Merge branch 'staging-next' into staging

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

@@ -0,0 +1,45 @@
+{ buildPythonPackage
+, fetchPypi
+, isPy27
+, aiohttp
+, pytest
+, pytest-aiohttp
+, pygments
+, lib
+}:
+
+buildPythonPackage rec {
+  pname = "aiojobs";
+  version = "0.2.2";
+  format = "flit";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "01a0msjh4w58fd7jplmblh0hwgpzwjs5xkgqz3d0p5yv3cykwjwf";
+  };
+
+  nativeBuildInputs = [
+    pygments
+  ];
+
+  propagatedBuildInputs = [
+    aiohttp
+  ];
+
+  checkInputs = [
+    pytest
+    pytest-aiohttp
+  ];
+
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/aio-libs/aiojobs";
+    description = "Jobs scheduler for managing background task (asyncio)";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ cmcdragonkai ];
+  };
+}

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

@@ -1,20 +1,30 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPy3k, pycodestyle, isort }:
+{ stdenv, buildPythonPackage, isPy3k, fetchPypi, pycodestyle, isort }:
 
 buildPythonPackage rec {
   pname = "avro";
   version = "1.10.0";
-  disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "bbf9f89fd20b4cf3156f10ec9fbce83579ece3e0403546c305957f9dac0d2f03";
   };
 
+  patchPhase = ''
+    # this test requires network access
+    sed -i 's/test_server_with_path/noop/' avro/test/test_ipc.py
+  '' + (stdenv.lib.optionalString isPy3k ''
+    # these files require twisted, which is not python3 compatible
+    rm avro/txipc.py
+    rm avro/test/txsample*
+  '');
+
   nativeBuildInputs = [ pycodestyle ];
   propagatedBuildInputs = [ isort ];
 
   meta = with stdenv.lib; {
     description = "A serialization and RPC framework";
     homepage = "https://pypi.python.org/pypi/avro/";
+    license = licenses.asl20;
+    maintainers = [ maintainers.zimbatm ];
   };
 }

pkgs/development/python-modules/azure-storage-blob/default.nix

@@ -2,23 +2,28 @@
 , buildPythonPackage
 , fetchPypi
 , azure-common
+, azure-core
 , azure-storage-common
+, msrest
 , isPy3k
 , futures
 }:
 
 buildPythonPackage rec {
   pname = "azure-storage-blob";
-  version = "2.1.0";
+  version = "12.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b90323aad60f207f9f90a0c4cf94c10acc313c20b39403398dfba51f25f7b454";
+    extension = "zip";
+    sha256 = "1s03daq5mxh9acbv8qpa55c2wmjvdf8jq071cwv65mrly8prp84n";
   };
 
   propagatedBuildInputs = [
     azure-common
+    azure-core
     azure-storage-common
+    msrest
   ] ++ lib.optional (!isPy3k) futures;
 
   # has no tests

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

@@ -1,30 +1,24 @@
-{ stdenv, fetchPypi, fetchpatch
-, buildPythonApplication, python, pythonOlder
-, mock, nose, pathpy, pyhamcrest, pytest_4
-, glibcLocales, parse, parse-type, six
-, traceback2
+{ stdenv, fetchFromGitHub
+, buildPythonApplication, python
+, mock, pathpy, pyhamcrest, pytest, pytest-html
+, glibcLocales
+, colorama, cucumber-tag-expressions, parse, parse-type, six
 }:
 
 buildPythonApplication rec {
   pname = "behave";
-  version = "1.2.6";
+  version = "1.2.7.dev1";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "11hsz365qglvpp1m1w16239c3kiw15lw7adha49lqaakm8kj6rmr";
+  src = fetchFromGitHub {
+    owner = "behave";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1ssgixmqlg8sxsyalr83a1970njc2wg3zl8idsmxnsljwacv7qwv";
   };
 
