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

pkgs/development/python-modules/Flask-PyMongo/default.nix

@@ -2,6 +2,7 @@
 , fetchPypi
 , flask
 , pymongo
+, vcversioner
 , lib
 , pytest
 }:
@@ -18,17 +19,17 @@ buildPythonPackage rec {
   checkInputs = [ pytest ];
 
   checkPhase = ''
-    py.test tests
+    py.test
   '';
 
   # Tests seem to hang
   doCheck = false;
 
-  propagatedBuildInputs = [ flask pymongo ];
+  propagatedBuildInputs = [ flask pymongo vcversioner ];
 
   meta = {
     homepage = "http://flask-pymongo.readthedocs.org/";
     description = "PyMongo support for Flask applications";
     license = lib.licenses.bsd2;
   };
-}
+}

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

@@ -1,18 +1,19 @@
 { stdenv, buildPythonPackage, fetchPypi, pythonOlder
 , cryptography
-, bcrypt, gssapi, libnacl, libsodium, nettle, pyopenssl }:
+, bcrypt, gssapi, libnacl, libsodium, nettle, pyopenssl
+, openssl }:
 
 buildPythonPackage rec {
   pname = "asyncssh";
-  version = "1.13.3";
+  version = "1.14.0";
   disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "eb5b190badc5cd2a506a1b6ced3e92f948166974eef7d1abab61acc67aa379e6";
+    sha256 = "0f1i5a760a3jylkj00bxkshnylzyhyqz50v8mb8s9ygllpzja058";
   };
 
-  propagatedBuildInputs = [ 
+  propagatedBuildInputs = [
     bcrypt
     cryptography
     gssapi
@@ -22,6 +23,8 @@ buildPythonPackage rec {
     pyopenssl
   ];
 
+  checkInputs = [ openssl ];
+
   # Disables windows specific test (specifically the GSSAPI wrapper for Windows)
   postPatch = ''
     rm ./tests/sspi_stub.py
@@ -29,8 +32,8 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Provides an asynchronous client and server implementation of the SSHv2 protocol on top of the Python asyncio framework";
-    homepage = https://pypi.python.org/pypi/asyncssh;
-    license = licenses.epl10;
+    homepage    = https://pypi.python.org/pypi/asyncssh;
+    license     = licenses.epl20;
     maintainers = with maintainers; [ worldofpeace ];
   };
 }

pkgs/development/python-modules/backports-shutil-which/default.nix

@@ -0,0 +1,24 @@
+{ stdenv, fetchPypi, fetchFromGitHub, buildPythonPackage, pytest }:
+
+buildPythonPackage rec {
+  pname = "backports.shutil_which";
+  version = "3.5.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "16sa3adkf71862cb9pk747pw80a2f1v5m915ijb4fgj309xrlhyx";
+  };
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test test
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Backport of shutil.which from Python 3.3";
+    homepage = https://github.com/minrk/backports.shutil_which;
+    license = licenses.psfl;
+    maintainers = with maintainers; [ jluttine ];
+  };
+}

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, libev, python }:
+
+buildPythonPackage rec {
+  pname = "bjoern";
+  version = "2.2.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1w5z9agacci4shmkg9gh46ifj2a724rrgbykdv14830f7jq3dcmi";
+  };
+
+  buildInputs = [ libev ];
+
+  checkPhase = ''
+    ${python.interpreter} tests/keep-alive-behaviour.py 2>/dev/null
+    ${python.interpreter} tests/test_wsgi_compliance.py
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/jonashaag/bjoern;
+    description = "A screamingly fast Python 2/3 WSGI server written in C";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ cmcdragonkai ];
+  };
+}

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

@@ -15,6 +15,12 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ persistent zope_interface ];
   checkInputs = [ zope_testrunner ];
 
+  # disable a failing test that looks broken
+  postPatch = ''
+    substituteInPlace BTrees/tests/common.py \
+      --replace "testShortRepr" "no_testShortRepr"
+  '';
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "dcc096c3cf92efd6b9365951f89118fd30bc209c9af83bf050a28151a9992786";

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

@@ -1,23 +1,26 @@
-{ stdenv, buildPythonPackage, fetchFromGitHub, six, pytest }:
+{ stdenv, buildPythonPackage, fetchFromGitHub
+, six, pytest, arrow
+}:
 
 buildPythonPackage rec {
-  pname = "construct";
-  version = "2.8.16";
-  name = pname + "-" + version;
+  pname   = "construct";
+  version = "2.9.45";
 
   src = fetchFromGitHub {
-    owner = "construct";
-    repo = "construct";
-    rev = "v${version}";
-    sha256 = "0lzz1dy419n254qccch7yx4nkpwd0fsyjhnsnaf6ysgwzqxxv63j";
+    owner  = pname;
+    repo   = pname;
+    rev    = "v${version}";
+    sha256 = "0ig66xrzswpkhhmw123p2nvr15a9lxz54a1fmycfdh09327c1d3y";
   };
 
   propagatedBuildInputs = [ six ];
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytest arrow ];
 
+  # TODO: figure out missing dependencies
+  doCheck = false;
   checkPhase = ''
-    py.test -k 'not test_numpy' tests
+    py.test -k 'not test_numpy and not test_gallery' tests
   '';
 
   meta = with stdenv.lib; {

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

@@ -1,4 +1,4 @@
-{ buildPythonPackage, fetchFromGitHub, lib,
+{ buildPythonPackage, isPy3k, fetchFromGitHub, lib,
   z3, ply, python-igraph, oset, ordered-set, dictionaries }:
 
 buildPythonPackage {
@@ -29,6 +29,8 @@ buildPythonPackage {
     $out/bin/cozy --help
   '';
 
+  disabled = !isPy3k;
+
   meta = {
     description = "The collection synthesizer";
     homepage = https://cozy.uwplse.org/;

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

@@ -4,7 +4,7 @@
 }:
 buildPythonPackage rec {
   pname = "daphne";
-  version = "2.1.0";
+  version = "2.2.2";
 
   disabled = !isPy3k;
 
@@ -12,7 +12,7 @@ buildPythonPackage rec {
     owner = "django";
     repo = pname;
     rev = version;
-    sha256 = "1lbpn0l796ar77amqy8dap30zxmsn6as8y2lbmp4lk8m9awscwi8";
+    sha256 = "1pr3b7zxjp2jx31lpiy1hfyprpmyiv2kd18n8x6kh6gd5nr0dgp8";
   };
 
   nativeBuildInputs = [ pytestrunner ];
@@ -21,9 +21,10 @@ buildPythonPackage rec {
 
   checkInputs = [ hypothesis pytest pytest-asyncio ];
 
+  doCheck = !stdenv.isDarwin; # most tests fail on darwin
+
   checkPhase = ''
-    # Other tests fail, seems to be due to filesystem access
-    py.test -k "test_cli or test_utils"
+    py.test
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/dask-glm/default.nix

@@ -0,0 +1,35 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, cloudpickle
+, dask
+, numpy, toolz # dask[array]
+, multipledispatch
+, scipy
+, scikitlearn
+, pytest
+}:
+
+buildPythonPackage rec {
+  version = "0.1.0";
+  pname = "dask-glm";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "5a38d17538558fe6a3457cd67eed0a90a5dff51a9eaebb496efb68fc432ed89a";
+  };
+
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ cloudpickle dask numpy toolz multipledispatch scipy scikitlearn ];
+
+  checkPhase = ''
+    py.test dask_glm
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://github.com/dask/dask-glm/;
+    description = "Generalized Linear Models with Dask";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/dask-image/default.nix

@@ -0,0 +1,30 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, dask
+, numpy, toolz # dask[array]
+, scipy
+, pims
+, pytest
+, scikitimage
+}:
+
+buildPythonPackage rec {
+  version = "0.1.1";
+  pname = "dask-image";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "e6294ac577a8fc0abec2b97a2c42d404f599feac61d6899bdf1bf2b7cfb0e015";
+  };
+
+  checkInputs = [ pytest scikitimage ];
+  propagatedBuildInputs = [ dask numpy toolz scipy pims ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/dask/dask-image;
+    description = "Distributed image processing";
+    license = licenses.bsdOriginal;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/dask-jobqueue/default.nix

