merge: fixing changes with nixpkgs since pull-request

- pytest-timeout: no longer requires patch
 - joblib: was improperly merged with the github merge tool (never
   using again)

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

@@ -47,6 +47,8 @@ buildPythonPackage rec {
     mkdir -p $out/share/{applications,alot}
     cp -r extra/themes $out/share/alot
 
+    install -D extra/completion/alot-completion.zsh $out/share/zsh/site-functions/_alot
+
     sed "s,/usr/bin,$out/bin,g" extra/alot.desktop > $out/share/applications/alot.desktop
   '';
 

pkgs/development/python-modules/confluent-kafka/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPy3k, rdkafka, requests, avro3k, avro}:
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, rdkafka, requests, avro3k, avro, futures}:
 
 buildPythonPackage rec {
   version = "0.11.5";
@@ -9,7 +9,7 @@ buildPythonPackage rec {
     sha256 = "bfb5807bfb5effd74f2cfe65e4e3e8564a9e72b25e099f655d8ad0d362a63b9f";
   };
 
-  buildInputs = [ rdkafka requests ] ++ (if isPy3k then [ avro3k ] else [ avro ]) ;
+  buildInputs = [ rdkafka requests ] ++ (if isPy3k then [ avro3k ] else [ avro futures ]) ;
 
   # Tests fail for python3 under this pypi release
   doCheck = if isPy3k then false else true;

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/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/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/genanki/default.nix

@@ -0,0 +1,38 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, cached-property, frozendict, pystache, pyyaml, pytest, pytestrunner
+}:
+
+buildPythonPackage rec {
+  pname = "genanki";
+  version = "0.6.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0xj8yd3acl8h457sh42balvcd0z4mg5idd4q63f7qlfzc5wgbb74";
+  };
+
+  propagatedBuildInputs = [
+		pytestrunner
+    cached-property
+    frozendict
+    pystache
+    pyyaml
+  ];
+
+  checkInputs = [ pytest ];
+
+  disabled = !isPy3k;
+
+  # relies on upstream anki
+	doCheck = false;
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://github.com/kerrickstaley/genanki;
+    description = "Generate Anki decks programmatically";
+    license = licenses.mit;
+    maintainers = with maintainers; [ teto ];
+  };
+}

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

@@ -1,23 +1,23 @@
 { stdenv, buildPythonPackage, fetchFromGitHub
 , pandas, shapely, fiona, descartes, pyproj
-, pytest }:
+, pytest, Rtree }:
 
 buildPythonPackage rec {
   pname = "geopandas";
-  version = "0.3.0";
+  version = "0.4.0";
   name = pname + "-" + version;
 
   src = fetchFromGitHub {
     owner = "geopandas";
     repo = "geopandas";
     rev = "v${version}";
-    sha256 = "0maafafr7sjjmlg2f19bizg06c8a5z5igmbcgq6kgmi7rklx8xxz";
+    sha256 = "025zpgck5pnmidvzk0805pr345rd7k6z66qb2m34gjh1814xjkhv";
   };
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytest Rtree ];
 
   checkPhase = ''
-    py.test geopandas
+    py.test geopandas -m "not web"
   '';
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,24 @@
+{ buildPythonPackage, fetchurl, isPyPy, gmp } :
+
+let
+  pname = "gmpy";
+  version = "1.17";
+in
+
+buildPythonPackage {
+  inherit pname version;
+
+  disabled = isPyPy;
+
+  src = fetchurl {
+    url = "mirror://pypi/g/gmpy/${pname}-${version}.zip";
+    sha256 = "1a79118a5332b40aba6aa24b051ead3a31b9b3b9642288934da754515da8fa14";
+  };
+
+  buildInputs = [ gmp ];
+
+  meta = {
+    description = "GMP or MPIR interface to Python 2.4+ and 3.x";
+    homepage = http://code.google.com/p/gmpy/;
+  };
+}

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

@@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchurl, isPyPy, gmp, mpfr, libmpc } :
+
+let
+  pname = "gmpy2";
+  version = "2.0.8";
+in
+
+buildPythonPackage {
+  inherit pname version;
+
+  disabled = isPyPy;
+
+  src = fetchurl {
+    url = "mirror://pypi/g/gmpy2/${pname}-${version}.zip";
+    sha256 = "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx";
+  };
+
+  buildInputs = [ gmp mpfr libmpc ];
+
+  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/;
+    license = licenses.gpl3Plus;
+  };
+}

