Merge master into staging-next

pkgs/development/python-modules/aiohttp-jinja2/default.nix

@@ -14,7 +14,7 @@ buildPythonPackage rec {
   checkInputs = [ pytest pytest-aiohttp ];
 
   checkPhase = ''
-    py.test
+    pytest -W ignore::DeprecationWarning
   '';
 
   meta = with lib; {

pkgs/development/python-modules/azure-core/default.nix

@@ -4,6 +4,8 @@
 , mock
 , msrest
 , pytest
+, pytest-asyncio
+, pytest-trio
 , pytestCheckHook
 , requests
 , six
@@ -33,13 +35,16 @@ buildPythonPackage rec {
     mock
     msrest
     pytest
+    pytest-trio
+    pytest-asyncio
     pytestCheckHook
     trio
     typing-extensions
   ];
 
   pytestFlagsArray = [ "tests/" ];
-  disabledTests = [ "response" "request" "timeout" ];
+  # disable tests which touch network
+  disabledTests = [ "aiohttp" "multipart_send" "response" "request" "timeout" ];
 
   meta = with lib; {
     description = "Microsoft Azure Core Library for Python";

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

@@ -6,6 +6,7 @@
 , isPy27
 , python
 , pexpect
+, bash
 }:
 
 buildPythonPackage rec {
@@ -26,6 +27,12 @@ buildPythonPackage rec {
     })
   ];
 
+  postPatch = ''
+    substituteInPlace bash_kernel/kernel.py \
+      --replace "'bash'" "'${bash}/bin/bash'" \
+      --replace "\"bash\"" "'${bash}/bin/bash'"
+  '';
+
   propagatedBuildInputs = [ ipykernel pexpect ];
 
   # no tests

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

@@ -0,0 +1,35 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, jupyterhub
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "batchspawner";
+  version = "1.0.0";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "jupyterhub";
+    repo = "batchspawner";
+    rev = "v${version}";
+    sha256 = "0yn312sjfjpjjfciagbczfmqprk2fj4lbb3vsbzj17p948acq5w2";
+  };
+
+  propagatedBuildInputs = [
+    jupyterhub
+  ];
+
+  # tests require a job scheduler e.g. slurm, pbs, etc.
+  doCheck = false;
+
+  pythonImportCheck = [ "batchspawner" ];
+
+  meta = with lib; {
+    description = "A spawner for Jupyterhub to spawn notebooks using batch resource managers";
+    homepage = "https://jupyter.org";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "bitarray";
-  version = "1.3.0";
+  version = "1.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1pz3yd9rhz3cb0yf7dbjhd1awm0w7vsbj73k4v95484j2kdxk3d4";
+    sha256 = "e1823b33d2caa7fc54ab5507eff316e74abfdc30434db8f3be908ab52a330021";
   };
 
   meta = with lib; {

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

@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, aenum
+}:
+
+buildPythonPackage rec {
+  pname = "bytecode";
+  version = "0.11.0";
+
+  src = fetchFromGitHub {
+    owner = "vstinner";
+    repo = pname;
+    rev = version;
+    sha256 = "097k83zr0z71pha7bafzhs4ink174wk9ls2883bic274rihsnc5r";
+  };
+
+  disabled = pythonOlder "3.5";
+
+  propagatedBuildInputs = lib.optionals (pythonOlder "3.6") [ aenum ];
+
+  meta = with lib; {
+    homepage = "https://github.com/vstinner/bytecode";
+    description = "Python module to generate and modify bytecode";
+    license = licenses.mit;
+    maintainers = with maintainers; [ raboof ];
+  };
+}

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

@@ -1,36 +1,27 @@
 { stdenv, buildPythonPackage, fetchPypi, isPy3k
 , setuptools_scm
 , cheroot, portend, more-itertools, zc_lockfile, routes
+, jaraco_collections
 , objgraph, pytest, pytestcov, pathpy, requests_toolbelt, pytest-services
 , fetchpatch
 }:
 
 buildPythonPackage rec {
   pname = "cherrypy";
-  version = "18.3.0";
+  version = "18.6.0";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     pname = "CherryPy";
     inherit version;
-    sha256 = "0q6cs4vrv0rwim4byxfizrlp4h6hmwg3n4baz0ga66vvgiz6hgk8";
+    sha256 = "16f410izp2c4qhn4n3l5l3qirmkf43h2amjqms8hkl0shgfqwq2n";
   };
 
