Merge branch 'master' into staging-next

A couple thousand rebuilds have accumulated on master.

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

@@ -8,33 +8,37 @@
 , async-timeout
 , yarl
 , idna-ssl
+, typing-extensions
+, pytestrunner
 , pytest
 , gunicorn
-, pytest-mock
-, async_generator
-, pytestrunner
 , pytest-timeout
+, async_generator
+, pytest_xdist
+, pytestcov
+, pytest-mock
+, trustme
+, brotlipy
 }:
 
 buildPythonPackage rec {
   pname = "aiohttp";
-  version = "3.4.4";
+  version = "3.5.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ykm6kdjkrg556j0zd7dx2l1rsrbh0d9g27ivr6dmaahz9pyrbsi";
+    sha256 = "7967b760d0e96eb7ac6b20a9143112ce5c03a00b4f74d8a5ee66c8e88e6b6800";
   };
 
   disabled = pythonOlder "3.5";
 
-  checkInputs = [ pytest gunicorn pytest-mock async_generator pytestrunner pytest-timeout ];
+  checkInputs = [
+    pytestrunner pytest gunicorn pytest-timeout async_generator pytest_xdist
+    pytest-mock pytestcov trustme brotlipy
+  ];
 
   propagatedBuildInputs = [ attrs chardet multidict async-timeout yarl ]
-    ++ lib.optional (pythonOlder "3.7") idna-ssl;
-
-
-  # Several test failures. Need to be looked into.
-  doCheck = false;
+    ++ lib.optionals (pythonOlder "3.7") [ idna-ssl typing-extensions ];
 
   meta = with lib; {
     description = "Asynchronous HTTP Client/Server for Python and asyncio";

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

@@ -0,0 +1,33 @@
+{ lib, buildPythonPackage, fetchPypi
+, redis
+, memcached
+, msgpack-python
+}:
+
+buildPythonPackage rec {
+  pname = "cachy";
+  version = "0.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0v6mjyhgx6j7ya20bk69cr3gdzdkdf6psay0h090rscclgji65dp";
+  };
+
+  propagatedBuildInputs = [
+    redis
+    memcached
+    msgpack-python
+  ];
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/cachy;
+    description = "Cachy provides a simple yet effective caching library";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ lib, buildPythonPackage, fetchPypi
+, pylev, pastel, clikit }:
+
+buildPythonPackage rec {
+  pname = "cleo";
+  version = "0.7.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "091nzpfp5incd2fzqych78rvyx4i3djr50cnizbjzr3dc7g00l3s";
+  };
+
+  propagatedBuildInputs = [
+    pylev
+    pastel
+    clikit
+  ];
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/cleo;
+    description = "Allows you to create beautiful and testable command-line interfaces";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ lib, buildPythonPackage, fetchPypi
+, isPy27, isPy34
+, pylev, pastel, typing, enum34 }:
+
+buildPythonPackage rec {
+  pname = "clikit";
+  version = "0.2.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zr1s0xhk62p9a6zcp5whvsb27lddyk8gx03k9l8q18jp7y3igbv";
+  };
+
+  propagatedBuildInputs = [
+    pylev pastel
+  ] ++ lib.optional (isPy27 || isPy34) typing
+    ++ lib.optional isPy27 enum34;
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/clikit;
+    description = "A group of utilities to build beautiful and testable command line interfaces";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/fido2/default.nix

@@ -1,4 +1,7 @@
-{ lib, buildPythonPackage, fetchPypi, six, cryptography }:
+{ lib, buildPythonPackage, fetchPypi
+, six, cryptography
+, mock, pyfakefs
+}:
 
 buildPythonPackage rec {
   pname = "fido2";
@@ -9,12 +12,10 @@ buildPythonPackage rec {
     sha256 = "1pl8d2pr6jzqj4y9qiaddhjgnl92kikjxy0bgzm2jshkzzic8mp3";
   };
 