-  patches = [
-    # Fix tests on Python 2.7
-    (fetchpatch {
-      url = "https://github.com/behave/behave/commit/0a9430a94881cd18437deb03d2ae23afea0f009c.patch";
-      sha256 = "1nrh9ii6ik6gw2kjh8a6jk4mg5yqw3jfjfllbyxardclsab62ydy";
-    })
-  ];
-
-  checkInputs = [ mock nose pathpy pyhamcrest pytest_4 ];
+  checkInputs = [ mock pathpy pyhamcrest pytest pytest-html ];
   buildInputs = [ glibcLocales ];
-  propagatedBuildInputs = [ parse parse-type six ] ++ stdenv.lib.optional (pythonOlder "3.0") traceback2;
+  propagatedBuildInputs = [ colorama cucumber-tag-expressions parse parse-type six ];
 
   postPatch = ''
     patchShebangs bin
@@ -36,7 +30,7 @@ buildPythonApplication rec {
     export LANG="en_US.UTF-8"
     export LC_ALL="en_US.UTF-8"
 
-    pytest test tests
+    pytest tests
 
     ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' features/
     ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' tools/test-features/
@@ -47,6 +41,6 @@ buildPythonApplication rec {
     homepage = "https://github.com/behave/behave";
     description = "behaviour-driven development, Python style";
     license = licenses.bsd2;
-    maintainers = with maintainers; [ alunduil ];
+    maintainers = with maintainers; [ alunduil maxxk ];
   };
 }

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

@@ -12,12 +12,13 @@
 , cramfsprogs
 , cramfsswap
 , lzma
+, matplotlib
 , nose
 , pycrypto
 , pyqtgraph ? null }:
 
 let
-  visualizationSupport = (pyqtgraph != null);
+  visualizationSupport = (pyqtgraph != null) && (matplotlib != null);
   version = "2.2.0";
 in
 buildPythonPackage {
@@ -32,7 +33,7 @@ buildPythonPackage {
   };
 
   propagatedBuildInputs = [ zlib xz ncompress gzip bzip2 gnutar p7zip cabextract cramfsswap cramfsprogs lzma pycrypto ]
-  ++ stdenv.lib.optional visualizationSupport pyqtgraph;
+  ++ stdenv.lib.optionals visualizationSupport [ matplotlib pyqtgraph ];
 
   # setup.py only installs version.py during install, not test
   postPatch = ''

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

@@ -73,6 +73,13 @@ let
       # This patch disables the test that tries to read /etc/os-release which
       # is not accessible in sandboxed builds.
       ./skip_test_linux_distro.patch
+
+      # fix compatibility with the latest SQLAlchemy
+      (fetchpatch {
+        url = "https://github.com/buildbot/buildbot/commit/96f3cd1c5f5c82b733baecb133576366ecf544fc.patch";
+        sha256 = "0n1jm13h08j7ksbs8ixayn3wziq5hzyp3kscz9fpgxd8gl885y5n";
+        stripLen = 1;
+      })
     ];
 
     postPatch = ''

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

@@ -1,10 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi
-, frozendict, simplejson, six
+, frozendict, simplejson, six, isPy27
 }:
 
 buildPythonPackage rec {
   pname = "canonicaljson";
   version = "1.3.0";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;

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

@@ -1,4 +1,13 @@
-{ lib, buildPythonPackage, fetchFromGitHub, stdenv, isPy3k, fetchpatch, humanfriendly, verboselogs, capturer, pytest, mock, utillinux }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, humanfriendly
+, verboselogs
+, capturer
+, pytest
+, mock
+, utillinux
+}:
 
 buildPythonPackage rec {
   pname = "coloredlogs";
@@ -11,13 +20,6 @@ buildPythonPackage rec {
     sha256 = "0rnmxwrim4razlv4vi3krxk5lc5ksck6h5374j8avqwplika7q2x";
   };
 
