f7')
+    version('0.7.1', 'c224fe3923d1dcfe418c65c8a7246316')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")

var/spack/packages/libxml2/package.py

@@ -9,11 +9,12 @@ class Libxml2(Package):
 
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
 
+    extends('python')
     depends_on('zlib')
     depends_on('xz')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
+        configure("--prefix=%s" % prefix)
-                  "--without-python")
+
         make()
         make("install")

var/spack/packages/lmdb/package.py

@@ -0,0 +1,39 @@
+import os
+from spack import *
+
+class Lmdb(Package):
+    """Read-only mirror of official repo on openldap.org. Issues and
+    pull requests here are ignored. Use OpenLDAP ITS for issues.
+    http://www.openldap.org/software/repo.html"""
+
+
+    homepage = "http://www.openldap.org/software/repo.html"
+    url      = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz"
+
+    version('0.9.16', '0de89730b8f3f5711c2b3a4ba517b648')
+
+    def install(self, spec, prefix):
+        os.chdir('libraries/liblmdb')
+
+        make()
+
+        mkdirp(prefix.bin)
+        mkdirp(prefix + '/man/man1')
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+
+        bins = ['mdb_stat', 'mdb_copy', 'mdb_dump', 'mdb_load']
+        for f in bins:
+            install(f, prefix.bin)
+
+        mans = ['mdb_stat.1', 'mdb_copy.1', 'mdb_dump.1', 'mdb_load.1']
+        for f in mans:
+            install(f, prefix + '/man/man1')
+
+        libs = ['liblmdb.a', 'liblmdb.so']
+        for f in libs:
+            install(f, prefix.lib)
+
+        includes = ['lmdb.h']
+        for f in includes:
+            install(f, prefix.include)

var/spack/packages/lua/package.py

@@ -0,0 +1,26 @@
+from spack import *
+import os
+
+class Lua(Package):
+    """ The Lua programming language interpreter and library """
+    homepage = "http://www.lua.org"
+    url      = "http://www.lua.org/ftp/lua-5.1.5.tar.gz"
+
+    version('5.3.1', '797adacada8d85761c079390ff1d9961')
+    version('5.3.0', 'a1b0a7e92d0c85bbff7a8d27bf29f8af')
+    version('5.2.4', '913fdb32207046b273fdb17aad70be13')
+    version('5.2.3', 'dc7f94ec6ff15c985d2d6ad0f1b35654')
+    version('5.2.2', 'efbb645e897eae37cad4344ce8b0a614')
+    version('5.2.1', 'ae08f641b45d737d12d30291a5e5f6e3')
+    version('5.2.0', 'f1ea831f397214bae8a265995ab1a93e')
+    version('5.1.5', '2e115fe26e435e33b0d5c022e4490567')
+    version('5.1.4', 'd0870f2de55d59c1c8419f36e8fac150')
+    version('5.1.3', 'a70a8dfaa150e047866dc01a46272599')
+
+    depends_on('ncurses')
+
+    def install(self, spec, prefix):
+        make('INSTALL_TOP=%s' % prefix,
+             'MYLDFLAGS=-L%s/lib' % spec['ncurses'].prefix,
+             'linux',
+             'install')

var/spack/packages/mesa/package.py

@@ -1,7 +1,7 @@
 from spack import *
 
 class Mesa(Package):
-    """Mesa is an open-source implementation of the OpenGL 
+    """Mesa is an open-source implementation of the OpenGL
     specification - a system for rendering interactive 3D graphics."""
 
     homepage = "http://www.mesa3d.org"
@@ -11,9 +11,10 @@ class Mesa(Package):
     # version('10.4.4', '8d863a3c209bf5116b2babfccccc68ce')
     version('8.0.5', 'cda5d101f43b8784fa60bdeaca4056f2')
 
-    # mesa 7.x, 8.x, 9.x 
+    # mesa 7.x, 8.x, 9.x
     depends_on("libdrm@2.4.33")
     depends_on("llvm@3.0")
+    depends_on("libxml2")
 
     # patch("llvm-fixes.patch") # using newer llvm
 

var/spack/packages/mpich/package.py

@@ -38,7 +38,6 @@ class Mpich(Package):
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@1:')
 