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

@@ -1,7 +1,8 @@
-{ lib, buildPythonPackage, fetchPypi, jsonschema, notebook }:
+{ lib, buildPythonPackage, fetchPypi, jsonschema, notebook, pythonOlder }:
 buildPythonPackage rec {
   pname = "jupyterlab_launcher";
   version = "0.13.1";
+  disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi, pythonAtLeast,
-  ipaddress, websocket_client, urllib3, pyyaml, requests_oauthlib, python-dateutil, google_auth,
+  ipaddress, websocket_client, urllib3, pyyaml, requests_oauthlib, python-dateutil, google_auth, adal,
   isort, pytest, coverage, mock, sphinx, autopep8, pep8, codecov, recommonmark, nose }:
 
 buildPythonPackage rec {
@@ -27,7 +27,7 @@ buildPythonPackage rec {
   };
 
   checkInputs = [ isort coverage pytest mock sphinx autopep8 pep8 codecov recommonmark nose ];
-  propagatedBuildInputs = [ ipaddress websocket_client urllib3 pyyaml requests_oauthlib python-dateutil google_auth ];
+  propagatedBuildInputs = [ ipaddress websocket_client urllib3 pyyaml requests_oauthlib python-dateutil google_auth adal ];
 
   meta = with stdenv.lib; {
     description = "Kubernetes python client";

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/locustio/default.nix

@@ -1,8 +1,8 @@
 { buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , mock
 , unittest2
-, msgpack-python
+, msgpack
 , requests
 , flask
 , gevent
@@ -11,18 +11,16 @@
 
 buildPythonPackage rec {
   pname = "locustio";
-  version = "0.8.1";
+  version = "0.9.0";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "64583987ba1c330bb071aee3e29d2eedbfb7c8b342fa064bfb74fafcff660d61";
+  src = fetchFromGitHub {
+    owner = "locustio";
+    repo = "locust";
+    rev = "${version}";
+    sha256 = "1645d63ig4ymw716b6h53bhmjqqc13p9r95k1xfx66ck6vdqnisd";
   };
 
-  patchPhase = ''
-    sed -i s/"pyzmq=="/"pyzmq>="/ setup.py
-  '';
-
-  propagatedBuildInputs = [ msgpack-python requests flask gevent pyzmq ];
+  propagatedBuildInputs = [ msgpack requests flask gevent pyzmq ];
   buildInputs = [ mock unittest2 ];
 
   meta = {

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 +1,34 @@
+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.

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

@@ -0,0 +1,30 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, setuptools
+, nose
+}:
+
+buildPythonPackage rec {
+  version = "0.6.0";
+  pname = "markerlib";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2fdb3939441f5bf4f090b1979a34f84a11d33eed6c0e3995de88ae5c06b6e3ae";
+  };
+
+  buildInputs = [ setuptools ];
+  checkInputs = [ nose ];
+
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://bitbucket.org/dholth/markerlib/;
+    description = "A compiler for PEP 345 environment markers";
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , paramiko
+, selectors2
 , lxml
 , libxml2
 , libxslt
@@ -21,7 +22,7 @@ buildPythonPackage rec {
   checkInputs = [ nose rednose ];
 
   propagatedBuildInputs = [
-    paramiko lxml libxml2 libxslt
+    paramiko lxml libxml2 libxslt selectors2
   ];
 
   checkPhase = ''

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

@@ -18,6 +18,8 @@
 , psutil
 , pydot
 , pytest
+, pytest_xdist
+, pytest-forked
 , scipy
 , simplejson
 , traits
@@ -47,8 +49,6 @@ buildPythonPackage rec {
   postPatch = ''
     substituteInPlace nipype/interfaces/base/tests/test_core.py \
       --replace "/usr/bin/env bash" "${bash}/bin/bash"
-
-    rm pytest.ini
   '';
 
   propagatedBuildInputs = [
@@ -56,7 +56,6 @@ buildPythonPackage rec {
     dateutil
     funcsigs
     future
-    futures
     networkx
     nibabel
     numpy
@@ -70,9 +69,10 @@ buildPythonPackage rec {
     xvfbwrapper
   ] ++ stdenv.lib.optional (!isPy3k) [
     configparser
+    futures
   ];
 