@@ -0,0 +1,33 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, dask
+, distributed
+, docrep
+, pytest
+}:
+
+buildPythonPackage rec {
+  version = "0.4.0";
+  pname = "dask-jobqueue";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "c73dae82b2a1d2a9f4ef17778f0de7a9237671a7fd3374aadd9d2bc07e92e848";
+  };
+
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ dask distributed docrep ];
+
+  # do not run entire tests suite (requires slurm, sge, etc.)
+  checkPhase = ''
+    py.test dask_jobqueue/tests/test_jobqueue_core.py
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/dask/dask-jobqueue;
+    description = "Deploy Dask on job schedulers like PBS, SLURM, and SGE";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/dask-ml/default.nix

@@ -0,0 +1,43 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, dask
+, numpy, toolz # dask[array]
+, numba
+, pandas
+, scikitlearn
+, scipy
+, dask-glm
+, six
+, multipledispatch
+, packaging
+, pytest
+, xgboost
+, tensorflow
+, joblib
+, distributed
+}:
+
+buildPythonPackage rec {
+  version = "0.10.0";
+  pname = "dask-ml";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4b6ca548c7282c1b6983e696e4bdfa0a2d7b51b168928b9322ea7a4b9a9f20f9";
+  };
+
+  checkInputs = [ pytest xgboost tensorflow joblib distributed ];
+  propagatedBuildInputs = [ dask numpy toolz numba pandas scikitlearn scipy dask-glm six multipledispatch packaging ];
+
+  # dask-ml has some heavy test requirements
+  # and requires some very new packages
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/dask/dask-ml;
+    description = "Scalable Machine Learn with Dask";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/dask-xgboost/default.nix

@@ -0,0 +1,36 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, xgboost
+, dask
+, distributed
+, pytest
+, scikitlearn
+, scipy
+}:
+
+buildPythonPackage rec {
+  version = "0.1.5";
+  pname = "dask-xgboost";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1860d06965fe68def1c83b9195130a92050fd4bc28bf2be689898a3a74ee1316";
+  };
+
+  checkInputs = [ pytest scikitlearn ];
+  propagatedBuildInputs = [ xgboost dask distributed ];
+
+  checkPhase = ''
+    py.test dask_xgboost/tests/test_core.py
+  '';
+
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/dask/dask-xgboost;
+    description = "Interactions between Dask and XGBoost";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,29 +1,33 @@
 { lib
 , pkgs
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
+, pytest
 }:
 
 buildPythonPackage rec {
   pname   = "DendroPy";
   version = "4.4.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c";
+  # tests are incorrectly packaged in pypi version
+  src = fetchFromGitHub {
+    owner = "jeetsukumaran";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9";
   };
 
-  prePatch = ''
-    # Test removed/disabled and reported upstream: https://github.com/jeetsukumaran/DendroPy/issues/74
-    rm -f dendropy/test/test_dataio_nexml_reader_tree_list.py
-  '';
-
   preCheck = ''
     # Needed for unicode python tests
     export LC_ALL="en_US.UTF-8"
+    cd tests  # to find the 'support' module
   '';
 
-  checkInputs = [ pkgs.glibcLocales ];
+  checkInputs = [ pytest pkgs.glibcLocales ];
+
+  checkPhase = ''
+    pytest -k 'not test_dataio_nexml_reader_tree_list and not test_pscores_with'
+  '';
 
   meta = {
     homepage = http://dendropy.org/;

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

@@ -0,0 +1,60 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, pytest-repeat
+, pytest-faulthandler
+, pytest-timeout
+, mock
+, joblib
+, click
+, cloudpickle
+, dask
+, msgpack
+, psutil
+, six
+, sortedcontainers
+, tblib
+, toolz
+, tornado
+, zict
+, pyyaml
+, pythonOlder
+, futures
+, singledispatch
+}:
+
+buildPythonPackage rec {
+  pname = "distributed";
+  version = "1.23.1";
+
+  # get full repository need conftest.py to run tests
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "9d4693442efe40e05e4304fe6d8174989c6eb4bad1afe70480c98263ef8e1cdb";
+  };
+
+  checkInputs = [ pytest pytest-repeat pytest-faulthandler pytest-timeout mock joblib ];
+  propagatedBuildInputs = [
+      click cloudpickle dask msgpack psutil six
+      sortedcontainers tblib toolz tornado zict pyyaml
+  ] ++ lib.optional (pythonOlder "3.2") [ futures ]
+    ++ lib.optional (pythonOlder "3.4") [ singledispatch ];
+
+  # tests take about 10-15 minutes
+  # ignore 5 cli tests out of 1000 total tests that fail due to subprocesses
+  # these tests are not critical to the library (only the cli)
+  checkPhase = ''
+    py.test distributed -m "not avoid-travis" -r s --timeout-method=thread --timeout=0 --durations=20 --ignore="distributed/cli/tests"
+  '';
+
+  # when tested random tests would fail and not repeatably
+  doCheck = false;
+
+  meta = {
+    description = "Distributed computation in Python.";
+    homepage = http://distributed.readthedocs.io/en/latest/;
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ teh costrouc ];
+  };
+}

pkgs/development/python-modules/django-raster/default.nix

@@ -1,11 +1,13 @@
-{ stdenv, buildPythonPackage, fetchPypi,
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k,
   numpy, django_colorful, pillow, psycopg2,
-  pyparsing, django, celery
+  pyparsing, django_2_1, celery, boto3
 }:
 buildPythonPackage rec {
   version = "0.6";
   pname = "django-raster";
 
+  disabled = !isPy3k;
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "9a0f8e71ebeeeb5380c6ca68e027e9de335f43bc15e89dd22e7a470c4eb7aeb8";
@@ -15,7 +17,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   propagatedBuildInputs = [ numpy django_colorful pillow psycopg2
-                            pyparsing django celery ];
+                            pyparsing django_2_1 celery boto3 ];
 
   meta = with stdenv.lib; {
     description = "Basic raster data integration for Django";

pkgs/development/python-modules/eth-hash/default.nix

@@ -0,0 +1,45 @@
+{ lib, fetchPypi, buildPythonPackage, pythonOlder, pytest, pysha3, pycrypto,
+  pycryptodome }:
+
+buildPythonPackage rec {
+  pname = "eth-hash";
+  version = "0.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0xpiz0wrxxj11ki9yapvsibl25qnki90bl3d39nqascg14nw17a9";
+  };
+
+  checkInputs = [ pytest ];
+
+  propagatedBuildInputs = [ pysha3 pycrypto pycryptodome ];
+
+  # setuptools-markdown uses pypandoc which is broken at the moment
+  preConfigure = ''
+    substituteInPlace setup.py --replace \'setuptools-markdown\' ""
+  '';
+
+  # Run tests separately because we don't want to run tests on tests/backends/
+  # but only on its selected subdirectories. Also, the directories under
+  # tests/backends/ must be run separately because they have identically named
+  # test files so pytest would raise errors because of that.
+  #
+  # Also, tests in tests/core/test_import.py are broken so just ignore them:
+  # https://github.com/ethereum/eth-hash/issues/25
+  # There is a pull request to fix the tests:
+  # https://github.com/ethereum/eth-hash/pull/26
+  checkPhase = ''
+    pytest tests/backends/pycryptodome/
+    pytest tests/backends/pysha3/
+    # pytest tests/core/
+  '';
+
+  disabled = pythonOlder "3.5";
+
+  meta = {
+    description = "The Ethereum hashing function keccak256";
+    homepage = https://github.com/ethereum/eth-hash;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ jluttine ];
+  };
+}

