Merge branch 'master' into staging

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

@@ -0,0 +1,15 @@
+{ buildPythonPackage, fetchPypi, attrs, protobuf, zeroconf }:
+
+buildPythonPackage rec {
+  pname = "aioesphomeapi";
+  version = "1.8.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "16ywa7yggmsx8m2r9azdq7w9fxjh736g1vd1aibgh24g7srhwwhj";
+  };
+
+  propagatedBuildInputs = [ attrs protobuf zeroconf ];
+
+  meta = {};
+}

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "altair";
-  version = "2.3.0";
+  version = "2.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9f4bc7cd132c0005deb6b36c7041ee213a69bbdfcd8c0b1a9f1ae8c1fba733f6";
+    sha256 = "1lqln4510qqqla6s8z4ca0271qrhq6yyznsijsdn3nssvxsynqpc";
   };
 
   postPatch = ''

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "amqp";
-  version = "2.4.1";
+  version = "2.4.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6816eed27521293ee03aa9ace300a07215b11fee4e845588a9b863a7ba30addb";
+    sha256 = "043beb485774ca69718a35602089e524f87168268f0d1ae115f28b88d27f92d7";
   };
 
   checkInputs = [ pytest case pytest-sugar ];

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "asynctest";
-  version = "0.12.2";
+  version = "0.12.3";
 
   disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "77520850ae21620ec31738f4a7b467acaa44de6d3752d8ac7a9f4dcf55d77853";
+    sha256 = "bbeb45bb41344d2cbb814b4c89c04f2c568742352736cabf7af6fcbed06f66cc";
   };
 
   postPatch = ''

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

@@ -0,0 +1,59 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, gym
+, scipy
+, tqdm
+, joblib
+, dill
+, progressbar2
+, cloudpickle
+, click
+, pyzmq
+, tensorflow
+, mpi4py
+}:
+
+buildPythonPackage rec {
+  pname = "baselines";
+  version = "0.1.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0n1mxkcg82gzhkb4j5zzwm335r3rc1sblknqs4x6nkrrh42d65cm";
+  };
+
+  patches = [
+    # already fixed upstream
+    ./fix-dep-names.patch
+  ];
+
+  propagatedBuildInputs = [
+    gym
+    scipy
+    tqdm
+    joblib
+    pyzmq
+    dill
+    progressbar2
+    mpi4py
+    cloudpickle
+    tensorflow
+    click
+  ];
+
+  # fails to create a daemon, probably because of sandboxing
+  doCheck = false;
+
+  checkInputs = [
+    pytest
+  ];
+
+  meta = with lib; {
+    description = "High-quality implementations of reinforcement learning algorithms";
+    homepage = https://github.com/openai/baselines;
+    license = licenses.mit;
+    maintainers = with maintainers; [ timokau ];
+  };
+}

pkgs/development/python-modules/baselines/fix-dep-names.patch

@@ -0,0 +1,18 @@
+diff --git a/setup.py b/setup.py
+index bf8badc..570be20 100644
+--- a/setup.py
++++ b/setup.py
+@@ -10,11 +10,11 @@ setup(name='baselines',
+       packages=[package for package in find_packages()
+                 if package.startswith('baselines')],
+       install_requires=[
+-          'gym[mujoco,atari,classic_control,robotics]',
++          'gym',
+           'scipy',
+           'tqdm',
+           'joblib',
+-          'zmq',
++          'pyzmq',
+           'dill',
+           'progressbar2',
+           'mpi4py',

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

@@ -2,42 +2,75 @@
 , buildPythonPackage
 , fetchFromGitHub
 , nose
+, pylibmc
+, memcached
+, redis
+, pymongo
 , mock
 , webtest
 , sqlalchemy
 , pycrypto
+, cryptography
 , isPy27
+, isPy3k
 , funcsigs
 , pycryptopp
 }:
 
 buildPythonPackage rec {
   pname = "Beaker";
-  version = "1.8.0";
+  version = "1.10.1";
 
   # The pypy release do not contains the tests
   src = fetchFromGitHub {
     owner = "bbangert";
     repo = "beaker";
     rev = "${version}";
-    sha256 = "17yfr7a307n8rdl09was4j60xqk2s0hk0hywdkigrpj4qnw0is7g";
+    sha256 = "0xrvg503xmi28w0hllr4s7fkap0p09fgw2wax3p1s2r6b3xjvbz7";
   };
 
-  buildInputs =
-    [ nose
-      mock
-      webtest
-    ];
   propagatedBuildInputs = [
     sqlalchemy
     pycrypto
+    cryptography
   ] ++ lib.optionals (isPy27) [
     funcsigs
     pycryptopp
   ];
 
+  checkInputs = [
+    nose
+    mock
+    webtest
+    pylibmc
+    memcached
+    redis
+    pymongo
+  ];
+
+
+  # Can not run memcached tests because it immediately tries to connect
+  postPatch = lib.optionalString isPy3k ''
+    substituteInPlace setup.py \
+      --replace "python-memcached" "python3-memcached"
+    '' + ''
+
+    rm tests/test_memcached.py
+  '';
+
+  # Disable external tests because they need to connect to a live database.
+  # Also disable a test in test_cache.py called "test_upgrade" because
+  # it currently fails on darwin.
+  # Please see issue https://github.com/bbangert/beaker/issues/166
+  checkPhase = ''
+    nosetests \
+      -e ".*test_ext_.*" \
+      -e "test_upgrade" \
+      -vv tests
+  '';
+
   meta = {
     description = "A Session and Caching library with WSGI Middleware";
     maintainers = with lib.maintainers; [ garbas domenkozar ];
   };
-}
+}