-  checkInputs = [ pytest mock pytestcov codecov which glibcLocales ];
+  checkInputs = [ pytest mock pytestcov pytest_xdist pytest-forked codecov which glibcLocales ];
 
   checkPhase = ''
     LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype

pkgs/development/python-modules/ordered-set/default.nix

@@ -1,10 +1,10 @@
-{ buildPythonPackage, fetchPypi, lib, pytest }:
+{ buildPythonPackage, fetchPypi, lib, pytest, pytestrunner }:
 
 buildPythonPackage rec {
   pname = "ordered-set";
   version = "3.0.1";
 
-  buildInputs = [ pytest ];
+  buildInputs = [ pytest pytestrunner ];
 
   src = fetchPypi {
     inherit pname version;
@@ -21,6 +21,3 @@ buildPythonPackage rec {
     maintainers = [ lib.maintainers.MostAwesomeDude ];
   };
 }
-
-
-

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

@@ -1,12 +1,14 @@
 { buildPythonPackage
 , fetchPypi
 , zope_interface
+, sphinx, manuel
 }:
 
 buildPythonPackage rec {
   pname = "persistent";
   version = "4.4.2";
 
+  nativeBuildInputs = [ sphinx manuel ];
   propagatedBuildInputs = [ zope_interface ];
 
   src = fetchPypi {

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

@@ -0,0 +1,29 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPyPy, isPy3k, click, gmpy2, numpy } :
+
+let
+  pname = "phe";
+  version = "1.4.0";
+in
+
+buildPythonPackage {
+  inherit pname version;
+
+  # https://github.com/n1analytics/python-paillier/issues/51
+  disabled = isPyPy || ! isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0wzlk7d24kp0f5kpm0kvvc88mm42144f5cg9pcpb1dsfha75qy5m";
+  };
+
+  buildInputs = [ click gmpy2 numpy ];
+
+  # 29/233 tests fail
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A library for Partially Homomorphic Encryption in Python";
+    homepage = https://github.com/n1analytics/python-paillier;
+    license = licenses.gpl3;
+  };
+}

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

@@ -10,9 +10,12 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [ numpy pyyaml matplotlib h5py ];
-  
+
   checkPhase = ''
-    cd test/phonopy
+    cd test
+    # dynamic structure factor test ocassionally fails do to roundoff
+    # see issue https://github.com/atztogo/phonopy/issues/79
+    rm spectrum/test_dynamic_structure_factor.py
     ${python.interpreter} -m unittest discover -b
     cd ../..
   '';
@@ -24,4 +27,3 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ psyanticy ];
   };
 }
-

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

@@ -17,7 +17,7 @@ buildPythonPackage rec {
   prePatch = ''
     substituteInPlace setup.py \
       --replace 'beautifulsoup4>=4.2.1,<4.5.0' \
-                'beautifulsoup4>=4.2.1,<=4.6.0'
+                'beautifulsoup4>=4.2.1,<=4.6.3'
   '';
 
   # don't require enum34 on python >= 3.4

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

@@ -1,17 +1,17 @@
-{ stdenv, buildPythonPackage, fetchPypi, glibcLocales, numpy, pydispatcher, sympy, requests, monty, ruamel_yaml, six, scipy, tabulate, enum34, matplotlib, palettable, spglib, pandas }:
+{ stdenv, buildPythonPackage, fetchPypi, glibcLocales, numpy, pydispatcher, sympy, requests, monty, ruamel_yaml, six, scipy, tabulate, enum34, matplotlib, palettable, spglib, pandas, networkx }:
 
 buildPythonPackage rec {
   pname = "pymatgen";
-  version = "2018.8.10";
+  version = "2018.9.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9bb3b170ca8654c956fa2efdd31107570c0610f7585d90e4a541eb99cee41603";
+    sha256 = "dee5dbd8008081de9f27759c20c550d09a07136eeebfe941e3d05fd88ccace18";
   };
 
   nativeBuildInputs = [ glibcLocales ];
-  propagatedBuildInputs = [ numpy pydispatcher sympy requests monty ruamel_yaml six scipy tabulate enum34 matplotlib palettable spglib pandas ];
-  
+  propagatedBuildInputs = [ numpy pydispatcher sympy requests monty ruamel_yaml six scipy tabulate enum34 matplotlib palettable spglib pandas networkx ];
+
   # No tests in pypi tarball.
   doCheck = false;
 
@@ -22,4 +22,3 @@ buildPythonPackage rec {
     maintainers = with maintainers; [ psyanticy ];
   };
 }
-

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

@@ -1,20 +1,30 @@
-{ stdenv, buildPythonPackage, isPy3k, fetchPypi }:
+{ stdenv, python, buildPythonPackage, isPy3k, fetchPypi }:
 
 buildPythonPackage rec {
   pname = "pymetar";
-  version = "0.21";
+  version = "1.0";
 