-  # patch by risicle
-  patches = lib.optional (stdenv.isDarwin && isPy3k) (fetchpatch {
-    name = "darwin-py3-capture-fix.patch";
-    url = "https://github.com/xolox/python-coloredlogs/pull/74.patch";
-    sha256 = "0pk7k94iz0gdripw623vzdl4hd83vwhsfzshl8pbvh1n6swi0xx9";
-  });
-
   checkPhase = ''
     PATH=$PATH:$out/bin pytest . -k "not test_plain_text_output_format \
                                      and not test_auto_install"

pkgs/development/python-modules/cucumber-tag-expressions/default.nix

@@ -0,0 +1,21 @@
+{ lib, fetchPypi, buildPythonPackage, pytest, pytest-html }:
+
+buildPythonPackage rec {
+  pname = "cucumber-tag-expressions";
+  version = "3.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0kb8dq458sflwl2agb2v9hp04qwygslrhdps819vq27wc44jabxw";
+  };
+
+  checkInputs = [ pytest pytest-html ];
+  checkPhase = "pytest tests/*/*.py";
+
+  meta = with lib; {
+    homepage = "https://github.com/cucumber/tag-expressions-python";
+    description = "Provides tag-expression parser for cucumber/behave";
+    license = licenses.mit;
+    maintainers = with maintainers; [ maxxk ];
+  };
+}

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

@@ -60,6 +60,7 @@ buildPythonPackage rec {
     "test_argwhere_str"
     "test_count_nonzero_str"
     "rolling_methods"  # floating percision error ~0.1*10^8 small
+    "num_workers_config" # flaky
   ];
 
   meta = {

pkgs/development/python-modules/django-widget-tweaks/default.nix

@@ -0,0 +1,25 @@
+{ buildPythonPackage, fetchFromGitHub, python, stdenv, django }:
+
+buildPythonPackage rec {
+  pname = "django-widget-tweaks";
+  version = "1.4.8";
+
+  src = fetchFromGitHub { # package from Pypi missing runtests.py
+    owner = "jazzband";
+    repo = pname;
+    rev = version;
+    sha256 = "00w1ja56dc7cyw7a3mph69ax6mkch1lsh4p98ijdhzfpjdy36rbg";
+  };
+
+  checkPhase = "${python.interpreter} runtests.py";
+  propagatedBuildInputs = [ django ];
+
+  meta = with stdenv.lib; {
+      description = "Tweak the form field rendering in templates, not in python-level form definitions.";
+      homepage = "https://github.com/jazzband/django-widget-tweaks";
+      license = licenses.mit;
+      maintainers = with maintainers; [
+          maxxk
+      ];
+  };
+}

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

@@ -17,7 +17,7 @@
 
 buildPythonPackage {
   pname = "dogtail";
-  version = "0.9.10";
+  version = "0.9.11";
 
   # https://gitlab.com/dogtail/dogtail/issues/1
   # src = fetchPypi {
@@ -26,7 +26,7 @@ buildPythonPackage {
   # };
   src = fetchurl {
     url = "https://gitlab.com/dogtail/dogtail/raw/released/dogtail-0.9.10.tar.gz";
-    sha256 = "14sycidl8ahj3fwlhpwlpnyd43c302yqr7nqg2hj39pyj7kgk15b";
+    sha256 = "EGyxYopupfXPYtTL9mm9ujZorvh8AGaNXVKBPWsGy3c=";
   };
 
   patches = [
@@ -54,7 +54,7 @@ buildPythonPackage {
   meta = {
     description = "GUI test tool and automation framework that uses Accessibility technologies to communicate with desktop applications";
     homepage = "https://gitlab.com/dogtail/dogtail";
-    license = lib.licenses.gpl2;
+    license = lib.licenses.gpl2Only;
     maintainers = with lib.maintainers; [ jtojnar ];
   };
 }

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

@@ -0,0 +1,56 @@
+{ buildPythonPackage
+, fetchFromGitHub
+, lib
+, isPy3k
+, cython
+, numpy
+, toml
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "finalfusion";
+  version = "0.7.1";
+
+  disabled = !isPy3k;
+
+  src = fetchFromGitHub {
+    owner = "finalfusion";
+    repo = "finalfusion-python";
+    rev = version;
+    sha256 = "0pwzflamxqvpl1wcz0zbhhd6aa4xn18rmza6rggaic3ckidhyrh4";
+  };
+
+  nativeBuildInputs = [
+    cython
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    toml
+  ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  postPatch = ''
+    patchShebangs tests/integration
+  '';
+
+  checkPhase = ''
+    # Regular unit tests.
+    pytest
+
+    # Integration tests for command-line utilities.
+    PATH=$PATH:$out/bin tests/integration/all.sh
+  '';
+
+  meta = with lib; {
+    description = "Python module for using finalfusion, word2vec, and fastText word embeddings";
+    homepage = "https://github.com/finalfusion/finalfusion-python/";
+    maintainers = with maintainers; [ danieldk ];
+    platforms = platforms.all;
+    license = licenses.blueOak100;
+  };
+}