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

@@ -1,16 +1,16 @@
 { stdenv, buildPythonPackage, fetchPypi, pythonOlder
-, attrs, click, toml, appdirs, aiohttp
+, attrs, click, toml, appdirs, aiohttp, aiohttp-cors
 , glibcLocales, pytest }:
 
 buildPythonPackage rec {
   pname = "black";
-  version = "18.9b0";
+  version = "19.3b0";
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1992ramdwv8sg4mbl5ajirwj5i4a48zjgsycib0fnbaliyiajc70";
+    sha256 = "073kd5rs02lisp6n3h7yai9lix520xnaa6c7rdmp2sci9pyhz5b8";
   };
 
   checkInputs =  [ pytest glibcLocales ];
@@ -23,7 +23,7 @@ buildPythonPackage rec {
       --deselect tests/test_black.py::BlackTestCase::test_failed_formatting_does_not_get_cached
   '';
 
-  propagatedBuildInputs = [ attrs appdirs click toml aiohttp ];
+  propagatedBuildInputs = [ attrs appdirs click toml aiohttp aiohttp-cors ];
 
   meta = with stdenv.lib; {
     description = "The uncompromising Python code formatter";

pkgs/development/python-modules/cassandra-driver/default.nix

@@ -21,11 +21,11 @@
 
 buildPythonPackage rec {
   pname = "cassandra-driver";
-  version = "3.16.0";
+  version = "3.17.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1gjs2lqy0ba6zhh13a1dhirk59i7lc4zcbl7h50619hdm5kv3g22";
+    sha256 = "1z49z6f9rj9kp1v03s1hs1rg8cj49rh0yk0fc2qi57w7slgy2hkd";
   };
 
   buildInputs = [

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

@@ -4,13 +4,18 @@
 
 buildPythonPackage rec {
   pname = "celery";
-  version = "4.3.0rc1";
+  version = "4.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1jmg47l0b3bnwmg44x48bwziwyk6xqs1y5plvr99a3ikz1l807yf";
+    sha256 = "4c4532aa683f170f40bd76f928b70bc06ff171a959e06e71bf35f2f9d6031ef9";
   };
 
+  postPatch = ''
+    substituteInPlace requirements/test.txt \
+      --replace "pytest>=4.3.1,<4.4.0" pytest
+  '';
+
   # make /etc/protocols accessible to fix socket.getprotobyname('tcp') in sandbox
   preCheck = stdenv.lib.optionalString stdenv.isLinux ''
     export NIX_REDIRECTS=/etc/protocols=${iana-etc}/etc/protocols \

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

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "Chameleon";
-  version = "3.5";
+  version = "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1a83jf211mqjhgbd3abqyrn4mp4vb077ql8fydmv80xg3whrf3yb";
+    sha256 = "0141kfwx553q73wzfl624pppmbhh7fpzvaj5pbj21pqlk2rhfx75";
   };
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/cherrypy/17.nix

@@ -0,0 +1,36 @@
+{ lib, buildPythonPackage, fetchPypi
+, setuptools_scm
+, cheroot, contextlib2, portend, routes, six, zc_lockfile
+, backports_unittest-mock, objgraph, pathpy, pytest, pytestcov, backports_functools_lru_cache, requests_toolbelt
+}:
+
+buildPythonPackage rec {
+  pname = "cherrypy";
+  version = "17.4.1";
+
+  src = fetchPypi {
+    pname = "CherryPy";
+    inherit version;
+    sha256 = "1kl17anzz535jgkn9qcy0c2m0zlafph0iv7ph3bb9mfrs2bgvagv";
+  };
+
+  propagatedBuildInputs = [
+    cheroot contextlib2 portend routes six zc_lockfile
+  ];
+
+  nativeBuildInputs = [ setuptools_scm ];
+
+  checkInputs = [
+    backports_unittest-mock objgraph pathpy pytest pytestcov backports_functools_lru_cache requests_toolbelt
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    homepage = https://www.cherrypy.org;
+    description = "A pythonic, object-oriented HTTP framework";
+    license = licenses.bsd3;
+  };
+}

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

@@ -1,54 +1,40 @@
 { lib, buildPythonPackage, fetchPypi, isPy3k
-, cheroot, contextlib2, portend, routes, six
-, setuptools_scm, zc_lockfile, more-itertools
-, backports_unittest-mock, objgraph, pathpy, pytest, pytestcov
-, backports_functools_lru_cache, requests_toolbelt, pytest-services
+, setuptools_scm
+, cheroot, portend, more-itertools, zc_lockfile, routes
+, objgraph, pytest, pytestcov, pathpy, requests_toolbelt, pytest-services
 }:
 