-  # Remove patches once 88d2163 and 713f672
-  # become part of a release - they're currently only present in master.
-  # ref: https://github.com/cherrypy/cherrypy/pull/1820
-  patches = [
-    (fetchpatch {
-      name = "test_HTTP11_Timeout.patch";
-      url = "https://github.com/cherrypy/cherrypy/commit/88d21630f68090c56d07000cabb6df4f1b612a71.patch";
-      sha256 = "1i6a3qs3ijyd9rgsxb8axigkzdlmr5sl3ljif9rvn0d90211bzwh";
-    })
-  ];
-
   propagatedBuildInputs = [
     # required
     cheroot portend more-itertools zc_lockfile
+    jaraco_collections
     # optional
     routes
   ];

pkgs/development/python-modules/cryptography/2.9.nix

@@ -0,0 +1,74 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, fetchpatch
+, isPy27
+, ipaddress
+, openssl
+, cryptography_vectors
+, darwin
+, packaging
+, six
+, pythonOlder
+, isPyPy
+, cffi
+, pytest
+, pretend
+, iso8601
+, pytz
+, hypothesis
+, enum34
+}:
+
+buildPythonPackage rec {
+  pname = "cryptography";
+  version = "2.9.2"; # Also update the hash in vectors.nix
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0af25w5mkd6vwns3r6ai1w5ip9xp0ms9s261zzssbpadzdr05hx0";
+  };
+
+  outputs = [ "out" "dev" ];
+
+  buildInputs = [ openssl ]
+             ++ stdenv.lib.optional stdenv.isDarwin darwin.apple_sdk.frameworks.Security;
+  propagatedBuildInputs = [
+    packaging
+    six
+  ] ++ stdenv.lib.optional (!isPyPy) cffi
+  ++ stdenv.lib.optionals isPy27 [ ipaddress enum34 ];
+
+  checkInputs = [
+    cryptography_vectors
+    hypothesis
+    iso8601
+    pretend
+    pytest
+    pytz
+  ];
+
+  checkPhase = ''
+    py.test --disable-pytest-warnings tests
+  '';
+
+  # IOKit's dependencies are inconsistent between OSX versions, so this is the best we
+  # can do until nix 1.11's release
+  __impureHostDeps = [ "/usr/lib" ];
+
+  meta = with stdenv.lib; {
+    description = "A package which provides cryptographic recipes and primitives";
+    longDescription = ''
+      Cryptography includes both high level recipes and low level interfaces to
+      common cryptographic algorithms such as symmetric ciphers, message
+      digests, and key derivation functions.
+      Our goal is for it to be your "cryptographic standard library". It
+      supports Python 2.7, Python 3.5+, and PyPy 5.4+.
+    '';
+    homepage = "https://github.com/pyca/cryptography";
+    changelog = "https://cryptography.io/en/latest/changelog/#v"
+      + replaceStrings [ "." ] [ "-" ] version;
+    license = with licenses; [ asl20 bsd3 psfl ];
+    maintainers = with maintainers; [ primeos ];
+  };
+}

pkgs/development/python-modules/cryptography/vectors-2.9.nix

@@ -0,0 +1,23 @@
+{ buildPythonPackage, fetchPypi, lib, cryptography }:
+
+buildPythonPackage rec {
+  pname = "cryptography_vectors";
+  # The test vectors must have the same version as the cryptography package:
+  version = cryptography.version;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1d4iykcv7cn9j399hczlxm5pzxmqy6d80h3j16dkjwlmv3293b4r";
+  };
+
+  # No tests included
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Test vectors for the cryptography package";
+    homepage = "https://cryptography.io/en/latest/development/test-vectors/";
+    # Source: https://github.com/pyca/cryptography/tree/master/vectors;
+    license = with licenses; [ asl20 bsd3 ];
+    maintainers = with maintainers; [ primeos ];
+  };
+}

pkgs/development/python-modules/csvs-to-sqlite/default.nix

@@ -13,14 +13,14 @@
 
 buildPythonPackage rec {
   pname = "csvs-to-sqlite";
-  version = "1.0";
+  version = "1.1";
   disabled = !isPy3k;
 
   src = fetchFromGitHub {
     owner = "simonw";
     repo = pname;
     rev = version;
-    sha256 = "0n80y9a6qhbhhbz64jdpscx0nha9jn9nygp9nkgszmw04ri5j5hm";
+    sha256 = "1xi9d8l1sf9vixzvqpz8lvhl6yqmz9x5659nvpsxinl317qzmc8m";
   };
 
   postPatch = ''

pkgs/development/python-modules/dash-renderer/default.nix

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "dash_renderer";
-  version = "1.5.1";
+  version = "1.6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "097195ebe69267732d2fba30825f72c2b6ec3e127f60648c64e8d248d275a89b";
+    sha256 = "8e9c0c0c2efb8ea562489c37665417cd608c30bca20425ac4d847420b5bbc128";
   };
 
   # No tests in archive

pkgs/development/python-modules/dash-table/default.nix

@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "dash_table";
-  version = "4.8.1";
+  version = "4.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16q0d9fidllxm7p51i5p4vzknnc09d114zqw3f4a2spr7llga7xj";
+    sha256 = "2f19000051730291100cd3a79b13fa62c478aea7908f2e4323c13b90f09e3320";
   };
 
