Implement review requests

- use two empty lines before `class`
- change version numbering scheme for packages, use `url_for_version` to make things work
- specify dependency types
- add comment about temporarily moved download location
- update two packages to newer versions

var/spack/repos/builtin/packages/bliss/package.py

@@ -25,6 +25,7 @@
 
 from spack import *
 
+
 class Bliss(Package):
     """bliss: A Tool for Computing Automorphism Groups and Canonical
     Labelings of Graphs"""
@@ -37,7 +38,7 @@ class Bliss(Package):
     # Note: Bliss can also be built without gmp, but we don't support this yet
 
     depends_on("gmp")
-    depends_on("libtool")
+    depends_on("libtool", type='build')
 
     patch("Makefile.spack.patch")
 

var/spack/repos/builtin/packages/cdd/package.py

@@ -25,6 +25,7 @@
 
 from spack import *
 
+
 class Cdd(Package):
     """The program cdd+ (cdd, respectively) is a C++ (ANSI C)
     implementation of the Double Description Method [MRTT53] for
@@ -34,9 +35,13 @@ class Cdd(Package):
     homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/cdd.html"
     url      = "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cdd-061a.tar.gz"
 
-    version('061a', '22c24a7a9349dd7ec0e24531925a02d9')
+    def url_for_version(self, version):
+        return ("ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cdd-%s.tar.gz" %
+                str(version.dotted()).replace('.', ''))
 
-    depends_on("libtool")
+    version('0.61a', '22c24a7a9349dd7ec0e24531925a02d9')
+
+    depends_on("libtool", type="build")
 
     patch("Makefile.spack.patch")
 

var/spack/repos/builtin/packages/cddlib/package.py

@@ -25,21 +25,32 @@
 
 from spack import *
 
+
 class Cddlib(Package):
     """The C-library cddlib is a C implementation of the Double Description 
     Method of Motzkin et al. for generating all vertices (i.e. extreme points)
     and extreme rays of a general convex polyhedron in R^d given by a system 
     of linear inequalities"""
     homepage = "https://www.inf.ethz.ch/personal/fukudak/cdd_home/"
+    # This is the original download url. It is currently down [2016-08-23],
+    # but should be reinstated or updated once the issue is resolved.
     # url      = "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-094h.tar.gz"
     url      = "http://pkgs.fedoraproject.org/lookaside/pkgs/cddlib/cddlib-094h.tar.gz/1467d270860bbcb26d3ebae424690e7c/cddlib-094h.tar.gz"
 
-    version('094h', '1467d270860bbcb26d3ebae424690e7c')
+    def url_for_version(self, version):
+        # Since the commit id is part of the version, we can't
+        # auto-generate the string, and we need to explicitly list all
+        # known versions here. Currently, there is only one version.
+        if str(version) == '0.94h':
+            return "http://pkgs.fedoraproject.org/lookaside/pkgs/cddlib/cddlib-094h.tar.gz/1467d270860bbcb26d3ebae424690e7c/cddlib-094h.tar.gz"
+        raise InstallError("Unsupported version %s" % str(version))
+
+    version('0.94h', '1467d270860bbcb26d3ebae424690e7c')
 
     # Note: It should be possible to build cddlib also without gmp
 
     depends_on("gmp")
-    depends_on("libtool")
+    depends_on("libtool", type="build")
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

var/spack/repos/builtin/packages/lrslib/package.py

@@ -25,24 +25,28 @@
 
 from spack import *
 
+
 class Lrslib(Package):
     """lrslib Ver 6.2 is a self-contained ANSI C implementation of the
     reverse search algorithm for vertex enumeration/convex hull
     problems and comes with a choice of three arithmetic packages"""
     homepage = "http://cgm.cs.mcgill.ca/~avis/C/lrs.html"
     url      = "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-062.tar.gz"
+    def url_for_version(self, version):
+        return ("http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-%s.tar.gz" %
+                ('0' + str(version).replace('.', '')))
 