-
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
         os.environ['MPICH_CC']  = 'cc'

var/spack/packages/munge/package.py

@@ -0,0 +1,20 @@
+from spack import *
+import os
+
+class Munge(Package):
+    """ MUNGE Uid 'N' Gid Emporium """
+    homepage = "https://code.google.com/p/munge/"
+    url      = "https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2"
+
+    version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2')
+
+    depends_on('openssl')
+    depends_on('libgcrypt')
+
+    def install(self, spec, prefix):
+        os.makedirs(os.path.join(prefix, "lib/systemd/system"))
+        configure("--prefix=%s" % prefix)
+
+        make()
+        make("install")
+

var/spack/packages/ncurses/package.py

@@ -21,3 +21,11 @@ def install(self, spec, prefix):
         make()
         make("install")
 
+        configure("--prefix=%s" % prefix,
+                  "--with-shared",
+                  "--disable-widec",
+                  "--disable-pc-files",
+                  "--without-ada")
+        make()
+        make("install")
+

var/spack/packages/netlib-blas/package.py

@@ -9,6 +9,8 @@ class NetlibBlas(Package):
 
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
 
+    variant('fpic', default=False, description="Build with -fpic compiler option")
+
     # virtual dependency
     provides('blas')
 
@@ -23,6 +25,10 @@ def patch(self):
         mf.filter('^LOADER.*',  'LOADER = f90')
         mf.filter('^CC =.*',  'CC = cc')
 
+        if '+fpic' in self.spec:
+            mf.filter('^OPTS.*=.*',  'OPTS = -O2 -frecursive -fpic')
+            mf.filter('^CFLAGS =.*',  'CFLAGS = -O3 -fpic')
+
 
     def install(self, spec, prefix):
         make('blaslib')

var/spack/packages/netlib-lapack/package.py

@@ -1,6 +1,6 @@
 from spack import *
 
-class Lapack(Package):
+class NetlibLapack(Package):
     """
     LAPACK version 3.X is a comprehensive FORTRAN library that does
     linear algebra operations including matrix inversions, least
@@ -18,9 +18,16 @@ class Lapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
+    variant('shared', default=False, description="Build shared library version")
+
+    # virtual dependency
+    provides('lapack')
+
     # blas is a virtual dependency.
     depends_on('blas')
 
+    depends_on('cmake')
+
     # Doesn't always build correctly in parallel
     parallel = False
 
@@ -39,7 +46,14 @@ def get_blas_libs(self):
 
     def install(self, spec, prefix):
         blas_libs = ";".join(self.get_blas_libs())
-        cmake(".", '-DBLAS_LIBRARIES=' + blas_libs, *std_cmake_args)
+        cmake_args = [".", '-DBLAS_LIBRARIES=' + blas_libs]
+
+        if '+shared' in spec:
+            cmake_args.append('-DBUILD_SHARED_LIBS=ON')
+
+        cmake_args += std_cmake_args
+
+        cmake(*cmake_args)
         make()
         make("install")
 

var/spack/packages/pidx/package.py

@@ -0,0 +1,21 @@
+from spack import *
+
+class Pidx(Package):
+    """PIDX Parallel I/O Library.
+
+    PIDX is an efficient parallel I/O library that reads and writes
+    multiresolution IDX data files.
+    """
+
+    homepage = "http://www.cedmav.com/pidx"
+
+    version('1.0', git='https://github.com/sci-visus/PIDX.git',
+            commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
+
+    depends_on("mpi")
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make("install")

var/spack/packages/pkg-config/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class PkgConfig(Package):
+    """pkg-config is a helper tool used when compiling applications and libraries"""
+    homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/"
+    url      = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz"
+
+    version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" %prefix, "--enable-shared")
+
+        make()
+        make("install")
+

var/spack/packages/protobuf/package.py

@@ -0,0 +1,16 @@
+import os
+from spack import *
+
+class Protobuf(Package):
+    """Google's data interchange format."""
+
+    homepage = "https://developers.google.com/protocol-buffers"
+    url      = "https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2"
+
+    version('2.5.0', 'a72001a9067a4c2c4e0e836d0f92ece4')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("check")
+        make("install")

