Merge staging into closure-size

The most complex problems were from dealing with switches reverted in
the meantime (gcc5, gmp6, ncurses6).
It's likely that darwin is (still) broken nontrivially.

pkgs/development/python-modules/dbus/default.nix

@@ -15,6 +15,10 @@ if isPyPy then throw "dbus-python not supported for interpreter ${python.executa
 
   doCheck = false; # https://bugs.freedesktop.org/show_bug.cgi?id=57140
 
+  # Set empty pythonPath, so that the package is recognized as a python package
+  # for python.buildEnv
+  pythonPath = [];
+
   meta = {
     description = "Python DBus bindings";
     license = stdenv.lib.licenses.mit;

pkgs/development/python-modules/fix_swiftclient_mocking.patch

@@ -0,0 +1,26 @@
+From f37947a7e083532676a9f2ed079dff6bdc19a8e9 Mon Sep 17 00:00:00 2001
+From: Sabari Kumar Murugesan <smurugesan@vmware.com>
+Date: Tue, 15 Sep 2015 14:22:11 -0700
+Subject: [PATCH] Fix swift store tests for latest swiftclient
+
+The latest swiftclient (2.6.0) breaks some of the swift store
+tests as a mock function's parameters got changed.
+
+Change-Id: I36512fbe642f4f12cf1382fdf0e37eccbf1acba4
+---
+ glance_store/tests/unit/test_swift_store.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/glance_store/tests/unit/test_swift_store.py b/glance_store/tests/unit/test_swift_store.py
+index f738cf9..3fe4699 100644
+--- a/glance_store/tests/unit/test_swift_store.py
++++ b/glance_store/tests/unit/test_swift_store.py
+@@ -92,7 +92,7 @@ def fake_head_container(url, token, container, **kwargs):
+     def fake_put_container(url, token, container, **kwargs):
+         fixture_containers.append(container)
+ 
+-    def fake_post_container(url, token, container, headers, http_conn=None):
++    def fake_post_container(url, token, container, headers, **kwargs):
+         for key, value in six.iteritems(headers):
+             fixture_container_headers[key] = value
+ 

pkgs/development/python-modules/generic/default.nix

@@ -59,7 +59,7 @@ if disabled
 then throw "${name} not supported for interpreter ${python.executable}"
 else
 
-python.stdenv.mkDerivation (attrs // {
+python.stdenv.mkDerivation (builtins.removeAttrs attrs ["disabled"] // {
   inherit doCheck;
 
   name = namePrefix + name;
@@ -161,15 +161,14 @@ python.stdenv.mkDerivation (attrs // {
     '';
 
   shellHook = attrs.shellHook or ''
+    ${preShellHook}
     if test -e setup.py; then
-       tmp_path=/tmp/`pwd | md5sum | cut -f 1 -d " "`-$name
-       mkdir -p $tmp_path/lib/${python.libPrefix}/site-packages
-       ${preShellHook}
+       tmp_path=$(mktemp -d)
        export PATH="$tmp_path/bin:$PATH"
-       export PYTHONPATH="$tmp_path/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
-       ${python}/bin/${python.executable} setup.py develop --prefix $tmp_path
-       ${postShellHook}
+       export PYTHONPATH="$tmp_path/${python.sitePackages}:$PYTHONPATH"
+       ${python.interpreter} setup.py develop --prefix $tmp_path
     fi
+    ${postShellHook}
   '';
 
   meta = with lib.maintainers; {

pkgs/development/python-modules/h5py/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, python, buildPythonPackage
-, numpy, hdf5, cython
+, numpy, hdf5, cython, six, pkgconfig
 , mpiSupport ? false, mpi4py ? null, mpi ? null }:
 
 assert mpiSupport == hdf5.mpiSupport;
@@ -12,24 +12,26 @@ assert mpiSupport -> mpi != null
 with stdenv.lib;
 
 buildPythonPackage rec {
-  name = "h5py-2.3.1";
+  name = "h5py-${version}";
+  version = "2.5.0";
 
   src = fetchurl {
     url = "https://pypi.python.org/packages/source/h/h5py/${name}.tar.gz";
-    md5 = "8f32f96d653e904d20f9f910c6d9dd91";
+    sha256 = "9833df8a679e108b561670b245bcf9f3a827b10ccb3a5fa1341523852cfac2f6";
   };
 
-  setupPyBuildFlags = [ "--hdf5=${hdf5}" ]
-    ++ optional mpiSupport "--mpi"
-    ;
-  setupPyInstallFlags = setupPyBuildFlags;
+  configure_flags = "--hdf5=${hdf5}" + optionalString mpiSupport " --mpi";
+
+  postConfigure = ''
+    ${python.executable} setup.py configure ${configure_flags}
+  '';
 
   preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";
 