-    version('062', 'be5da7b3b90cc2be628dcade90c5d1b9')
+    version('6.2', 'be5da7b3b90cc2be628dcade90c5d1b9')
-    version('061', '0b3687c8693cd7d1f234a3f65e147551')
+    version('6.1', '0b3687c8693cd7d1f234a3f65e147551')
-    version('060', 'd600a2e62969ad03f7ab2f85f1b3709c')
+    version('6.0', 'd600a2e62969ad03f7ab2f85f1b3709c')
-    version('051', 'cca323eee8bf76f598a13d7bf67cc13d')
+    version('5.1', 'cca323eee8bf76f598a13d7bf67cc13d')
-    version('043', '86dd9a45d20a3a0069f77e61be5b46ad')
+    version('4.3', '86dd9a45d20a3a0069f77e61be5b46ad')
 
     # Note: lrslib can also be built with Boost, and probably without gmp
 
     # depends_on("boost")
     depends_on("gmp")
-    depends_on("libtool")
+    depends_on("libtool", type="build")
 
     patch("Makefile.spack.patch")
 

var/spack/repos/builtin/packages/nauty/package.py

@@ -26,14 +26,20 @@
 import shutil
 from spack import *
 
+
 class Nauty(Package):
     """nauty and Traces are programs for computing automorphism groups of
     graphsq and digraphs"""
     homepage = "http://pallini.di.uniroma1.it/index.html"
-    url      = "http://pallini.di.uniroma1.it/nauty26r5.tar.gz"
+    url      = "http://pallini.di.uniroma1.it/nauty26r7.tar.gz"
 
-    version('26r5', '91b03a7b069962e94fc9aac8831ce8d2')
+    def url_for_version(self, version):
-    version('25r9', 'e8ecd08b0892a1fb13329c147f08de6d')
+        return ("http://pallini.di.uniroma1.it/nauty%s.tar.gz" %
+                str(version).replace('.', ''))
+
+    version('2.6r7', 'b2b18e03ea7698db3fbe06c5d76ad8fe')
+    version('2.6r5', '91b03a7b069962e94fc9aac8831ce8d2')
+    version('2.5r9', 'e8ecd08b0892a1fb13329c147f08de6d')
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)

var/spack/repos/builtin/packages/panda/package.py

@@ -25,16 +25,17 @@
 
 from spack import *
 
+
 class Panda(Package):
     """PANDA: Parallel AdjaceNcy Decomposition Algorithm"""
     homepage = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/index.html"
     url      = "http://comopt.ifi.uni-heidelberg.de/software/PANDA/downloads/current_panda.tar"
 
-    version('panda', 'b06dc312ee56e13eefea9c915b70fcef')
+    version('current', 'b06dc312ee56e13eefea9c915b70fcef')
 
     # Note: Panda can also be built without MPI support
 
-    depends_on("cmake")
+    depends_on("cmake", type="build")
     depends_on("mpi")
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/polymake/package.py

@@ -25,11 +25,13 @@
 
 from spack import *
 
+
 class Polymake(Package):
     """polymake is open source software for research in polyhedral geometry"""
     homepage = "https://polymake.org/doku.php"
     url      = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.0r1.tar.bz2"
 
+    version('3.0r2', '08584547589f052ea50e2148109202ab')
     version('3.0r1', '63ecbecf9697c6826724d8a041d2cac0')
 
     # Note: Could also be built with nauty instead of bliss

var/spack/repos/builtin/packages/porta/package.py

@@ -25,6 +25,7 @@
 
 from spack import *
 
+
 class Porta(Package):
     """PORTA is a collection of routines for analyzing polytopes and
     polyhedra"""
@@ -33,7 +34,7 @@ class Porta(Package):
 
     version('1.4.1', '585179bf19d214ed364663a5d17bd5fc')
 
-    depends_on("libtool")
+    depends_on("libtool", type="build")
 
     patch("Makefile.spack.patch")
 

var/spack/repos/builtin/packages/sympol/package.py

@@ -25,6 +25,7 @@
 
 from spack import *
 
+
 class Sympol(Package):
     """SymPol is a C++ tool to work with symmetric polyhedra"""
     homepage = "http://www.math.uni-rostock.de/~rehn/software/sympol.html"