-  # The pypi package does not include tests
-  # Check https://github.com/Yubico/python-fido2/pull/8
-  doCheck = false;
-
   propagatedBuildInputs = [ six cryptography ];
 
+  checkInputs = [ mock pyfakefs ];
+
   meta = with lib; {
     description = "Provides library functionality for FIDO 2.0, including communication with a device over USB.";
     homepage = https://github.com/Yubico/python-fido2;

pkgs/development/python-modules/google-i18n-address/default.nix

@@ -0,0 +1,22 @@
+{ buildPythonPackage, fetchPypi, lib, requests, pytest, pytestcov, mock }:
+
+buildPythonPackage rec {
+  pname = "google-i18n-address";
+  version = "2.3.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0f1j1lp9bmllkzhciw0lxi7ipm8w461n0p97mz9714br0cs9glm1";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  checkInputs = [ pytest pytestcov mock ];
+
+  meta = with lib; {
+    description = "Google's i18n address data packaged for Python";
+    homepage = https://pypi.org/project/google-i18n-address/;
+    maintainers = with maintainers; [ ma27 ];
+    license = licenses.bsd3;
+  };
+}

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

@@ -10,12 +10,12 @@ let
   mpi = hdf5.mpi;
   mpiSupport = hdf5.mpiSupport;
 in buildPythonPackage rec {
-  version = "2.8.0";
+  version = "2.9.0";
   pname = "h5py";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6";
+    sha256 = "9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002";
   };
 
   configure_flags = "--hdf5=${hdf5}" + optionalString mpiSupport " --mpi";
@@ -37,9 +37,6 @@ in buildPythonPackage rec {
   propagatedBuildInputs = [ numpy six]
     ++ optionals mpiSupport [ mpi4py openssh ];
 
-  # https://github.com/h5py/h5py/issues/1088
-  doCheck = false;
-
   meta = {
     description =
       "Pythonic interface to the HDF5 binary data format";

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, glibcLocales
 }:
 
 buildPythonPackage rec {
@@ -12,6 +13,10 @@ buildPythonPackage rec {
     sha256 = "8eec9c1f4bfae3408a3f30500261f7e6a65912dc138526ea054f9ad98892e9d2";
   };
 
+  buildInputs = [ glibcLocales ];
+
+  LANG = "en_US.UTF-8";
+
   meta = with stdenv.lib; {
     description = "Pure-Python HPACK header compression";
     homepage = "http://hyper.rtfd.org";

pkgs/development/python-modules/mt-940/default.nix

@@ -3,14 +3,15 @@
 }:
 
 buildPythonPackage rec {
-  version = "4.12.2";
+  version = "4.13.0";
   pname = "mt-940";
 
+  # No tests in PyPI tarball
   src = fetchFromGitHub {
     owner = "WoLpH";
     repo = "mt940";
     rev = "v${version}";
-    sha256 = "0l7q8v00dhpbc9mh6baaaqc55kf44rszygx28dq3pwp5b5x33nir";
+    sha256 = "0p6z4ipj0drph3ryn8mnb3xn0vjfv54y1c5w5i9ixrxwz48h6bga";
   };
 
   postPatch = ''
@@ -24,9 +25,8 @@ buildPythonPackage rec {
 
   checkInputs = [ pyyaml pytestpep8 pytestflakes pytest glibcLocales ];
 
-  # See https://github.com/WoLpH/mt940/issues/64 for the disabled test
   checkPhase = ''
-    py.test -k "not mt940.models.FixedOffset"
+    py.test
   '';
 
   meta = with stdenv.lib; {

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "multidict";
-  version = "4.4.2";
+  version = "4.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3c11e92c3dfc321014e22fb442bc9eb70e01af30d6ce442026b0c35723448c66";
+    sha256 = "024b8129695a952ebd93373e45b5d341dbb87c17ce49637b34000093f243dd4f";
   };
 
   checkInputs = [ pytest pytestrunner pytestcov ];