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyCython(Package):
-    """The Cython compiler for writing C extensions for the Python language."""
-    homepage = "http://www.cython.org"
-    version("0.21.2", "d21adb870c75680dc857cd05d41046a4",
-            url="https://pypi.python.org/packages/source/C/Cython/Cython-0.21.2.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

var/spack/packages/py-Distutils2/package.py

@@ -1,15 +0,0 @@
-from spack import *
-
-class PyDistutils2(Package):
-    """Python Packaging Library."""
-    
-    homepage = "https://hg.python.org/distutils2"
-    url      = "https://pypi.python.org/packages/source/D/Distutils2/Distutils2-1.0a4.tar.gz"
-
-    version('1.0a4', '52bc9dffb394970c27e02853ae3a3241')
-
-    depends_on("python")
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)
-

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyAstroml(Package):
-    """tools for machine learning and data mining in Astronomy"""
-    homepage = "http://astroML.github.com"
-    version("0.2", "85f558368546660564f20b30efafb024",
-            url="https://pypi.python.org/packages/source/a/astroML/astroML-0.2.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyAstropy(Package):
-    """Community-developed python astronomy tools"""
-    homepage = "http://astropy.org"
-    version("0.4.2", "6dc4f643cde37ba0a8b4967dc8becee8",
-            url="https://pypi.python.org/packages/source/a/astropy/astropy-0.4.2.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

var/spack/packages/py-autopep8/package.py

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyAutopep8(Package):
-    """A tool that automatically formats Python code to conform to the PEP 8 style guide"""
-    homepage = "https://github.com/hhatto/autopep8"
-    version("1.1", "7998358d8f0efd77dcb2cc8e34e3cb5c",
-            url="https://pypi.python.org/packages/source/a/autopep8/autopep8-1.1.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyCertifi(Package):
-    """Python package for providing Mozilla's CA Bundle."""
-    homepage = "http://python-requests.org"
-    version("14.05.14", "315ea4e50673a16ab047099f816fd32a",
-            url="https://pypi.python.org/packages/source/c/certifi/certifi-14.05.14.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyDecorator(Package):
-    """Better living through Python with decorators"""
-    homepage = "https://github.com/micheles/decorator"
-    version("4.0.4", "dd3a0669e1e6f09699eefa2c7fbd9756",
-            url="https://pypi.python.org/packages/source/d/decorator/decorator-4.0.4.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyEmcee(Package):
-    """Kick ass affine-invariant ensemble MCMC sampling"""
-    homepage = "http://dan.iel.fm/emcee/"
-    version("2.1.0", "c6b6fad05c824d40671d4a4fc58dfff7",
-            url="https://pypi.python.org/packages/source/e/emcee/emcee-2.1.0.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,13 +0,0 @@
-from spack import *
-
-class PyFitsio(Package):
-    """A full featured python library to read from and write to FITS files."""
-    homepage = "https://github.com/esheldon/fitsio"
-    version("0.9.7", "75fa05f999ae8f55c8290bd78ada49e7",
-            url="https://pypi.python.org/packages/source/f/fitsio/fitsio-0.9.7.tar.gz")
-
-    extends("python")
-    depends_on("py-numpy")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyGnureadline(Package):
-    """The standard Python readline extension statically linked against the GNU readline library."""
-    homepage = "http://github.com/ludwigschwardt/python-gnureadline"
-    version("6.3.3", "c4af83c9a3fbeac8f2da9b5a7c60e51c",
-            url="https://pypi.python.org/packages/source/g/gnureadline/gnureadline-6.3.3.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -3,29 +3,14 @@
 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('3.0.0','b3f00f3c0be036fafef3b0b9d663f27e',
+    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf')
-           url='https://pypi.python.org/packages/source/i/ipython/ipython-3.0.0.tar.gz')
-    version('4.0.0','c2fecbcf1c0fbdc82625c77a50733dd6',
-           url='https://pypi.python.org/packages/source/i/ipython/ipython-4.0.0.tar.gz')
-    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf',
-            url="https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz")
     version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
-    version('3.2.1', 'f4c93d67ac4b2d4fc69df693b6f3c9e0',
-            url='https://github.com/ipython/ipython/archive/rel-3.2.1.tar.gz')
 
