Merge branch master into security-updatesorigin/security-updatesgitlab.intr/security-updates

This merge mostly take the changes made to the master branch.

Some conflict happen in top-level/default.nix due to a reformating of the
code of which is computing the fix-point. This merge fixes these issues by
adding the pkgsIndex argument, needed to re-evaluate the fix-point with
another set of packages, and also re-add the second fix-point made to
support the dependencies.

9 files changed, 60 insertions, 13 deletions

diff --git a/pkgs/development/python-modules/bootstrapped-pip/default.nix b/pkgs/development/python-modules/bootstrapped-pip/default.nix
index 31436d0ea38e..0fd6c1873b53 100644
--- a/pkgs/development/python-modules/bootstrapped-pip/default.nix
+++ b/pkgs/development/python-modules/bootstrapped-pip/default.nix
@@ -14,7 +14,7 @@ let
     sha256 = "0533cr5w14da8wdb2q4py6aizvbvsdbk3sj7m1jx9lwznvnlf5n3";
   };
 in stdenv.mkDerivation rec {
-  name = "python-${python.version}-bootstrapped-pip-${version}";
+  name = "${python.libPrefix}-bootstrapped-pip-${version}";
   version = "8.1.2";
 
   src = fetchurl {
diff --git a/pkgs/development/python-modules/cython_test.patch b/pkgs/development/python-modules/cython_test.patch
new file mode 100644
index 000000000000..5b1cece3aa50
--- /dev/null
+++ b/pkgs/development/python-modules/cython_test.patch
@@ -0,0 +1,15 @@
+diff --git a/tests/run/numpy_math.pyx b/tests/run/numpy_math.pyx
+index eafd23a..4a15522 100644
+--- a/tests/run/numpy_math.pyx
++++ b/tests/run/numpy_math.pyx
+@@ -37,8 +37,8 @@ def test_fp_classif():
+     assert not npmath.isnan(d_zero)
+     assert not npmath.isnan(f_zero)
+ 
+-    assert npmath.isinf(npmath.INFINITY) == 1
+-    assert npmath.isinf(-npmath.INFINITY) == -1
++    assert npmath.isinf(npmath.INFINITY) != 0
++    assert npmath.isinf(-npmath.INFINITY) != 0
+     assert npmath.isnan(npmath.NAN)
+ 
+     assert npmath.signbit(npmath.copysign(1., -1.))
diff --git a/pkgs/development/python-modules/matplotlib/default.nix b/pkgs/development/python-modules/matplotlib/default.nix
index 7c1b8b503a3a..a9dced9b6c4a 100644
--- a/pkgs/development/python-modules/matplotlib/default.nix
+++ b/pkgs/development/python-modules/matplotlib/default.nix
@@ -18,11 +18,11 @@ assert enableTk -> (tcl != null)
 
 buildPythonPackage rec {
   name = "matplotlib-${version}";
-  version = "1.5.1";
+  version = "1.5.3";
 
   src = fetchurl {
     url = "mirror://pypi/m/matplotlib/${name}.tar.gz";
-    sha256 = "3ab8d968eac602145642d0db63dd8d67c85e9a5444ce0e2ecb2a8fedc7224d40";
+    sha256 = "1g7bhr6v3wdxyx29rfxgf57l9w19s79cdlpyi0h4y0c5ywwxr9d0";
   };
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";
@@ -40,7 +40,7 @@ buildPythonPackage rec {
     ]
     ++ stdenv.lib.optional enableGtk2 pygtk
     ++ stdenv.lib.optionals enableGtk3 [ cairo pycairo gtk3 gobjectIntrospection pygobject3 ]
-    ++ stdenv.lib.optionals enableTk [ tcl tk tkinter libX11 ];
+    ++ stdenv.lib.optionals enableTk [ python.tkinter tcl tk tkinter libX11 ];
 
   patches =
     [ ./basedirlist.patch ] ++
diff --git a/pkgs/development/python-modules/numpy-distutils-C++.patch b/pkgs/development/python-modules/numpy-distutils-C++.patch
new file mode 100644
index 000000000000..4b2d5c640e64
--- /dev/null
+++ b/pkgs/development/python-modules/numpy-distutils-C++.patch
@@ -0,0 +1,23 @@
+diff --git a/numpy/distutils/unixccompiler.py b/numpy/distutils/unixccompiler.py
+index a92ccd3..9630e91 100644
+--- a/numpy/distutils/unixccompiler.py
++++ b/numpy/distutils/unixccompiler.py
+@@ -43,10 +43,15 @@ def UnixCCompiler__compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts
+         if opt not in llink_s:
+             self.linker_so = llink_s.split() + opt.split()
+ 
+-    display = '%s: %s' % (os.path.basename(self.compiler_so[0]), src)
+     try:
+-        self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
+-                   extra_postargs, display = display)
++        if self.detect_language(src) == 'c++':
++            display = '%s: %s' % (os.path.basename(self.compiler_so_cxx[0]), src)
++            self.spawn(self.compiler_so_cxx + cc_args + [src, '-o', obj] +
++                       extra_postargs, display = display)
++        else:
++            display = '%s: %s' % (os.path.basename(self.compiler_so[0]), src)
++            self.spawn(self.compiler_so + cc_args + [src, '-o', obj] +
++                       extra_postargs, display = display)
+     except DistutilsExecError:
+         msg = str(get_exception())
+         raise CompileError(msg)
diff --git a/pkgs/development/python-modules/numpy.nix b/pkgs/development/python-modules/numpy.nix
index 141c8b14fa6d..14504d925438 100644
--- a/pkgs/development/python-modules/numpy.nix
+++ b/pkgs/development/python-modules/numpy.nix
@@ -1,4 +1,4 @@
-{lib, python, buildPythonPackage, isPyPy, gfortran, nose, blas}:
+{lib, python, buildPythonPackage, isPy27, isPyPy, gfortran, nose, blas}:
 
 args:
 