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "netdisco";
-  version = "2.2.0";
+  version = "2.3.0";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b5e810721a266660f7f90fc43f12c4635ec95c3db87d9e30ca408bb922cb1007";
+    sha256 = "2571fc094f3bf8c60be211e90474515f565f3ef1c92e857176daab8577493a3b";
   };
 
   propagatedBuildInputs = [ requests zeroconf netifaces ];

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

@@ -30,21 +30,28 @@
 , which
 , bash
 , glibcLocales
+, callPackage
 }:
 
 assert !isPy3k -> configparser != null;
 
+let
+
+ # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
+ neurdflib = callPackage ./neurdflib.nix { };
+
+in
+
 buildPythonPackage rec {
   pname = "nipype";
-  version = "1.1.5";
+  version = "1.1.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d49bbe531cdbf0a049f1581e4d3c63231ff5978445cb380aa6e7f8f1d256a29c";
+    sha256 = "0iyi5w2h42bpssqj52ixm2kxp56yxfxdacb6xv5r24yv3hmwd4yn";
   };
 
-  # see https://github.com/nipy/nipype/issues/2240
-  patches = [ ./prov-version.patch ];
+  patches = [ ./move-uneeded-requires.patch ];
 
   postPatch = ''
     substituteInPlace nipype/interfaces/base/tests/test_core.py \
@@ -57,6 +64,7 @@ buildPythonPackage rec {
     funcsigs
     future
     networkx
+    neurdflib
     nibabel
     numpy
     packaging
@@ -72,12 +80,24 @@ buildPythonPackage rec {
     futures
   ];
 
-  checkInputs = [ pytest mock pytestcov pytest_xdist pytest-forked codecov which glibcLocales ];
+  checkInputs = [
+    codecov
+    glibcLocales
+    mock
+    pytest
+    pytest-forked
+    pytest_xdist
+    pytestcov
+    which
+  ];
 
   checkPhase = ''
-    LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype
+    LC_ALL="en_US.UTF-8" pytest -v --doctest-modules nipype
   '';
 
+  # See: https://github.com/nipy/nipype/issues/2839
+  doCheck = false;
+
   meta = with stdenv.lib; {
     homepage = http://nipy.org/nipype/;
     description = "Neuroimaging in Python: Pipelines and Interfaces";

pkgs/development/python-modules/nipype/move-uneeded-requires.patch

@@ -0,0 +1,31 @@
+diff --git a/nipype/info.py b/nipype/info.py
+index c6503ac..4379643 100644
+--- a/nipype/info.py
++++ b/nipype/info.py
+@@ -147,9 +147,6 @@ REQUIRES = [
+     'neurdflib',
+     'click>=%s' % CLICK_MIN_VERSION,
+     'funcsigs',
+-    'pytest>=%s' % PYTEST_MIN_VERSION,
+-    'pytest-xdist',
+-    'mock',
+     'pydotplus',
+     'pydot>=%s' % PYDOT_MIN_VERSION,
+     'packaging',
+@@ -159,7 +156,15 @@ REQUIRES = [
+ if sys.version_info <= (3, 4):
+     REQUIRES.append('configparser')
+ 
+-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
++TESTS_REQUIRES = [
++    'pytest>=%s' % PYTEST_MIN_VERSION,
++    'pytest-xdist',
++    'mock',
++    'pytest-cov',
++    'codecov',
++    'pytest-env',
++    'coverage<5'
++]
+ 
+ EXTRA_REQUIRES = {
+     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

pkgs/development/python-modules/nipype/neurdflib.nix

@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isodate
+, html5lib
+, SPARQLWrapper
+, networkx
+, nose
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "neurdflib";
+  version = "5.0.0.post1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qgmprixqxycxpjk9wjdmjykma14qqa2wcbx4nsldxi0ga7i7vv5";
+  };
+
+  propagatedBuildInputs = [ isodate html5lib SPARQLWrapper ];
+
+  checkInputs = [ networkx nose ];
+
+  # Python 2 syntax
+  # Failing doctest
+  doCheck = false;
+
+  checkPhase = ''
+    ${python.interpreter} run_tests.py
+  '';
+
+  meta = with lib; {
+    description = "A temporary convenience package for changes waiting to be merged into the primary rdflib repo";
+    homepage = https://pypi.org/project/neurdflib;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/python-modules/nipype/prov-version.patch