pkgs/development/python-modules/eth-typing/default.nix

@@ -0,0 +1,35 @@
+{ lib, fetchFromGitHub, buildPythonPackage, pythonOlder, pytest }:
+
+buildPythonPackage rec {
+  pname = "eth-typing";
+  version = "1.3.0";
+
+  # Tests are missing from the PyPI source tarball so let's use GitHub
+  # https://github.com/ethereum/eth-typing/issues/8
+  src = fetchFromGitHub {
+    owner = "ethereum";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0703z7vlsfa3dvgcq22f9rzmj0svyp2a8wc7h73d0aac28ydhpv9";
+  };
+
+  # setuptools-markdown uses pypandoc which is broken at the moment
+  preConfigure = ''
+    substituteInPlace setup.py --replace \'setuptools-markdown\' ""
+  '';
+
+  disabled = pythonOlder "3.5";
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    pytest .
+  '';
+
+  meta = {
+    description = "Common type annotations for Ethereum Python packages";
+    homepage = https://github.com/ethereum/eth-typing;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ jluttine ];
+  };
+}

pkgs/development/python-modules/eth-utils/default.nix

@@ -0,0 +1,35 @@
+{ lib, fetchFromGitHub, buildPythonPackage, pytest, eth-hash, eth-typing,
+  cytoolz, hypothesis }:
+
+buildPythonPackage rec {
+  pname = "eth-utils";
+  version = "1.2.1";
+
+  # Tests are missing from the PyPI source tarball so let's use GitHub
+  # https://github.com/ethereum/eth-utils/issues/130
+  src = fetchFromGitHub {
+    owner = "ethereum";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0g8f5vdjh7qd8kgsqqd9qkm6m79rx3w9yp0rf9vpdsv3xfzrkh1w";
+  };
+
+  checkInputs = [ pytest hypothesis ];
+  propagatedBuildInputs = [ eth-hash eth-typing cytoolz ];
+
+  # setuptools-markdown uses pypandoc which is broken at the moment
+  preConfigure = ''
+    substituteInPlace setup.py --replace \'setuptools-markdown\' ""
+  '';
+
+  checkPhase = ''
+    pytest .
+  '';
+
+  meta = {
+    description = "Common utility functions for codebases which interact with ethereum";
+    homepage = https://github.com/ethereum/eth-utils;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ jluttine ];
+  };
+}

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

@@ -1,5 +1,5 @@
-{ stdenv, buildPythonPackage, fetchPypi, flask, jinja2, itsdangerous, events
-, markupsafe, pymongo, flask-pymongo, werkzeug, simplejson, cerberus }:
+{ stdenv, buildPythonPackage, fetchPypi, flask, events
+, pymongo, simplejson, cerberus }:
 
 buildPythonPackage rec {
   pname = "Eve";
@@ -13,14 +13,9 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     cerberus
     events
-    flask-pymongo
     flask
-    itsdangerous
-    jinja2
-    markupsafe
     pymongo
     simplejson
-    werkzeug
   ];
 
   # tests call a running mongodb instance

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

@@ -12,6 +12,8 @@ buildPythonPackage rec {
     sha256 = "a156129f0904cb7eb24aa0745b6075da54f2c31db168ed3bcac8a4bd716d77b2";
   };
 
+  CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11";
+
   buildInputs = [
     gdal
   ];

pkgs/development/python-modules/flask-ldap-login/default.nix

@@ -1,16 +1,27 @@
-{ stdenv, buildPythonPackage, fetchPypi
+{ stdenv, buildPythonPackage, isPy3k, fetchFromGitHub, fetchpatch
 , flask, flask_wtf, flask_testing, ldap
 , mock, nose }:
 
 buildPythonPackage rec {
   pname = "flask-ldap-login";
-  version = "0.3.0";
+  version = "0.3.4";
+  disabled = isPy3k;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "085rik7q8xrp5g95346p6jcp9m2yr8kamwb2kbiw4q0b0fpnnlgq";
+  src = fetchFromGitHub {
+    owner = "ContinuumIO";
+    repo = "flask-ldap-login";
+    rev = version;
+    sha256 = "1l6zahqhwn5g9fmhlvjv80288b5h2fk5mssp7amdkw5ysk570wzp";
   };
 
+  patches = [
+    # Fix flask_wtf>=0.9.0 incompatibility. See https://github.com/ContinuumIO/flask-ldap-login/issues/41
+    (fetchpatch {
+      url = https://github.com/ContinuumIO/flask-ldap-login/commit/ed08c03c818dc63b97b01e2e7c56862eaa6daa43.patch;
+      sha256 = "19pkhbldk8jq6m10kdylvjf1c8m84fvvj04v5qda4cjyks15aq48";
+    })
+  ];
+
   checkInputs = [ nose mock flask_testing ];
   propagatedBuildInputs = [ flask flask_wtf ldap ];
 

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, pkgconfig, fuse }:
+
+buildPythonPackage rec {
+  pname = "fuse-python";
+  version = "0.3.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0p1f01gah1y8skirrwsbxapz3g6drqihnkjh27b45ifg43h45g7x";
+  };
+
+  buildInputs = [ fuse ];
+  nativeBuildInputs = [ pkgconfig ];
+  
+  # no tests in the Pypi archive
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Python bindings for FUSE";
+    homepage = https://github.com/libfuse/python-fuse;
+    license = licenses.lgpl21;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+

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

@@ -19,6 +19,6 @@ buildPythonPackage {
 
   meta = {
     description = "GMP or MPIR interface to Python 2.4+ and 3.x";
-    homepage = http://code.google.com/p/gmpy/;
+    homepage = https://github.com/aleaxit/gmpy/;
   };
 }

pkgs/development/python-modules/gmpy2/default.nix

@@ -19,7 +19,7 @@ buildPythonPackage {
 
   meta = with stdenv.lib; {
     description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x";
-    homepage = http://code.google.com/p/gmpy/;
+    homepage = https://github.com/aleaxit/gmpy/;
     license = licenses.gpl3Plus;
   };
 }

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

@@ -1,29 +1,36 @@
 { lib
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , sphinx
 , numpydoc
 , pytest
+, python-lz4
 }:
 
 
 buildPythonPackage rec {
   pname = "joblib";
-  version = "0.12.3";
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "333b9bf16ff015d6b56bf80b9831afdd243443cb84c7ff7b6e342f117e354c42";
+  version = "0.12.4";
+
+  # get full repository inorder to run tests
+  src = fetchFromGitHub {
+    owner = "joblib";
+    repo = pname;
+    rev = version;
+    sha256 = "06zszgp7wpa4jr554wkk6kkigp4k9n5ad5h08i6w9qih963rlimb";
   };
 
   checkInputs = [ sphinx numpydoc pytest ];
+  propagatedBuildInputs = [ python-lz4 ];
 
   checkPhase = ''
-    py.test -k 'not test_disk_used and not test_nested_parallel_warnings' joblib/test
+    py.test joblib
   '';
 
   meta = {
     description = "Lightweight pipelining: using Python functions as pipeline jobs";
     homepage = https://pythonhosted.org/joblib/;
     license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ costrouc ];
   };
 }

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

@@ -1,5 +1,5 @@
 { stdenv, fetchPypi, buildPythonPackage, hidapi
-, pycrypto, pillow, protobuf, future, ecpy
+, pycrypto, pillow, protobuf, future, ecpy, python-u2flib-host, pycryptodomex
 }:
 
 buildPythonPackage rec {
@@ -11,7 +11,12 @@ buildPythonPackage rec {
     sha256 = "3969b3c375c0f3fb60ff1645621ebf2f39fb697a53851620705f27ed7b283097";
   };
 
-  buildInputs = [ hidapi pycrypto pillow protobuf future ecpy ];
+  propagatedBuildInputs = [
+    hidapi pycrypto pillow protobuf future ecpy python-u2flib-host pycryptodomex
+  ];
+
+  # No tests
+  doCheck = false;
 
   meta = with stdenv.lib; {
     description = "Python library to communicate with Ledger Blue/Nano S";

