Merge staging-next into staging

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

@@ -23,11 +23,11 @@
 
 buildPythonPackage rec {
   pname = "aiohttp";
-  version = "3.5.3";
+  version = "3.5.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7967b760d0e96eb7ac6b20a9143112ce5c03a00b4f74d8a5ee66c8e88e6b6800";
+    sha256 = "9c4c83f4fa1938377da32bc2d59379025ceeee8e24b89f72fcbccd8ca22dc9bf";
   };
 
   disabled = pythonOlder "3.5";

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi, pythonOlder
-, attrs, click, toml, appdirs
+, attrs, click, toml, appdirs, aiohttp
 , glibcLocales, pytest }:
 
 buildPythonPackage rec {
@@ -15,14 +15,15 @@ buildPythonPackage rec {
 
   checkInputs =  [ pytest glibcLocales ];
 
+  # Don't know why these tests fails
   checkPhase = ''
-    # no idea, why those fail.
-    LC_ALL="en_US.UTF-8" HOME="$NIX_BUILD_TOP" \
-      pytest \
-        -k "not test_cache_multiple_files and not test_failed_formatting_does_not_get_cached"
+    LC_ALL="en_US.UTF-8" pytest \
+      --deselect tests/test_black.py::BlackTestCase::test_expression_diff \
+      --deselect tests/test_black.py::BlackTestCase::test_cache_multiple_files \
+      --deselect tests/test_black.py::BlackTestCase::test_failed_formatting_does_not_get_cached
   '';
 
-  propagatedBuildInputs = [ attrs appdirs click toml ];
+  propagatedBuildInputs = [ attrs appdirs click toml aiohttp ];
 
   meta = with stdenv.lib; {
     description = "The uncompromising Python code formatter";

pkgs/development/python-modules/css-parser/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "css-parser";
+  version = "1.0.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "c7ab355512ae51334ba6791a7e4d553f87bef17ba2026f1cc9bf3b17a7779d44";
+  };
+
+  # Test suite not included in tarball yet
+  # See https://github.com/ebook-utils/css-parser/pull/2
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A CSS Cascading Style Sheets library for Python";
+    homepage = https://github.com/ebook-utils/css-parser;
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ jethro ];
+  };
+}

pkgs/development/python-modules/cypari2/default.nix

@@ -23,8 +23,7 @@ buildPythonPackage rec {
   # That is because while the default install phase succeeds to build the package,
   # it fails to generate the file "auto_paridecl.pxd".
   installPhase = ''
-    mkdir -p "$out/lib/${python.sitePackages}"
-    export PYTHONPATH="$out/lib/${python.sitePackages}:$PYTHONPATH"
+    export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
 
     # install "." instead of "*.whl"
     ${python.pythonForBuild.pkgs.bootstrapped-pip}/bin/pip install --no-index --prefix=$out --no-cache --build=tmpdir .

pkgs/development/python-modules/django/2_1.nix

@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "Django";
-  version = "2.1.4";
+  version = "2.1.5";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mxbrqdzim3xcy18dmd08xh2am0q7whbf0nf6bmnrl43802m3386";
+    sha256 = "1hwqqsfg8jgnn039yxrq6xrksk11y7vwpfvba6lk01c3v8c3jffn";
   };
 
   patches = stdenv.lib.optionals withGdal [

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "fonttools";
-  version = "3.33.0";
+  version = "3.34.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "196yl6m3fycrbsclcmg550821j18ga6dpghmk5nb1xi4j4yb62gq";
+    sha256 = "1ahs82jnc8f7gksh51asg9dcifhslyfdz9dry9sxq424q1p5k9lz";
     extension = "zip";
   };
 