@@ -1,21 +0,0 @@
-diff --git a/nipype/info.py b/nipype/info.py
-index 1daa382e2..da338d0ea 100644
---- a/nipype/info.py
-+++ b/nipype/info.py
-@@ -108,7 +108,6 @@ DATEUTIL_MIN_VERSION = '2.2'
- PYTEST_MIN_VERSION = '3.0'
- FUTURE_MIN_VERSION = '0.16.0'
- SIMPLEJSON_MIN_VERSION = '3.8.0'
--PROV_VERSION = '1.5.0'
- CLICK_MIN_VERSION = '6.6.0'
- PYDOT_MIN_VERSION = '1.2.3'
- 
-@@ -140,7 +139,7 @@ REQUIRES = [
-     'traits>=%s' % TRAITS_MIN_VERSION,
-     'future>=%s' % FUTURE_MIN_VERSION,
-     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
--    'prov==%s' % PROV_VERSION,
-+    'prov<2',
-     'click>=%s' % CLICK_MIN_VERSION,
-     'funcsigs',
-     'pytest>=%s' % PYTEST_MIN_VERSION,

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

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchFromGitHub, isPy3k, pytest }:
+
+buildPythonPackage rec {
+  pname = "pastel";
+  version = "0.1.0";
+
+  # No tests in PyPi tarball
+  src = fetchFromGitHub {
+    owner = "sdispater";
+    repo = "pastel";
+    rev = version;
+    sha256 = "1b4ag7jr7j0sxly5g29imdq8g0d4ixhbck55dblr45mlsidydx0s";
+  };
+
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    pytest tests -sq
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/pastel;
+    description = "Bring colors to your terminal";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,35 @@
+{ stdenv
+, python
+, fetchPypi
+, buildPythonPackage
+, postgresql }:
+
+buildPythonPackage rec {
+  pname = "pgsanity";
+  version = "0.2.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "de0bbd6fe4f98bf5139cb5f466eac2e2abaf5a7b050b9e4867b87bf360873173";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s test
+  '';
+
+  propagatedBuildInputs = [ postgresql ];
+
+  meta = with stdenv.lib; {
+    homepage = "http://github.com/markdrago/pgsanity";
+    description = "Checks the syntax of Postgresql SQL files";
+    longDescription = ''
+      PgSanity checks the syntax of Postgresql SQL files by
+      taking a file that has a list of bare SQL in it, 
+      making that file look like a C file with embedded SQL, 
+      run it through ecpg and 
+      let ecpg report on the syntax errors of the SQL.
+    '';
+    license = stdenv.lib.licenses.mit;
+    maintainers = with maintainers; [ nalbyuites ];
+  };
+}

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

@@ -1,21 +1,21 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, nose
 , pygments
-, isPy3k
 }:
 
 buildPythonPackage rec {
-  version = "0.8.0";
+  version = "0.9.2";
   pname = "piep";
-  disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1wgkg1kc28jpya5k4zvbc9jmpa60b3d5c3gwxfbp15hw6smyqirj";
+    sha256 = "0b5anpsq16xkiisws95jif5s5mplkl1kdnhy0w0i6m0zcy50jnxq";
   };
 
   propagatedBuildInputs = [ pygments ];
+  checkInputs = [ nose ];
 
   meta = with stdenv.lib; {
     description = "Bringing the power of python to stream editing";

pkgs/development/python-modules/pika-pool/default.nix

@@ -11,6 +11,10 @@ buildPythonPackage rec {
     sha256 = "f3985888cc2788cdbd293a68a8b5702a9c955db6f7b8b551aeac91e7f32da397";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py --replace "pika >=0.9,<0.11" "pika"
+  '';
+
   # Tests require database connections
   doCheck = false;
 

