Merge remote-tracking branch 'upstream/develop' into develop

.mailmap

@@ -0,0 +1,11 @@
+Todd Gamblin       <tgamblin@llnl.gov>          George Todd Gamblin <gamblin2@llnl.gov>
+Adam Moody         <moody20@llnl.gov>           Adam T. Moody       <moody20@llnl.gov>
+Alfredo Gimenez    <gimenez1@llnl.gov>          Alfredo Gimenez     <alfredo.gimenez@gmail.com>
+David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra324.llnl.gov>
+David Boehme       <boehme3@llnl.gov>           David Boehme        <boehme3@sierra648.llnl.gov>
+Kevin Brandstatter <kjbrandstatter@gmail.com>   Kevin Brandstatter  <kbrandst@hawk.iit.edu>
+Luc Jaulmes        <luc.jaulmes@bsc.es>         Luc Jaulmes         <jaulmes1@llnl.gov>
+Saravan Pantham    <saravan.pantham@gmail.com>  Saravan Pantham     <pantham1@surface86.llnl.gov
+Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <scogland1@llnl.gov>
+Tom Scogland       <tscogland@llnl.gov>         Tom Scogland        <tom.scogland@gmail.com>
+Joachim Protze     <protze@rz.rwth-aachen.de>   jprotze             <protze@rz.rwth-aachen.de>

lib/spack/external/pyqver2.py

@@ -165,12 +165,24 @@ def visitCallFunc(self, node):
         def rollup(n):
             if isinstance(n, compiler.ast.Name):
                 return n.name
+            elif isinstance(n, compiler.ast.Const):
+                return type(n.value).__name__
             elif isinstance(n, compiler.ast.Getattr):
                 r = rollup(n.expr)
                 if r:
                     return r + "." + n.attrname
         name = rollup(node.node)
         if name:
+            # Special handling for empty format strings, which aren't
+            # allowed in Python 2.6
+            if name in ('unicode.format', 'str.format'):
+                n = node.node
+                if isinstance(n, compiler.ast.Getattr):
+                    n = n.expr
+                    if isinstance(n, compiler.ast.Const):
+                        if '{}' in n.value:
+                            self.add(node, (2,7), name + ' with {} format string')
+
             v = Functions.get(name)
             if v is not None:
                 self.add(node, v, name)

lib/spack/spack/build_environment.py

@@ -88,10 +88,10 @@ def set_compiler_environment_variables(pkg):
     compiler = pkg.compiler
 
     # Set compiler variables used by CMake and autotools
-    os.environ['CC']  = 'cc'
-    os.environ['CXX'] = 'c++'
-    os.environ['F77'] = 'f77'
-    os.environ['FC']  = 'f90'
+    os.environ['CC']  = join_path(spack.build_env_path, 'cc')
+    os.environ['CXX'] = join_path(spack.build_env_path, 'c++')
+    os.environ['F77'] = join_path(spack.build_env_path, 'f77')
+    os.environ['FC']  = join_path(spack.build_env_path, 'f90')
 
     # Set SPACK compiler variables so that our wrapper knows what to call
     if compiler.cc:

lib/spack/spack/cmd/find.py

@@ -92,7 +92,7 @@ def display_specs(specs, **kwargs):
             # Print one spec per line along with prefix path
             width = max(len(s) for s in abbreviated)
             width += 2
-            format = "    %-{}s%s".format(width)
+            format = "    %%-%ds%%s" % width
 
             for abbrv, spec in zip(abbreviated, specs):
                 if hashes:

lib/spack/spack/fetch_strategy.py

@@ -425,12 +425,21 @@ def fetch(self):
             if self.git_version > ver('1.7.10'):
                 args.append('--single-branch')
 
+            cloned = False
             # Yet more efficiency, only download a 1-commit deep tree
             if self.git_version >= ver('1.7.1'):
-                args.extend(['--depth','1'])
+                try:
+                    self.git(*(args + ['--depth','1', self.url]))
+                    cloned = True
+                except spack.error.SpackError:
+                    # This will fail with the dumb HTTP transport
+                    # continue and try without depth, cleanup first
+                    pass
+
+            if not cloned:
+                args.append(self.url)
+                self.git(*args)
 
-            args.append(self.url)
-            self.git(*args)
             self.stage.chdir_to_source()
 
             # For tags, be conservative and check them out AFTER

lib/spack/spack/test/python_version.py

@@ -41,13 +41,10 @@
 
 class PythonVersionTest(unittest.TestCase):
 
-    def spack_python_files(self):
+    def pyfiles(self, *search_paths):
         # first file is the spack script.
         yield spack.spack_file
 
-        # Next files are all the source files and package files.
-        search_paths = [spack.lib_path, spack.var_path]
-
         # Iterate through the whole spack source tree.
         for path in search_paths:
             for root, dirnames, filenames in os.walk(path):
@@ -56,16 +53,20 @@ def spack_python_files(self):
                         yield os.path.join(root, filename)
 