   # No tests in archive

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

@@ -16,13 +16,13 @@
 
 buildPythonPackage rec {
   pname = "dash";
-  version = "1.13.3";
+  version = "1.14.0";
 
   src = fetchFromGitHub {
     owner = "plotly";
     repo = pname;
     rev = "v${version}";
-    sha256 = "131p725rc731ynksp12h9j1faq3vl51d5p64ln22r7zx4pvahss5";
+    sha256 = "1f7gal9x0bjsmwxlbvlkwfwz1cyyg5d0n6jh4399wkjilpd966d5";
   };
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,49 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, aiohttp
+, colorlog
+, cryptography
+, traitlets
+, go
+, isPy27
+}:
+
+buildPythonPackage rec {
+  pname = "dask-gateway-server";
+  # update dask-gateway-server lock step with dask-gateway
+  version = "0.8.0";
+  disabled = isPy27;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "272134933b7e2068cd89a17a5012c76a29fbd9e40a78164345a2b15353d4b40a";
+  };
+
+  nativeBuildInputs = [
+    go
+  ];
+
+  propagatedBuildInputs = [
+    aiohttp
+    colorlog
+    cryptography
+    traitlets
+  ];
+
+  preBuild = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  # tests requires cluster for testing
+  doCheck = false;
+
+  pythonImportsCheck = [ "dask_gateway_server" ];
+
+  meta = with lib; {
+    description = "A multi-tenant server for securely deploying and managing multiple Dask clusters";
+    homepage = "https://gateway.dask.org/";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,36 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, aiohttp
+, dask
+, distributed
+}:
+
+buildPythonPackage rec {
+  pname = "dask-gateway";
+  # update dask-gateway lock step with dask-gateway-server
+  version = "0.8.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "519818f3598ddd726882c5a6bf7053941613d8517b80e8a2c28467e30d57da9b";
+  };
+
+  propagatedBuildInputs = [
+    aiohttp
+    dask
+    distributed
+  ];
+
+  # tests requires cluster for testing
+  doCheck = false;
+
+  pythonImportsCheck = [ "dask_gateway" ];
+
+  meta = with lib; {
+    description = "A client library for interacting with a dask-gateway server";
+    homepage = "https://gateway.dask.org/";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -1,25 +1,43 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , dask
 , numpy, toolz # dask[array]
 , scipy
 , pims
 , pytest
+, pytest-flake8
 , scikitimage
 }:
 
 buildPythonPackage rec {
-  version = "0.2.0";
+  version = "0.3.0";
   pname = "dask-image";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bece2ea347f963dc0168c7d5fdfd11e51b47d9c857d3bc56144d7c146964a23f";
+    sha256 = "15svy8y57i30878pijyd0pxn10bnk7ffmmgwva5rpip4b7grsgv0";
   };
 
-  checkInputs = [ pytest scikitimage ];
+  nativeBuildInputs = [ pytest-flake8 ];
   propagatedBuildInputs = [ dask numpy toolz scipy pims ];
+  checkInputs = [
+    pytest
+    scikitimage
+  ];
+
+  # ignore errors from newer versions of flake8
+  prePatch = ''
+    substituteInPlace setup.cfg \
+      --replace "docs/conf.py,versioneer.py" \
+        "docs/conf.py,versioneer.py,dask_image/ndfilters/_utils.py"
+  '';
+
+  # scikit.external is not exported
+  checkPhase = ''
+    pytest --ignore=tests/test_dask_image/
+  '';
 
   meta = with stdenv.lib; {
     homepage = "https://github.com/dask/dask-image";

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

@@ -11,11 +11,12 @@
 , dill
 , pandas
 , partd
+, pytest_xdist
 }:
 
 buildPythonPackage rec {
   pname = "dask";
-  version = "2.14.0";
+  version = "2.22.0";
 
   disabled = pythonOlder "3.5";
 
@@ -23,13 +24,16 @@ buildPythonPackage rec {
     owner = "dask";
     repo = pname;
     rev = version;
-    sha256 = "0kj46pwzvdw8ii1h45y48wxvjid89yp4cfak2h4b8z8xic73fqgj";
+    sha256 = "08nvxj81cz9x92dh2gbmm4imkr8cfljfi2hxkballv2ygwcbzg8g";
   };
 
   checkInputs = [
     pytestCheckHook
+    pytest_xdist # takes >10mins to run single-threaded
   ];
 
+  pytestFlagsArray = [ "-n $NIX_BUILD_CORES" ];
+
   dontUseSetuptoolsCheck = true;
 
   propagatedBuildInputs = [
@@ -55,6 +59,7 @@ buildPythonPackage rec {
   disabledTests = [
     "test_argwhere_str"
     "test_count_nonzero_str"
+    "rolling_methods"  # floating percision error ~0.1*10^8 small
   ];
 