-  disabled = isPy3k;
+  disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1sh3nm5ilnsgpnzbb2wv4xndnizjayw859qp72798jadqpcph69k";
+    sha256 = "1n4k5aic4sgp43ki6j3zdw9b21r3biqqws8ah57b77n44b8wzrap";
   };
 
+  checkPhase = ''
+    cd testing/smoketest
+    tar xzf reports.tgz
+    mkdir logs
+    patchShebangs runtests.sh
+    substituteInPlace runtests.sh --replace "break" "exit 1"  # fail properly
+    export PYTHONPATH="$PYTHONPATH:$out/${python.sitePackages}"
+    ./runtests.sh
+  '';
+
   meta = with stdenv.lib; {
     description = "A command-line tool to show the weather report by a given station ID";
     homepage = http://www.schwarzvogel.de/software/pymetar.html;
-    license = licenses.gpl2;
+    license = licenses.gpl2Plus;
     maintainers = with maintainers; [ erosennin ];
   };
 }

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyslurm";
-  version = "20180604";
+  version = "20180908";
 
   src = fetchFromGitHub {
     repo = "pyslurm";
     owner = "PySlurm";
-    rev = "9dd4817e785fee138a9e29c3d71d2ea44898eedc";
-    sha256 = "14ivwc27sjnk0z0jpfgyy9bd91m2bhcz11lzp1kk9xn4495i7wvj";
+    rev = "50dc113e99d82e70e84fc2e812333733708be4ed";
+    sha256 = "1j2i4rvhmk2ihhcvsjdlqlxqb5a05jg8k9bqkv3zrvdj71yn4z9k";
   };
 
   buildInputs = [ cython slurm ];

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

@@ -10,21 +10,11 @@ buildPythonPackage rec {
   pname = "pytest-timeout";
   version = "1.3.2";
 
-  # remove after version 1.3.1
-  patches = [
-    (fetchpatch {
-      name = "fix-installation-27-3-with-encoding-issue.patch";
-      url = "https://bitbucket.org/pytest-dev/pytest-timeout/commits/9de81d3fc57a71a36d418d4aa181c241a7c5350f/raw";
-      sha256 = "0g081j6iyc9825f63ssmmi40rkcgk4p9vvhy9g0lqd0gc6xzwa2p";
-    })
-  ];
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "1117fc0536e1638862917efbdc0895e6b62fa61e6cf4f39bb655686af7af9627";
   };
 
-  buildInputs = [ pytest ];
   checkInputs = [ pytest pexpect ];
   checkPhase = ''pytest -ra'';
 

pkgs/development/python-modules/selectors2/default.nix

@@ -0,0 +1,29 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, nose, psutil, mock }:
+
+buildPythonPackage rec {
+  version = "2.0.1";
+  pname = "selectors2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "81b77c4c6f607248b1d6bbdb5935403fef294b224b842a830bbfabb400c81884";
+  };
+
+  checkInputs = [ nose psutil mock ];
+
+  checkPhase = ''
+    # https://github.com/NixOS/nixpkgs/pull/46186#issuecomment-419450064
+    # Trick to disable certain tests that depend on timing which
+    # will always fail on hydra
+    export TRAVIS=""
+    nosetests tests/test_selectors2.py
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://www.github.com/SethMichaelLarson/selectors2;
+    description = "Back-ported, durable, and portable selectors";
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ buildPythonPackage, lib, fetchPypi, glibcLocales, isPy3k, contextvars
+, pythonOlder
+}:
+
+buildPythonPackage rec {
+  pname = "sniffio";
+  version = "1.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1dzb0nx3m1hpjgsv6s6w5ac2jcmywcz6gqnfkw8rwz1vkr1836rf";
+  };
+
+  # breaks with the following error:
+  # > TypeError: 'encoding' is an invalid keyword argument for this function
+  disabled = !isPy3k;
+
+  buildInputs = [ glibcLocales ];
+
+  propagatedBuildInputs = lib.optionals (pythonOlder "3.7") [ contextvars ];
+
+  # no tests distributed with PyPI
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/python-trio/sniffio;
+    license = licenses.asl20;
+    description = "Sniff out which async library your code is running under";
+  };
+}