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

@@ -1,6 +1,6 @@
-{ stdenv, fetchPypi, buildPythonPackage, ed25519, ecdsa
-, semver, keepkey, trezor, mnemonic, ledgerblue, unidecode, mock, pytest
-}:
+{ stdenv, fetchPypi, buildPythonPackage, ed25519, ecdsa , semver, mnemonic,
+  unidecode, mock, pytest , backports-shutil-which, ConfigArgParse,
+  pythondaemon, pymsgbox }:
 
 buildPythonPackage rec {
   pname = "libagent";
@@ -11,12 +11,8 @@ buildPythonPackage rec {
     sha256 = "55af1ad2a6c95aef1fc5588c2002c9e54edbb14e248776b64d00628235ceda3e";
   };
 
-  buildInputs = [
-    ed25519 ecdsa semver keepkey
-    trezor mnemonic ledgerblue
-  ];
-
-  propagatedBuildInputs = [ unidecode ];
+  propagatedBuildInputs = [ unidecode backports-shutil-which ConfigArgParse
+    pythondaemon pymsgbox ecdsa ed25519 mnemonic semver ];
 
   checkInputs = [ mock pytest ];
 

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

@@ -14,8 +14,9 @@ buildPythonPackage rec {
   buildInputs = [ pytest ];
   propagatedBuildInputs = [ libsodium ];
 
-  postPatch = ''
-    substituteInPlace "./libnacl/__init__.py" --replace "ctypes.cdll.LoadLibrary('libsodium.so')" "ctypes.cdll.LoadLibrary('${libsodium}/lib/libsodium.so')"
+  postPatch =
+    let soext = stdenv.hostPlatform.extensions.sharedLibrary; in ''
+    substituteInPlace "./libnacl/__init__.py" --replace "ctypes.cdll.LoadLibrary('libsodium${soext}')" "ctypes.cdll.LoadLibrary('${libsodium}/lib/libsodium${soext}')"
   '';
 
   checkPhase = ''
@@ -27,6 +28,6 @@ buildPythonPackage rec {
     description = "Python bindings for libsodium based on ctypes";
     homepage = https://pypi.python.org/pypi/libnacl;
     license = licenses.asl20;
-    platforms = platforms.linux;
+    platforms = platforms.unix;
   };
 }

pkgs/development/python-modules/libusb1/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, python, libusb1 }:
+{ stdenv, lib, buildPythonPackage, fetchPypi, python, libusb1, pytest }:
 
 buildPythonPackage rec {
   pname = "libusb1";
@@ -9,7 +9,7 @@ buildPythonPackage rec {
     sha256 = "a49917a2262cf7134396f6720c8be011f14aabfc5cdc53f880cc672c0f39d271";
   };
 
-  postPatch = lib.optionalString stdenv.isLinux ''
+  postPatch = ''
     substituteInPlace usb1/libusb1.py --replace \
       "ctypes.util.find_library(base_name)" \
       "'${libusb1}/lib/libusb-1.0${stdenv.hostPlatform.extensions.sharedLibrary}'"
@@ -17,8 +17,12 @@ buildPythonPackage rec {
 
   buildInputs = [ libusb1 ];
 
+  checkInputs = [ pytest ];
+
   checkPhase = ''
-    ${python.interpreter} -m usb1.testUSB1
+    # USBPollerThread is unreliable. Let's not test it.
+    # See: https://github.com/vpelletier/python-libusb1/issues/16
+    py.test -k 'not testUSBPollerThreadExit' usb1/testUSB1.py
   '';
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,33 @@
+{ buildPythonPackage, fetchFromGitHub, nose, pillow, scipy, numpy, imread, stdenv }:
+
+buildPythonPackage rec {
+  pname = "mahotas";
+  version = "1.4.2";
+
+  src = fetchFromGitHub {
+    owner = "luispedro";
+    repo = "mahotas";
+    rev = "v${version}";
+    sha256 = "1d2hciag5sxw00qj7qz7lbna477ifzmpgl0cv3xqzjkhkn5m4d7r";
+  };
+
+  # remove this as soon as https://github.com/luispedro/mahotas/issues/97 is fixed
+  patches = [ ./disable-impure-tests.patch ];
+
+  propagatedBuildInputs = [ numpy imread pillow scipy ];
+  checkInputs = [ nose ];
+
+  checkPhase= ''
+    python setup.py test
+  '';
+
+  disabled = stdenv.isi686; # Failing tests
+
+  meta = with stdenv.lib; {
+    description = "Computer vision package based on numpy";
+    homepage = http://mahotas.readthedocs.io/;
+    maintainers = with maintainers; [ luispedro ];
+    license = licenses.mit;
+    platforms = platforms.linux;
+  };
+}

pkgs/development/python-modules/mahotas/disable-impure-tests.patch

@@ -0,0 +1,76 @@
+diff --git a/mahotas/tests/test_colors.py b/mahotas/tests/test_colors.py
+index 8a8183b..0d34c9f 100644
+--- a/mahotas/tests/test_colors.py
++++ b/mahotas/tests/test_colors.py
+@@ -2,7 +2,9 @@ import mahotas
+ import numpy as np
+ from mahotas.tests.utils import luispedro_jpg
+ from mahotas.colors import rgb2xyz, rgb2lab, xyz2rgb, rgb2grey, rgb2sepia
++from nose.tools import nottest
+ 
++@nottest
+ def test_colors():
+     f = luispedro_jpg()
+     lab = rgb2lab(f)
+diff --git a/mahotas/tests/test_features_shape.py b/mahotas/tests/test_features_shape.py
+index 462f467..2381793 100644
+--- a/mahotas/tests/test_features_shape.py
++++ b/mahotas/tests/test_features_shape.py
+@@ -2,6 +2,7 @@ import mahotas.features.shape
+ import numpy as np
+ import mahotas as mh
+ from mahotas.features.shape import roundness, eccentricity
++from nose.tools import nottest
+ 
+ def test_eccentricity():
+     D = mh.disk(32, 2)
+@@ -29,6 +30,7 @@ def test_zeros():
+     I[8:4:12] = 1
+     assert eccentricity(I) == 0
+ 
++@nottest
+ def test_ellipse_axes():
+     Y,X = np.mgrid[:1024,:1024]
+     Y = Y/1024.
+diff --git a/mahotas/tests/test_moments.py b/mahotas/tests/test_moments.py
+index 686c7c3..ba3487b 100644
+--- a/mahotas/tests/test_moments.py
++++ b/mahotas/tests/test_moments.py
+@@ -1,6 +1,7 @@
+ import numpy as np
+ import mahotas as mh
+ from mahotas.features.moments import moments
++from nose.tools import nottest
+ 
+ def _slow(A, p0, p1, cm):
+     c0,c1 = cm
+@@ -28,7 +29,7 @@ def test_against_slow():
+     yield perform, 1, 2, (0, 0), A
+     yield perform, 1, 0, (0, 0), A
+ 
+-
++@nottest
+ def test_normalize():
+     A,B = np.meshgrid(np.arange(128),np.arange(128))
+     for p0,p1 in [(1,1), (1,2), (2,1), (2,2)]:
+diff --git a/mahotas/tests/test_texture.py b/mahotas/tests/test_texture.py
+index 7e101ba..af1305d 100644
+--- a/mahotas/tests/test_texture.py
++++ b/mahotas/tests/test_texture.py
+@@ -2,7 +2,7 @@ import numpy as np
+ from mahotas.features import texture
+ import mahotas as mh
+ import mahotas.features._texture
+-from nose.tools import raises
++from nose.tools import raises, nottest
+ 
+ def test__cooccurence():
+     cooccurence = mahotas.features._texture.cooccurence
+@@ -149,6 +149,7 @@ def test_float_haralick():
+     A[2,2]=12
+     texture.haralick(A)
+ 
++@nottest
+ def test_haralick3d():
+     np.random.seed(22)
+     img = mahotas.stretch(255*np.random.rand(20,20,4))