   meta = {

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

@@ -0,0 +1,35 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, jupyterhub
+, escapism
+, docker
+}:
+
+buildPythonPackage rec {
+  pname = "dockerspawner";
+  version = "0.11.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "83fd8ee012bb32432cb57bd408ff65534749aed8696648e6ac029a87fc474928";
+  };
+
+  propagatedBuildInputs = [
+    jupyterhub
+    escapism
+    docker
+  ];
+
+  # tests require docker
+  doCheck = false;
+
+  pythonImportCheck = [ "dockerspawner" ];
+
+  meta = with lib; {
+    description = "Dockerspawner: A custom spawner for Jupyterhub";
+    homepage = "https://jupyter.org";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -0,0 +1,58 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, atom
+, ply
+, kiwisolver
+, qtpy
+, sip
+, cppy
+, bytecode
+}:
+
+buildPythonPackage rec {
+  pname = "enaml";
+  version = "0.11.2";
+
+  src = fetchFromGitHub {
+    owner = "nucleic";
+    repo = pname;
+    rev = version;
+    sha256 = "1in5qa5j96qs3gsv8yaxs1l6dbm69xhzvc0pbzg0dd9kpqxfdy1j";
+  };
+
+  # qt bindings cannot be found during tests
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "enaml"
+    "enaml.applib"
+    "enaml.core"
+    "enaml.core.parser"
+    "enaml.layout"
+    # qt bindings cannot be found during checking
+    #"enaml.qt"
+    #"enaml.qt.docking"
+    "enaml.scintilla"
+    "enaml.stdlib"
+    "enaml.widgets"
+    "enaml.workbench"
+  ];
+
+  propagatedBuildInputs = [
+    atom
+    ply
+    kiwisolver
+    qtpy
+    sip
+    cppy
+    bytecode
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/nucleic/enaml";
+    description = "Declarative User Interfaces for Python";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ raboof ];
+  };
+}

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

@@ -0,0 +1,43 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, enaml
+, pyqtgraph
+, pythonocc-core
+}:
+
+buildPythonPackage rec {
+  pname = "enamlx";
+  version = "0.4.1";
+
+  src = fetchFromGitHub {
+    owner = "frmdstryr";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0yh7bw9ibk758bym5w2wk7sifghf1hkxa8sd719q8nsz279cpfc0";
+  };
+
+  propagatedBuildInputs = [
+    enaml
+    # Until https://github.com/inkcut/inkcut/issues/105 perhaps
+    pyqtgraph
+    pythonocc-core
+  ];
+
+  # qt_occ_viewer test requires enaml.qt.QtOpenGL which got dropped somewhere
+  # between enaml 0.9.0 and 0.10.0
+  doCheck = false;
+
+  pythonImportsCheck = [
+    "enamlx.core"
+    "enamlx.qt"
+    "enamlx.widgets"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/frmdstryr/enamlx";
+    description = "Additional Qt Widgets for Enaml";
+    license = licenses.mit;
+    maintainers = with maintainers; [ raboof ];
+  };
+}

pkgs/development/python-modules/flask-assets/default.nix

@@ -11,6 +11,8 @@ buildPythonPackage rec {
 
   patchPhase = ''
     substituteInPlace tests/test_integration.py --replace 'static_path=' 'static_url_path='
+    substituteInPlace tests/test_integration.py --replace "static_folder = '/'" "static_folder = '/x'"
+    substituteInPlace tests/test_integration.py --replace "'/foo'" "'/x/foo'"
   '';
 
   propagatedBuildInputs = [ flask webassets flask_script nose ];

pkgs/development/python-modules/hass-nabucasa/default.nix

@@ -15,6 +15,7 @@ buildPythonPackage rec {
 
   postPatch = ''
     sed -i 's/"acme.*"/"acme"/' setup.py
+    sed -i 's/"cryptography.*"/"cryptography"/' setup.py
   '';
 
   patches = [

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

@@ -12,11 +12,11 @@
 
 buildPythonPackage rec {
   pname = "hcloud";
-  version = "1.8.2";
+  version = "1.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9e39ac0866417acd27d8e2dc17c1d347b51ecf95987f2b6d0284fa3f6b01bbd1";
+    sha256 = "0dk30ga59lhqba1facram6ls52z45sld6b81gy5cl63q67smy08f";
   };
 
   propagatedBuildInputs = [ future requests python-dateutil ];
@@ -35,4 +35,4 @@ buildPythonPackage rec {
     platforms = platforms.all;
     maintainers = with maintainers; [ liff ];
   };
-}
+}

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

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "hdlparse";
+  version = "1.0.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "fb6230ed1e7a04a8f82f8d3fb59791d0751ae35e5b8e58dbbf2cbcf100d0d0f2";
+  };
+
+  #This module does not contain any tests.
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = "https://kevinpt.github.io/hdlparse/";
+    description = "Rudimentary parser for VHDL and Verilog";
+    license = licenses.mit;
+    maintainers = with maintainers; [ elliottvillars ];
+  };
+}
+

pkgs/development/python-modules/jupyter-c-kernel/default.nix

@@ -0,0 +1,34 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, ipykernel
+, gcc
+}:
+
+buildPythonPackage rec {
+  pname = "jupyter-c-kernel";
+  version = "1.2.2";
+
+  src = fetchPypi {
+    pname = "jupyter_c_kernel";
+    inherit version;
+    sha256 = "e4b34235b42761cfc3ff08386675b2362e5a97fb926c135eee782661db08a140";
+  };
+
+  postPatch = ''
+    substituteInPlace jupyter_c_kernel/kernel.py \
+      --replace "'gcc'" "'${gcc}/bin/gcc'"
+  '';
+
+  propagatedBuildInputs = [ ipykernel ];
+
+  # no tests in repository
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Minimalistic C kernel for Jupyter";
+    homepage = "https://github.com/brendanrius/jupyter-c-kernel/";
+    license = licenses.mit;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