-let
-  srcInfo = if isPy3k then {
-    version = "18.1.0";
-    sha256 = "4dd2f59b5af93bd9ca85f1ed0bb8295cd0f5a8ee2b84d476374d4e070aa5c615";
-  } else {
-    version = "17.4.1";
-    sha256 = "1kl17anzz535jgkn9qcy0c2m0zlafph0iv7ph3bb9mfrs2bgvagv";
-  };
-in buildPythonPackage rec {
-  pname = "CherryPy";
-  inherit (srcInfo) version;
+buildPythonPackage rec {
+  pname = "cherrypy";
+  version = "18.1.1";
+
+  disabled = !isPy3k;
 
   src = fetchPypi {
-    inherit pname;
-    inherit (srcInfo) version sha256;
+    pname = "CherryPy";
+    inherit version;
+    sha256 = "6585c19b5e4faffa3613b5bf02c6a27dcc4c69a30d302aba819639a2af6fa48b";
   };
 
-  propagatedBuildInputs = if isPy3k then [
+  propagatedBuildInputs = [
     # required
     cheroot portend more-itertools zc_lockfile
     # optional
     routes
-  ] else [
-    cheroot contextlib2 portend routes six zc_lockfile
   ];
 
-  buildInputs = [ setuptools_scm ];
+  nativeBuildInputs = [ setuptools_scm ];
 
-  checkInputs = if isPy3k then [
+  checkInputs = [
     objgraph pytest pytestcov pathpy requests_toolbelt pytest-services
-  ] else [
-    backports_unittest-mock objgraph pathpy pytest pytestcov backports_functools_lru_cache requests_toolbelt
   ];
 
   checkPhase = ''
-    # 3 out of 5 SignalHandlingTests need network access
-    # test_2_File_Concurrency also fails upstream: https://github.com/cherrypy/cherrypy/issues/1306
-    # ...and skipping it makes 2 other tests fail
-    LANG=en_US.UTF-8 pytest -k "not SignalHandlingTests and not test_4_Autoreload \
-                            and not test_2_File_Concurrency and not test_3_Redirect and not test_4_File_deletion"
+    pytest
   '';
 
   meta = with lib; {
-    homepage = "http://www.cherrypy.org";
+    homepage = https://www.cherrypy.org;
     description = "A pythonic, object-oriented HTTP framework";
     license = licenses.bsd3;
   };

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

@@ -2,16 +2,14 @@
 
 buildPythonPackage rec {
   pname = "contextvars";
-  version = "2.3";
+  version = "2.4";
   disabled = !isPy36;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09fnni8cyxm070bfv9ay030qbyk0dfds5nq77s0p38h33hp08h93";
+    sha256 = "f38c908aaa59c14335eeea12abea5f443646216c4e29380d7bf34d2018e2c39e";
   };
 
-  # pull request for this patch is https://github.com/MagicStack/contextvars/pull/9
-  patches = [ ./immutables_version.patch ];
   propagatedBuildInputs = [ immutables ];
 
   meta = {

pkgs/development/python-modules/contextvars/immutables_version.patch

@@ -1,11 +0,0 @@
---- ./setup.py	2018-07-30 15:40:14.000000000 +0000
-+++ ./setup.py	2019-02-12 18:33:24.984430303 +0000
-@@ -17,7 +17,7 @@
-     packages=['contextvars'],
-     provides=['contextvars'],
-     install_requires=[
--        'immutables==0.6',
-+        'immutables>=0.6',
-     ],
-     license='Apache License, Version 2.0',
-     classifiers=[

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

@@ -1,19 +1,27 @@
-{ buildPythonPackage, stdenv, fetchPypi, pandas, plotly, colorlover
+{ buildPythonPackage, stdenv, fetchPypi
+, numpy, pandas, plotly, six, colorlover
+, ipython, ipywidgets, nose
 }:
 
 buildPythonPackage rec {
   pname = "cufflinks";
-  version = "0.14.6";
+  version = "0.15";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4188324361cc584214150aadaeb28ed07e9d150adb714b53c5f09d5b3fcdd28a";
+    sha256 = "014098a4568199957198c0a7fe3dbeb3b4010b6de8d692a41fe3b3ac107b660e";
   };
 
-  propagatedBuildInputs = [ pandas plotly colorlover ];
+  propagatedBuildInputs = [
+    numpy pandas plotly six colorlover
+    ipython ipywidgets
+  ];
 
-  # tests not included in archive
-  doCheck = false;
+  checkInputs = [ nose ];
+
+  checkPhase = ''
+    nosetests -xv tests.py
+  '';
 
   meta = {
     homepage = https://github.com/santosjorge/cufflinks;

pkgs/development/python-modules/devpi-common/default.nix

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, requests, py, pytest }:
+{ lib, buildPythonPackage, fetchPypi, requests, py, pytest, pytest-flakes }:
 
 buildPythonPackage rec {
   pname = "devpi-common";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [ requests py ];
-  checkInputs = [ pytest ];
+  checkInputs = [ pytest pytest-flakes ];
 
   checkPhase = ''
     py.test

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

@@ -1,12 +1,17 @@
-{ buildPythonPackage, dlib, python, pytest }:
+{ buildPythonPackage, dlib, python, pytest, avxSupport ? true }:
 
 buildPythonPackage {
   inherit (dlib) name src nativeBuildInputs buildInputs meta;
 
+  # although AVX can be enabled, we never test with it. Some Hydra machines
+  # fail because of this, however their build results are probably used on hardware
+  # with AVX support.
   checkPhase = ''
     ${python.interpreter} nix_run_setup test --no USE_AVX_INSTRUCTIONS
   '';
 
