Merge staging-next into staging

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

@@ -1,7 +1,7 @@
 { stdenv, lib, buildPythonPackage, fetchPypi, makeWrapper, isPy3k,
   python, twisted, jinja2, zope_interface, future, sqlalchemy,
   sqlalchemy_migrate, dateutil, txaio, autobahn, pyjwt, treq, txrequests,
-  txgithub, pyjade, boto3, moto, mock, lz4, setuptoolsTrial, isort, pylint,
+  txgithub, pyjade, boto3, moto, mock, python-lz4, setuptoolsTrial, isort, pylint,
   flake8, buildbot-worker, buildbot-pkg, glibcLocales }:
 
 let
@@ -55,7 +55,7 @@ let
       boto3
       moto
       mock
-      lz4
+      python-lz4
       setuptoolsTrial
       isort
       pylint

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

@@ -4,6 +4,7 @@
 , isPy3k
 , oauth2client
 , gdata
+, google_api_python_client
 , simplejson
 , httplib2
 , keyring
@@ -21,7 +22,7 @@ buildPythonPackage rec {
     sha256 = "139a98d646d5c5963670944d5cfcc1a107677ee11fa98329221bd600457fda6d";
   };
 
-  propagatedBuildInputs = [ oauth2client gdata simplejson httplib2 keyring six rsa ];
+  propagatedBuildInputs = [ oauth2client gdata google_api_python_client simplejson httplib2 keyring six rsa ];
 
   preConfigure = ''
     sed -i '/distribute/d' setup.py

pkgs/development/python-modules/jsonrpclib-pelix/default.nix

@@ -12,6 +12,8 @@ buildPythonPackage rec {
     sha256 = "14d288d1b3d3273cf96a729dd21a2470851c4962be8509f3dd62f0137ff90339";
   };
 
+  doCheck = false; # test_suite="tests" in setup.py but no tests in pypi.
+
   meta = with lib; {
     description = "JSON RPC client library - Pelix compatible fork";
     homepage = https://pypi.python.org/pypi/jsonrpclib-pelix/;

pkgs/development/python-modules/lz4/default.nix

@@ -1,29 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, pytestrunner
-, pytest
-, psutil
-, pkgconfig
-, setuptools_scm
-}:
-
-buildPythonPackage rec {
-  pname = "lz4";
-  version = "2.1.2";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "ec265f7c3fc3df706e9579bde632ceeef9278858d7ae87c376a2954d11e9ea39";
-  };
-
-  buildInputs = [ setuptools_scm pytestrunner pkgconfig ];
-  checkInputs = [ pytest psutil ];
-
-  meta = with stdenv.lib; {
-    description = "Compression library";
-    homepage = https://github.com/python-lz4/python-lz4;
-    license = licenses.bsd3;
-  };
-
-}

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

@@ -3,6 +3,7 @@
 , fetchPypi
 , six
 , beautifulsoup4
+, lxml
 }:
 
 buildPythonPackage rec {
@@ -14,7 +15,7 @@ buildPythonPackage rec {
     sha256 = "d8c81fd5089332106da1a2e8919c412c7c677f08af04d557ca767701a04e0918";
   };
 
-  propagatedBuildInputs = [ six beautifulsoup4 ];
+  propagatedBuildInputs = [ six beautifulsoup4 lxml ];
 
   meta = with stdenv.lib; {
     homepage = "http://sites.google.com/site/ofxparse";

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

@@ -1,8 +1,9 @@
-{ stdenv
+{ lib
 , buildPythonPackage
 , fetchPypi
 , pytest
 , pytestrunner
+, functools32
 , six
 , w3lib
 , lxml
@@ -19,13 +20,13 @@ buildPythonPackage rec {
   };
 
   buildInputs = [ pytest pytestrunner ];
-  propagatedBuildInputs = [ six w3lib lxml cssselect ];
+  propagatedBuildInputs = [ functools32 six w3lib lxml cssselect ];
 
   checkPhase = ''
     py.test
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/scrapy/parsel";
     description = "Parsel is a library to extract data from HTML and XML using XPath and CSS selectors";
     license = licenses.bsd3;

pkgs/development/python-modules/python-lz4/default.nix

@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "python-lz4";
-  version = "2.1.0";
+  version = "2.1.2";
 