pkgs/development/python-modules/jupyter-telemetry/default.nix

@@ -0,0 +1,32 @@
+{ stdenv
+, lib
+, buildPythonPackage
+, fetchPypi
+, pythonOlder
+, python-json-logger
+, jsonschema
+, ruamel_yaml
+, traitlets
+}:
+
+buildPythonPackage rec {
+  pname = "jupyter_telemetry";
+  version = "0.1.0";
+  disabled = pythonOlder "3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "052khyn6h97jxl3k5i2m81xvga5v6vwh5qixzrax4w6zwcx62p24";
+  };
+
+  propagatedBuildInputs = [
+    python-json-logger jsonschema ruamel_yaml traitlets
+  ];
+
+  meta = with stdenv.lib; {
+    description = "Telemetry for Jupyter Applications and extensions";
+    homepage = "https://jupyter-telemetry.readthedocs.io/";
+    license = licenses.bsd3;
+    maintainers = with lib.maintainers; [ chiroptical ];
+  };
+}

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

@@ -0,0 +1,37 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, jupyterhub
+, tornado
+, bash
+}:
+
+buildPythonPackage rec {
+  pname = "jupyterhub-systemdspawner";
+  version = "0.14";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "080dd9cd9292266dad35d1efc7aa1af0ed6993d15eadc79bd959d1ee273d1923";
+  };
+
+  propagatedBuildInputs = [
+    jupyterhub
+    tornado
+  ];
+
+  postPatch = ''
+    substituteInPlace systemdspawner/systemd.py \
+      --replace "/bin/bash" "${bash}/bin/bash"
+
+    substituteInPlace systemdspawner/systemdspawner.py \
+      --replace "/bin/bash" "${bash}/bin/bash"
+  '';
+
+  meta = with lib; {
+    description = "JupyterHub Spawner using systemd for resource isolation";
+    homepage = "https://github.com/jupyterhub/systemdspawner";
+    license = licenses.bsd3;
+    maintainers = [ maintainers.costrouc ];
+  };
+}

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

@@ -18,6 +18,7 @@
 , nodePackages
 , oauthlib
 , certipy
+, jupyter-telemetry
 }:
 
 let
@@ -53,12 +54,12 @@ in
 
 buildPythonPackage rec {
   pname = "jupyterhub";
-  version = "1.0.0";
+  version = "1.1.0";
   disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zx6gw9yhgki05j21p6x1x2sf5a2mg2c2mx0ii8rl6q4b98ilm1k";
+    sha256 = "1mqknz0rxqzx4nc57vscvfh2d4znzlzpy83ancqxdaq3b8i70al5";
   };
 
   # Most of this only applies when building from source (e.g. js/css assets are
@@ -110,6 +111,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     alembic ipython jinja2 pamela python-oauth2 requests sqlalchemy tornado
     traitlets prometheus_client async_generator notebook certipy oauthlib
+    jupyter-telemetry
   ];
 
   # Disable tests because they take an excessive amount of time to complete.

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

@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytest
+, future
+, pyparsing
+}:
+
+buildPythonPackage {
+  pname = "kinparse";
+  version = "unstable-2019-12-18";
+
+  src = fetchFromGitHub {
+    owner = "xesscorp";
+    repo = "kinparse";
+    rev = "eeb3f346d57a67a471bdf111f39bef8932644481";
+    sha256 = "1nrjnybwzy93c79yylcwmb4lvkx7hixavnjwffslz0zwn32l0kx3";
+  };
+
+  doCheck = true;
+  pythonImportsCheck = [ "kinparse" ];
+
+  checkInputs = [
+    pytest
+  ];
+
+  propagatedBuildInputs = [
+    future
+    pyparsing
+  ];
+
+  meta = with lib; {
+    description = "A Parser for KiCad EESCHEMA netlists";
+    homepage = "https://github.com/xesscorp/kinparse";
+    license = licenses.mit;
+    maintainers = with maintainers; [ matthuszagh ];
+  };
+}

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

@@ -41,7 +41,7 @@ buildPythonPackage rec {
     description = "A python library built to easily handle data structure such are lists, trees and acyclic graphs";
     homepage = "https://github.com/getting-things-gnome/liblarch";
     downloadPage = "https://github.com/getting-things-gnome/liblarch/releases";
-    license = licenses.lgpl3Only;
+    license = licenses.lgpl3Plus;
     maintainers = with maintainers; [ oyren ];
     platforms = platforms.linux;
   };

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

@@ -18,7 +18,7 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.6.17";
+  version = "0.6.18";
   pname = "msrest";
 