pkgs/development/python-modules/geoip2/default.nix

@@ -1,7 +1,8 @@
 { buildPythonPackage, lib, fetchPypi, isPy27
-, ipaddress
+, aiohttp
 , maxminddb
 , mock
+, mocket
 , requests
 , requests-mock
 }:
@@ -9,16 +10,20 @@
 buildPythonPackage rec {
   version = "4.0.2";
   pname = "geoip2";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "4afb5d899eac08444e461239c8afb165c90234adc0b5dc952792d9da74c9091b";
   };
 
-  propagatedBuildInputs = [ requests maxminddb ]
-    ++ lib.optionals isPy27 [ ipaddress ];
+  patchPhase = ''
+    substituteInPlace requirements.txt --replace "requests>=2.24.0,<3.0.0" "requests"
+  '';
 
-  checkInputs = [ requests-mock ];
+  propagatedBuildInputs = [ aiohttp requests maxminddb ];
+
+  checkInputs = [ mocket requests-mock ];
 
   meta = with lib; {
     description = "MaxMind GeoIP2 API";

pkgs/development/python-modules/m2crypto/default.nix

@@ -11,12 +11,12 @@
 
 
 buildPythonPackage rec {
-  version = "0.35.2";
+  version = "0.36.0";
   pname = "M2Crypto";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09yirf3w77w6f49q6nxhrjm9c3a4y9s30s1k09chqrw8zdgx8sjc";
+    sha256 = "1hadbdckmjzfb8qzbkafypin6sakfx35j2qx0fsivh757s7c2hhm";
   };
 
   patches = [

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

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, pythonAtLeast
+{ stdenv, lib, buildPythonPackage, pythonOlder, pythonAtLeast
 , fetchPypi
 , libmaxminddb
 , ipaddress
@@ -9,6 +9,7 @@
 buildPythonPackage rec {
   version = "2.0.2";
   pname = "maxminddb";
+  disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;

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

@@ -0,0 +1,43 @@
+{ lib, buildPythonPackage, fetchPypi, pythonOlder, isPy27
+, decorator
+, importlib-metadata
+, python
+, python_magic
+, six
+, urllib3 }:
+
+buildPythonPackage rec {
+  pname = "mocket";
+  version = "3.8.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0yqls2hqmfs6i4p2nb89j5icyrqwabalsmwfixfvbjir4fmgad2l";
+  };
+
+  patchPhase = ''
+    substituteInPlace requirements.txt \
+      --replace "python-magic==0.4.18" "python-magic" \
+      --replace "urllib3==1.25.10" "urllib3"
+    substituteInPlace setup.py --replace 'setup_requires=["pipenv"]' "setup_requires=[]"
+  '';
+
+  propagatedBuildInputs = [
+    decorator
+    python_magic
+    urllib3
+    six
+  ] ++ lib.optionals (isPy27) [ six ];
+
+  # Pypi has no runtests.py, github has no requirements.txt. No way to test, no way to install.
+  doCheck = false;
+
+  pythonImportsCheck = [ "mocket" ];
+
+  meta = with lib; {
+    description = "A socket mock framework - for all kinds of socket animals, web-clients included";
+    homepage = "https://github.com/mindflayer/python-mocket";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ hexa ];
+  };
+}