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

@@ -4,11 +4,11 @@
 
 python.pkgs.buildPythonPackage rec {
   pname = "memory_profiler";
-  version = "0.54.0";
+  version = "0.55.0";
 
   src = python.pkgs.fetchPypi {
     inherit pname version;
-    sha256 = "06ld8h8mhm8pk0sv7fxgx0y2q8nri65qlh4vjbs0bq9j7yi44hyn";
+    sha256 = "1hdgh5f59bya079w4ahx4l0hf4gc5yvaz44irp5x57cj9hkpp92z";
   };
 
   propagatedBuildInputs = with python.pkgs; [

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

@@ -1,19 +1,24 @@
 { stdenv
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
+, nose
 }:
 
 buildPythonPackage rec {
   pname = "munkres";
-  version = "1.0.6";
+  version = "1.0.12";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "c78f803b9b776bfb20a25c9c7bb44adbf0f9202c2024d51aa5969d21e560208d";
+  # No sdist for 1.0.12, see https://github.com/bmc/munkres/issues/25
+  src = fetchFromGitHub {
+    owner = "bmc";
+    repo = pname;
+    rev = "release-${version}";
+    sha256 = "0m3rkn0z3ialndxmyg26xn081znna34i5maa1i4nkhy6nf0ixdjm";
   };
 
-  # error: invalid command 'test'
-  doCheck = false;
+  checkInputs = [ nose ];
+
+  checkPhase = "nosetests";
 
   meta = with stdenv.lib; {
     homepage = http://bmc.github.com/munkres/;

pkgs/development/python-modules/numpy-stl/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "numpy-stl";
-  version = "2.7.0";
+  version = "2.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ede911118cfee5a8fd4c341b418fc55bfcd70a557686febc4efb6693297e3aa2";
+    sha256 = "0mh7p19rhx800dd54ij1pgln5ny03fdyvadyhrsb380fgjby2nh3";
   };
 
   checkInputs = [ pytest pytestrunner ];

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

@@ -16,7 +16,10 @@ buildPythonPackage rec {
     sha256 = "18n14ha2d3j3ghg2f2aqnf2mks94nn7ma9ii7vkiwcay93zm82cf";
   };
 
-  buildInputs = [ pkgs.swig1 pkgs.coin3d pkgs.soqt pkgs.libGLU_combined pkgs.xorg.libXi ];
+  buildInputs = with pkgs; with xorg; [
+    swig1 coin3d soqt libGLU_combined
+    libXi libXext libSM libICE libX11
+  ];
 
   meta = with stdenv.lib; {
     homepage = http://pivy.coin3d.org/;

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

@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "pycares";
-  version = "2.3.0";
+  version = "2.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0h4fxw5drrhfyslzmfpljk0qnnpbhhb20hnnndzahhbwylyw1x1n";
+    sha256 = "15pwsxsj1nr33n6x2918bfbzdnqv1qkwd2d5jgvxsm81zxnvgk0f";
   };
 
   propagatedBuildInputs = [ pkgs.c-ares ];

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

@@ -1,16 +1,12 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, python, pytest, glibcLocales }:
+{ stdenv, buildPythonPackage, fetchPypi, python, pytest, glibcLocales }:
 
 buildPythonPackage rec {
-  version = "3.5.5";
+  version = "3.5.6";
   pname = "pyfakefs";
 
-  # no tests in PyPI tarball
-  # https://github.com/jmcgeheeiv/pyfakefs/pull/361
-  src = fetchFromGitHub {
-    owner = "jmcgeheeiv";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "1pww444ih4bf84a0jgl1r446mjywhlls890mnw76flx8maahlik1";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "efe9c318b2a37ae498a555889684c30ccb6a1b06bd391cb3baf0eb5ba68e9062";
   };
 
   postPatch = ''

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

@@ -5,6 +5,7 @@
 , flask
 , pyquery
 , pytest
+, pytestrunner
 , cairosvg
 , tinycss
 , cssselect
@@ -22,7 +23,24 @@ buildPythonPackage rec {
     sha256 = "9204f05380b02a8a32f9bf99d310b51aa2a932cba5b369f7a4dc3705f0a4ce83";
   };
 
-  buildInputs = [ flask pyquery pytest ];
+  buildInputs = [
+    flask
+    pyquery
+
+    # Should be a check input, but upstream lists it under "setup_requires".
+    # https://github.com/Kozea/pygal/issues/430
+    pytestrunner
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  preCheck = ''
+    # necessary on darwin to pass the testsuite
+    export LANG=en_US.UTF-8
+  '';
+
   propagatedBuildInputs = [ cairosvg tinycss cssselect ]
     ++ stdenv.lib.optionals (!isPyPy) [ lxml ];
 