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

@@ -0,0 +1,76 @@
+{ lib, buildPythonPackage, fetchPypi, callPackage
+, isPy27, isPy34
+, cleo
+, requests
+, cachy
+, requests-toolbelt
+, pyrsistent
+, pyparsing
+, cachecontrol
+, pkginfo
+, html5lib
+, shellingham
+, tomlkit
+, typing
+, pathlib2
+, virtualenv
+, functools32
+, pytest
+}:
+
+let
+  cleo6 = cleo.overrideAttrs (oldAttrs: rec {
+    version = "0.6.8";
+    src = fetchPypi {
+      inherit (oldAttrs) pname;
+      inherit version;
+      sha256 = "06zp695hq835rkaq6irr1ds1dp2qfzyf32v60vxpd8rcnxv319l5";
+    };
+  });
+
+  jsonschema3 = callPackage ./jsonschema.nix { };
+
+in buildPythonPackage rec {
+  pname = "poetry";
+  version = "0.12.10";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "00npb0jlimnk4r01zkhfmns4843j1hfhd388s326da5pd8n0dq7l";
+  };
+
+  postPatch = ''
+    substituteInPlace pyproject.toml --replace "3.0a3" "3.0.0a3"
+    substituteInPlace setup.py --replace "3.0a3" "3.0.0a3"
+  '';
+
+  propagatedBuildInputs = [
+    cleo6
+    requests
+    cachy
+    requests-toolbelt
+    jsonschema3
+    pyrsistent
+    pyparsing
+    cachecontrol
+    pkginfo
+    html5lib
+    shellingham
+    tomlkit
+  ] ++ lib.optionals (isPy27 || isPy34) [ typing pathlib2 ]
+    ++ lib.optionals isPy27 [ virtualenv functools32 ];
+
+  # No tests in Pypi tarball
+  doCheck = false;
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/poetry;
+    description = "Python dependency management and packaging made easy";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/poetry/jsonschema.nix

@@ -0,0 +1,37 @@
+{ lib, buildPythonPackage, fetchPypi, isPy27, callPackage
+, attrs
+, pyrsistent
+, six
+, functools32
+, lockfile
+, setuptools_scm
+}:
+
+buildPythonPackage rec {
+  pname = "jsonschema";
+  version = "3.0.0a3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0pkhsq91rhk6384p0jxjkhc9yml2ya2l0mysyq78sb4981h45n6z";
+  };
+
+  nativeBuildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [
+    attrs
+    pyrsistent
+    six
+    lockfile
+  ] ++ lib.optional isPy27 functools32;
+
+  # tests for latest version rely on custom version of betterpaths that is
+  # difficult to deal with and isn't used on master
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/Julian/jsonschema;
+    description = "An implementation of JSON Schema validation for Python";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/py3status/default.nix

@@ -19,11 +19,11 @@
 
 buildPythonPackage rec {
   pname = "py3status";
-  version = "3.14";
+  version = "3.15";
   
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8775fb3903458a519593fc22b712ccac598464e319a12b9fdf04803fa60a1583";
+    sha256 = "78aa7fa0af707641e215ea93bfd4bb5fd47f18a7193d84ed60bb9e6cccb75b7f";
   };
 
   doCheck = false;

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

@@ -1,5 +1,18 @@
 { stdenv, buildPythonPackage, fetchPypi, thrift, isPy3k }:
 
+let
+
+  thrift' = thrift.overridePythonAttrs (old: rec {
+    version = "0.9.3";
+    src= fetchPypi {
+      inherit (old) pname;
+      inherit version;
+      sha256 = "0zl7cgckqy9j5vq8wyfzw82q1blkdpsblnmhv8c6ffcxs4xkvg6z";
+    };
+  });
+
+in
+
 buildPythonPackage rec {
   pname = "pycassa";
   version = "1.11.2";
@@ -15,7 +28,7 @@ buildPythonPackage rec {
   # running
   doCheck = false;
 