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

@@ -1,8 +1,8 @@
-{ stdenv, buildPythonPackage, fetchzip, pyopenssl, python }:
+{ stdenv, buildPythonPackage, fetchzip, gobject-introspection, idna, libsoup, precis-i18n, pygobject3, pyopenssl }:
 
 let
   pname = "nbxmpp";
-  version = "0.6.10";
+  version = "1.0.2";
   name = "${pname}-${version}";
 in buildPythonPackage {
   inherit pname version;
@@ -11,16 +11,12 @@ in buildPythonPackage {
     name = "${name}.tar.bz2";
     url = "https://dev.gajim.org/gajim/python-nbxmpp/repository/archive.tar.bz2?"
         + "ref=${name}";
-    sha256 = "1w31a747mj9rvlp3n20z0fnvyvihphkgkyr22sk2kap3migw8vai";
+    sha256 = "1rhzsakqrybzq5j5b9400wjd14pncph47c1ggn5a6f3di03lk4az";
   };
 
-  propagatedBuildInputs = [ pyopenssl ];
-
-  checkPhase = ''
-    # Disable tests requiring networking
-    echo "" > test/unit/test_xmpp_transports_nb2.py
-    ${python.executable} test/runtests.py
-  '';
+  buildInputs = [ precis-i18n ];
+  checkInputs = [ gobject-introspection libsoup pygobject3 ];
+  propagatedBuildInputs = [ idna pyopenssl ];
 
   meta = with stdenv.lib; {
     homepage = "https://dev.gajim.org/gajim/python-nbxmpp";

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

@@ -1,19 +1,21 @@
-{ stdenv, buildPythonPackage , fetchFromGitHub , bashInteractive , urlgrabber, m2crypto, rpm }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, bashInteractive, urlgrabber
+, m2crypto, rpm, chardet
+}:
 
 buildPythonPackage rec {
   pname = "osc";
-  version = "0.167.1";
+  version = "0.170.0";
 
   src = fetchFromGitHub {
     owner = "openSUSE";
     repo = "osc";
     rev = version;
-    sha256 = "0f3c6mzvk9yjicwfdh47j4s2l1wrfgpa6lmqdchasdqfsacps4r6";
+    sha256 = "10dj9kscz59qm8rw5084gf0m8ail2rl7r8rg66ij92x88wvi9mbz";
   };
 
   buildInputs = [ bashInteractive ]; # needed for bash-completion helper
   checkInputs = [ rpm ];
-  propagatedBuildInputs = [ urlgrabber m2crypto ];
+  propagatedBuildInputs = [ urlgrabber m2crypto chardet ];
 
   postInstall = ''
     ln -s $out/bin/osc-wrapper.py $out/bin/osc

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

@@ -1,6 +1,6 @@
 { lib, buildPythonPackage, fetchPypi
 , requests, cryptography, pybrowserid, hawkauthlib, six
-, grequests, mock, responses, pytest }:
+, grequests, mock, responses, pytest, pyjwt }:
 
 buildPythonPackage rec {
   pname = "PyFxA";
@@ -17,15 +17,16 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [
-    requests cryptography pybrowserid hawkauthlib six
+    pyjwt requests cryptography pybrowserid hawkauthlib six
   ];
 
   checkInputs = [
     grequests mock responses pytest
   ];
 
+  # test_oath is mostly network calls
   checkPhase = ''
-    pytest
+    pytest --ignore=fxa/tests/test_oauth.py
   '';
 
   meta = with lib; {

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

@@ -6,18 +6,23 @@
 # pythonPackages
 , django
 , pylint-plugin-utils
+
+# pythonPackages for checkInputs
+, coverage
+, factory_boy
+, pytest
 }:
 
 buildPythonPackage rec {
   pname = "pylint-django";
-  version = "2.1.0";
+  version = "2.3.0";
   disabled = !isPy3k;
 
   src = fetchFromGitHub {
     owner = "PyCQA";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1gvbh2a480x3ddrq6xzray7kdsz8nb8n16xm2lf03w2nqnsdbkwy";
+    sha256 = "1088waraiigi2bnlighn7bvnvqmpx5fbw70c8jd8sh25mj38wgly";
   };
 
   propagatedBuildInputs = [
@@ -25,8 +30,14 @@ buildPythonPackage rec {
     pylint-plugin-utils
   ];
 