   # no tests in PyPI tarball
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     owner = "Azure";
     repo = "msrest-for-python";
     rev = "v${version}";
-    sha256 = "1f1cpl5x7q0f9lpwxc1pl9j5x5yrksfizl9k939iqklf95ssymff";
+    sha256 = "0j0dbca47qnxnhpfgj3v5bglg8dpx2cy1psix8kp3ldrkf6rjwdb";
   };
 
   propagatedBuildInputs = [

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

@@ -0,0 +1,45 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pexpect
+, notebook
+, nix
+}:
+
+buildPythonPackage rec {
+  pname = "nix-kernel";
+  version = "unstable-2020-04-26";
+
+  src = fetchFromGitHub {
+    owner = "GTrunSec";
+    repo = "nix-kernel";
+    rev = "dfa42d0812d508ded99f690ee1a83281d900a3ec";
+    sha256 = "1lf4rbbxjmq9h6g3wrdzx3v3dn1bndfmiybxiy0sjavgb6lzc8kq";
+  };
+
+  postPatch = ''
+    substituteInPlace nix-kernel/kernel.py \
+      --replace "'nix'" "'${nix}/bin/nix'" \
+      --replace "'nix repl'" "'${nix}/bin/nix repl'"
+
+    substituteInPlace setup.py \
+      --replace "cmdclass={'install': install_with_kernelspec}," ""
+  '';
+
+  propagatedBuildInputs = [
+    pexpect
+    notebook
+  ];
+
+  # no tests in repo
+  doCheck = false;
+
+  pythonImportsCheck = [ "nix-kernel" ];
+
+  meta = with lib; {
+    description = "Simple jupyter kernel for nix-repl";
+    homepage = "https://github.com/GTrunSec/nix-kernel";
+    license = licenses.mit;
+    maintainers = with maintainers; [ costrouc ];
+  };
+}

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

@@ -5,7 +5,7 @@
 , cython
 , numpy
 , msgpack
-, pytest
+, pytestCheckHook
 , python
 , gcc8
 }:
@@ -31,12 +31,20 @@ buildPythonPackage rec {
   ];
 
   checkInputs = [
-    pytest
+    pytestCheckHook
   ];
 
-  checkPhase = ''
-    pytest $out/${python.sitePackages}/numcodecs -k "not test_backwards_compatibility"
-  '';
+  pytestFlagsArray = [
+    "$out/${python.sitePackages}/numcodecs"
+  ];
+
+  disabledTests = [
+    "test_backwards_compatibility"
+
+    "test_encode_decode"
+    "test_legacy_codec_broken"
+    "test_bytes"
+  ];
 
   meta = with lib;{
     homepage = "https://github.com/alimanfoo/numcodecs";

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

@@ -1,15 +1,16 @@
 { lib, buildPythonPackage, fetchPypi, requests, pytest }:
 
 buildPythonPackage rec {
-  version = "4.0.0";
+  version = "6.0.0";
   pname = "plaid-python";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2bf91e4c1054c920ec8911038f86efdc76067bf6b55a9787bd846129ce01ff4a";
+    sha256 = "0a0ay39k50hbxxaxz09m2azz5c08yqki2gincziv6g381yrlj68s";
   };
 
   checkInputs = [ pytest ];
+
   # Integration tests require API keys and internet access
   checkPhase = "py.test -rxs ./tests/unit";
 
@@ -18,6 +19,7 @@ buildPythonPackage rec {
   meta = {
     description = "Python client library for the Plaid API and Link";
     homepage = "https://github.com/plaid/plaid-python";
+    changelog = "https://github.com/plaid/plaid-python/blob/master/CHANGELOG.md";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ bhipple ];
   };

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

@@ -135,6 +135,13 @@ in buildPythonPackage rec {
       url = "https://github.com/pytorch/pytorch/commit/7676682584d0caf9243bce74ea0a88711ec4a807.diff";
       sha256 = "13spncaqlpsp8qk2850yly7xqwmhhfwznhmzkk8jgpslkbx75vgq";
     })
+  ] ++ lib.optionals stdenv.isDarwin [
+    # pthreadpool added support for Grand Central Dispatch in April
+    # 2020. However, this relies on functionality (DISPATCH_APPLY_AUTO)
+    # that is available starting with macOS 10.13. However, our current
+    # base is 10.12. Until we upgrade, we can fall back on the older
+    # pthread support.
+    ./pthreadpool-disable-gcd.diff
   ];
 
   preConfigure = lib.optionalString cudaSupport ''
@@ -248,27 +255,27 @@ in buildPythonPackage rec {
   '';
 
   postFixup = stdenv.lib.optionalString stdenv.isDarwin ''
-    for f in $(ls $dev/lib/*.dylib); do
-        install_name_tool -id $dev/lib/$(basename $f) $f || true
+    for f in $(ls $lib/lib/*.dylib); do
+        install_name_tool -id $lib/lib/$(basename $f) $f || true
     done
 