-  propagatedBuildInputs = [ thrift ];
+  propagatedBuildInputs = [ thrift' ];
 
   meta = {
     description = "A python client library for Apache Cassandra";

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

@@ -1,7 +1,7 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, python, pytest, glibcLocales }:
 
 buildPythonPackage rec {
-  version = "3.4.3";
+  version = "3.5.5";
   pname = "pyfakefs";
 
   # no tests in PyPI tarball
@@ -10,7 +10,7 @@ buildPythonPackage rec {
     owner = "jmcgeheeiv";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0rhbkcb5h2x8kmyxivr5jr1db2xvmpjdbsfjxl142qhfb29hr2hp";
+    sha256 = "1pww444ih4bf84a0jgl1r446mjywhlls890mnw76flx8maahlik1";
   };
 
   postPatch = ''
@@ -33,7 +33,8 @@ buildPythonPackage rec {
   checkPhase = ''
     export LC_ALL=en_US.UTF-8
     ${python.interpreter} -m pyfakefs.tests.all_tests
-    ${python.interpreter} -m pytest pyfakefs/tests/pytest_plugin_test.py
+    ${python.interpreter} -m pyfakefs.tests.all_tests_without_extra_packages
+    ${python.interpreter} -m pytest pyfakefs/tests/pytest/pytest_plugin_test.py
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/pygit2/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, fetchpatch, isPyPy, libgit2, six, cffi }:
+{ stdenv, lib, buildPythonPackage, fetchPypi, fetchpatch, isPyPy, libgit2_0_27, six, cffi }:
 
 buildPythonPackage rec {
   pname = "pygit2";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
   };
 
   preConfigure = lib.optionalString stdenv.isDarwin ''
-    export DYLD_LIBRARY_PATH="${libgit2}/lib"
+    export DYLD_LIBRARY_PATH="${libgit2_0_27}/lib"
   '';
 
   patches = [ (fetchpatch {
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     sha256 = "18x1fpmywhjjr4lvakwmy34zpxfqi8pqqj48g1wcib39lh3s7l4f";
   }) ];
 
-  propagatedBuildInputs = [ libgit2 six ] ++ lib.optional (!isPyPy) cffi;
+  propagatedBuildInputs = [ libgit2_0_27 six ] ++ lib.optional (!isPyPy) cffi;
 
   preCheck = ''
     # disable tests that require networking

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyhomematic";
-  version = "0.1.53";
+  version = "0.1.54";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1crqdqbv7yqw2pasydy51ps048phbdn7s37xaba9npd1xm8g7jvh";
+    sha256 = "3c27f303e6a424229d2d5133af593c21f7d660bdf19d3d00641fbac08a6992c5";
   };
 
   # PyPI tarball does not include tests/ directory

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

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "pylev";
+  version = "1.3.0";
+
+  # No tests in PyPi tarball
+  src = fetchFromGitHub {
+    owner = "toastdriven";
+    repo = "pylev";
+    # Can't use a tag because it's missing
+    # https://github.com/toastdriven/pylev/issues/10
+    # rev = "v${version};
+    rev = "72e3d490515c3188e2acac9c15ea1b466f9ff938";
+    sha256 = "18dg1rfnqgfl6x4vafiq4la9d7f65xak19gcvngslq0bm1z6hyd8";
+  };
+
+  meta = with lib; {
+    homepage = https://github.com/toastdriven/pylev;
+    description = "A pure Python Levenshtein implementation that's not freaking GPL'd";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -4,6 +4,7 @@
 , six
 , pytest
 , hypothesis
+, pytestrunner
 }:
 
 buildPythonPackage rec {
@@ -16,11 +17,11 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [ six ];
-  buildInputs = [ pytest hypothesis ];
 