   # get full repository inorder to run tests
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "1vjfplj37jcw1mf8l810dv76dx0raia3ylgyfy7sfsb3g17brjq6";
+    sha256 = "1kzzdfkrq9nnlh0wssa6ccncvv0sk4wmhivhgyndjxz6d6przl5d";
   };
 
   buildInputs = [ setuptools_scm pkgconfig pytestrunner ];
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   meta = {
      description = "LZ4 Bindings for Python";
      homepage = https://github.com/python-lz4/python-lz4;
-     license = lib.licenses.bsd0;
+     license = lib.licenses.bsd3;
      maintainers = with lib.maintainers; [ costrouc ];
   };
 }

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

@@ -1,6 +1,6 @@
-{ buildPythonPackage, pythonOlder,
+{ stdenv, fetchurl, buildPythonPackage, pythonOlder,
   cudaSupport ? false, cudatoolkit ? null, cudnn ? null,
-  fetchFromGitHub, lib, numpy, pyyaml, cffi, typing, cmake,
+  fetchFromGitHub, lib, numpy, pyyaml, cffi, typing, cmake, hypothesis, numactl,
   linkFarm, symlinkJoin,
   utillinux, which }:
 
@@ -25,7 +25,7 @@ let
     "LD_LIBRARY_PATH=${cudaStub}\${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH} ";
 
 in buildPythonPackage rec {
-  version = "0.4.1";
+  version = "1.0.0";
   pname = "pytorch";
 
   src = fetchFromGitHub {
@@ -33,9 +33,17 @@ in buildPythonPackage rec {
     repo   = "pytorch";
     rev    = "v${version}";
     fetchSubmodules = true;
-    sha256 = "1cr8h47jxgfar5bamyvlayvqymnb2qvp7rr0ka2d2d4rdldf9lrp";
+    sha256 = "076cpbig4sywn9vv674c0xdg832sdrd5pk1d0725pjkm436kpvlm";
   };
 
+  patches =
+    [ # Skips two tests that are only meant to run on multi GPUs
+      (fetchurl {
+        url = "https://github.com/pytorch/pytorch/commit/bfa666eb0deebac21b03486e26642fd70d66e478.patch";
+        sha256 = "1fgblcj02gjc0y62svwc5gnml879q3x2z7m69c9gax79dpr37s9i";
+      })
+    ];
+
   preConfigure = lib.optionalString cudaSupport ''
     export CC=${cudatoolkit.cc}/bin/gcc CXX=${cudatoolkit.cc}/bin/g++
   '' + lib.optionalString (cudaSupport && cudnn != null) ''
@@ -58,12 +66,24 @@ in buildPythonPackage rec {
     done
   '';
 
+  # Override the (weirdly) wrong version set by default. See
+  # https://github.com/NixOS/nixpkgs/pull/52437#issuecomment-449718038
+  # https://github.com/pytorch/pytorch/blob/v1.0.0/setup.py#L267
+  PYTORCH_BUILD_VERSION = version;
+  PYTORCH_BUILD_NUMBER = 0;
+
+  # Suppress a weird warning in mkl-dnn, part of ideep in pytorch
+  # (upstream seems to have fixed this in the wrong place?)
+  # https://github.com/intel/mkl-dnn/commit/8134d346cdb7fe1695a2aa55771071d455fae0bc
+  NIX_CFLAGS_COMPILE = lib.optionals (numpy.blasImplementation == "mkl") [ "-Wno-error=array-bounds" ];
+
   buildInputs = [
      cmake
      numpy.blas
      utillinux
      which
-  ] ++ lib.optionals cudaSupport [cudatoolkit_joined cudnn];
+  ] ++ lib.optionals cudaSupport [ cudatoolkit_joined cudnn ]
+    ++ lib.optionals stdenv.isLinux [ numactl ];
 
   propagatedBuildInputs = [
     cffi
@@ -71,15 +91,16 @@ in buildPythonPackage rec {
     pyyaml
   ] ++ lib.optional (pythonOlder "3.5") typing;
 
+  checkInputs = [ hypothesis ];
   checkPhase = ''
-    ${cudaStubEnv}python test/run_test.py --exclude dataloader sparse torch utils distributed
+    ${cudaStubEnv}python test/run_test.py --exclude dataloader sparse torch utils thd_distributed distributed cpp_extensions
   '';
 
   meta = {
-    description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration.";
-    homepage = https://pytorch.org/;
-    license = lib.licenses.bsd3;
-    platforms = lib.platforms.linux;
-    maintainers = with lib.maintainers; [ teh ];
+    description = "Open source, prototype-to-production deep learning platform";
+    homepage    = https://pytorch.org/;
+    license     = lib.licenses.bsd3;
+    platforms   = lib.platforms.linux;
+    maintainers = with lib.maintainers; [ teh thoughtpolice ];
   };
 }