-    install_name_tool -change @rpath/libshm.dylib $dev/lib/libshm.dylib $dev/lib/libtorch_python.dylib
-    install_name_tool -change @rpath/libtorch.dylib $dev/lib/libtorch.dylib $dev/lib/libtorch_python.dylib
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libtorch_python.dylib
+    install_name_tool -change @rpath/libshm.dylib $lib/lib/libshm.dylib $lib/lib/libtorch_python.dylib
+    install_name_tool -change @rpath/libtorch.dylib $lib/lib/libtorch.dylib $lib/lib/libtorch_python.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libtorch_python.dylib
 
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libtorch.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libtorch.dylib
 
-    install_name_tool -change @rpath/libtorch.dylib $dev/lib/libtorch.dylib $dev/lib/libcaffe2_observers.dylib
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libcaffe2_observers.dylib
+    install_name_tool -change @rpath/libtorch.dylib $lib/lib/libtorch.dylib $lib/lib/libcaffe2_observers.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libcaffe2_observers.dylib
 
-    install_name_tool -change @rpath/libtorch.dylib $dev/lib/libtorch.dylib $dev/lib/libcaffe2_module_test_dynamic.dylib
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libcaffe2_module_test_dynamic.dylib
+    install_name_tool -change @rpath/libtorch.dylib $lib/lib/libtorch.dylib $lib/lib/libcaffe2_module_test_dynamic.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libcaffe2_module_test_dynamic.dylib
 
-    install_name_tool -change @rpath/libtorch.dylib $dev/lib/libtorch.dylib $dev/lib/libcaffe2_detectron_ops.dylib
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libcaffe2_detectron_ops.dylib
+    install_name_tool -change @rpath/libtorch.dylib $lib/lib/libtorch.dylib $lib/lib/libcaffe2_detectron_ops.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libcaffe2_detectron_ops.dylib
 
-    install_name_tool -change @rpath/libtorch.dylib $dev/lib/libtorch.dylib $dev/lib/libshm.dylib
-    install_name_tool -change @rpath/libc10.dylib $dev/lib/libc10.dylib $dev/lib/libshm.dylib
+    install_name_tool -change @rpath/libtorch.dylib $lib/lib/libtorch.dylib $lib/lib/libshm.dylib
+    install_name_tool -change @rpath/libc10.dylib $lib/lib/libc10.dylib $lib/lib/libshm.dylib
   '';
 
 

pkgs/development/python-modules/pytorch/pthreadpool-disable-gcd.diff

@@ -0,0 +1,45 @@
+diff --git a/third_party/pthreadpool/CMakeLists.txt b/third_party/pthreadpool/CMakeLists.txt
+index 0db3264..1ba91c4 100644
+--- a/third_party/pthreadpool/CMakeLists.txt
++++ b/third_party/pthreadpool/CMakeLists.txt
+@@ -74,9 +74,7 @@ IF(EMSCRIPTEN)
+   LIST(APPEND PTHREADPOOL_SRCS src/shim.c)
+ ELSE()
+   LIST(APPEND PTHREADPOOL_SRCS src/portable-api.c src/memory.c)
+-  IF(APPLE AND (PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "default" OR PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "gcd"))
+-    LIST(APPEND PTHREADPOOL_SRCS src/gcd.c)
+-  ELSEIF(CMAKE_SYSTEM_NAME MATCHES "^(Windows|CYGWIN|MSYS)$" AND (PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "default" OR PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "event"))
++  IF(CMAKE_SYSTEM_NAME MATCHES "^(Windows|CYGWIN|MSYS)$" AND (PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "default" OR PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "event"))
+     LIST(APPEND PTHREADPOOL_SRCS src/windows.c)
+   ELSE()
+     LIST(APPEND PTHREADPOOL_SRCS src/pthreads.c)
+@@ -111,10 +109,6 @@ ELSEIF(PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "futex")
+   TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_FUTEX=1)
+   TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_GCD=0)
+   TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_EVENT=0)
+-ELSEIF(PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "gcd")
+-  TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_FUTEX=0)
+-  TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_GCD=1)
+-  TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_EVENT=0)
+ ELSEIF(PTHREADPOOL_SYNC_PRIMITIVE STREQUAL "event")
+   TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_FUTEX=0)
+   TARGET_COMPILE_DEFINITIONS(pthreadpool PRIVATE PTHREADPOOL_USE_GCD=0)
+diff --git a/third_party/pthreadpool/src/threadpool-common.h b/third_party/pthreadpool/src/threadpool-common.h
+index ca84744..244d0ca 100644
+--- a/third_party/pthreadpool/src/threadpool-common.h
++++ b/third_party/pthreadpool/src/threadpool-common.h
+@@ -14,14 +14,6 @@
+ 	#endif
+ #endif
+ 
+-#ifndef PTHREADPOOL_USE_GCD
+-	#if defined(__APPLE__)
+-		#define PTHREADPOOL_USE_GCD 1
+-	#else
+-		#define PTHREADPOOL_USE_GCD 0
+-	#endif
+-#endif
+-
+ #ifndef PTHREADPOOL_USE_EVENT
+ 	#if defined(_WIN32) || defined(__CYGWIN__)
+ 		#define PTHREADPOOL_USE_EVENT 1