-  checkPhase = ''
-    py.test
-  '';
+  checkInputs = [ pytestrunner pytest hypothesis ];
+
+  # pytestrunner is only needed to run tests
+  patches = [ ./no-setup-requires-pytestrunner.patch ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/tobgu/pyrsistent/;

pkgs/development/python-modules/pyrsistent/no-setup-requires-pytestrunner.patch

@@ -0,0 +1,15 @@
+diff --git a/setup.py b/setup.py
+index 90a39a5..7bf444f 100644
+--- a/setup.py
++++ b/setup.py
+@@ -77,9 +77,8 @@ setup(
+         'Programming Language :: Python :: Implementation :: PyPy',
+     ],
+     test_suite='tests',
+-    tests_require=['pytest','hypothesis'],
++    tests_require=['pytest-runner', 'pytest','hypothesis'],
+     scripts=[],
+-    setup_requires=['pytest-runner'],
+     ext_modules=extensions,
+     cmdclass={'build_ext': custom_build_ext},
+     install_requires=['six'],

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "scapy";
-  version = "2.4.0";
+  version = "2.4.2";
 
   disabled = isPyPy;
 
@@ -21,13 +21,16 @@ buildPythonPackage rec {
     owner = "secdev";
     repo = "scapy";
     rev = "v${version}";
-    sha256 = "0dw6kl1qi9bf3rbm79gb1h40ms8y0b5dbmpip841p2905d5r2isj";
+    sha256 = "03xzjklvc6y4d87k0rqpx5h112ld5nvgfldrbd8c4mx6f9mmd11n";
   };
 
   # TODO: Temporary workaround
-  patches = [ ./fix-version-1.patch ./fix-version-2.patch ];
+  patches = [ ./fix-version.patch ];
 
-  postPatch = lib.optionalString withManufDb ''
+  postPatch = ''
+    sed -i "s/NIXPKGS_SCAPY_VERSION/${version}/" \
+      setup.py scapy/__init__.py
+  '' + lib.optionalString withManufDb ''
     substituteInPlace scapy/data.py --replace "/opt/wireshark" "${wireshark}"
   '';
 

pkgs/development/python-modules/scapy/fix-version-1.patch

@@ -1,11 +0,0 @@
---- a/setup.py	2018-02-15 22:14:08.531591678 +0100
-+++ b/setup.py	2018-03-27 17:15:38.617315539 +0200
-@@ -47,7 +47,7 @@
- 
- setup(
-     name='scapy',
--    version=__import__('scapy').VERSION,
-+    version='2.4.0',
-     packages=[
-         'scapy',
-         'scapy/arch',

pkgs/development/python-modules/scapy/fix-version.patch

@@ -1,3 +1,14 @@
+--- a/setup.py	2018-02-15 22:14:08.531591678 +0100
++++ b/setup.py	2018-03-27 17:15:38.617315539 +0200
+@@ -47,7 +47,7 @@
+ 
+ setup(
+     name='scapy',
+-    version=__import__('scapy').VERSION,
++    version='NIXPKGS_SCAPY_VERSION',
+     packages=[
+         'scapy',
+         'scapy/arch',
 --- a/scapy/__init__.py	2018-03-27 17:38:52.706481269 +0200
 +++ b/scapy/__init__.py	2018-03-27 17:39:56.576688890 +0200
 @@ -82,9 +82,10 @@
@@ -5,10 +16,10 @@
                  return "git-archive.dev" + match.group(1)
              elif sha1:
 -                return "git-archive.dev" + sha1
-+                return '2.4.0'
++                return 'NIXPKGS_SCAPY_VERSION'
              else:
 -                return 'unknown.version'
-+                return '2.4.0'
++                return 'NIXPKGS_SCAPY_VERSION'
 +
  
  VERSION = _version()