+  setupPyBuildFlags = [ "--${if avxSupport then "yes" else "no"} USE_AVX_INSTRUCTIONS" ];
+
   patches = [ ./build-cores.patch ];
 
   checkInputs = [ pytest ];

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

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "face_recognition";
-  version = "1.2.2";
+  version = "1.2.3";
 
   src = fetchFromGitHub {
     repo = pname;
     owner = "ageitgey";
-    rev = "v${version}";
-    sha256 = "17jnyr80j1p74gyvh1jabvwd3zsxvip2y7cjhh2g6gsjv2dpvrjv";
+    rev = "634db2e4309a365cee2503cb65d6f2e88f519d1e";
+    sha256 = "06zw5hq417d5yp17zynhxhb73074lx2qy64fqfzf711rw5vrn2mx";
   };
 
   postPatch = ''
@@ -19,6 +19,15 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ pillow click dlib numpy face_recognition_models ];
 
+  # Our dlib is compiled with AVX instructions by default which breaks
+  # with "Illegal instruction" on some builders due to missing hardware features.
+  #
+  # As this makes the build fairly unreliable, it's better to skip the test and to ensure that
+  # the build is working and after each change to the package, manual testing should be done.
+  doCheck = false;
+
+  # Although tests are disabled by default, checkPhase still exists, so
+  # maintainers can check the package's functionality locally before modifying it.
   checkInputs = [ flake8 pytest glibcLocales ];
   checkPhase = ''
     LC_ALL="en_US.UTF-8" py.test

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

@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "first";
-  version = "2.0.1";
+  version = "2.0.2";
   name = pname + "-" + version;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0pn9hl2y0pz61la1xhkdz6vl9i2dg3nh0ksizcf0f9ybh8sxxcrv";
+    sha256 = "1gykyrm6zlrbf9iz318p57qwk594mx1jf0d79v79g32zql45na7z";
   };
 
   doCheck = false; # no tests

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

@@ -14,11 +14,11 @@
 
 buildPythonPackage rec {
   pname = "folium";
-  version = "0.7.0";
+  version = "0.8.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04mhdl3k644j45rlfkamxz1paf58fxrmnwgvkrvza2fcwcs4nr9n";
+    sha256 = "0f25fhwxnix8hddzf67barzjwwsvpww112zisrvz2lpl08j388rn";
   };
 
   checkInputs = [ pytest nbconvert pandas mock ];

pkgs/development/python-modules/importlib-metadata/default.nix

@@ -1,29 +1,36 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, setuptools_scm
+, zipp
 , pathlib2
 , contextlib2
+, configparser
 , isPy3k
 , importlib-resources
+, packaging
 }:
 
 buildPythonPackage rec {
   pname = "importlib-metadata";
-  version = "0.6";
+  version = "0.8";
 
   src = fetchPypi {
     pname = "importlib_metadata";
     inherit version;
-    sha256 = "36b02c84f9001adf65209fefdf951be8e9014a95eab9938c0779ad5670359b1c";
+    sha256 = "b50191ead8c70adfa12495fba19ce6d75f2e0275c14c5a7beb653d6799b512bd";
   };
 
-  propagatedBuildInputs = [] ++ lib.optionals (!isPy3k) [ pathlib2 contextlib2 ];
+  nativeBuildInputs = [ setuptools_scm ];
 
-  checkInputs = [ importlib-resources ];
+  propagatedBuildInputs = [ zipp ]
+    ++ lib.optionals (!isPy3k) [ pathlib2 contextlib2 configparser ];
+
+  checkInputs = [ importlib-resources packaging ];
 
   meta = with lib; {
     description = "Read metadata from Python packages";
     homepage = https://importlib-metadata.readthedocs.io/;
     license = licenses.asl20;
   };
-}
+}

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

@@ -13,6 +13,7 @@
 , tornado
 , traitlets
 , requests
+, notebook
 , pythonOlder
 , nodePackages
 }:
@@ -106,7 +107,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     alembic ipython jinja2 pamela python-oauth2 requests sqlalchemy tornado
-    traitlets prometheus_client async_generator
+    traitlets prometheus_client async_generator notebook
   ];
 
   # Disable tests because they take an excessive amount of time to complete.

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "kombu";
-  version = "4.3.0";
+  version = "4.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "529df9e0ecc0bad9fc2b376c3ce4796c41b482cf697b78b71aea6ebe7ca353c8";
+    sha256 = "389ba09e03b15b55b1a7371a441c894fd8121d174f5583bbbca032b9ea8c9edd";
   };
 
   postPatch = ''

pkgs/development/python-modules/lark-parser/default.nix

@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "lark-parser";
-  version = "0.6.5";
+  version = "0.6.6";
 
   src = fetchFromGitHub {
     owner = "lark-parser";
     repo = "lark";
     rev = version;
-    sha256 = "0mf10xm9blqik8mwrpw0r07vqlk2y4r98yqvk1sq849zqlxmqpsr";
+    sha256 = "0kaiw8zzzcp92p6mzm9zkyhv578p0x4lzjsyl8b4rnsafplmbscs";
   };
 
   checkPhase = ''

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

@@ -66,8 +66,9 @@ buildPythonPackage rec {
 
   enableParallelBuilding = true;
 