-  # Testing requires checkout from other repositories
-  doCheck = false;
+  checkInputs = [ coverage factory_boy pytest ];
+
+  # Check command taken from scripts/test.sh
+  # Skip test external_django_tables2_noerror_meta_class:
+  # requires an unpackaged django_tables2
+  checkPhase = ''
+      python pylint_django/tests/test_func.py -v -k "not tables2"
+  '';
 
   meta = with lib; {
     description = "A Pylint plugin to analyze Django applications";

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

@@ -0,0 +1,46 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, isPy27
+, future
+, pytestCheckHook
+, pytorch
+, pyyaml
+, tensorflow-tensorboard
+, tqdm }:
+
+buildPythonPackage rec {
+  pname = "pytorch-lightning";
+  version = "0.8.5";
+
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "PyTorchLightning";
+    repo = pname;
+    rev = version;
+    sha256 = "12zhq4pnfcwbgcx7cs99c751gp3w0ysaf5ykv2lv8f4i360w3r5a";
+  };
+
+  propagatedBuildInputs = [ 
+    future
+    pytorch
+    pyyaml
+    tensorflow-tensorboard
+    tqdm
+  ];
+
+  checkInputs = [ pytestCheckHook ];
+  # Some packages are not in NixPkgs; other tests try to build distributed
+  # models, which doesn't work in the sandbox.
+  doCheck = false;
+
+  pythonImportsCheck = [ "pytorch_lightning" ];
+
+  meta = with lib; {
+    description = "Lightweight PyTorch wrapper for machine learning researchers";
+    homepage = "https://pytorch-lightning.readthedocs.io";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ tbenst ];
+  };
+}

pkgs/development/python-modules/rdflib-jsonld/default.nix

@@ -0,0 +1,21 @@
+{ buildPythonPackage, fetchPypi, lib, rdflib, nose }:
+
+buildPythonPackage rec {
+  pname = "rdflib-jsonld";
+  version = "0.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4f7d55326405071c7bce9acf5484643bcb984eadb84a6503053367da207105ed";
+  };
+
+  nativeBuildInputs = [ nose ];
+  propagatedBuildInputs = [ rdflib ];
+
+  meta = with lib; {
+    homepage = "https://github.com/RDFLib/rdflib-jsonld";
+    license = licenses.bsdOriginal;
+    description = "rdflib extension adding JSON-LD parser and serializer";
+    maintainers = [ maintainers.koslambrou ];
+  };
+}

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

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , six
+, setuptools
 }:
 
 buildPythonPackage rec {
@@ -13,7 +14,7 @@ buildPythonPackage rec {
     sha256 = "945b5efdc10f468fc056bd53a4e4224ec4c2fe1a7e83ae47443bbb6e7c7a1f7d";
   };
 
-  propagatedBuildInputs = [ six ];
+  propagatedBuildInputs = [ six setuptools ];
 
   doCheck = false;
   pythonImportsCheck = [ "rethinkdb" ];
@@ -21,7 +22,7 @@ buildPythonPackage rec {
   meta = with stdenv.lib; {
     description = "Python driver library for the RethinkDB database server";
     homepage = "https://pypi.python.org/pypi/rethinkdb";
-    license = licenses.agpl3;
+    license = licenses.asl20;
   };
 
 }

pkgs/development/python-modules/shamir-mnemonic/default.nix

@@ -17,6 +17,6 @@ buildPythonPackage rec {
     description = "Reference implementation of SLIP-0039";
     homepage = "https://github.com/trezor/python-shamir-mnemonic";
     license = licenses.mit;
-    maintainers = with maintainers; [ maintainers."1000101" ];
+    maintainers = with maintainers; [ _1000101 ];
   };
 }

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

@@ -5,9 +5,10 @@
 , praw
 , pyenchant
 , pygeoip
-, pytest
+, pytestCheckHook
 , python
 , pytz
+, sqlalchemy
 , xmltodict
 }:
 
@@ -29,20 +30,26 @@ buildPythonPackage rec {
     pyenchant
     pygeoip
     pytz
+    sqlalchemy
     xmltodict
   ];
 