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

@@ -1,20 +1,21 @@
-{ stdenv, fetchPypi, buildPythonPackage, lxml, typed-ast, psutil, isPy3k }:
+{ stdenv, fetchPypi, buildPythonPackage, lxml, typed-ast, psutil, isPy3k
+,mypy_extensions }:
 
 buildPythonPackage rec {
   pname = "mypy";
-  version = "0.620";
+  version = "0.630";
 
   # Tests not included in pip package.
   doCheck = false;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c770605a579fdd4a014e9f0a34b6c7a36ce69b08100ff728e96e27445cef3b3c";
+    sha256 = "1p8rnap4ngczfm2q4035mcmn5nsprbljnhksx2jxzxrb9immh137";
   };
 
   disabled = !isPy3k;
 
-  propagatedBuildInputs = [ lxml typed-ast psutil ];
+  propagatedBuildInputs = [ lxml typed-ast psutil mypy_extensions ];
 
   meta = with stdenv.lib; {
     description = "Optional static typing for Python";

pkgs/development/python-modules/mypy/extensions.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchPypi, buildPythonPackage, typing, isPy3k }:
+
+buildPythonPackage rec {
+  pname = "mypy_extensions";
+  version = "0.4.1";
+
+  # Tests not included in pip package.
+  doCheck = false;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "04h8brrbbx151dfa2cvvlnxgmb5wa00mhd2z7nd20s8kyibfkq1p";
+  };
+
+  propagatedBuildInputs = [ typing ];
+
+  meta = with stdenv.lib; {
+    description = "Experimental type system extensions for programs checked with the mypy typechecker";
+    homepage    = "http://www.mypy-lang.org";
+    license     = licenses.mit;
+    maintainers = with maintainers; [ martingms lnl7 ];
+  };
+}

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

@@ -11,9 +11,13 @@ buildPythonPackage rec {
     sha256 = "5049363eb6da2e7c35589477dfc79bf69929ca66de2d7ed2e9dc07acf78636f4";
   };
 
-  checkPhase = "nosetests --exclude with_expand_user nilearn/tests";
+  # disable some failing tests
+  checkPhase = ''
+    nosetests nilearn/tests \
+    -e test_cache_mixin_with_expand_user -e test_clean_confounds -e test_detrend
+  '';
 
-  buildInputs = [ nose ];
+  checkInputs = [ nose ];
 
   propagatedBuildInputs = [
     matplotlib

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, pytest, psycopg2, click, sqlparse }:
+
+buildPythonPackage rec {
+  pname = "pgspecial";
+  version = "1.11.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1yq3cmpdcvwsz3nifc0db125433vxbgbpmbhxfj46b9s5k81xs30";
+  };
+
+  buildInputs = [ pytest psycopg2 ];
+  propagatedBuildInputs = [ click sqlparse ];
+
+  checkPhase = ''
+    find tests -name \*.pyc -delete
+    py.test tests
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Meta-commands handler for Postgres Database";
+    homepage = https://pypi.python.org/pypi/pgspecial;
+    license = licenses.bsd3;
+  };
+}

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

@@ -0,0 +1,34 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, slicerator
+, scikitimage
+, six
+, numpy
+, tifffile
+, pytest
+, nose
+}:
+
+buildPythonPackage rec {
+  version = "0.4.1";
+  pname = "PIMS";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6a53a155e900b44e71127a1e1fccbfbaed7eec3c2b52497c40c23a05f334c9dd";
+  };
+
+  checkInputs = [ nose ];
+  propagatedBuildInputs = [ slicerator six numpy tifffile scikitimage ];
+
+  # not everything packaged with pypi release
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/soft-matter/pims;
+    description = "Python Image Sequence: Load video and sequential images in many formats with a simple, consistent interface";
+    license = licenses.bsdOriginal;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/psycopg2/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, lib, buildPythonPackage, isPyPy, fetchPypi, postgresql, openssl }:
+
+buildPythonPackage rec {
+  pname = "psycopg2";
+  version = "2.7.5";
+
+  disabled = isPyPy;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17klx964gw8z0znl0raz3by8vdc7cq5gxj4pdcrfcina84nrdkzc";
+  };
+
+  buildInputs = lib.optional stdenv.isDarwin openssl;
+  propagatedBuildInputs = [ postgresql ];
+
+  doCheck = false;
+
+  meta = with lib; {
+    description = "PostgreSQL database adapter for the Python programming language";
+    license = with licenses; [ gpl2 zpl20 ];
+  };
+}

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

@@ -1,19 +1,29 @@
-{ stdenv, buildPythonPackage, fetchPypi, scipy, ffmpeg-full }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, scipy, ffmpeg-full }:
 
 buildPythonPackage rec {
   pname = "pydub";
   version = "0.22.1";
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "20beff39e9959a3b2cb4392802aecb9b2417837fff635d2b00b5ef5f5326d313";
+  # pypi version doesn't include required data files for tests
+  src = fetchFromGitHub {
+    owner = "jiaaro";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0xqyvzgdfy01p98wnvsrf6iwdfq91ad377r6j12r8svm13ygx5bv";
   };
 
-  patches = [
-    ./pyaudioop-python3.patch
-  ];
+
+  # disable a test that fails on aarch64 due to rounding errors
+  postPatch = stdenv.lib.optionalString stdenv.isAarch64 ''
+    substituteInPlace test/test.py \
+      --replace "test_overlay_with_gain_change" "notest_overlay_with_gain_change"
+  '';
 
   checkInputs = [ scipy ffmpeg-full ];
 
+  checkPhase = ''
+    python test/test.py
+  '';
+
   meta = with stdenv.lib; {
     description = "Manipulate audio with a simple and easy high level interface.";
     homepage    = "http://pydub.com/";

pkgs/development/python-modules/pydub/pyaudioop-python3.patch

@@ -1,46 +0,0 @@
-diff --git i/pydub/pyaudioop.py w/pydub/pyaudioop.py
-index 8f8f017..aa6bb8c 100644
---- i/pydub/pyaudioop.py
-+++ w/pydub/pyaudioop.py
-@@ -1,4 +1,4 @@
--import __builtin__
-+import builtins
- import math
- import struct
- from fractions import gcd
-@@ -79,7 +79,7 @@ def _get_minval(size, signed=True):
- def _get_clipfn(size, signed=True):
-     maxval = _get_maxval(size, signed)
-     minval = _get_minval(size, signed)
--    return lambda val: __builtin__.max(min(val, maxval), minval)
-+    return lambda val: builtins.max(min(val, maxval), minval)
- 
- 
- def _overflow(val, size, signed=True):
-@@ -109,7 +109,7 @@ def max(cp, size):
-     if len(cp) == 0:
-         return 0
- 
--    return __builtin__.max(abs(sample) for sample in _get_samples(cp, size))
-+    return builtins.max(abs(sample) for sample in _get_samples(cp, size))
- 
- 
- def minmax(cp, size):
-@@ -117,8 +117,8 @@ def minmax(cp, size):
- 
-     max_sample, min_sample = 0, 0
-     for sample in _get_samples(cp, size):
--        max_sample = __builtin__.max(sample, max_sample)
--        min_sample = __builtin__.min(sample, min_sample)
-+        max_sample = builtins.max(sample, max_sample)
-+        min_sample = builtins.min(sample, min_sample)
- 
-     return min_sample, max_sample
- 
-@@ -542,4 +542,4 @@ def lin2adpcm(cp, size, state):
- 
- 
- def adpcm2lin(cp, size, state):
--    raise NotImplementedError()
-\ No newline at end of file
-+    raise NotImplementedError()

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

@@ -1,7 +1,7 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, python, pytest, glibcLocales }:
 
 buildPythonPackage rec {
-  version = "3.4.1";
+  version = "3.4.3";
   pname = "pyfakefs";
 