+  nativeBuildInputs = [ cmake ];
+
   buildInputs = [
-    cmake
     cython
     nose
   ];

pkgs/development/python-modules/matplotlib/2.nix

@@ -5,7 +5,8 @@
 , enableGhostscript ? false, ghostscript ? null, gtk3
 , enableGtk2 ? false, pygtk ? null, gobject-introspection
 , enableGtk3 ? false, cairo
-, enableTk ? false, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
+# darwin has its own "MacOSX" backend
+, enableTk ? !stdenv.isDarwin, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
 , enableQt ? false, pyqt4
 , libcxx
 , Cocoa

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

@@ -4,7 +4,8 @@
 , enableGhostscript ? true, ghostscript ? null, gtk3
 , enableGtk2 ? false, pygtk ? null, gobject-introspection
 , enableGtk3 ? false, cairo
-, enableTk ? false, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
+# darwin has its own "MacOSX" backend
+, enableTk ? !stdenv.isDarwin, tcl ? null, tk ? null, tkinter ? null, libX11 ? null
 , enableQt ? false, pyqt4
 , libcxx
 , Cocoa

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

@@ -0,0 +1,24 @@
+{ stdenv, lib, buildPythonPackage, isPy3k, fetchPypi
+, urllib3, python-dateutil , pytz, faker, mock, nose }:
+
+buildPythonPackage rec {
+  pname = "minio";
+  version = "4.0.13";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1sbmv1lskm5cs3jmn8f2688pimgibly16g8ycc6fgnsjanyby35l";
+  };
+
+  disabled = !isPy3k;
+
+  checkInputs = [ faker mock nose ];
+  propagatedBuildInputs = [ urllib3 python-dateutil pytz ];
+
+  meta = with lib; {
+    description = "Simple APIs to access any Amazon S3 compatible object storage server";
+    homepage = https://github.com/minio/minio-py;
+    maintainers = with maintainers; [ peterromfeldhk ];
+    license = licenses.asl20;
+  };
+}

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

@@ -12,6 +12,8 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ twisted ];
 
+  checkInputs = [ twisted ];
+
   checkPhase = ''
     trial formless nevow
   '';

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "nvchecker";
-  version = "1.3";
+  version = "1.4.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0lgcc05c515d7692zvcmf36n2qpyn0bi018i1z3jy73abm04230j";
+    sha256 = "0v340wkq4sn9pvcpjh076l8mcqkn3nrn7if8p6iysk02bjxvknbv";
   };
 
   propagatedBuildInputs = [ setuptools structlog tornado pycurl ];

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

@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "osmnx";
-  version = "0.8.1";
+  version = "0.9";
 
   src = fetchFromGitHub {
     owner  = "gboeing";
     repo   = pname;
     rev    = "v${version}";
-    sha256 = "1pn2v3dhbmb0yhqif9padg7x3sdx27pgfr95i3kxj4v0yrviaf9k";
+    sha256 = "1k3y5kl4k93vxaxyanc040x44s2fyyc3m1ndy2j3kg0037z8ad4z";
   };
 
   propagatedBuildInputs = [ geopandas descartes matplotlib networkx numpy pandas requests Rtree shapely folium scikitlearn scipy ];

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

@@ -1,16 +1,21 @@
-{ stdenv, fetchPypi, buildPythonPackage, pytest, tox }:
+{ stdenv, fetchPypi, buildPythonPackage, pytest }:
 
 buildPythonPackage rec {
   version = "1.0.0";
   pname = "pluginbase";
 
-  buildInputs = [ pytest tox ];
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "497894df38d0db71e1a4fbbfaceb10c3ef49a3f95a0582e11b75f8adaa030005";
   };
 
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    cd tests
+    PYTHONPATH=.. pytest
+  '';
+
   meta = with stdenv.lib; {
     homepage = https://github.com/mitsuhiko/pluginbase;
     description = "A support library for building plugins sytems in Python";

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

@@ -5,17 +5,14 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.4";
+  version = "1.5";
   pname = "progress";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5e2f9da88ed8236a76fffbee3ceefd259589cf42dfbc2cec2877102189fae58a";
+    sha256 = "0wj3wvdgfmqj44n32wag3mzpp5fjqkkd321x67v1prxvs78yvv39";
   };
 
-  # tests not packaged with pypi release
-  doCheck = false;
-
   checkPhase = ''
     ${python.interpreter} test_progress.py
   '';

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

@@ -4,9 +4,6 @@ buildPythonPackage rec {
   pname = "progressbar";
   version = "2.5";
 
-  # https://github.com/niltonvolpato/python-progressbar/issues/54
-  disabled = isPy3k;
-
   src = fetchPypi {
     inherit pname version;
     sha256 = "5d81cb529da2e223b53962afd6c8ca0f05c6670e40309a7219eacc36af9b6c63";