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

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "pyment";
+  version = "0.3.3";
+
+  src = fetchPypi {
+    pname = "Pyment";
+    inherit version;
+    sha256 = "951a4c52d6791ccec55bc739811169eed69917d3874f5fe722866623a697f39d";
+  };
+
+  # Tests are not included in PyPI tarball
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/dadadel/pyment;
+    description = "Create, update or convert docstrings in existing Python files, managing several styles";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ jethro ];
+  };
+}

pkgs/development/python-modules/pysaml2/default.nix

@@ -1,62 +1,42 @@
 { stdenv
 , buildPythonPackage
-, fetchPypi
-, fetchpatch
-, repoze_who
-, paste
-, cryptography
-, pycrypto
-, pyopenssl
-, ipaddress
-, six
-, cffi
-, idna
-, enum34
-, pytz
-, setuptools
-, zope_interface
-, dateutil
-, requests
-, pyasn1
-, webob
-, decorator
-, pycparser
-, defusedxml
-, Mako
-, pytest
-, memcached
-, pymongo
-, mongodict
-, pkgs
+, fetchFromGitHub
+, substituteAll
+, xmlsec
+, cryptography, defusedxml, future, pyopenssl, dateutil, pytz, requests, six
+, mock, pyasn1, pymongo, pytest, responses
 }:
 
 buildPythonPackage rec {
   pname = "pysaml2";
-  version = "3.0.2";
+  version = "4.6.5";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "0y2iw1dddcvi13xjh3l52z1mvnrbc41ik9k4nn7lwj8x5kimnk9n";
+  # No tests in PyPI tarball
+  src = fetchFromGitHub {
+    owner = "IdentityPython";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0xlbr52vzx1j9sg65jhqv01vp4a49afjy03lc2zb0ggx0xxzngvb";
   };
 
   patches = [
-    (fetchpatch {
-      name = "CVE-2016-10127.patch";
-      url = "https://sources.debian.net/data/main/p/python-pysaml2/3.0.0-5/debian/patches/fix-xxe-in-xml-parsing.patch";
-      sha256 = "184lkwdayjqiahzsn4yp15parqpmphjsb1z7zwd636jvarxqgs2q";
+    (substituteAll {
+      src = ./hardcode-xmlsec1-path.patch;
+      inherit xmlsec;
     })
   ];
 
-  propagatedBuildInputs = [ repoze_who paste cryptography pycrypto pyopenssl ipaddress six cffi idna enum34 pytz setuptools zope_interface dateutil requests pyasn1 webob decorator pycparser defusedxml ];
-  buildInputs = [ Mako pytest memcached pymongo mongodict pkgs.xmlsec ];
+  propagatedBuildInputs = [ cryptography defusedxml future pyopenssl dateutil pytz requests six ];
 
-  preConfigure = ''
-    sed -i 's/pymongo==3.0.1/pymongo/' setup.py
+  checkInputs = [ mock pyasn1 pymongo pytest responses ];
+
+  # Disabled tests try to access the network
+  checkPhase = ''
+    py.test -k "not test_load_extern_incommon \
+            and not test_load_remote_encoding \
+            and not test_load_external"
   '';
 
-  # 16 failed, 427 passed, 17 error in 88.85 seconds
-  doCheck = false;
-
   meta = with stdenv.lib; {
     homepage = "https://github.com/rohe/pysaml2";
     description = "Python implementation of SAML Version 2 Standard";

