Merge remote-tracking branch 'upstream/master' into HEAD

Conflicts:
	pkgs/development/tools/misc/binutils/default.nix

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

@@ -1,6 +1,6 @@
 { stdenv, fetchPypi, buildPythonPackage
 , more-itertools, six
-, coverage, codecov, pytest, pytestcov, pytest-sugar, portend
+, pytest, pytestcov, portend
 , backports_unittest-mock, setuptools_scm }:
 
 buildPythonPackage rec {
@@ -16,7 +16,7 @@ buildPythonPackage rec {
 
   buildInputs = [ setuptools_scm ];
 
-  checkInputs = [ coverage codecov pytest pytestcov pytest-sugar portend backports_unittest-mock  ];
+  checkInputs = [ pytest pytestcov portend backports_unittest-mock ];
 
   checkPhase = ''
     py.test cheroot

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

@@ -1,11 +1,10 @@
 { lib, buildPythonPackage, fetchPypi
 , cheroot, portend, routes, six
 , setuptools_scm
-, backports_unittest-mock, codecov, coverage, objgraph, pathpy, pytest, pytest-sugar, pytestcov
+, backports_unittest-mock, objgraph, pathpy, pytest, pytestcov
 }:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "CherryPy";
   version = "14.0.1";
 
@@ -18,7 +17,7 @@ buildPythonPackage rec {
 
   buildInputs = [ setuptools_scm ];
 
-  checkInputs = [ backports_unittest-mock codecov coverage objgraph pathpy pytest pytest-sugar pytestcov ];
+  checkInputs = [ backports_unittest-mock objgraph pathpy pytest pytestcov ];
 
   checkPhase = ''
     LANG=en_US.UTF-8 pytest

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

@@ -0,0 +1,55 @@
+{ stdenv
+, bootstrapped-pip
+, buildPythonPackage
+, python
+, fetchPypi
+, pari
+, gmp
+, cython
+, cysignals
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "cypari2";
+  version = "1.1.4"; # remove six dependency on upgrade to >1.1.4
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0n0mp8qmvvzmfaawg39d3mkyzf65q2zkz7bnqyk4sfjbz4xwc6mb";
+  };
+
+  # This differs slightly from the default python installPhase in that it pip-installs
+  # "." instead of "*.whl".
+  # 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.libPrefix}/site-packages"
+    export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
+
+    # install "." instead of "*.whl"
+    ${bootstrapped-pip}/bin/pip install --no-index --prefix=$out --no-cache --build=tmpdir .
+  '';
+
+  buildInputs = [
+    pari
+    gmp
+  ];
+
+  propagatedBuildInputs = [
+    cysignals
+    cython
+    six # after 1.1.4: will not be needed
+  ];
+
+  checkPhase = ''
+    make check
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Cython bindings for PARI";
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ timokau ];
+    homepage = https://github.com/defeo/cypari2;
+  };
+}

pkgs/development/python-modules/django/1_11.nix

@@ -6,14 +6,13 @@
 
 buildPythonPackage rec {
   pname = "Django";
-  name = "${pname}-${version}";
-  version = "1.11.9";
+  version = "1.11.12";
 
   disabled = pythonOlder "2.7";
 
   src = fetchurl {
-    url = "http://www.djangoproject.com/m/releases/1.11/${name}.tar.gz";
-    sha256 = "0d0hh9sh2rwazi7z2lnqvz1424bq6ps6c5h6ss04klp14agi4g9m";
+    url = "http://www.djangoproject.com/m/releases/1.11/${pname}-${version}.tar.gz";
+    sha256 = "1szjha338grhf9dq0wpbrqwvak597shsx474pm5j67kn09xqqfad";
   };
 
   patches = stdenv.lib.optionals withGdal [

pkgs/development/python-modules/flask-babel/default.nix

@@ -0,0 +1,44 @@
+{ stdenv
+, buildPythonPackage
+, python
+, fetchPypi
+, flask
+, Babel
+, jinja2
+, pytz
+, speaklater
+}:
+
+buildPythonPackage rec {
+  pname = "Flask-Babel";
+  version = "0.11.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0ff9n165vhf1nhv6807ckhpp224jw7k7sd7jz5kfh3sbpl85gmy0";
+  };
+
+  propagatedBuildInputs = [
+    flask
+    Babel
+    jinja2
+    pytz
+    speaklater
+  ];
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s tests
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Adds i18n/l10n support to Flask applications";
+    longDescription = ''
+      Implements i18n and l10n support for Flask.
+      This is based on the Python babel module as well as pytz both of which are
+      installed automatically for you if you install this library.
+    '';
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ timokau ];
+    homepage = https://github.com/python-babel/flask-babel;
+  };
+}