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

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, libGLU_combined
+, xorg
+}:
+
+buildPythonPackage rec {
+  pname = "pybullet";
+  version = "2.4.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0b6dkrac5zydxqfrf827xhamsimychrn77dsfnz1kf7c1crlwcw9";
+  };
+
+  buildInputs = [
+    libGLU_combined
+    xorg.libX11
+  ];
+
+  patches = [
+    # make sure X11 and OpenGL can be found at runtime
+    ./static-libs.patch
+  ];
+
+  meta = with lib; {
+    description = "Open-source software for robot simulation, integrated with OpenAI Gym";
+    homepage = https://pybullet.org/;
+    license = licenses.zlib;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.linux;
+  };
+}

pkgs/development/python-modules/pybullet/static-libs.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 98efabdbf..e69e79084 100644
+--- a/setup.py
++++ b/setup.py
+@@ -563,6 +563,8 @@ print("-----")
+ 
+ extensions = []
+ 
++libraries += [ "X11", "GL" ] # statically link x11 and opengl
++
+ pybullet_ext = Extension("pybullet",
+         sources =  sources,
+         libraries = libraries,

pkgs/development/python-modules/pyls-black/default.nix

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "pyls-black";
-  version = "0.3.0";
+  version = "0.4.4";
 
   src = fetchFromGitHub {
     owner = "rupert";
     repo = "pyls-black";
     rev = "v${version}";
-    sha256 = "1pagbafb9r9glzy7nbvrq19msjy4wqahrvmc0wll0a0r4msqpi1d";
+    sha256 = "1ynynay9g6yma39szbzf15ypq3c72fg1i0kjmq1dwxarj68i2gf9";
   };
 
   disabled = !isPy3k;

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

@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "pyodbc";
-  version = "4.0.25";
+  version = "4.0.26";
   disabled = isPyPy;  # use pypypdbc instead
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1bbwrb812w5i0x56jfn0l86mxc2ck904hl8y87mziay96znwia0f";
+    sha256 = "1qrxnf7ji5hml7z4y669k4wmk3iz2pcsr05bnn1n912asash09z5";
   };
 
   buildInputs = [ unixODBC ];

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

@@ -1,34 +1,31 @@
-{ stdenv, lib, fetchPypi, buildPythonPackage, libvorbis, flac, libogg, libopus, opusfile }:
+{ stdenv, lib, fetchPypi, buildPythonPackage, libvorbis, flac, libogg, libopus, opusfile, substituteAll }:
 
 buildPythonPackage rec {
     pname = "PyOgg";
-    version = "0.6.6a1";
+    version = "0.6.9a1";
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1ihzgl8p0rc3yjsp27zdrrs2r4qar5yf5l4v8wg0lilvan78h0rs";
+      sha256 = "0xabqwyknpvfc53s7il5pq6b07fcaqvz5bi5vbs3pbaw8602qvim";
     };
 
     buildInputs = [ libvorbis flac libogg libopus ];
     propagatedBuidInputs = [ libvorbis flac libogg libopus opusfile ];
     # There are no tests in this package.
     doCheck = false;
-    postPatch = ''
-      substituteInPlace pyogg/vorbis.py --replace \
-        'libvorbisfile = ExternalLibrary.load("vorbisfile")' "libvorbisfile = ctypes.CDLL('${libvorbis}/lib/libvorbisfile${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/vorbis.py --replace \
-        'libvorbisenc = ExternalLibrary.load("vorbisenc")' "libvorbisenc = ctypes.CDLL('${libvorbis}/lib/libvorbisenc${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/vorbis.py --replace \
-        'libvorbis = ExternalLibrary.load("vorbis")' "libvorbis = ctypes.CDLL('${libvorbis}/lib/libvorbis${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/flac.py --replace \
-        'libflac = ExternalLibrary.load("flac")' "libflac = ctypes.CDLL('${flac.out}/lib/libFLAC${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/ogg.py --replace \
-        'libogg = ExternalLibrary.load("ogg")' "libogg = ctypes.CDLL('${libogg}/lib/libogg${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/opus.py --replace \
-        'libopus = ExternalLibrary.load("opus")' "libopus = ctypes.CDLL('${libopus}/lib/libopus${stdenv.hostPlatform.extensions.sharedLibrary}')"
-      substituteInPlace pyogg/opus.py --replace \
-        'libopusfile = ExternalLibrary.load("opusfile")' "libopusfile = ctypes.CDLL('${opusfile}/lib/libopusfile${stdenv.hostPlatform.extensions.sharedLibrary}')"
-    '';
+    patchFlags = [ "-p1" "--binary" ]; # patch has dos style eol
+    patches = [
+      (substituteAll {
+        src = ./pyogg-paths.patch;
+        flacLibPath="${flac.out}/lib/libFLAC${stdenv.hostPlatform.extensions.sharedLibrary}";
+        oggLibPath="${libogg}/lib/libogg${stdenv.hostPlatform.extensions.sharedLibrary}";
+        vorbisLibPath="${libvorbis}/lib/libvorbis${stdenv.hostPlatform.extensions.sharedLibrary}";
+        vorbisFileLibPath="${libvorbis}/lib/libvorbisfile${stdenv.hostPlatform.extensions.sharedLibrary}";
+        vorbisEncLibPath="${libvorbis}/lib/libvorbisenc${stdenv.hostPlatform.extensions.sharedLibrary}";
+        opusLibPath="${libopus}/lib/libopus${stdenv.hostPlatform.extensions.sharedLibrary}";
+        opusFileLibPath="${opusfile}/lib/libopusfile${stdenv.hostPlatform.extensions.sharedLibrary}";
+      })
+    ];
 
   meta = {
     description = "Xiph.org's Ogg Vorbis, Opus and FLAC for Python";