   # no tests in PyPI tarball
@@ -10,22 +10,30 @@ buildPythonPackage rec {
     owner = "jmcgeheeiv";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0i8kq7sl8bczr927hllgfhsmirjqjh89c9184kcqmprc13ac4kxy";
+    sha256 = "0rhbkcb5h2x8kmyxivr5jr1db2xvmpjdbsfjxl142qhfb29hr2hp";
   };
 
   postPatch = ''
     # test doesn't work in sandbox
-    substituteInPlace tests/fake_filesystem_test.py \
+    substituteInPlace pyfakefs/tests/fake_filesystem_test.py \
       --replace "test_expand_root" "notest_expand_root"
-    substituteInPlace tests/fake_os_test.py \
-      --replace "test_append_mode" "notest_append_mode"
-  '';
+    substituteInPlace pyfakefs/tests/fake_os_test.py \
+      --replace "test_path_links_not_resolved" "notest_path_links_not_resolved" \
+      --replace "test_append_mode_tell_linux_windows" "notest_append_mode_tell_linux_windows"
+    substituteInPlace pyfakefs/tests/fake_filesystem_unittest_test.py \
+      --replace "test_copy_real_file" "notest_copy_real_file"
+  '' + (stdenv.lib.optionalString stdenv.isDarwin ''
+    # this test fails on darwin due to case-insensitive file system
+    substituteInPlace pyfakefs/tests/fake_os_test.py \
+      --replace "test_rename_dir_to_existing_dir" "notest_rename_dir_to_existing_dir"
+  '');
 
   checkInputs = [ pytest glibcLocales ];
 
   checkPhase = ''
-    LC_ALL=en_US.UTF-8 ${python.interpreter} -m tests.all_tests
-    py.test tests/pytest_plugin_test.py
+    export LC_ALL=en_US.UTF-8
+    ${python.interpreter} -m pyfakefs.tests.all_tests
+    ${python.interpreter} -m pytest pyfakefs/tests/pytest_plugin_test.py
   '';
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,26 @@
+{ lib, fetchPypi, buildPythonPackage
+, lxml, pycryptodome, construct
+, argon2_cffi, dateutil, enum34
+}:
+
+buildPythonPackage rec {
+  pname   = "pykeepass";
+  version = "3.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1kfnh42nimsbdpwpny2c9df82b2n4fb5fagh54ck06f3x483vd90";
+  };
+
+  propagatedBuildInputs = [
+    lxml pycryptodome construct
+    argon2_cffi dateutil enum34
+  ];
+
+  meta = {
+    homepage = https://github.com/pschmitt/pykeepass;
+    description = "Python library to interact with keepass databases (supports KDBX3 and KDBX4)";
+    license = lib.licenses.gpl3;
+  };
+
+}

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

@@ -0,0 +1,24 @@
+{ stdenv, fetchPypi, buildPythonPackage, tkinter }:
+
+buildPythonPackage rec {
+  pname = "PyMsgBox";
+  version = "1.0.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0kmd00w7p6maiyqpqqb2j8m6v2gh9c0h5i198pa02bc1c1m1321q";
+    extension = "zip";
+  };
+
+  propagatedBuildInputs = [ tkinter ];
+
+  # Finding tests fails
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A simple, cross-platform, pure Python module for JavaScript-like message boxes";
+    homepage = https://github.com/asweigart/PyMsgBox;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ jluttine ];
+  };
+}

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPyPy, libiodbc }:
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy, unixODBC }:
 
 buildPythonPackage rec {
   pname = "pyodbc";
@@ -10,7 +10,9 @@ buildPythonPackage rec {
     sha256 = "4326abb737dec36156998d52324921673d30f575e1e0998f0c5edd7de20e61d4";
   };
 
-  buildInputs = [ libiodbc ];
+  buildInputs = [ unixODBC ];
+
+  doCheck = false; # tests require a database server
 
   meta = with stdenv.lib; {
     description = "Python ODBC module to connect to almost any database";

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, requests }:
+{ lib, buildPythonPackage, fetchPypi, requests, geojson }:
 
 buildPythonPackage rec {
   pname = "pyowm";
@@ -9,11 +9,13 @@ buildPythonPackage rec {
     sha256 = "ed175873823a2fedb48e453505c974ca39f3f75006ef1af54fdbcf72e6796849";
   };
 
-  propagatedBuildInputs = [ requests ];
+  propagatedBuildInputs = [ requests geojson ];
 
   # This may actually break the package.
   postPatch = ''
-    substituteInPlace setup.py --replace "requests>=2.18.2,<2.19" "requests"
+    substituteInPlace setup.py \
+      --replace "requests>=2.18.2,<2.19" "requests"  \
+      --replace "geojson>=2.3.0,<2.4" "geojson<2.5,>=2.3.0"
   '';
 
   # No tests in archive

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

@@ -0,0 +1,26 @@
+{ lib, fetchPypi, buildPythonPackage
+, requests, chardet, cssselect, lxml
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname   = "PyReadability";
+  version = "0.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1k6fq416pdmjcdqh6gdxl0y0k8kj1zlpzwp5574xsvsha18p2zpn";
+  };
+
+  propagatedBuildInputs = [ requests chardet cssselect lxml ];
+
+  # ModuleNotFoundError: No module named 'tests'
+  doCheck = false;
+
+  meta = {
+    homepage = https://github.com/hyperlinkapp/python-readability;
+    description = "fast python port of arc90's readability tool, updated to match latest readability.js!";
+    license = lib.licenses.asl20;
+  };
+
+}

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyslurm";
-  version = "20180811";
+  version = "20180908";
 
   src = fetchFromGitHub {
     repo = "pyslurm";
     owner = "PySlurm";
-    rev = "2d4f0553de971309b7e465d4d64528b8a5fafb05";
-    sha256 = "1cy57gyvvmzx0c8fx4h6p8dgan0ay6pdivdf24k1xiancjnw20xr";
+    rev = "50dc113e99d82e70e84fc2e812333733708be4ed";
+    sha256 = "1j2i4rvhmk2ihhcvsjdlqlxqb5a05jg8k9bqkv3zrvdj71yn4z9k";
   };
 
   buildInputs = [ cython slurm ];

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

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+, pytest
+, pytest-mock
+, pythonOlder
+, faulthandler
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-faulthandler";
+  version = "1.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "bf8634c3fd6309ef786ec03b913a5366163fdb094ebcfdebc35626400d790e0d";
+  };
+
+  buildInputs = [ setuptools_scm pytest ];
+  checkInputs = [ pytest-mock ];
+  propagatedBuildInputs = lib.optional (pythonOlder "3.0") faulthandler;
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = {
+    description = "Py.test plugin that activates the fault handler module for tests";
+    homepage = https://github.com/pytest-dev/pytest-faulthandler;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi
-, pytestpep8, pytest, pyflakes, pytestcache }:
+, pytestpep8, pytest, pyflakes }:
 
 buildPythonPackage rec {
   pname = "pytest-flakes";
@@ -11,10 +11,11 @@ buildPythonPackage rec {
   };
 
   buildInputs = [ pytestpep8 pytest ];
-  propagatedBuildInputs = [ pyflakes pytestcache ];
+  propagatedBuildInputs = [ pyflakes ];
 
+  # disable one test case that looks broken
   checkPhase = ''
-    py.test test_flakes.py
+    py.test test_flakes.py -k 'not test_syntax_error'
   '';
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-repeat";
+  version = "0.6.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "84aba2fcca5dc2f32ae626a01708f469f17b3384ec3d1f507698077f274909d6";
+  };
+
+  buildInputs = [ setuptools_scm pytest ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = {
+    description = "Pytest plugin for repeating tests";
+    homepage = https://github.com/pytest-dev/pytest-repeat;
+    maintainers = with lib.maintainers; [ costrouc ];
+    license = lib.licenses.mpl20;
+  };
+}

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

@@ -9,10 +9,13 @@ buildPythonPackage rec {
     sha256 = "be6bf93ed618c8899aeb6721c24f8009c769879a3b4931e05650f3c173ec17c5";
   };
 
-  checkInputs = [ pytest mock ];
+  checkInputs = [ mock ];
 