-  buildInputs = [ hdf5 cython ]
+  buildInputs = [ hdf5 cython pkgconfig ]
     ++ optional mpiSupport mpi
     ;
-  propagatedBuildInputs = [ numpy ]
+  propagatedBuildInputs = [ numpy six]
     ++ optional mpiSupport mpi4py
     ;
 

pkgs/development/python-modules/matplotlib/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, python, buildPythonPackage, pycairo
-, which, dateutil, nose, numpy, pyparsing, tornado
+, which, cycler, dateutil, nose, numpy, pyparsing, sphinx, tornado
 , freetype, libpng, pkgconfig, mock, pytz, pygobject3
 , enableGhostscript ? false, ghostscript ? null, gtk3
 , enableGtk2 ? false, pygtk ? null, gobjectIntrospection
@@ -10,25 +10,34 @@ assert enableGhostscript -> ghostscript != null;
 assert enableGtk2 -> pygtk != null;
 
 buildPythonPackage rec {
-  name = "matplotlib-1.4.3";
+  name = "matplotlib-${version}";
+  version = "1.5.0";
 
   src = fetchurl {
-    url = "mirror://sourceforge/matplotlib/${name}.tar.gz";
-    sha256 = "1dn05cvd0g984lzhh72wa0z93psgwshbbg93fkab6slx5m3l95av";
+    url = "https://pypi.python.org/packages/source/m/matplotlib/${name}.tar.gz";
+    sha256 = "67b08b1650a00a6317d94b76a30a47320087e5244920604c5462188cba0c2646";
   };
   
   XDG_RUNTIME_DIR = "/tmp";
 
-  buildInputs = [ python which stdenv ]
+  buildInputs = [ python which sphinx stdenv ]
     ++ stdenv.lib.optional enableGhostscript ghostscript;
 
   propagatedBuildInputs =
-    [ dateutil nose numpy pyparsing tornado freetype 
+    [ cycler dateutil nose numpy pyparsing tornado freetype 
       libpng pkgconfig mock pytz  
     ]
     ++ stdenv.lib.optional enableGtk2 pygtk
     ++ stdenv.lib.optionals enableGtk3 [ cairo pycairo gtk3 gobjectIntrospection pygobject3 ];
 
+  patchPhase = ''
+    # Failing test: ERROR: matplotlib.tests.test_style.test_use_url
+    sed -i 's/test_use_url/fails/' lib/matplotlib/tests/test_style.py
+    # Failing test: ERROR: test suite for <class 'matplotlib.sphinxext.tests.test_tinypages.TestTinyPages'>
+    sed -i 's/TestTinyPages/fails/' lib/matplotlib/sphinxext/tests/test_tinypages.py
+  '';
+
+
   meta = with stdenv.lib; {
     description = "python plotting library, making publication quality plots";
     homepage    = "http://matplotlib.sourceforge.net/";

pkgs/development/python-modules/pyatspi/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, pkgconfig, python3, python3Packages, at_spi2_core }:
 
 stdenv.mkDerivation rec {
-  version = "2.16.0";
+  version = "2.18.0";
   name = "pyatspi-${version}";
 
   src = fetchurl {
-    url = "mirror://gnome/sources/pyatspi/2.16/${name}.tar.xz";
-    sha256 = "185lwgv9bk1fc6vw2xypznzr7p8fhp84ggnrb706zwgalmy8aym6";
+    url = "mirror://gnome/sources/pyatspi/2.18/${name}.tar.xz";
+    sha256 = "0imbyk2v6c11da7pkwz91313pkkldxs8zfg81zb2ql6h0nnh6vzq";
   };
 
   buildInputs = [

pkgs/development/python-modules/pycairo/default.nix

@@ -1,6 +1,6 @@
-{ stdenv, fetchurl, fetchpatch, python, pkgconfig, cairo, xlibsWrapper, isPyPy }:
+{ stdenv, fetchurl, fetchpatch, python, pkgconfig, cairo, xlibsWrapper, isPyPy, isPy35 }:
 
-if isPyPy then throw "pycairo not supported for interpreter ${python.executable}" else stdenv.mkDerivation rec {
+if (isPyPy || isPy35) then throw "pycairo not supported for interpreter ${python.executable}" else stdenv.mkDerivation rec {
   version = "1.10.0";
   name = "pycairo-${version}";
   src = if python.is_py3k or false
@@ -36,4 +36,6 @@ if isPyPy then throw "pycairo not supported for interpreter ${python.executable}
   '';
   buildPhase = "${python.executable} waf";
   installPhase = "${python.executable} waf install";
+
+  meta.platforms = stdenv.lib.platforms.linux;
 }

pkgs/development/python-modules/setuptools/default.nix

@@ -4,7 +4,7 @@ stdenv.mkDerivation rec {
   shortName = "setuptools-${version}";
   name = "${python.executable}-${shortName}";
 