@@ -12,6 +12,12 @@ in buildPythonPackage (args // rec {
   buildInputs = args.buildInputs or [ gfortran nose ];
   propagatedBuildInputs = args.propagatedBuildInputs or [ passthru.blas ];
 
+  patches = lib.optionals (python.hasDistutilsCxxPatch or false) [
+    # See cpython 2.7 patches.
+    # numpy.distutils is used by cython during it's check phase
+    ./numpy-distutils-C++.patch
+  ];
+
   preConfigure = ''
     sed -i 's/-faltivec//' numpy/distutils/system_info.py
   '';
diff --git a/pkgs/development/python-modules/pycairo/default.nix b/pkgs/development/python-modules/pycairo/default.nix
index fb95a9fa4683..23e06ff4cb4e 100644
--- a/pkgs/development/python-modules/pycairo/default.nix
+++ b/pkgs/development/python-modules/pycairo/default.nix
@@ -1,9 +1,9 @@
-{ lib, fetchurl, fetchpatch, python, mkPythonDerivation, pkgconfig, cairo, xlibsWrapper, isPyPy, isPy35 }:
+{ lib, fetchurl, fetchpatch, python, mkPythonDerivation, pkgconfig, cairo, xlibsWrapper, isPyPy, isPy35, isPy3k }:
 
 if (isPyPy) then throw "pycairo not supported for interpreter ${python.executable}" else mkPythonDerivation rec {
   version = "1.10.0";
   name = "${python.libPrefix}-pycairo-${version}";
-  src = if python.is_py3k or false
+  src = if isPy3k
     then fetchurl {
       url = "http://cairographics.org/releases/pycairo-${version}.tar.bz2";
       sha256 = "1gjkf8x6hyx1skq3hhwcbvwifxvrf9qxis5vx8x5igmmgs70g94s";
diff --git a/pkgs/development/python-modules/pygobject/3.nix b/pkgs/development/python-modules/pygobject/3.nix
index 797d89fd4822..dfddd7dddbdb 100644
--- a/pkgs/development/python-modules/pygobject/3.nix
+++ b/pkgs/development/python-modules/pygobject/3.nix
@@ -1,13 +1,13 @@
 { stdenv, fetchurl, mkPythonDerivation, python, pkgconfig, glib, gobjectIntrospection, pycairo, cairo, which, ncurses}:
 
 mkPythonDerivation rec {
-  major = "3.20";
+  major = "3.22";
   minor = "0";
   name = "pygobject-${major}.${minor}";
 
   src = fetchurl {
     url = "mirror://gnome/sources/pygobject/${major}/${name}.tar.xz";
-    sha256 = "0ikzh3l7g1gjh8jj8vg6mdvrb25svp63gxcam4m0i404yh0lgari";
+    sha256 = "08b29cfb08efc80f7a8630a2734dec65a99c1b59f1e5771c671d2e4ed8a5cbe7";
   };
 
   buildInputs = [ pkgconfig glib gobjectIntrospection ]
diff --git a/pkgs/development/python-modules/searx.patch b/pkgs/development/python-modules/searx.patch
index 6cd25babb332..1fd7dcbde6d4 100644
--- a/pkgs/development/python-modules/searx.patch
+++ b/pkgs/development/python-modules/searx.patch
@@ -16,7 +16,8 @@ index 0d2f61b..46481b3 100644
  pyasn1-modules==0.0.8
 -pygments==2.1.3
 +pygments==2.*
- pyopenssl==0.15.1
+-pyopenssl==0.15.1
++pyopenssl==16.*
 -python-dateutil==2.5.3
 +python-dateutil==2.*
 -pyyaml==3.11
diff --git a/pkgs/development/python-modules/wxPython/3.0.nix b/pkgs/development/python-modules/wxPython/3.0.nix
index 5f224428fce4..8dc99955af31 100644
--- a/pkgs/development/python-modules/wxPython/3.0.nix
+++ b/pkgs/development/python-modules/wxPython/3.0.nix
@@ -1,16 +1,18 @@
 { fetchurl
 , lib
-, pythonPackages
 , openglSupport ? true
 , libX11
 , wxGTK
 , pkgconfig
+, buildPythonPackage
+, pyopengl
+, isPy3k
+, isPyPy
+, python
 }:
 
 assert wxGTK.unicode;
 
-with pythonPackages;
-
 buildPythonPackage rec {
   name = "wxPython-${version}";
   version = "3.0.2.0";