pkgs/development/python-modules/flask-silk/default.nix

@@ -0,0 +1,26 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, flask
+}:
+
+buildPythonPackage rec {
+  pname = "Flask-Silk";
+  version = "0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1gjzighx4f0w39sq9xvzr1kwb4y7yv9qrgzvli1p89gy16piz8l0";
+  };
+
+  propagatedBuildInputs = [
+    flask
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Adds silk icons to your Flask application or module, or extension";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ timokau ];
+    homepage = https://github.com/sublee/flask-silk;
+  };
+}

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

@@ -17,7 +17,9 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ entrypoints ] ++ stdenv.lib.optional stdenv.isLinux secretstorage;
 
-  doCheck = !stdenv.isDarwin;
+  # all tests with flake8 are broken right now
+  # https://github.com/tholo/pytest-flake8/issues/45
+  doCheck = false;
 
   checkPhase = ''
     py.test

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

@@ -33,7 +33,7 @@ buildPythonPackage rec {
   libraryPath = lib.makeLibraryPath (
     []
     ++ lib.optionals cudaSupport [ cudatoolkit.lib cudatoolkit.out ]
-    ++ lib.optionals openclSupport [ ocl-icd clblas ]
+    ++ lib.optionals openclSupport ([ clblas ] ++ lib.optional (!stdenv.isDarwin) ocl-icd)
   );
 
   preBuild = ''
@@ -47,7 +47,7 @@ buildPythonPackage rec {
 
   postFixup = ''
     rm $out/lib/libgpuarray-static.a
-
+  '' + stdenv.lib.optionalString (!stdenv.isDarwin) ''
     function fixRunPath {
       p=$(patchelf --print-rpath $1)
       patchelf --set-rpath "$p:$libraryPath" $1
@@ -75,7 +75,7 @@ buildPythonPackage rec {
     description = "Library to manipulate tensors on GPU.";
     license = licenses.free;
     maintainers = with maintainers; [ artuuge ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
   };
 
 }

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

@@ -0,0 +1,22 @@
+{ lib, fetchPypi, buildPythonPackage, cffi }:
+buildPythonPackage rec {
+  pname = "misaka";
+  version = "2.1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1yqrq3a5rracirmvk52n28nn6ckdaz897gnigv89a9gmyn87sqw7";
+  };
+
+  propagatedBuildInputs = [ cffi ];
+
+  # The tests require write access to $out
+  doCheck = false;
+
+  meta = with lib; {
+    description = "A CFFI binding for Hoedown, a markdown parsing library";
+    homepage = "http://misaka.61924.nl/";
+    license = licenses.mit;
+    maintainers = with maintainers; [ fgaz ];
+  };
+}

pkgs/development/python-modules/mysql-connector/default.nix

@@ -4,17 +4,20 @@
 
 buildPythonPackage rec {
   pname = "mysql-connector";
-  version = "8.0.6";
+  version = "8.0.11";
 
   src = fetchFromGitHub {
     owner = "mysql";
     repo = "mysql-connector-python";
     rev = version;
-    sha256 = "1ygr7va56da12yp3gr7kzss9zgbs28q2lmdkw16rpxj108id4rkp";
+    sha256 = "0w5sxy0zdkdj5cj35wwfjy9y8yn5yzk9biwwsglvhkqlkrms8fw1";
   };
 
   propagatedBuildInputs = [ protobuf ];
 
+  # Tests are failing (TODO: unknown reason)
+  # TypeError: __init__() missing 1 required positional argument: 'string'
+  # But the library should be working as expected.
   doCheck = false;
 
   meta = {

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

@@ -1,20 +1,25 @@
 { stdenv, buildPythonPackage, fetchPypi
-, pytest, pytest-sugar, pytest-warnings, setuptools_scm
-, tempora }:
+, pytest, setuptools_scm, tempora }:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "portend";
   version = "2.2";
 