+  propagatedBuildInputs = [ pytest ];
+
+  # disable tests that fail with pytest 3.7.4
   checkPhase = ''
-    py.test
+    py.test test_pytest_rerunfailures.py -k 'not test_reruns_with_delay'
   '';
 
   meta = with stdenv.lib; {

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

@@ -1,5 +1,6 @@
 { buildPythonPackage
 , fetchPypi
+, fetchpatch
 , lib
 , pexpect
 , pytest
@@ -13,7 +14,7 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "1117fc0536e1638862917efbdc0895e6b62fa61e6cf4f39bb655686af7af9627";
   };
-  buildInputs = [ pytest ];
+
   checkInputs = [ pytest pexpect ];
   checkPhase = ''pytest -ra'';
 
@@ -21,6 +22,6 @@ buildPythonPackage rec {
     description = "py.test plugin to abort hanging tests";
     homepage = https://bitbucket.org/pytest-dev/pytest-timeout/;
     license = licenses.mit;
-    maintainers = with maintainers; [ makefu ];
+    maintainers = with maintainers; [ makefu costrouc ];
   };
 }

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

@@ -1,27 +0,0 @@
-{ lib
-, pkgconfig
-, fetchurl
-, fuse
-, buildPythonPackage
-, isPy3k
-}:
-
-buildPythonPackage rec {
-  pname = "fuse";
-  version = "0.2.1";
-
-  disabled = isPy3k;
-
-  src = fetchurl {
-    url = "mirror://sourceforge/fuse/fuse-python-${version}.tar.gz";
-    sha256 = "06rmp1ap6flh64m81j0n3a357ij2vj9zwcvvw0p31y6hz1id9shi";
-  };
-
-  nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ fuse ];
-
-  meta = {
-    description = "Python bindings for FUSE";
-    license = lib.licenses.lgpl21;
-  };
-}

pkgs/development/python-modules/python-jsonrpc-server/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub, pythonOlder
+, pytest, mock, pytestcov, coverage
+, future, futures
+}:
+
+buildPythonPackage rec {
+  pname = "python-jsonrpc-server";
+  version = "0.0.1";
+
+  src = fetchFromGitHub {
+    owner = "palantir";
+    repo = "python-jsonrpc-server";
+    rev = version;
+    sha256 = "0p5dj1hxx3yz8vjk59dcp3h6ci1hrjkbzf9lr3vviy0xw327409k";
+  };
+
+  checkInputs = [
+    pytest mock pytestcov coverage
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  propagatedBuildInputs = [ future ]
+    ++ stdenv.lib.optional (pythonOlder "3.2") futures;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/palantir/python-jsonrpc-server;
+    description = "A Python 2 and 3 asynchronous JSON RPC server";
+    license = licenses.mit;
+    maintainers = [ maintainers.mic92 ];
+  };
+}

pkgs/development/python-modules/python-language-server/default.nix

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, pythonOlder, isPy27
-, configparser, futures, future, jedi, pluggy
+, configparser, futures, future, jedi, pluggy, python-jsonrpc-server
 , pytest, mock, pytestcov, coverage
 , # Allow building a limited set of providers, e.g. ["pycodestyle"].
   providers ? ["*"]
@@ -20,13 +20,13 @@ in
 
 buildPythonPackage rec {
   pname = "python-language-server";
-  version = "0.19.0";
+  version = "0.21.2";
 
   src = fetchFromGitHub {
     owner = "palantir";
     repo = "python-language-server";
     rev = version;
-    sha256 = "0glnhnjmsnnh1vs73n9dglknfkhcgp03nkjbpz0phh1jlqrkrwm6";
+    sha256 = "11fvrpv1kymj2fzh8fhys4qk1xc64j1rbdrz252awyab7b3509i7";
   };
 
   # The tests require all the providers, disable otherwise.
@@ -43,7 +43,7 @@ buildPythonPackage rec {
     HOME=$TEMPDIR pytest
   '';
 
-  propagatedBuildInputs = [ jedi pluggy future ]
+  propagatedBuildInputs = [ jedi pluggy future python-jsonrpc-server ]
     ++ stdenv.lib.optional (withProvider "autopep8") autopep8
     ++ stdenv.lib.optional (withProvider "mccabe") mccabe
     ++ stdenv.lib.optional (withProvider "pycodestyle") pycodestyle

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

@@ -0,0 +1,40 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestrunner
+, pytest
+, psutil
+, setuptools_scm
+, pkgconfig
+, isPy3k
+, future
+}:
+
+buildPythonPackage rec {
+  pname = "python-lz4";
+  version = "2.1.0";
+
+  # get full repository inorder to run tests
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1vjfplj37jcw1mf8l810dv76dx0raia3ylgyfy7sfsb3g17brjq6";
+  };
+
+  buildInputs = [ setuptools_scm pkgconfig pytestrunner ];
+  checkInputs = [ pytest psutil ];
+  propagatedBuildInputs = lib.optionals (!isPy3k) [ future ];
+
+  # give a hint to setuptools_scm on package version
+  preBuild = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="v${version}"
+  '';
+
+  meta = {
+     description = "LZ4 Bindings for Python";
+     homepage = https://github.com/python-lz4/python-lz4;
+     license = lib.licenses.bsd0;
+     maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/python-u2flib-host/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchPypi, buildPythonPackage, requests, hidapi }:
+
+buildPythonPackage rec {
+  pname = "python-u2flib-host";
+  version = "3.0.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "02pwafd5kyjpc310ys0pgnd0adff1laz18naxxwsfrllqafqnrxb";
+  };
+
+  propagatedBuildInputs = [ requests hidapi ];
+
+  # Tests fail: "ValueError: underlying buffer has been detached"
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Python based U2F host library";
+    homepage = https://github.com/Yubico/python-u2flib-host;
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ jluttine ];
+  };
+}

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

@@ -27,7 +27,8 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    py.test
+    # disable one failing test case
+    py.test -k "not test_invalid_link"
   '';
 
   meta = {

pkgs/development/python-modules/requests-file/default.nix

@@ -0,0 +1,20 @@
+{ lib, fetchPypi, buildPythonPackage, requests, six }:
+
+buildPythonPackage rec {
+  pname   = "requests-file";
+  version = "1.4.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1yp2jaxg3v86pia0q512dg3hz6s9y5vzdivsgrba1kds05ial14g";
+  };
+
+  propagatedBuildInputs = [ requests six ];
+
+  meta = {
+    homepage = https://github.com/dashea/requests-file;
+    description = "Transport adapter for fetching file:// URLs with the requests python library";
+    license = lib.licenses.asl20;
+  };
+
+}

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , docutils
 , readme_renderer
 , pygments
@@ -19,6 +20,15 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ docutils readme_renderer pygments ];
   checkInputs = [ mock ];
 
+  patches = [
+    # fix tests after readme_renderer update
+    # TODO remove on next update
+    (fetchpatch {
+      url = "https://github.com/mgedmin/restview/commit/541743ded13ae55dea4c437046984a5f13d06e8b.patch";
+      sha256 = "031b1dlqx346bz7afpc011lslnq771lnxb6iy1l2285pph534bci";
+    })
+  ];
+
   postPatch = ''
     # dict order breaking tests
     sed -i 's@<a href="http://www.example.com" rel="nofollow">@...@' src/restview/tests.py

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

@@ -1,4 +1,4 @@
-{ lib, fetchPypi, buildPythonPackage, pytest }:
+{ lib, fetchPypi, buildPythonPackage, pytest, hypothesis, eth-utils }:
 
 buildPythonPackage rec {
   pname = "rlp";
@@ -9,8 +9,18 @@ buildPythonPackage rec {
     sha256 = "040fb5172fa23d27953a886c40cac989fc031d0629db934b5a9edcd2fb28df1e";
   };
 
-  checkInputs = [ pytest ];
-  propagatedBuildInputs = [ ];
+  checkInputs = [ pytest hypothesis ];
+  propagatedBuildInputs = [ eth-utils ];
+
+  # setuptools-markdown uses pypandoc which is broken at the moment
+  preConfigure = ''
+    substituteInPlace setup.py --replace \'setuptools-markdown\' ""
+    substituteInPlace setup.py --replace "long_description_markdown_filename='README.md'," ""
+  '';
+
+  checkPhase = ''
+    pytest .
+  '';
 
   meta = {
     description = "A package for encoding and decoding data in and from Recursive Length Prefix notation";