pkgs/development/python-modules/pysaml2/hardcode-xmlsec1-path.patch

@@ -0,0 +1,39 @@
+diff --git a/src/saml2/sigver.py b/src/saml2/sigver.py
+index 59fe2dee..0c24fbcc 100644
+--- a/src/saml2/sigver.py
++++ b/src/saml2/sigver.py
+@@ -165,33 +165,7 @@ def get_xmlsec_binary(paths=None):
+     :return: full name of the xmlsec1 binary found. If no binaries are
+         found then an exception is raised.
+     """
+-    if os.name == 'posix':
+-        bin_name = ['xmlsec1']
+-    elif os.name == 'nt':
+-        bin_name = ['xmlsec.exe', 'xmlsec1.exe']
+-    else:  # Default !?
+-        bin_name = ['xmlsec1']
+-
+-    if paths:
+-        for bname in bin_name:
+-            for path in paths:
+-                fil = os.path.join(path, bname)
+-                try:
+-                    if os.lstat(fil):
+-                        return fil
+-                except OSError:
+-                    pass
+-
+-    for path in os.environ['PATH'].split(os.pathsep):
+-        for bname in bin_name:
+-            fil = os.path.join(path, bname)
+-            try:
+-                if os.lstat(fil):
+-                    return fil
+-            except OSError:
+-                pass
+-
+-    raise SigverError('Cannot find {binary}'.format(binary=bin_name))
++    return '@xmlsec@/bin/xmlsec1'
+ 
+ 
+ def _get_xmlsec_cryptobackend(path=None, search_paths=None):

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

@@ -5,12 +5,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.3.2";
+  version = "0.3.3";
   pname = "pysmi";
 
  src = fetchPypi {
     inherit pname version;
-    sha256 = "309039ab9bd458cc721692ffff10b4ad2c4a8e731e6507c34866ca2727323353";
+    sha256 = "0bzhmi4691rf306n4y82js52532h3fp1sy6phvh6hnms6nww4daf";
   };
 
   propagatedBuildInputs = [ ply ];

pkgs/development/python-modules/pytest-rerunfailures/default.nix

@@ -2,24 +2,23 @@
 
 buildPythonPackage rec {
   pname = "pytest-rerunfailures";
-  version = "4.2";
+  version = "6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "97216f8a549f74da3cc786236d9093fbd43150a6fbe533ba622cb311f7431774";
+    sha256 = "978349ae00687504fd0f9d0970c37199ccd89cbdb0cb8c4ed7ee417ede582b40";
   };
 
   checkInputs = [ mock ];
 
   propagatedBuildInputs = [ pytest ];
 
-  # disable tests that fail with pytest 3.7.4
   checkPhase = ''
-    py.test test_pytest_rerunfailures.py -k 'not test_reruns_with_delay'
+    py.test test_pytest_rerunfailures.py
   '';
 
   meta = with stdenv.lib; {
-    description = "pytest plugin to re-run tests to eliminate flaky failures.";
+    description = "pytest plugin to re-run tests to eliminate flaky failures";
     homepage = https://github.com/pytest-dev/pytest-rerunfailures;
     license = licenses.mpl20;
     maintainers = with maintainers; [ jgeerds ];

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

@@ -24,7 +24,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Invoke py.test as distutils command with dependency resolution";
-    homepage = https://bitbucket.org/pytest-dev/pytest-runner;
+    homepage = https://github.com/pytest-dev/pytest-runner;
     license = licenses.mit;
   };
 }

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

@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+, six
+, pytest }:
+
+buildPythonPackage rec {
+  version = "0.1.4";
+  pname = "pyvcd";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0dv9wac5y5z9j54ypyc59csxdiy9ybpphw9ipxp1k8nfg65q9jxx";
+  };
+
+  buildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [ six ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  checkInputs = [ pytest ];
+
+  meta = with lib; {
+    description = "Python package for writing Value Change Dump (VCD) files";
+    homepage = https://github.com/SanDisk-Open-Source/pyvcd;
+    license = licenses.mit;
+    maintainers = [ maintainers.sb0 ];
+  };
+}

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

@@ -10,16 +10,15 @@
 
 buildPythonPackage rec {
   pname = "qrcode";
-  version = "6.0";
+  version = "6.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "037b0db4c93f44586e37f84c3da3f763874fcac85b2974a69a98e399ac78e1bf";
+    sha256 = "505253854f607f2abf4d16092c61d4e9d511a3b4392e60bff957a68592b04369";
   };
 
   propagatedBuildInputs = [ six pillow pymaging_png ];
   checkInputs = [ mock ];
-  doCheck = isPy27; # https://github.com/lincolnloop/python-qrcode/issues/163
 
   meta = with stdenv.lib; {
     description = "Quick Response code generation for Python";