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

@@ -1,5 +1,6 @@
 { stdenv
 , buildPythonPackage
+, isPy27
 , fetchPypi
 , six
 , pillow
@@ -18,6 +19,7 @@ buildPythonPackage rec {
 
   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/secretstorage/2.nix

@@ -0,0 +1,24 @@
+{ lib, fetchPypi, buildPythonPackage, cryptography, dbus-python }:
+
+buildPythonPackage rec {
+  pname = "secretstorage";
+  version = "2.3.1";
+
+  src = fetchPypi {
+    pname = "SecretStorage";
+    inherit version;
+    sha256 = "1di9gx4m27brs6ar774m64s017iz742mnmw39kvfc8skfs3mrxis";
+  };
+
+  propagatedBuildInputs = [ cryptography dbus-python ];
+
+  # Needs a D-Bus Sesison
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/mitya57/secretstorage;
+    description = "Python bindings to FreeDesktop.org Secret Service API";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ orivej ];
+  };
+}

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

@@ -24,7 +24,7 @@ buildPythonPackage rec {
   meta = with lib; {
     homepage = https://github.com/mitya57/secretstorage;
     description = "Python bindings to FreeDesktop.org Secret Service API";
-    license = licenses.bsdOriginal;
+    license = licenses.bsd3;
     maintainers = with maintainers; [ teto ];
   };
 }

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

@@ -5,6 +5,7 @@
 , tox
 , six
 , dateutil
+, kitchen
 , pytz
 , pkgs
 }:
@@ -28,7 +29,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   buildInputs = [ nose pkgs.taskwarrior tox ];
-  propagatedBuildInputs = [ six dateutil pytz ];
+  propagatedBuildInputs = [ six dateutil kitchen pytz ];
 
   meta = with stdenv.lib; {
     homepage =  https://github.com/ralphbean/taskw;

pkgs/development/python-modules/taskw/use-template-for-taskwarrior-install-path.patch

@@ -4,45 +4,11 @@ Date:   Sun Nov 16 15:19:38 2014 +0100
 
     Use a template for taskwarrior install path.
 
-diff --git a/taskw/warrior.py b/taskw/warrior.py
-index 21dde88..e0509f2 100644
 --- a/taskw/warrior.py
 +++ b/taskw/warrior.py
-@@ -451,17 +451,17 @@ class TaskWarriorShellout(TaskWarriorBase):
-     def _execute(self, *args):
-         """ Execute a given taskwarrior command with arguments
- 
-         Returns a 2-tuple of stdout and stderr (respectively).
- 
-         """
-         command = (
-             [
+@@ -449 +449 @@ class TaskWarriorShellout(TaskWarriorBase):
 -                'task',
 +                '@@taskwarrior@@/bin/task',
-                 'rc:%s' % self.config_filename,
-             ]
-             + self.get_configuration_override_args()
-             + [six.text_type(arg) for arg in args]
-         )
- 
-         # subprocess is expecting bytestrings only, so nuke unicode if present
-         for i in range(len(command)):
-@@ -525,17 +525,17 @@ class TaskWarriorShellout(TaskWarriorBase):
-         except OSError:
-             # OSError is raised if subprocess.Popen fails to find
-             # the executable.
-             return False
- 
-     @classmethod
-     def get_version(cls):
-         taskwarrior_version = subprocess.Popen(
--            ['task', '--version'],
-+            ['@@taskwarrior@@/bin/task', '--version'],
-             stdout=subprocess.PIPE
-         ).communicate()[0]
-         return LooseVersion(taskwarrior_version.decode())
- 
-     def sync(self, init=False):
-         if self.get_version() < LooseVersion('2.3'):
-             raise UnsupportedVersionException(
-                 "'sync' requires version 2.3 of taskwarrior or later."
+@@ -553 +553 @@ class TaskWarriorShellout(TaskWarriorBase):
+-                ['task', '--version'],
++                ['@@taskwarrior@@/bin/task', '--version'],