pkgs/development/python-modules/pyogg/pyogg-paths.patch

@@ -0,0 +1,79 @@
+diff --git a/pyogg/flac.py b/pyogg/flac.py
+index 37cc788..9fb7e95 100644
+--- a/pyogg/flac.py
++++ b/pyogg/flac.py
+@@ -49,7 +49,7 @@ __here = os.getcwd()
+ libflac = None
+ 
+ try:
+-    libflac = ExternalLibrary.load("FLAC", tests = [lambda lib: hasattr(lib, "FLAC__EntropyCodingMethodTypeString")])
++    libflac = ctypes.CDLL('@flacLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+diff --git a/pyogg/ogg.py b/pyogg/ogg.py
+index 7264774..2702e24 100644
+--- a/pyogg/ogg.py
++++ b/pyogg/ogg.py
+@@ -54,7 +54,7 @@ __here = os.getcwd()
+ libogg = None
+ 
+ try:
+-    libogg = ExternalLibrary.load("ogg", tests = [lambda lib: hasattr(lib, "oggpack_writeinit")])
++    libogg = ctypes.CDLL('@oggLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+diff --git a/pyogg/opus.py b/pyogg/opus.py
+index 81e73da..640e59c 100644
+--- a/pyogg/opus.py
++++ b/pyogg/opus.py
+@@ -130,7 +130,7 @@ __here = os.getcwd()
+ libopus = None
+ 
+ try:
+-    libopus = ExternalLibrary.load("opus", tests = [lambda lib: hasattr(lib, "opus_encoder_get_size")])
++    libopus = ctypes.CDLL('@opusLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+@@ -139,7 +139,7 @@ except:
+ libopusfile = None
+ 
+ try:
+-    libopusfile = ExternalLibrary.load("opusfile", tests = [lambda lib: hasattr(lib, "opus_head_parse")])
++    libopusfile = ctypes.CDLL('@opusFileLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+diff --git a/pyogg/vorbis.py b/pyogg/vorbis.py
+index a8e4792..6f44d2d 100644
+--- a/pyogg/vorbis.py
++++ b/pyogg/vorbis.py
+@@ -52,7 +52,7 @@ __here = os.getcwd()
+ libvorbis = None
+ 
+ try:
+-    libvorbis = ExternalLibrary.load("vorbis", tests = [lambda lib: hasattr(lib, "vorbis_info_init")])
++    libvorbis = ctypes.CDLL('@vorbisLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+@@ -61,7 +61,7 @@ except:
+ libvorbisfile = None
+ 
+ try:
+-    libvorbisfile = ExternalLibrary.load("vorbisfile", tests = [lambda lib: hasattr(lib, "ov_clear")])
++    libvorbisfile = ctypes.CDLL('@vorbisFileLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:
+@@ -70,7 +70,7 @@ except:
+ libvorbisenc = None
+ 
+ try:
+-    libvorbisenc = ExternalLibrary.load("vorbisenc", tests = [lambda lib: hasattr(lib, "vorbis_encode_init")])
++    libvorbisenc = ctypes.CDLL('@vorbisEncLibPath@')
+ except ExternalLibraryError:
+     pass
+ except:

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

@@ -14,7 +14,7 @@ buildPythonPackage rec {
     py.test -k 'not test_includeme' pyramid_beaker/tests.py
   '';
 
-  buildInputs = [ pytest ];
+  checkInputs = [ pytest ];
 
   propagatedBuildInputs = [ beaker pyramid ];
 

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

@@ -2,14 +2,14 @@
 
 buildPythonPackage rec {
   pname = "pytest-rerunfailures";
-  version = "6.0";
+  version = "7.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "978349ae00687504fd0f9d0970c37199ccd89cbdb0cb8c4ed7ee417ede582b40";
+    sha256 = "1zfm9v80bqfdapygy9wmi6j6y5c179ixpnh9ih27py4v6cqwzjgk";
   };
 
-  checkInputs = [ mock ];
+  checkInputs = [ mock pytest ];
 
   propagatedBuildInputs = [ pytest ];
 

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

@@ -0,0 +1,73 @@
+{ lib
+, buildPythonPackage
+, python
+, fetchFromGitHub
+, fetchpatch
+, qt5
+, boost
+, assimp
+, gym
+, bullet-roboschool
+, pkgconfig
+, which
+}:
+
+buildPythonPackage rec {
+  pname = "roboschool";
+  version = "1.0.39";
+
+  src = fetchFromGitHub {
+    owner = "openai";
+    repo = "roboschool";
+    rev = version;
+    sha256 = "1s7rp5bbiglnrfm33wf7x7kqj0ks3b21bqyz18c5g6vx39rxbrmh";
+  };
+
+  propagatedBuildInputs = [
+    gym
+  ];
+
+  nativeBuildInputs = [
+    pkgconfig
+    qt5.qtbase # needs the `moc` tool
+    which
+  ];
+
+  buildInputs = [
+    bullet-roboschool
+    assimp
+    qt5.qtbase
+    boost
+  ];
+
+  NIX_CFLAGS_COMPILE="-I ${python}/include/${python.libPrefix}";
+
+  patches = [
+    # Remove kwarg that was removed in upstream gym
+    # https://github.com/openai/roboschool/pull/180
+    (fetchpatch {
+      name = "remove-close-kwarg.patch";
+      url = "https://github.com/openai/roboschool/pull/180/commits/334f489c8ce7af4887e376139ec676f89da5b16f.patch";
+      sha256 = "0bbz8b63m40a9lrwmh7c8d8gj9kpa8a7svdh08qhrddjkykvip6r";
+    })
+  ];
+
+  preBuild = ''
+    # First build the cpp dependencies
+    cd roboschool/cpp-household
+    make \
+      MOC=moc \
+      -j$NIX_BUILD_CORES
+    cd ../..
+  '';
+
+  # Does a QT sanity check, but QT is not expected to work in isolation
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Open-source software for robot simulation, integrated with OpenAI Gym";
+    homepage = https://github.com/openai/roboschool;
+    license = licenses.mit;
+    maintainers = with maintainers; [ timokau ];
+  };
+}