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

@@ -11,7 +11,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6";
+    sha256 = "1ri9kx0yrn85h6ivkaja35afbyhimxn8lsairgns2wi5xv3wfnxw";
   };
 
   buildInputs = [ pillow gfortran glibcLocales ];

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

@@ -1,22 +1,30 @@
-{ lib, buildPythonPackage, fetchPypi, pythonOlder, fetchurl, aiodns, pyasn1, pyasn1-modules, gnupg }:
+{ lib, buildPythonPackage, fetchPypi, isPy3k, substituteAll, aiodns, pyasn1, pyasn1-modules, aiohttp, gnupg, nose }:
 
 buildPythonPackage rec {
   pname = "slixmpp";
   version = "1.4.1";
 
-  disabled = pythonOlder "3.4";
+  disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "020acd4507fd00c38835b78b5f338db60d3df840187623e0d41ab2ca89d7ae57";
   };
 
-  patchPhase = ''
-    substituteInPlace slixmpp/thirdparty/gnupg.py \
-      --replace "gpgbinary='gpg'" "gpgbinary='${gnupg}/bin/gpg'"
-  '';
+  patches = [
+    (substituteAll {
+      src = ./hardcode-gnupg-path.patch;
+      inherit gnupg;
+    })
+  ];
 
-  propagatedBuildInputs = [ aiodns pyasn1 pyasn1-modules gnupg ];
+  propagatedBuildInputs = [ aiodns pyasn1 pyasn1-modules aiohttp ];
+
+  checkInputs = [ nose ];
+
+  checkPhase = ''
+    nosetests --where=tests --exclude=live -i slixtest.py
+  '';
 
   meta = {
     description = "Elegant Python library for XMPP";

pkgs/development/python-modules/slixmpp/hardcode-gnupg-path.patch

@@ -0,0 +1,26 @@
+diff --git a/slixmpp/plugins/xep_0027/gpg.py b/slixmpp/plugins/xep_0027/gpg.py
+index a0b1df4..7cfb3bd 100644
+--- a/slixmpp/plugins/xep_0027/gpg.py
++++ b/slixmpp/plugins/xep_0027/gpg.py
+@@ -41,7 +41,7 @@ class XEP_0027(BasePlugin):
+     dependencies = set()
+     stanza = stanza
+     default_config = {
+-        'gpg_binary': 'gpg',
++        'gpg_binary': '@gnupg@/bin/gpg',
+         'gpg_home': '',
+         'use_agent': True,
+         'keyring': None,
+diff --git a/slixmpp/thirdparty/gnupg.py b/slixmpp/thirdparty/gnupg.py
+index a89289f..46dd9b7 100644
+--- a/slixmpp/thirdparty/gnupg.py
++++ b/slixmpp/thirdparty/gnupg.py
+@@ -468,7 +468,7 @@ class GPG(object):
+     }
+ 
+     "Encapsulate access to the gpg executable"
+-    def __init__(self, gpgbinary='gpg', gnupghome=None, verbose=False,
++    def __init__(self, gpgbinary='@gnupg@/bin/gpg', gnupghome=None, verbose=False,
+                  use_agent=False, keyring=None):
+         """Initialize a GPG process wrapper.  Options are:
+ 

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

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchFromGitHub, requests, nose, mock }:
+
+buildPythonPackage rec {
+  pname = "yarg";
+  version = "0.1.9";
+
+  src = fetchFromGitHub {
+    owner = "kura";
+    repo = pname;
+    rev = version;
+    sha256 = "1isq02s404fp9whkm8w2kvb2ik1sz0r258iby0q532zw81lga0d0";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  checkInputs = [ nose mock ];
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = with lib; {
+    description = "An easy to use PyPI client";
+    homepage = https://yarg.readthedocs.io;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}