     extends('python')
     depends_on('py-pygments')
-    depends_on('py-setuptools@18.1')
+    depends_on('py-setuptools')
-    depends_on('py-traitlets')
-    depends_on('py-pyzmq')
-    depends_on('py-pexpect')
-    depends_on('py-tornado')
-    depends_on('py-jinja2')
 
     def install(self, spec, prefix):
-        import os
-        # os.system("spack activate py-setuptools@18.1")
-        # os.system("easy_install pip")
-        # os.system("pip install ipython[notebook]")
         python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -1,27 +0,0 @@
-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"
-
-    version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf',
-            url="https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz")
-    version('3.1.0', 'a749d90c16068687b0ec45a27e72ef8f')
-    version('3.2.1', 'f4c93d67ac4b2d4fc69df693b6f3c9e0',
-            url='https://github.com/ipython/ipython/archive/rel-3.2.1.tar.gz')
-
-    extends('python')
-    depends_on('py-pygments')
-    depends_on('py-setuptools@18.1')
-    depends_on('py-traitlets')
-    depends_on('py-pyzmq')
-    depends_on('py-pexpect')
-    depends_on('py-tornado')
-    depends_on('py-Jinja2')
-
-    def install(self, spec, prefix):
-        import os
-        # os.system("spack activate py-setuptools@18.1")
-        # os.system("easy_install pip")
-        # os.system("pip install ipython[notebook]")
-        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyIpythonGenutils(Package):
-    """Vestigial utilities from IPython"""
-    homepage = "http://ipython.org"
-    version("0.1.0", "9a8afbe0978adbcbfcb3b35b2d015a56",
-            url="https://pypi.python.org/packages/source/i/ipython_genutils/ipython_genutils-0.1.0.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyJoblib(Package):
-    """Lightweight pipelining: using Python functions as pipeline jobs."""
-    homepage = "http://packages.python.org/joblib/"
-    version("0.8.4", "90a1c25cc4dc4a8e3536093dbc35cff3",
-            url="https://pypi.python.org/packages/source/j/joblib/joblib-0.8.4.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,16 +0,0 @@
-from spack import *
-
-class PyJsonschema(Package):
-    """implementation of JSON Schema validation for Python"""
-    homepage = "https://github.com/Julian/jsonschema"
-    url      = "https://pypi.python.org/packages/source/j/jsonschema/jsonschema-2.5.1.tar.gz"
-
-    version('2.4.0','661f85c3d23094afbb9ac3c0673840bf',
-           url='https://pypi.python.org/packages/source/j/jsonschema/jsonschema-2.4.0.tar.gz')
-    version('2.5.1', '374e848fdb69a3ce8b7e778b47c30640')
-
-    extends("python")
-    depends_on("py-setuptools@18.1")
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -12,6 +12,7 @@ class PyMatplotlib(Package):
     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')

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

@@ -1,12 +1,17 @@
 from spack import *
 
 class PyMock(Package):
-    """A Python Mocking and Patching Library for Testing"""
+    """mock is a library for testing in Python. It allows you to replace parts
-    homepage = "http://www.voidspace.org.uk/python/mock/"
+    of your system under test with mock objects and make assertions about how
-    version("1.0.1", "c3971991738caa55ec7c356bbc154ee2",
+    they have been used."""
-            url="https://pypi.python.org/packages/source/m/mock/mock-1.0.1.tar.gz")
 
-    extends("python")
+    homepage = "https://github.com/testing-cabal/mock"
+    url      = "https://pypi.python.org/packages/source/m/mock/mock-1.3.0.tar.gz"
+
+    version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb')
+
+    extends('python')
+    depends_on('py-setuptools@17.1:')
 
     def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)
+        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyNumexpr(Package):
-    """Fast numerical expression evaluator for NumPy"""
-    homepage = "https://github.com/pydata/numexpr"
-    version("2.4", "df7e8d9e9dbb145b56d43c465c2bf854",
-            url="https://pypi.python.org/packages/source/n/numexpr/numexpr-2.4.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -7,9 +7,22 @@ class PyNumpy(Package):
 