   # remove once https://github.com/sopel-irc/sopel/pull/1653 lands
   postPatch = ''
     substituteInPlace requirements.txt \
-      --replace "praw<6.0.0" "praw<7.0.0"
+      --replace "praw>=4.0.0,<6.0.0" "praw"
   '';
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytestCheckHook ];
 
-  checkPhase = ''
-    HOME=$PWD # otherwise tries to create tmpdirs at root
-    pytest .
+  preCheck = ''
+    export TESTDIR=$(mktemp -d)
+    cp -R ./test $TESTDIR
+    pushd $TESTDIR
+  '';
+
+  postCheck = ''
+    popd
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/spacy/annotation-test/annotate.py

@@ -0,0 +1,69 @@
+import pytest
+import spacy
+
+en_text = (
+    "When Sebastian Thrun started working on self-driving cars at "
+    "Google in 2007, few people outside of the company took him "
+    "seriously. “I can tell you very senior CEOs of major American "
+    "car companies would shake my hand and turn away because I wasn’t "
+    "worth talking to,” said Thrun, in an interview with Recode earlier "
+    "this week.")
+
+
+@pytest.fixture
+def en_core_web_sm():
+    return spacy.load("en_core_web_sm")
+
+
+@pytest.fixture
+def doc_en_core_web_sm(en_core_web_sm):
+    return en_core_web_sm(en_text)
+
+
+def test_entities(doc_en_core_web_sm):
+    entities = list(map(lambda e: (e.text, e.label_),
+                        doc_en_core_web_sm.ents))
+
+    assert entities == [
+        ('Sebastian Thrun', 'PERSON'),
+        ('Google', 'ORG'), ('2007', 'DATE'),
+        ('American', 'NORP'),
+        ('Thrun', 'ORG'),
+        ('earlier this week', 'DATE')
+    ]
+
+
+def test_nouns(doc_en_core_web_sm):
+    assert [
+        chunk.text for chunk in doc_en_core_web_sm.noun_chunks] == [
+        'Sebastian Thrun',
+        'self-driving cars',
+        'Google',
+        'few people',
+        'the company',
+        'him',
+        'I',
+        'you',
+        'very senior CEOs',
+        'major American car companies',
+        'my hand',
+        'I',
+        'Thrun',
+        'an interview',
+        'Recode']
+
+
+def test_verbs(doc_en_core_web_sm):
+    assert [
+        token.lemma_ for token in doc_en_core_web_sm if token.pos_ == "VERB"] == [
+        'start',
+        'work',
+        'drive',
+        'take',
+        'can',
+        'tell',
+        'would',
+        'shake',
+        'turn',
+        'talk',
+        'say']

pkgs/development/python-modules/spacy/annotation-test/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, pytest, spacy_models }:
+
+stdenv.mkDerivation {
+  name = "spacy-annotation-test";
+
+  src = ./.;
+
+  dontConfigure = true;
+  dontBuild = true;
+  doCheck = true;
+
+  checkInputs = [ pytest spacy_models.en_core_web_sm ];
+
+  checkPhase = ''
+    pytest annotate.py
+  '';
+
+  installPhase = ''
+    touch $out
+  '';
+
+  meta.timeout = 60;
+}

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

@@ -1,5 +1,6 @@
 { lib
 , buildPythonPackage
+, callPackage
 , fetchPypi
 , pythonOlder
 , pytest
@@ -55,6 +56,7 @@ buildPythonPackage rec {
 
   postPatch = ''
     substituteInPlace setup.cfg \
+      --replace "blis>=0.4.0,<0.5.0" "blis>=0.4.0,<1.0" \
       --replace "catalogue>=0.0.7,<1.1.0" "catalogue>=0.0.7,<3.0" \
       --replace "plac>=0.9.6,<1.2.0" "plac>=0.9.6,<2.0" \
       --replace "srsly>=1.0.2,<1.1.0" "srsly>=1.0.2,<3.0" \
@@ -63,6 +65,8 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "spacy" ];
 