-  buildInputs = [ pytest pytest-sugar pytest-warnings setuptools_scm ];
-  propagatedBuildInputs = [ tempora ];
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "bc48d3d99e1eaf2e9406c729f8848bfdaf87876cd3560dc3ec6c16714f529586";
   };
 
+  nativeBuildInputs = [ setuptools_scm ];
+
+  propagatedBuildInputs = [ tempora ];
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test
+  '';
+
   meta = with stdenv.lib; {
     description = "Monitor TCP ports for bound or unbound states";
     homepage = https://github.com/jaraco/portend;

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

@@ -5,15 +5,20 @@
 
 buildPythonPackage rec {
   pname = "praw";
-  version = "5.2.0";
+  version = "5.4.0";
 
   src = fetchFromGitHub {
     owner = "praw-dev";
     repo = "praw";
     rev = "v${version}";
-    sha256 = "0nwfadczxa1fyq65zc3sfv8g2r4w3xrx3bdi5fv9xpn97wh2ifgw";
+    sha256 = "13vbh2r952ai2m6sc79psfwaj5fc8cssdg2pqpizg2mwd0l1s6lb";
   };
 
+  postPatch = ''
+    # drop upper bound of prawcore requirement
+    sed -ri "s/'(prawcore >=.+), <.+'/'\1'/" setup.py
+  '';
+
   propagatedBuildInputs = [
     requests
     decorator

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

@@ -0,0 +1,65 @@
+{ lib, buildPythonPackage, python, isPy3k, fetchurl, arrow-cpp, cmake, cython, futures, numpy, pandas, pytest, pytestrunner, parquet-cpp, pkgconfig, setuptools_scm, six }:
+
+let
+  _arrow-cpp = arrow-cpp.override { inherit python;};
+  _parquet-cpp = parquet-cpp.override { arrow-cpp = _arrow-cpp; };
+in
+
+buildPythonPackage rec {
+  pname = "pyarrow";
+  version = "0.9.0";
+
+  src = fetchurl {
+    url = "mirror://apache/arrow/arrow-${version}/apache-arrow-${version}.tar.gz";
+    sha256 = "16l91fixb5dgx3v6xc73ipn1w1hjgbmijyvs81j7ywzpna2cdcdy";
+  };
+
+  sourceRoot = "apache-arrow-${version}/python";
+
+  nativeBuildInputs = [ cmake cython pkgconfig setuptools_scm ];
+  propagatedBuildInputs = [ numpy six ] ++ lib.optionals (!isPy3k) [ futures ];
+  checkInputs = [ pandas pytest pytestrunner ];
+
+  PYARROW_BUILD_TYPE = "release";
+  PYARROW_CMAKE_OPTIONS = "-DCMAKE_INSTALL_RPATH=${ARROW_HOME}/lib;${PARQUET_HOME}/lib";
+
+  preBuild = ''
+    substituteInPlace CMakeLists.txt --replace "\''${ARROW_ABI_VERSION}" '"0.0.0"'
+    substituteInPlace CMakeLists.txt --replace "\''${ARROW_SO_VERSION}" '"0"'
+
+    # fix the hardcoded value
+    substituteInPlace cmake_modules/FindParquet.cmake --replace 'set(PARQUET_ABI_VERSION "1.0.0")' 'set(PARQUET_ABI_VERSION "${_parquet-cpp.version}")'
+  '';
+
+  preCheck = ''
+    rm pyarrow/tests/test_hdfs.py
+
+    # fails: "ArrowNotImplementedError: Unsupported numpy type 22"
+    substituteInPlace pyarrow/tests/test_feather.py --replace "test_timedelta_with_nulls" "_disabled"
+
+    # runs out of memory on @grahamcofborg linux box
+    substituteInPlace pyarrow/tests/test_feather.py --replace "test_large_dataframe" "_disabled"
+
+    # probably broken on python2
+    substituteInPlace pyarrow/tests/test_feather.py --replace "test_unicode_filename" "_disabled"
+
+    # fails "error: [Errno 2] No such file or directory: 'test'" because
+    # nix_run_setup invocation somehow manages to import deserialize_buffer.py
+    # when it is not intended to be imported at all
+    rm pyarrow/tests/deserialize_buffer.py
+    substituteInPlace pyarrow/tests/test_feather.py --replace "test_deserialize_buffer_in_different_process" "_disabled"
+  '';
+
+  ARROW_HOME = _arrow-cpp;
+  PARQUET_HOME = _parquet-cpp;
+
+  setupPyBuildFlags = ["--with-parquet" ];
+
+  meta = with lib; {
+    description = "A cross-language development platform for in-memory data";
+    homepage = https://arrow.apache.org/;
+    license = lib.licenses.asl20;
+    platforms = platforms.unix;
+    maintainers = with lib.maintainers; [ veprbl ];
+  };
+}