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

@@ -0,0 +1,32 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, python
+, six
+}:
+
+buildPythonPackage rec {
+  version = "0.9.8";
+  pname = "slicerator";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "b91dd76a415fd8872185cbd6fbf1922fe174359053d4694983fc719e4a0f5667";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  checkPhase = ''
+    ${python.interpreter} run_tests.py
+  '';
+
+  # run_tests.py not packaged with pypi release
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = http://github.com/soft-matter/slicerator;
+    description = "A lazy-loading, fancy-sliceable iterable";
+    license = licenses.bsdOriginal;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,5 +1,5 @@
 { lib, stdenv, fetchPypi, buildPythonPackage, isPy27, pythonOlder
-, numpy, nose, enum34, futures }:
+, numpy, nose, enum34, futures, pathlib }:
 
 buildPythonPackage rec {
   pname = "tifffile";
@@ -16,7 +16,7 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [ numpy ]
-    ++ lib.optional isPy27 futures
+    ++ lib.optional isPy27 [ futures pathlib ]
     ++ lib.optional (pythonOlder "3.0") enum34;
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,24 @@
+{ lib, fetchPypi, buildPythonPackage
+, requests, requests-file, idna, pytest
+, responses
+}:
+
+buildPythonPackage rec {
+  pname   = "tldextract";
+  version = "2.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1d5s8v6kpsgazyahflhji1cfdcf89rv7l7z55v774bhzvcjp2y99";
+  };
+
+  propagatedBuildInputs = [ requests requests-file idna ];
+  checkInputs = [ pytest responses ];
+
+  meta = {
+    homepage = https://github.com/john-kurkowski/tldextract;
+    description = "Accurately separate the TLD from the registered domain and subdomains of a URL, using the Public Suffix List.";
+    license = lib.licenses.bsd3;
+  };
+
+}

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

@@ -8,12 +8,25 @@
 , singledispatch
 , pythonOlder
 , futures
+, version ? "5.1"
 }:
 
+let
+  versionMap = {
+    "4.5.3" = {
+      sha256 = "02jzd23l4r6fswmwxaica9ldlyc2p6q8dk6dyff7j58fmdzf853d";
+    };
+    "5.1" = {
+      sha256 = "4f66a2172cb947387193ca4c2c3e19131f1c70fa8be470ddbbd9317fd0801582";
+    };
+  };
+in
+
+with versionMap.${version};
+
 buildPythonPackage rec {
   pname = "tornado";
-  version = "5.1";
-
+  inherit version;
 
   propagatedBuildInputs = [ backports_abc  certifi singledispatch ]
     ++ lib.optional (pythonOlder "3.5") backports_ssl_match_hostname
@@ -26,8 +39,7 @@ buildPythonPackage rec {
   '';
 
   src = fetchPypi {
-    inherit pname version;
-    sha256 = "4f66a2172cb947387193ca4c2c3e19131f1c70fa8be470ddbbd9317fd0801582";
+    inherit pname sha256 version;
   };
 
   meta = {

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

@@ -15,7 +15,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [ pycurl ];
 
   meta = with stdenv.lib; {
-    homepage = "urlgrabber.baseurl.org";
+    homepage = http://urlgrabber.baseurl.org;
     license = licenses.lgpl2Plus;
     description = "Python module for downloading files";
     maintainers = with maintainers; [ qknight ];

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

@@ -15,6 +15,13 @@ buildPythonPackage rec {
     sha256 = "1niglalkp7pinibzbxjdz9mxx9qmwkrh8884dag3kr72cfkrpp09";
   };
 
+  # Upstream requires jellyfish==0.5.6 but we have 0.6.1
+  postPatch = ''
+    substituteInPlace setup.py --replace "jellyfish==" "jellyfish>="
+  '';
+
+  doCheck = false; # pypi version doesn't include tests
+
   meta = {
     description = "A package for easily working with US and state metadata";
     longDescription = ''

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

@@ -6,27 +6,28 @@
 , msgpack
 , mecab-python3
 , jieba
-, nose
+, pytest
 , pythonOlder
 , fetchFromGitHub
 }:
 
 buildPythonPackage rec {
   pname = "wordfreq";
-  version = "2.0";
+  version = "2.2.0";
 
    src = fetchFromGitHub {
     owner = "LuminosoInsight";
     repo = "wordfreq";
-    rev = "e3a1b470d9f8e0d82e9f179ffc41abba434b823b";
-    sha256 = "1wjkhhj7nxfnrghwvmvwc672s30lp4b7yr98gxdxgqcq6wdshxwv";
+    # upstream don't tag by version
+    rev = "bc12599010c8181a725ec97d0b3990758a48da36";
+    sha256 = "195794vkzq5wsq3mg1dgfhlnz2f7vi1xajlifq6wkg4lzwyq262m";
    };
 
-  checkInputs = [ nose ];
+  checkInputs = [ pytest ];
 
   checkPhase = ''
     # These languages require additional dictionaries
-    nosetests -e test_japanese -e test_korean -e test_languages
+    pytest tests -k 'not test_japanese and not test_korean and not test_languages and not test_french_and_related'
   '';
    
   propagatedBuildInputs = [ regex langcodes ftfy msgpack mecab-python3 jieba ];

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

@@ -4,7 +4,6 @@
 , zope_testrunner
 , transaction
 , six
-, wheel
 , zope_interface
 , zodbpickle
 , zconfig
@@ -24,15 +23,16 @@ buildPythonPackage rec {
     };
 
     patches = [
-      ./ZODB-5.3.0-fix-tests.patch
+      ./ZODB-5.3.0-fix-tests.patch # still needeed with 5.4.0
+      # Upstream patch to fix tests with persistent 4.4,
+      # cannot fetchpatch because only one hunk of the upstream commit applies.
+      # TODO remove on next release
+      ./fix-tests-with-persistent-4.4.patch
     ];
 
     propagatedBuildInputs = [
-      manuel
       transaction
-      zope_testrunner
       six
-      wheel
       zope_interface
       zodbpickle
       zconfig
@@ -41,6 +41,11 @@ buildPythonPackage rec {
       BTrees
     ];
 
+    checkInputs = [
+      manuel
+      zope_testrunner
+    ];
+
     meta = with stdenv.lib; {
       description = "Zope Object Database: object database and persistence";
       homepage = https://pypi.python.org/pypi/ZODB;

pkgs/development/python-modules/zodb/fix-tests-with-persistent-4.4.patch

@@ -0,0 +1,26 @@
+From 2d0ae7199501795617a82a32bafe19b4b5ae89c3 Mon Sep 17 00:00:00 2001
+From: Jason Madden <jamadden@gmail.com>
+Date: Wed, 22 Aug 2018 10:43:19 -0500
+Subject: [PATCH] Fix tests with, and depend on, persistent 4.4.
+
+Fixes #213.
+---
+ src/ZODB/tests/util.py | 5 +++++
+ 3 files changed, 9 insertions(+), 3 deletions(-)
+
+diff --git a/src/ZODB/tests/util.py b/src/ZODB/tests/util.py
+index 4ffde92c1..e9bf547fa 100644
+--- a/src/ZODB/tests/util.py
++++ b/src/ZODB/tests/util.py
+@@ -37,6 +37,11 @@
+      r"\1"),
+     (re.compile('b(".*?")'),
+      r"\1"),
++    # Persistent 4.4 changes the repr of persistent subclasses,
++    # and it is slightly different with the C extension and
++    # pure-Python module
++    (re.compile('ZODB.tests.testcrossdatabasereferences.'),
++     ''),
+     # Python 3 adds module name to exceptions.
+     (re.compile("ZODB.interfaces.BlobError"),
+      r"BlobError"),