     version('1.9.1', '78842b73560ec378142665e712ae4ad9')
     version('1.9.2', 'a1ed53432dbcd256398898d35bc8e645')
-
+    
     extends('python')
     depends_on('py-nose')
+    depends_on('netlib-blas+fpic')
+    depends_on('netlib-lapack+shared')
+
+    def patch(self):
+        filter_file(
+            "possible_executables = \['(gfortran|g77|ifort|efl)",
+            "possible_executables = ['fc",
+            "numpy/distutils/fcompiler/gnu.py",
+            "numpy/distutils/fcompiler/intel.py")
 
     def install(self, spec, prefix):
+        with open('site.cfg', 'w') as f:
+            f.write('[DEFAULT]\n')
+            f.write('libraries=lapack,blas\n')
+            f.write('library_dirs=%s/lib:%s/lib\n' % (spec['blas'].prefix, spec['lapack'].prefix))
         python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -6,8 +6,6 @@ class PyPandas(Package):
     homepage = "http://pandas.pydata.org/"
     url      = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73"
 
-    version('0.15.1','f6fd8d49fc801f6f3fa48f9117a6290b',
-           url='https://pypi.python.org/packages/source/p/pandas/pandas-0.15.1.tar.gz')
     version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
 

var/spack/packages/py-pep8/package.py

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPep8(Package):
-    """Python style guide checker"""
-    homepage = "http://pep8.readthedocs.org/"
-    version("1.6.1", "76cf60b245f8549cb458ffcd85710738",
-            url="https://pypi.python.org/packages/source/p/pep8/pep8-1.6.1.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPickleshare(Package):
-    """Tiny 'shelve'-like database with concurrency support"""
-    homepage = "https://github.com/vivainio/pickleshare"
-    version("0.5", "25337740507cb855ad58bfcf60f7710e",
-            url="https://pypi.python.org/packages/source/p/pickleshare/pickleshare-0.5.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPip(Package):
-    """The PyPA recommended tool for installing Python packages."""
-    homepage = "https://pip.pypa.io/"
-    version("7.1.2", "3823d2343d9f3aaab21cf9c917710196",
-            url="https://pypi.python.org/packages/source/p/pip/pip-7.1.2.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPy(Package):
-    """library with cross-python path, ini-parsing, io, code, log facilities"""
-    homepage = "http://pylib.readthedocs.org/"
-    version("1.4.26", "30c3fd92a53f1a5ed6f3591c1fe75c0e",
-            url="https://pypi.python.org/packages/source/p/py/py-1.4.26.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

var/spack/packages/py-py4j/package.py

@@ -1,15 +0,0 @@
-from spack import *
-
-
-class PyPy4j(Package):
-    """Enables Python programs to dynamically access arbitrary Java objects"""
-    homepage = "https://www.py4j.org/"
-    url      = "https://pypi.python.org/packages/source/p/py4j/py4j-0.9.tar.gz"
-
-    version('0.9', 'b6fed5faef81a5368e3d50a91a5c9a60')
-
-    extends("python")
-    depends_on("py-setuptools@18.1")
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -8,9 +8,12 @@ class PyPyside(Package):
 
     version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d')
 
+    # TODO: make build dependency
+    # depends_on("cmake")
+
     extends('python')
     depends_on('py-setuptools')
-    depends_on('qt@5.4.0')
+    depends_on('qt@:4')
 
     def patch(self):
         """Undo PySide RPATH handling and add Spack RPATH."""

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPytest(Package):
-    """pytest: simple powerful testing with Python"""
-    homepage = "http://pytest.org"
-    version("2.6.4", "14341e122f7e9031a0948eb6b01a2640",
-            url="https://pypi.python.org/packages/source/p/pytest/pytest-2.6.4.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyPythonDateutil(Package):
-    """Extensions to the standard Python datetime module"""
-    homepage = "http://labix.org/python-dateutil"
-    version("2.2", "c1f654d0ff7e33999380a8ba9783fd5c",
-            url="https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.2.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -5,8 +5,6 @@ class PyPytz(Package):
     homepage = "https://pypi.python.org/pypi/pytz"
     url      = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz"
 
