Add new versions of several Python packages (#3195)

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

@@ -30,10 +30,12 @@ class PyNose(PythonPackage):
     making it easier to write, find and run tests."""
 
     homepage = "https://pypi.python.org/pypi/nose"
-    url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz"
+    url      = "https://pypi.io/packages/source/n/nose/nose-1.3.4.tar.gz"
+    list_url = "https://pypi.python.org/pypi/nose/"
+    list_depth = 2
 
-    version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
-    version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
     version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b')
+    version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
+    version('1.3.4', '6ed7169887580ddc9a8e16048d38274d')
 
     depends_on('py-setuptools', type='build')

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

@@ -36,6 +36,8 @@ class PyNumpy(PythonPackage):
     homepage = "http://www.numpy.org/"
     url      = "https://pypi.io/packages/source/n/numpy/numpy-1.9.1.tar.gz"
 
+    version('1.12.0', '33e5a84579f31829bbbba084fe0a4300',
+            url="https://pypi.io/packages/source/n/numpy/numpy-1.12.0.zip")
     version('1.11.2', '03bd7927c314c43780271bf1ab795ebc')
     version('1.11.1', '2f44a895a8104ffac140c3a70edbd450')
     version('1.11.0', 'bc56fb9fc2895aa4961802ffbdb31d0b')
@@ -43,11 +45,10 @@ class PyNumpy(PythonPackage):
     version('1.9.2',  'a1ed53432dbcd256398898d35bc8e645')
     version('1.9.1',  '78842b73560ec378142665e712ae4ad9')
 
-    variant('blas',   default=True)
+    variant('blas',   default=True, description='Build with BLAS support')
-    variant('lapack', default=True)
+    variant('lapack', default=True, description='Build with LAPACK support')
 
-    depends_on('python@2.6:2.8,3.2:')
+    depends_on('python@2.7:2.8,3.4:')
-    depends_on('py-nose', type='build')
     depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
@@ -122,3 +123,12 @@ def patch(self):
                 if not ((platform.system() == "Darwin") and
                         (platform.mac_ver()[0] == '10.12')):
                     f.write('rpath=%s\n' % dirs)
+
+    def build_args(self, spec, prefix):
+        args = []
+
+        # From NumPy 1.10.0 on it's possible to do a parallel build
+        if self.version >= Version('1.10.0'):
+            args = ['-j', str(make_jobs)]
+
+        return args

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

@@ -33,4 +33,5 @@ class PyPip(PythonPackage):
 
     version('9.0.1', '35f01da33009719497f01a4ba69d63c9')
 
+    depends_on('python@2.6:2.7,3.3:')
     depends_on('py-setuptools', type='build')

var/spack/repos/builtin/packages/py-pytest-flake8/package.py

@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyPytestFlake8(PythonPackage):
+    """pytest plugin to check FLAKE8 requirements."""
+
+    homepage = "https://github.com/tholo/pytest-flake8"
+    url      = "https://pypi.io/packages/source/p/pytest-flake8/pytest-flake8-0.8.1.tar.gz"
+
+    version('0.8.1', '39b64ebceb2849805975a2ff4ea7e947')
+
+    depends_on('py-setuptools', type='build')
+
+    # Install requires:
+    depends_on('py-flake8@3.0:', type=('build', 'run'))
+    depends_on('py-pytest@2.8:', type=('build', 'run'))

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

@@ -27,13 +27,18 @@
 
 class PyScikitLearn(PythonPackage):
     """A set of python modules for machine learning and data mining."""
-    homepage = "https://pypi.python.org/pypi/scikit-learn"
-    url      = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz"
 
+    homepage = "https://pypi.python.org/pypi/scikit-learn"
+    url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.18.1.tar.gz"
+    list_url = "https://pypi.python.org/pypi/scikit-learn"
+    list_depth = 2
+
+    version('0.18.1', '6b0ff1eaa5010043895dd63d1e3c60c9')
     version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
     version('0.17.1', 'a2f8b877e6d99b1ed737144f5a478dfc')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('python@2.6:2.7,3.3:')
-    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-setuptools',   type='build')
-    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-numpy@1.6.1:', type=('build', 'run'))
+    depends_on('py-scipy@0.9:',   type=('build', 'run'))

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

@@ -31,21 +31,22 @@ class PyScipy(PythonPackage):
     as routines for numerical integration and optimization."""
 
     homepage = "http://www.scipy.org/"
-    url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz"
+    url = "https://pypi.io/packages/source/s/scipy/scipy-0.18.1.tar.gz"
 
-    version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327',
+    version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327')
-            url="https://pypi.python.org/packages/22/41/b1538a75309ae4913cdbbdc8d1cc54cae6d37981d2759532c1aa37a41121/scipy-0.18.1.tar.gz")
     version('0.17.0', '5ff2971e1ce90e762c59d2cd84837224')
     version('0.15.1', 'be56cd8e60591d6332aac792a5880110')
     version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a')
 
     depends_on('python@2.6:2.8,3.2:')
-    depends_on('py-nose', type='build')
+    depends_on('py-setuptools', type='build')
-    # Known not to work with 2.23, 2.25
-    depends_on('binutils@2.26:', type='build')
     depends_on('py-numpy@1.7.1:+blas+lapack', type=('build', 'run'))
 
     # NOTE: scipy picks up Blas/Lapack from numpy, see
     # http://www.scipy.org/scipylib/building/linux.html#step-4-build-numpy-1-5-0
     depends_on('blas')
     depends_on('lapack')
+
+    def build_args(self, spec, prefix):
+        # Build in parallel
+        return ['-j', str(make_jobs)]

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

@@ -30,14 +30,15 @@ class PySetuptools(PythonPackage):
        upgrading, installing, and uninstalling Python packages."""
 
     homepage = "https://pypi.python.org/pypi/setuptools"
-    url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
+    url      = "https://pypi.io/packages/source/s/setuptools/setuptools-25.2.0.tar.gz"
 
-    version('25.2.0', 'a0dbb65889c46214c691f6c516cf959c',
+    version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be',
-            url="https://pypi.python.org/packages/9f/32/81c324675725d78e7f6da777483a3453611a427db0145dfb878940469692/setuptools-25.2.0.tar.gz")
+            url="https://pypi.io/packages/source/s/setuptools/setuptools-34.2.0.zip")
+    version('25.2.0', 'a0dbb65889c46214c691f6c516cf959c')
     version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615')
     version('20.6.7', '45d6110f3ec14924e44c33411db64fe6')
-    version('20.5', 'fadc1e1123ddbe31006e5e43e927362b')
+    version('20.5',   'fadc1e1123ddbe31006e5e43e927362b')
-    version('19.2', '78353b1f80375ca5e088f4b4627ffe03')
+    version('19.2',   '78353b1f80375ca5e088f4b4627ffe03')
-    version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06')
+    version('18.1',   'f72e87f34fbf07f299f6cb46256a0b06')
-    version('16.0', '0ace0b96233516fc5f7c857d086aa3ad')
+    version('16.0',   '0ace0b96233516fc5f7c857d086aa3ad')
     version('11.3.1', '01f69212e019a2420c1693fb43593930')