pkgs/development/python-modules/spacy/models.json

@@ -1,42 +1,78 @@
 [{
-  "pname": "es_core_web_md",
-  "version": "1.0.0",
-  "sha256": "0ikyakdhnj6rrfpr8k83695d1gd3z9n60a245hwwchv94jmr7r6s",
+  "pname": "de_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "13fs4f46qg9mlxd9ynmh81gxizm11kfq3g52pk8d2m7wp89xfc6a",
   "license": "cc-by-sa-40"
 },
 {
-  "pname": "fr_depvec_web_lg",
-  "version": "1.0.0",
-  "sha256": "0nxmdszs1s5by2874cz37azrmwamh1ngdsiylffkfihzq6s8bhka",
-  "license": "cc-by-nc-sa-40"
+  "pname": "en_core_web_lg",
+  "version": "2.0.0",
+  "sha256": "1r33l02jrkzjn78nd0bzzzd6rwjlz7qfgs3bg5yr2ki6q0m7qxvw",
+  "license": "cc-by-sa-40"
 },
 {
   "pname": "en_core_web_md",
-  "version": "1.2.1",
-  "sha256": "12prr4hcbfdaky9rcna1y1ykr417jkhkks2r8l06g8fb7am3pvp3",
-  "license": "cc-by-sa-40"
-},
-{
-  "pname": "en_depent_web_md",
-  "version": "1.2.1",
-  "sha256": "0giyr35q5lpp5drpcamyvb5gsjnhj62mk3ndfr49nm1s6d5f6m52",
+  "version": "2.0.0",
+  "sha256": "1b5g5gma1gzm8ffj0pgli1pllccx5jpjvb7a19n7c8bfswpifxzc",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "en_core_web_sm",
-  "version": "1.2.0",
-  "sha256": "0vc4l77dcwa9lmzyqdci8ikjc0m2rhasl2zvyba547vf76qb0528",
+  "version": "2.0.0",
+  "sha256": "161298pl6kzc0cgf2g7ji84xbqv8ayrgsrmmg0hxiflwghfj77cx",
   "license": "cc-by-sa-40"
 },
 {
-  "pname": "de_core_news_md",
-  "version": "1.0.0",
-  "sha256": "072jz2rdi1nckny7k16avp86vjg4didfdsw816kfl9zwr88iny6g",
+  "pname": "en_vectors_web_lg",
+  "version": "2.0.0",
+  "sha256": "15qfd8vzdv56x41fzghy7k5x1c8ql92ds70r37b6a8hkb87z9byw",
   "license": "cc-by-sa-40"
 },
 {
-  "pname": "en_vectors_glove_md",
-  "version": "1.0.0",
-  "sha256": "1jbr27xnh5fdww8yphpvk2brfnzb174wfnxkzdqwv3iyi02zsin6",
+  "pname": "es_core_news_md",
+  "version": "2.0.0",
+  "sha256": "03056qz866r641q4nagymw6pc78qnn5vdvcp7p1ph2cvxh7081kp",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "es_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "1b91lcmw2kyqmcrxlfq7m5vlj1a57i3bb9a5h4y31smjgzmsr81s",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "fr_core_news_md",
+  "version": "2.0.0",
+  "sha256": "06kva46l1nw819bidzj2vks69ap1a9fa7rnvpd28l3z2haci38ls",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "fr_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "1zlhm9646g3cwcv4cs33160f3v8gxmzdr02x8hx7jpw1fbnmc5mx",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "it_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "0fs68rdq19migb3x3hb510b96aabibsi01adlk1fipll1x48msaz",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "nl_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "0n5x61jp8rdxa3ki250ipbd68rjpp9li6xwbx3fbzycpngffwy8z",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "pt_core_news_sm",
+  "version": "2.0.0",
+  "sha256": "1sg500b3f3qnx1ga32hbq9p4qfynqhpdzhlmdjrxgqw8i58ys23g",
+  "license": "cc-by-sa-40"
+},
+{
+  "pname": "xx_ent_wiki_sm",
+  "version": "2.0.0",
+  "sha256": "0mc3mm6nfjp31wbjysdj2x72akyi52hgprm1g54djxfypm3pmn35",
   "license": "cc-by-sa-40"
 }]

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/trio/default.nix

@@ -8,6 +8,7 @@
 , pytest
 , pyopenssl
 , trustme
+, sniffio
 }:
 
 buildPythonPackage rec {
@@ -31,6 +32,7 @@ buildPythonPackage rec {
     async_generator
     idna
     outcome
+    sniffio
   ] ++ lib.optionals (pythonOlder "3.7") [ contextvars ];
 
   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 ];