-    version('2014.9','d42bda2f4c1e873e02fbd1e4acfd1b8c',
-           url='https://pypi.python.org/packages/source/p/pytz/pytz-2014.9.tar.gz')
     version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7')
     version('2015.4', '417a47b1c432d90333e42084a605d3d8')
 

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

@@ -1,16 +0,0 @@
-from spack import *
-
-class PyPyzmq(Package):
-    """official Python binding for the ZeroMQ Messaging Library"""
-    homepage = "https://github.com/zeromq/pyzmq"
-    url      = "https://pypi.python.org/packages/source/p/pyzmq/pyzmq-14.7.0.tar.gz"
-
-    version('14.4.1','a6a7fb6950b1bf5333c6795f3edf196c',
-           url='https://pypi.python.org/packages/source/p/pyzmq/pyzmq-14.4.1.tar.gz')
-    version('14.7.0', '87e3abb33af5794db5ae85c667bbf324')
-
-    extends('python')
-    depends_on('py-setuptools@18.1')
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -9,9 +9,6 @@ class PyScikitLearn(Package):
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
 
     extends('python')
-    depends_on('python@2.7.10')
-    depends_on('py-numpy@1.9.2')
-    depends_on('py-scipy@0.15.1')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -5,14 +5,14 @@ class PyScipy(Package):
     homepage = "https://pypi.python.org/pypi/scipy"
     url      = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
 
-    version('0.14.0','d7c7f4ccf8b07b08d6fe49d5cd51f85d',
-           url='https://pypi.python.org/packages/source/s/scipy/scipy-0.14.0.tar.gz')
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
 
     extends('python')
     depends_on('py-nose')
     depends_on('py-numpy')
+    depends_on('blas')
+    depends_on('lapack')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PySeaborn(Package):
-    """Seaborn: statistical data visualization"""
-    homepage = "http://stanford.edu/~mwaskom/software/seaborn/"
-    version("0.5.1", "2ce6ea7d3c67858c0b1f5793fa2043b8",
-            url="https://pypi.python.org/packages/source/s/seaborn/seaborn-0.5.1.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -3,12 +3,11 @@
 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('18.1', 'f72e87f34fbf07f299f6cb46256a0b06',
+    version('11.3.1', '01f69212e019a2420c1693fb43593930')
-            url='https://pypi.python.org/packages/source/s/setuptools/setuptools-18.1.tar.gz')
+    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
-    version('11.3.1', '01f69212e019a2420c1693fb43593930',
+    version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
-            url="https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz")
-    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad',)
 
     extends('python')
 

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

@@ -5,8 +5,6 @@ class PySix(Package):
     homepage = "https://pypi.python.org/pypi/six"
     url      = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz"
 
-    version('1.8.0','1626eb24cc889110c38f7e786ec69885',
-           url='https://pypi.python.org/packages/source/s/six/six-1.8.0.tar.gz')
     version('1.9.0', '476881ef4012262dfc8adc645ee786c4')
 
     extends('python')

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyStatsmodels(Package):
-    """Statistical computations and models for use with SciPy"""
-    homepage = "http://statsmodels.sourceforge.net/"
-    version("0.6.1", "f7580ebf7d2a2c9b87abfad190dcb9a3",
-            url="https://pypi.python.org/packages/source/s/statsmodels/statsmodels-0.6.1.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyTables(Package):
-    """Hierarchical datasets for Python"""
-    homepage = "http://www.pytables.org/"
-    version("3.1.1", "38d917f0c6dfb0bc28ce9ea0c3492524",
-            url="https://pypi.python.org/packages/source/t/tables/tables-3.1.1.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

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

@@ -1,17 +0,0 @@
-from spack import *
-
-class PyTornado(Package):
-    """Python web framework and asynchronous networking library"""
-    homepage = "http://www.tornadoweb.org/"
-    url = "https://pypi.python.org/packages/source/t/tornado/tornado-4.2.1.tar.gz"
-
-    version('4.0.2','985c0e704b765c33a6193d49d1935588',
-           url='https://pypi.python.org/packages/source/t/tornado/tornado-4.0.2.tar.gz')
-    version('4.2.1', 'd523204389cfb70121bb69709f551b20')
-
-    extends('python')
-    depends_on('py-certifi')
-    depends_on('py-setuptools@18.1')
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -1,14 +0,0 @@
-from spack import *
-
-class PyTraitlets(Package):
-    """A lightweight Traits like module"""
-    homepage = "http://traitlets.readthedocs.org/"
-    url      = "https://github.com/ipython/traitlets/archive/4.0.0.tar.gz"
-
-    version('4.0.0', 'b5b95ea5941fd9619b4704dfd8201568')
-
-    extends('python')
-    depends_on("py-setuptools@18.1")
-
-    def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)