-  version = "18.2";
+  version = "18.2";  # 18.4 breaks python34Packages.characteristic and many others
 
   src = fetchurl {
     url = "http://pypi.python.org/packages/source/s/setuptools/${shortName}.tar.gz";

pkgs/development/python-modules/sphinx-1.3.1-pr-1946.patch

@@ -0,0 +1,35 @@
+From 7ce3b991229c74262f81ab7692a1dc6bde2416ee Mon Sep 17 00:00:00 2001
+From: Barry Warsaw <barry@python.org>
+Date: Thu, 25 Jun 2015 11:54:05 -0400
+Subject: [PATCH] One way to work around the lack of
+ html.parser.HTMLParserError in Python 3.5
+
+---
+ sphinx/builders/linkcheck.py | 12 +++++++++++-
+ 1 file changed, 11 insertions(+), 1 deletion(-)
+
+diff --git a/sphinx/builders/linkcheck.py b/sphinx/builders/linkcheck.py
+index 9f5c213..b05c5b2 100644
+--- a/sphinx/builders/linkcheck.py
++++ b/sphinx/builders/linkcheck.py
+@@ -19,9 +19,19 @@
+ from six.moves.urllib.request import build_opener, Request, HTTPRedirectHandler
+ from six.moves.urllib.parse import unquote, urlsplit, quote
+ from six.moves.urllib.error import HTTPError
+-from six.moves.html_parser import HTMLParser, HTMLParseError
++from six.moves.html_parser import HTMLParser
+ from docutils import nodes
+ 
++# 2015-06-25 barry@python.org.  This exception was deprecated in Python 3.3 and
++# removed in Python 3.5, however for backward compatibility reasons, we're not
++# going to just remove it.  If it doesn't exist, define an exception that will
++# never be caught but leaves the code in check_anchor() intact.
++try:
++    from six.moves.html_parser import HTMLParseError
++except ImportError:
++    class HTMLParseError(Exception):
++        pass
++
+ from sphinx.builders import Builder
+ from sphinx.util.console import purple, red, darkgreen, darkgray, \
+     darkred, turquoise

pkgs/development/python-modules/suds-0.4-CVE-2013-2217.patch

@@ -0,0 +1,19 @@
+--- suds.orig/suds/cache.py	2013-06-29 16:26:16.930326017 +0200
++++ suds.orig/suds/cache.py	2013-06-29 16:02:15.000000000 +0200
+@@ -19,6 +19,7 @@ 
+ """
+ 
+ import os
++import tempfile
+ import suds
+ from tempfile import gettempdir as tmp
+ from suds.transport import *
+@@ -138,7 +139,7 @@ 
+         @type duration: {unit:value}
+         """
+         if location is None:
+-            location = os.path.join(tmp(), 'suds')
++            location = tempfile.mkdtemp()
+         self.location = location
+         self.duration = (None, 0)
+         self.setduration(**duration)

pkgs/development/python-modules/tables/default.nix

@@ -2,12 +2,12 @@
 , cython, bzip2, lzo, numpy, numexpr, hdf5 }:
 
 buildPythonPackage rec {
-  version = "3.1.1";
+  version = "3.2.2";
   name = "tables-${version}";
 
   src = fetchurl {
-    url = "mirror://sourceforge/pytables/${name}.tar.gz";
-    sha256 = "18rdzv9xwiapb5c8y47rk2fi3fdm2dpjf68wfycma67ifrih7f9r";
+    url = "https://pypi.python.org/packages/source/t/tables/${name}.tar.gz";
+    sha256 = "3564b351a71ec1737b503b001eb7ceae1f65d5d6e3ffe1ea75aafba10f37fa84";
   };
 
   buildInputs = [ hdf5 cython bzip2 lzo ];

pkgs/development/python-modules/testtools_support_unittest2.patch

@@ -0,0 +1,22 @@
+From e600d12980ccb807ba1ca3fb6a4da1d0b89c02f6 Mon Sep 17 00:00:00 2001
+From: Robert Collins <robertc@robertcollins.net>
+Date: Wed, 1 Jul 2015 15:46:28 +1200
+Subject: [PATCH] Fix tests with unittest2 1.1.0 and higher.
+
+Change-Id: I4613d47852fbf901819f197f6e388ccaa717b53e
+---
+ testtools/tests/test_run.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/testtools/tests/test_run.py b/testtools/tests/test_run.py
+index ead716b..433b6f8 100644
+--- a/testtools/tests/test_run.py
++++ b/testtools/tests/test_run.py
+@@ -201,6 +201,7 @@ def test_run_list_failed_import(self):
+             run.main, ['prog', 'discover', '-l', broken.package.base, '*.py'], out)
+         self.assertEqual(2, exc.args[0])
+         self.assertThat(out.getvalue(), DocTestMatches("""\
++unittest2.loader._FailedTest.runexample
+ Failed to import test module: runexample
+ Traceback (most recent call last):
+   File ".../loader.py", line ..., in _find_test_path