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

@@ -1,11 +1,12 @@
 { lib, fetchFromGitHub, buildPythonPackage, pillow, six
-, tesseract, cuneiform
+, tesseract, cuneiform, isPy3k
 }:
 
 buildPythonPackage rec {
   pname = "pyocr";
   version = "0.4.7";
   name = pname + "-" + version;
+  disabled = !isPy3k;
 
   # Don't fetch from PYPI because it doesn't contain tests.
   src = fetchFromGitHub {

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

@@ -19,5 +19,9 @@ buildPythonPackage rec {
     description = "A plugin that changes the default look and feel of py.test";
     homepage = https://github.com/Frozenball/pytest-sugar;
     license = licenses.bsd3;
+
+    # incompatible with pytest 3.5
+    # https://github.com/Frozenball/pytest-sugar/issues/134
+    broken = true; # 2018-04-20
   };
 }

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

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "raven";
-  version = "6.6.0";
+  version = "6.7.0";
 
   src = fetchFromGitHub {
     owner = "getsentry";
     repo = "raven-python";
     rev = version;
-    sha256 = "184wpr0zdcm260pxqll9kpmp2ywisn75k8pdm8gc6xmk740in1hj";
+    sha256 = "0vb6zczfgrrh0qw5wlbvk703r11y091k6r53fbbhpbwh4hva30nx";
   };
 
   # way too many dependencies to run tests

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

@@ -6,7 +6,6 @@
 buildPythonPackage rec {
   pname = "scapy";
   version = "2.4.0";
-  name = pname + "-" + version;
 
   disabled = isPyPy;
 

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

@@ -35,4 +35,8 @@ buildPythonPackage rec {
     pyramid sqlalchemy simplejson mozsvc cornice pyramid_hawkauth pymysql
     pymysqlsa umemcache WSGIProxy requests pybrowserid
   ];
+
+  meta = {
+    broken = true; # 2018-11-04
+  };
 }

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

@@ -33,6 +33,7 @@ buildPythonPackage rec {
     homepage = http://weboob.org;
     description = "Collection of applications and APIs to interact with websites without requiring the user to open a browser";
     license = stdenv.lib.licenses.agpl3;
+    broken = true; # 2018-04-11
   };
 }
 

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi
+{ lib, buildPythonPackage, fetchPypi, isPy3k
 , wrapGAppsHook, gobjectIntrospection, pygobject3, graphviz, gnome3 }:
 
 buildPythonPackage rec {
@@ -10,6 +10,8 @@ buildPythonPackage rec {
     sha256 = "01v9vmgdxz1q2m2vq2b4aqx4ycw7grc0l4is673ygvyg9rk02dx3";
   };
 
+  disabled = !isPy3k;
+
   nativeBuildInputs = [ wrapGAppsHook ];
   propagatedBuildInputs = [ gobjectIntrospection pygobject3 graphviz gnome3.gtk ];
 

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

@@ -17,7 +17,7 @@ buildPythonApplication rec {
   meta = {
     description = "Command-line tool for querying PyPI and Python packages installed on your system";
     homepage = https://github.com/cakebread/yolk;
-    maintainer = with maintainers; [];
+    maintainers = with maintainers; [];
     license = licenses.bsd3;
   };
 }

pkgs/development/python-modules/zipfile36/default.nix

@@ -28,6 +28,6 @@ buildPythonPackage rec {
     description = "Read and write ZIP files - backport of the zipfile module from Python 3.6";
     homepage = https://gitlab.com/takluyver/zipfile36;
     license = lib.licenses.psfl;
-    maintainer = lib.maintainers.fridh;
+    maintainers = lib.maintainers.fridh;
   };
-}
+}