Revert "added a bunch of packages and added submodule"

This reverts commit 79808da7.

.gitignore

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

.gitmodules

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

python_recipe_parser @ 3158074a

+Subproject commit 3158074a2d74f99aa72289dfcf093b1b0ba4474e

var/spack/packages/asciidoc/package.py

+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

+--- 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

+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

+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

+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

+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

+#------------------------------------------------------------------------------
+# 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

-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

+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

+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

+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

+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

+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

+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

 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")
-    depends_on("freetype@2.1.10")
-    depends_on("fontconfig")
-    depends_on("zlib@1.2.3")
-    # depends_on("libpng@1.2.10")
-    # depends_on("expat@2.0.0")
-    # depends_on("gd@2.0.34")
+    parallel = False
+
+    depends_on("swig")
+    depends_on("python")
+    depends_on("ghostscript")
 
     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

+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')