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

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "sasmodels";
-  version = "0.98";
+  version = "0.99";
 
   src = fetchFromGitHub {
     owner = "SasView";
     repo = "sasmodels";
     rev = "v${version}";
-    sha256 = "02y4lpjwaa73pr46ylk0pw0kbill4nfzqgnfv16v5m0z9smd76ir";
+    sha256 = "1lcvn42h29i0mg4i75xn0dbk711q9ycyhm3h95skqy8i61qmjrx6";
   };
 
   buildInputs = [ opencl-headers ];

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

@@ -6,19 +6,17 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.1.0";
+  version = "0.1.2";
   pname = "shouldbe";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07pchxpv1xvjbck0xy44k3a1jrvklg0wbyccn14w0i7d135d4174";
+    sha256 = "16zbvjxf71dl4yfbgcr6idyim3mdrfvix1dv8b95p0s9z07372pj";
   };
 
-  buildInputs = [ nose ];
+  checkInputs = [ nose ];
   propagatedBuildInputs = [ forbiddenfruit ];
 
-  doCheck = false;  # Segmentation fault on py 3.5
-
   meta = with stdenv.lib; {
     description = "Python Assertion Helpers inspired by Shouldly";
     homepage =  https://pypi.python.org/pypi/shouldbe/;

pkgs/development/python-modules/speedtest-cli/default.nix

@@ -7,11 +7,11 @@
 # required for home-assistant
 buildPythonPackage rec {
   pname = "speedtest-cli";
-  version = "2.0.2";
+  version = "2.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2f3d5aa1086d9b367c03b99db6e3207525af174772d877c6b982289b8d2bdefe";
+    sha256 = "1s3ylvkclzdsyqmpjnsd6ixrbmj7vd4bfsdplkjaz1c2czyy3j9p";
   };
 
   # tests require working internet connection

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

@@ -63,7 +63,10 @@ buildPythonPackage rec {
     substituteInPlace setup.py \
       --replace "pathlib==1.0.1" "pathlib>=1.0.0,<2.0.0" \
       --replace "plac>=0.9.6,<1.0.0" "plac>=0.9.6" \
-      --replace "msgpack-numpy<0.4.4" "msgpack-numpy"
+      --replace "msgpack-numpy<0.4.4" "msgpack-numpy" \
+      --replace "wheel>=0.32.0,<0.33.0" "wheel" \
+      --replace "wrapt>=1.10.0,<1.11.0" "wrapt" \
+      --replace "msgpack>=0.5.6,<0.6.0" "msgpack"
   '';
 
   # Cannot find cython modules.

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

@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "twilio";
-  version = "6.24.0";
+  version = "6.26.0";
   # tests not included in PyPi, so fetch from github instead
   src = fetchFromGitHub {
     owner = "twilio";
     repo = "twilio-python";
     rev = version;
-    sha256 = "16lxns59fms75swfjz46484464q4b1fw3ybf8f2k56aas9gyzb2j";
+    sha256 = "0l50n5hljkp7w2l4c36arxf4dxhkfhs7ywwck9y1gvcgsnvccmss";
   };
 
   buildInputs = [ nose mock ];

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

@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "vine";
-  version = "1.2.0";
+  version = "1.3.0";
 
   disable = pythonOlder "2.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0xjz2sjbr5jrpjk411b7alkghdskhphgsqqrbi7abqfh2pli6j7f";
+    sha256 = "133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87";
   };
 
   buildInputs = [ case pytest ];

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

@@ -4,18 +4,18 @@
 
 buildPythonPackage rec {
   pname = "Werkzeug";
-  version = "0.14.1";
+  version = "0.15.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c";
+    sha256 = "ca5c2dcd367d6c0df87185b9082929d255358f5391923269335782b213d52655";
   };
 
   propagatedBuildInputs = [ itsdangerous ];
-  checkInputs = [ pytest requests glibcLocales hypothesis ];
+  checkInputs = [ pytest requests hypothesis ];
 
   checkPhase = ''
-    LC_ALL="en_US.UTF-8" py.test ${stdenv.lib.optionalString stdenv.isDarwin "-k 'not test_get_machine_id'"}
+    pytest ${stdenv.lib.optionalString stdenv.isDarwin "-k 'not test_get_machine_id'"}
   '';
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+, pytest
+, pytest-flake8
+}:
+
+buildPythonPackage rec {
+  pname = "zipp";
+  version = "0.3.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "55ca87266c38af6658b84db8cfb7343cdb0bf275f93c7afaea0d8e7a209c7478";
+  };
+
+  nativeBuildInputs = [ setuptools_scm ];
+
+  checkInputs = [ pytest pytest-flake8 ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  meta = with lib; {
+    description = "Pathlib-compatible object wrapper for zip files";
+    homepage = https://github.com/jaraco/zipp;
+    license = licenses.mit;
+  };
+}