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, six
 }:
 
 buildPythonPackage rec {
@@ -12,6 +13,8 @@ buildPythonPackage rec {
     sha256 = "7d59ac4fdcb2c58037ebd4a9da5f9a49e3e034bf75b3f26d9fe48ba3d8806e6b";
   };
 
+  propagatedBuildInputs = [ six ];
+
   # No tests. Breaks when not disabling.
   doCheck = false;
 

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

@@ -3,6 +3,7 @@
 , fetchPypi
 , pytest
 , python
+, cython
 , cssutils
 , isPyPy
 }:
@@ -18,6 +19,17 @@ buildPythonPackage rec {
 
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ cssutils ];
+  nativeBuildInputs = [
+    cython
+  ];
+
+  preBuild = ''
+    # Force cython to re-generate this file. If it is present, cython will
+    # think it is "up to date" even though it was generated with an older,
+    # incompatible version of cython. See
+    # https://github.com/Kozea/tinycss/issues/17.
+    rm tinycss/speedups.c
+  '';
 
   checkPhase = ''
     py.test $out/${python.sitePackages}

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

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchPypi, isPy27, isPy34
+, enum34, functools32, typing
+}:
+
+buildPythonPackage rec {
+  pname = "tomlkit";
+  version = "0.5.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hjfzlb6y694pkadygcaq1n63di97pxgq2zpc74in1axc5166l6n";
+  };
+
+  propagatedBuildInputs =
+    lib.optionals isPy27 [ enum34 functools32 ]
+    ++ lib.optional (isPy27 || isPy34) typing;
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/tomlkit;
+    description = "Style-preserving TOML library for Python";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/xml2rfc/default.nix

@@ -1,4 +1,6 @@
-{ lib, fetchPypi, buildPythonPackage, intervaltree, pyflakes, requests, lxml }:
+{ lib, fetchPypi, buildPythonPackage, intervaltree, pyflakes, requests, lxml, google-i18n-address
+, pycountry, html5lib, six
+}:
 
 buildPythonPackage rec {
   pname = "xml2rfc";
@@ -9,7 +11,20 @@ buildPythonPackage rec {
     sha256 = "64609a2194d18c03e2348f1ea2fb97208b3455dfb76a16900143813aa61b6d3c";
   };
 
-  propagatedBuildInputs = [ intervaltree pyflakes requests lxml ];
+  propagatedBuildInputs = [
+    intervaltree
+    pyflakes
+    requests
+    lxml
+    google-i18n-address
+    pycountry
+    html5lib
+    six
+  ];
+
+  preCheck = ''
+    export HOME=$(mktemp -d)
+  '';
 
   meta = with lib; {
     description = "Tool generating IETF RFCs and drafts from XML sources";

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

@@ -15,6 +15,9 @@ buildPythonPackage rec {
   };
   propagatedBuildInputs = [ xorgserver ];
 
+  # See: https://github.com/cgoldberg/xvfbwrapper/issues/30
+  doCheck = false;
+
   checkInputs = [ mock ];
 
   meta = with stdenv.lib; {

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

@@ -1,16 +1,13 @@
-{ stdenv, pkgconfig, fetchpatch, fetchFromGitHub, buildPythonPackage
+{ stdenv, pkgconfig, fetchpatch, fetchPypi, buildPythonPackage
 , zstd, pytest }:
 
 buildPythonPackage rec {
   pname = "zstd";
-  version = "1.3.5.1";
+  version = "1.3.8.1";
 
-  # Switch back to fetchPypi when tests/ is included, see https://github.com/NixOS/nixpkgs/pull/49339
-  src = fetchFromGitHub {
-    owner = "sergey-dryabzhinsky";
-    repo = "python-zstd";
-    rev = "v${version}";
-    sha256 = "08n1vz4zavas4cgzpdfcbpy33lnv39xxhq5mgj0zv3xi03ypc1rl";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "d89e884da59c35e480439f1663cb3cb4cf372e42ba0eb0bdf22b9625414702a3";
   };
 
   postPatch = ''