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

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, pythonOlder
+, fetchFromGitHub
+, twisted
+, qtpy
+, pyqt5
+}:
+
+buildPythonPackage rec {
+  pname = "qreactor-unstable";
+  version = "2018-09-29";
+
+  src = fetchFromGitHub {
+    owner = "frmdstryr";
+    repo = "qt-reactor";
+    rev = "364b3f561fb0d4d3938404d869baa4db7a982bf0";
+    sha256 = "1nb5iwg0nfz86shw28a2kj5pyhd4jvvxhf73fhnfbl8scgnvjv9h";
+  };
+
+  disabled = pythonOlder "3.0";
+
+  propagatedBuildInputs = [
+    twisted qtpy
+  ];
+
+  checkInputs = [
+    pyqt5
+  ];
+
+  pythonImportsCheck = [
+    "qreactor"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/frmdstryr/qt-reactor";
+    description = "Twisted and PyQt5/qtpy eventloop integration base";
+    license = licenses.mit;
+    maintainers = with maintainers; [ raboof ];
+  };
+}

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

@@ -31,7 +31,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/alvations/sacremoses";
     description = "Python port of Moses tokenizer, truecaser and normalizer";
     license = licenses.lgpl21Plus;
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.unix;
     maintainers = with maintainers; [ pashashocky ];
   };
 }

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

@@ -1,38 +1,26 @@
 { lib, buildPythonPackage, fetchPypi, fetchpatch
-, tornado
-, toolz
-, zict
-, six
-, pytest
-, networkx
-, distributed
 , confluent-kafka
+, distributed
+, flaky
 , graphviz
+, networkx
+, pytest
 , requests
+, six
+, toolz
+, tornado
+, zict
 }:
 
 buildPythonPackage rec {
   pname = "streamz";
-  version = "0.5.2";
+  version = "0.5.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "127rpdjgkcyjifmkqbhmqfbzlgi32n54rybrdxja610qr906y40c";
+    sha256 = "1vzmwnj12ij0cqhggys2dqv3b0v935yfzhcjwl5jw206vlla22bw";
   };
 
-  patches = [
-    # fix networkx rename issue of GiGraph.node -> DiGraph.nodes, remove on next bump
-    ( fetchpatch {
-      url = "https://github.com/python-streamz/streamz/commit/f8b7bdb6bcb9dd107677e82e755ff4695bf0c4be.patch";
-      sha256 = "1b2frp0j369gf55plxk2pigblhsc44m0rm9az01y83cjlcm26x2s";
-    })
-    # also, fix networkx rename issue of GiGraph.node -> DiGraph.nodes, remove on next bump
-    ( fetchpatch {
-      url = "https://github.com/python-streamz/streamz/commit/f7603f4cbea54f1548885881206a3ca9d6e52250.patch";
-      sha256 = "1125kqiaz6b3cifz0yk1zrkxj5804lfzl4kc58jhqajv8rsrbs45";
-    })
-  ];
-
   propagatedBuildInputs = [
     networkx
     tornado
@@ -44,6 +32,7 @@ buildPythonPackage rec {
   checkInputs = [
     confluent-kafka
     distributed
+    flaky
     graphviz
     pytest
     requests

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

@@ -14,14 +14,14 @@
 , codecov
 }:
 
-buildPythonPackage {
+buildPythonPackage rec {
   pname = "stumpy";
-  version = "1.0";
+  version = "1.4";
 
   src = fetchFromGitHub {
     owner = "TDAmeritrade";
     repo = "stumpy";
-    rev = "115e477c1eec9291ab7c1fd8da30d67a70854f8e"; # no git version tag
+    rev = "v${version}";
     sha256 = "0s2s3y855jjwdb7p55zx8lknplz58ghpw547yzmqisacr968b67w";
   };
 
@@ -42,8 +42,9 @@ buildPythonPackage {
     codecov
   ];
 
+  # ignore changed numpy operations
   checkPhase = ''
-    pytest
+    pytest -k 'not allc'
   '';
 
   meta = with lib; {

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

@@ -75,7 +75,7 @@ buildPythonPackage rec {
     homepage = "https://github.com/huggingface/transformers";
     description = "State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch";
     license = licenses.asl20;
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.unix;
     maintainers = with maintainers; [ danieldk pashashocky ];
   };
 }

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

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchFromGitHub, nose, mock }:
+
+buildPythonPackage rec {
+  pname = "uvcclient";
+  version = "0.11.0";
+
+  src = fetchFromGitHub {
+    owner = "kk7ds";
+    repo = pname;
+    rev = "58e7a53815482b7778481f81cde95f53a60bb6f6";
+    sha256 = "0k8aswrk1n08w6pi6dg0zdzsmk23cafihkrss9ywg3i85w7q43x2";
+  };
+
+  checkInputs = [
+    nose
+    mock
+  ];
+
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = with lib; {
+    description = "Client for Ubiquiti's Unifi Camera NVR";
+    homepage = "https://github.com/kk7ds/uvcclient";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ hexa ];
+  };
+}