+  passthru.tests = callPackage ./annotation-test {};
+
   meta = with lib; {
     description = "Industrial-strength Natural Language Processing (NLP) with Python and Cython";
     homepage = "https://github.com/explosion/spaCy";

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

@@ -14,6 +14,8 @@ let
     propagatedBuildInputs = [ spacy ]
       ++ lib.optionals (lang == "zh") [ jieba pkuseg ];
 
+    pythonImportsCheck = [ pname ];
+
     meta = with stdenv.lib; {
       description = "Models for the spaCy NLP library";
       homepage    = "https://github.com/explosion/spacy-models";

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

@@ -60,6 +60,7 @@ buildPythonPackage rec {
 
   postPatch = ''
     substituteInPlace setup.py \
+      --replace "blis>=0.4.0,<0.5.0" "blis>=0.4.0,<1.0" \
       --replace "catalogue>=0.0.7,<1.1.0" "catalogue>=0.0.7,<3.0" \
       --replace "plac>=0.9.6,<1.2.0" "plac>=0.9.6,<2.0" \
       --replace "srsly>=0.0.6,<1.1.0" "srsly>=0.0.6,<3.0"

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

@@ -55,6 +55,6 @@ buildPythonPackage rec {
     description = "Python library for communicating with TREZOR Bitcoin Hardware Wallet";
     homepage = "https://github.com/trezor/trezor-firmware/tree/master/python";
     license = licenses.gpl3;
-    maintainers = with maintainers; [ np prusnak mmahut maintainers."1000101" ];
+    maintainers = with maintainers; [ np prusnak mmahut _1000101 ];
   };
 }

pkgs/development/python-modules/wtf-peewee/default.nix

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "wtf-peewee";
-  version = "3.0.1";
+  version = "3.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4ac1b457f3255ee2d72915267884a16e5fb502e1e7bb793f2f1301c926e3599a";
+    sha256 = "03qs6np5s9r0nmsryfzll29ajcqk27b18kcbgd9plf80ys3nb6kd";
   };
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchFromGitHub, xcffib, pillow }:
+
+buildPythonPackage rec {
+  pname = "xpybutil";
+  version = "0.0.6";
+
+  # Pypi only offers a wheel
+  src = fetchFromGitHub {
+    owner = "BurntSushi";
+    repo = pname;
+    rev = version;
+    sha256 = "17gbqq955fcl29aayn8l0x14azc60cxgkvdxblz9q8x3l50w0xpg";
+  };
+
+  # pillow is a dependency in image.py which is not listed in setup.py
+  propagatedBuildInputs = [ xcffib pillow ];
+
+  meta = with lib; {
+    homepage = "https://github.com/BurntSushi/xpybutil";
+    description = "An incomplete xcb-util port plus some extras";
+    license = licenses.wtfpl;
+    maintainers = with maintainers; [ artturin ];
+  };
+}

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

@@ -1,8 +1,8 @@
 { stdenv
 , fetchPypi
-, fetchpatch
 , buildPythonPackage
 , python
+, pythonAtLeast
 , zope_testrunner
 , transaction
 , six
@@ -17,26 +17,21 @@
 
 buildPythonPackage rec {
     pname = "ZODB";
-    version = "5.5.1";
+    version = "5.6.0";
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "20155942fa326e89ad8544225bafd74237af332ce9d7c7105a22318fe8269666";
+      sha256 = "1zh7rd182l15swkbkm3ib0wgyn16xasdz2mzry8k4lwk6dagnm26";
     };
 
-    patches = [
-      # Compatibility with transaction v3.0
-      (fetchpatch {
-        url = "https://github.com/zopefoundation/ZODB/commit/0adcc6877f690186c97cc5da7e13788946d5e0df.patch";
-        sha256 = "1zmbgm7r36nj5w7icpinp61fm81svh2wk213pzr3l0jxzr9i5qi4";
-      })
-    ];
-
     # remove broken test
     postPatch = ''
       rm -vf src/ZODB/tests/testdocumentation.py
     '';
 
+    # ZConfig 3.5.0 is not compatible with Python 3.8
+    disabled = pythonAtLeast "3.8";
+
     propagatedBuildInputs = [
       transaction
       six