var/spack/packages/py-triangle-plot/package.py

@@ -1,12 +0,0 @@
-from spack import *
-
-class PyTrianglePlot(Package):
-    """Make some beautiful corner plots of samples."""
-    homepage = "https://github.com/dfm/triangle.py"
-    version("0.0.6", "970a35a9bde6002d673e3188fe39f0ed",
-            url="https://pypi.python.org/packages/source/t/triangle_plot/triangle_plot-0.0.6.tar.gz")
-
-    extends("python")
-
-    def install(self, spec, prefix):
-        python("setup.py", "install", "--prefix=%s" % prefix)

var/spack/packages/samtools/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Samtools(Package):
+    """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
+       including sorting, merging, indexing and generating
+       alignments in a per-position format"""
+
+    homepage = "www.htslib.org"
+    version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2")
+
+    depends_on("zlib")
+    depends_on("mpc")
+    parallel=False
+    patch("samtools1.2.patch",level=0)
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "install")
+

var/spack/packages/samtools/samtools1.2.patch

@@ -0,0 +1,20 @@
+--- Makefile	2015-02-03 08:27:34.000000000 -0800
++++ Makefile.new	2015-07-21 10:38:27.881406892 -0700
+@@ -26,7 +26,7 @@
+ CFLAGS   = -g -Wall -O2
+ LDFLAGS  =
+ LDLIBS   =
+-DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
++DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0
+ LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
+             sam_header.o bam_plbuf.o
+ AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
+@@ -37,7 +37,7 @@
+             faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
+             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
+ INCLUDES=   -I. -I$(HTSDIR)
+-LIBCURSES=  -lcurses # -lXCurses
++#LIBCURSES=  -lcurses # -lXCurses
+ 
+ prefix      = /usr/local
+ exec_prefix = $(prefix)

var/spack/packages/scorep/package.py

@@ -1,11 +1,10 @@
 # FIXME: Add copyright statement
 
 from spack import *
-from contextlib import closing
 
 class Scorep(Package):
-    """The Score-P measurement infrastructure is a highly scalable and 
+    """The Score-P measurement infrastructure is a highly scalable and
-       easy-to-use tool suite for profiling, event tracing, and online 
+       easy-to-use tool suite for profiling, event tracing, and online
        analysis of HPC applications."""
 
     # FIXME: add a proper url for your package's homepage here.
@@ -20,7 +19,7 @@ class Scorep(Package):
     depends_on("mpi")
     depends_on("papi")
     # depends_on("otf2@1.2:1.2.1") # only Score-P 1.2.x
-    depends_on("otf2") 
+    depends_on("otf2")
     depends_on("opari2")
     depends_on("cube@4.2:4.2.3")
 
@@ -53,12 +52,12 @@ def install(self, spec, prefix):
         # Use a custom compiler configuration, otherwise the score-p
         # build system messes with spack's compiler settings.
         # Create these three files in the build directory
-        with closing(open("platform-backend-user-provided", "w")) as backend_file:
+        with open("platform-backend-user-provided", "w") as backend_file:
             backend_file.write(self.backend_user_provided)
-        with closing(open("platform-frontend-user-provided", "w")) as frontend_file:
+        with open("platform-frontend-user-provided", "w") as frontend_file:
             frontend_file.write(self.frontend_user_provided)
-        with closing(open("platform-mpi-user-provided", "w")) as mpi_file:
+        with open("platform-mpi-user-provided", "w") as mpi_file:
-            mpi_file.write(self.mpi_user_provided)            
+            mpi_file.write(self.mpi_user_provided)
 
         configure_args = ["--prefix=%s" % prefix,
                           "--with-custom-compilers",