 
-    def all_package_py_files(self):
+    def package_py_files(self):
         for name in spack.db.all_package_names():
             yield spack.db.filename_for_package_name(name)
 
 
-    def check_python_versions(self, files):
+    def check_python_versions(self, *files):
         # dict version -> filename -> reasons
         all_issues = {}
 
         for fn in files:
+            if fn != '/Users/gamblin2/src/spack/var/spack/packages/vim/package.py':
+                continue
+            print fn
+
             with open(fn) as pyfile:
                 versions = pyqver2.get_versions(pyfile.read())
                 for ver, reasons in versions.items():
@@ -101,8 +102,8 @@ def check_python_versions(self, files):
 
 
     def test_core_module_compatibility(self):
-        self.check_python_versions(self.spack_python_files())
+        self.check_python_versions(*self.pyfiles(spack.lib_path))
 
 
     def test_package_module_compatibility(self):
-        self.check_python_versions(self.all_package_py_files())
+        self.check_python_versions(*self.pyfiles(spack.packages_path))

lib/spack/spack/util/executable.py

@@ -34,6 +34,7 @@
 import spack
 import spack.error
 
+
 class Executable(object):
     """Class representing a program that can be run on the command line."""
     def __init__(self, name):
@@ -58,7 +59,20 @@ def __call__(self, *args, **kwargs):
         return_output = kwargs.get("return_output", False)
         fail_on_error = kwargs.get("fail_on_error", True)
         ignore_errors = kwargs.get("ignore_errors", ())
+
+        output        = kwargs.get("output", sys.stdout)
         error         = kwargs.get("error", sys.stderr)
+        input         = kwargs.get("input", None)
+
+        def streamify(arg, mode):
+            if isinstance(arg, basestring):
+                return open(arg, mode), True
+            elif arg is None and mode != 'r':
+                return open(os.devnull, mode), True
+            return arg, False
+        output, ostream = streamify(output, 'w')
+        error,  estream = streamify(error,  'w')
+        input,  istream = streamify(input,  'r')
 
         # if they just want to ignore one error code, make it a tuple.
         if isinstance(ignore_errors, int):
@@ -77,16 +91,12 @@ def __call__(self, *args, **kwargs):
         cmd_line = ' '.join(cmd)
         tty.debug(cmd_line)
 
-        close_error = False
         try:
-            if error is None:
-                error = open(os.devnull, 'w')
-                close_error = True
-
             proc = subprocess.Popen(
                 cmd,
+                stdin=input,
                 stderr=error,
-                stdout=subprocess.PIPE if return_output else sys.stdout)
+                stdout=subprocess.PIPE if return_output else output)
             out, err = proc.communicate()
             self.returncode = proc.returncode
 
@@ -110,8 +120,9 @@ def __call__(self, *args, **kwargs):
                     % (proc.returncode, cmd_line))
 
         finally:
-            if close_error:
-                error.close()
+            if ostream: output.close()
+            if estream: error.close()
+            if istream: input.close()
 
 
     def __eq__(self, other):

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/bear/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class Bear(Package):
+    """Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems."""
+    homepage = "https://github.com/rizsotto/Bear"
+    url      = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz"
+
+    version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011')
+
+    depends_on("cmake")
+    depends_on("python")
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make("all")
+        make("install")

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/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/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

@@ -0,0 +1,21 @@
+from spack import *
+
+class Libpciaccess(Package):
+    """Generic PCI access library."""
+
+    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):
+        from subprocess import call
+        call(["./autogen.sh"])
+        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,
-                  "--without-python")
+        configure("--prefix=%s" % prefix)
+
         make()
         make("install")

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/mpfr/package.py

@@ -33,6 +33,8 @@ class Mpfr(Package):
     version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138')
     # version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19')
 
+    depends_on('gmp')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()

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/py-mock/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+class PyMock(Package):
+    """mock is a library for testing in Python. It allows you to replace parts
+    of your system under test with mock objects and make assertions about how
+    they have been used."""
+
+    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)

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

@@ -16,6 +16,10 @@ class PyPandas(Package):
     depends_on('py-scipy')
     depends_on('py-setuptools')
     depends_on('py-pytz')
+    depends_on('libdrm')
+    depends_on('libpciaccess')
+    depends_on('llvm')
+    depends_on('mesa')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)

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

@@ -7,6 +7,7 @@ class PySetuptools(Package):
 
     version('11.3.1', '01f69212e019a2420c1693fb43593930')
     version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
+    version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
 
     extends('python')
 

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(
-              feature_set,
-              fs))
+            tty.error("Only one feature set allowed, both %s and %s specified"
+                      % (feature_set, 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")

var/spack/packages/zsh/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+class Zsh(Package):
+    """ The ZSH shell """
+    homepage = "http://www.zsh.org"
+    url      = "http://www.zsh.org/pub/zsh-5.0.8.tar.bz2"
+
+    version('5.0.8', 'e6759e8dd7b714d624feffd0a73ba0fe')
+
+    depends_on("pcre")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")