var/spack/packages/snappy/package.py

@@ -0,0 +1,15 @@
+import os
+from spack import *
+
+class Snappy(Package):
+    """A fast compressor/decompressor: https://code.google.com/p/snappy"""
+
+    homepage = "https://code.google.com/p/snappy"
+    url      = "https://github.com/google/snappy/releases/download/1.1.3/snappy-1.1.3.tar.gz"
+
+    version('1.1.3', '7358c82f133dc77798e4c2062a749b73')
+
+    def install(self, spec, prefix):
+        configure("--prefix=" + prefix)
+        make()
+        make("install")

var/spack/packages/stat/package.py

@@ -9,17 +9,20 @@ class Stat(Package):
     version('2.1.0', 'ece26beaf057aa9134d62adcdda1ba91')
     version('2.0.0', 'c7494210b0ba26b577171b92838e1a9b')
 
+    variant('dysect', default=False, description="enable DySectAPI")
+
     depends_on('libelf')
     depends_on('libdwarf')
     depends_on('dyninst')
     depends_on('graphlib')
+    depends_on('graphviz')
     depends_on('launchmon')
     depends_on('mrnet')
 
     patch('configure_mpicxx.patch', when='@2.1.0')
 
     def install(self, spec, prefix):
-        configure(
+        configure_args = [
             "--enable-gui",
             "--prefix=%s" % prefix,
             "--disable-examples", # Examples require MPI: avoid this dependency.
@@ -27,7 +30,11 @@ def install(self, spec, prefix):
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
-            "--with-libdwarf=%s"    % spec['libdwarf'].prefix)
+            "--with-libdwarf=%s"    % spec['libdwarf'].prefix
+            ]
+        if '+dysect' in spec:
+            configure_args.append('--enable-dysectapi')
+        configure(*configure_args)
 
         make(parallel=False)
         make("install")

var/spack/packages/vim/package.py

@@ -35,15 +35,26 @@ class Vim(Package):
     variant('ruby', default=False, description="build with Ruby")
     depends_on('ruby', when='+ruby')
 
+    variant('cscope', default=False, description="build with cscope support")
+    depends_on('cscope', when='+cscope')
+
+    variant('gui', default=False, description="build with gui (gvim)")
+    # virtual dependency?
+
     def install(self, spec, prefix):
       feature_set = None
       for fs in self.feature_sets:
         if "+" + fs in spec:
           if feature_set is not None:
-            tty.error("Only one feature set allowed, both {} and {} specified".format(
+            tty.error("Only one feature set allowed, both %s and %s specified"
-              feature_set,
+                      % (feature_set, fs))
-              fs))
           feature_set = fs
+      if '+gui' in spec:
+        if feature_set is not None:
+          if feature_set is not 'huge':
+            tty.error("+gui variant requires 'huge' feature set, %s was specified"
+                      % feature_set)
+        feature_set = 'huge'
       if feature_set is None:
         feature_set = 'normal'
 
@@ -60,6 +71,12 @@ def install(self, spec, prefix):
       else:
         configure_args.append("--enable-rubyinterp=dynamic")
 
+      if '+gui' in spec:
+        configure_args.append("--enable-gui=auto")
+
+      if '+cscope' in spec:
+        configure_args.append("--enable-cscope")
+
       configure("--prefix=%s" % prefix, *configure_args)
 
       make()

var/spack/packages/zeromq/package.py

@@ -0,0 +1,20 @@
+from spack import *
+
+class Zeromq(Package):
+    """ The ZMQ networking/concurrency library and core API """
+    homepage = "http://zguide.zeromq.org/"
+    url      = "http://download.zeromq.org/zeromq-4.1.2.tar.gz"
+
+    version('4.1.2', '159c0c56a895472f02668e692d122685')
+    version('4.1.1', '0a4b44aa085644f25c177f79dc13f253')
+    version('4.0.7', '9b46f7e7b0704b83638ef0d461fd59ab')
+    version('4.0.6', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6')
+    version('4.0.5', '73c39f5eb01b9d7eaf74a5d899f1d03d')
+
+    depends_on("libsodium")
+
+    def install(self, spec, prefix):
+        configure("--with-libsodium","--prefix=%s" % prefix)
+
+        make()
+        make("install")