Merge master into staging-next

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

@@ -0,0 +1,20 @@
+{ stdenv, buildPythonPackage, fetchPypi, cython, numpy, pysam, matplotlib
+}:
+buildPythonPackage rec {
+  version = "0.11.2";
+  pname = "HTSeq";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc";
+  };
+
+  buildInputs = [ cython numpy pysam ];
+  propagatedBuildInputs = [ numpy pysam matplotlib ];
+
+  meta = with stdenv.lib; {
+    description = "A framework to work with high-throughput sequencing data";
+    maintainers = with maintainers; [ unode ];
+    platforms = platforms.unix;
+  };
+}

pkgs/development/python-modules/addic7ed-cli/default.nix

@@ -2,11 +2,11 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "addic7ed-cli";
-  version = "1.4.5";
+  version = "1.4.6";
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "16nmyw7j2igx5dxflwiwblf421g69rxb879n1553wv6hxi4x27in";
+    sha256 = "182cpwxpdybsgl1nps850ysvvjbqlnx149kri4hxhgm58nqq0qf5";
   };
 
   propagatedBuildInputs = with python3Packages; [

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

@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "alot";
-  version = "0.8";
+  version = "0.8.1";
   outputs = [ "out" ] ++ lib.optional withManpage "man";
 
   disabled = !isPy3k;
@@ -16,7 +16,7 @@ buildPythonPackage rec {
     owner = "pazz";
     repo = "alot";
     rev = version;
-    sha256 = "1isn0p0i2a7dlbrdk5ib01xa1wgi6bi9ka4xl4vj8iw1q4i5fqv9";
+    sha256 = "1gzis6w45d860mr2qbmjhnbrhy6d9xwhw27wpmvs56vndafvv9d3";
   };
 
   nativeBuildInputs = lib.optional withManpage sphinx;
@@ -57,6 +57,6 @@ buildPythonPackage rec {
     description = "Terminal MUA using notmuch mail";
     license = licenses.gpl3;
     platforms = platforms.linux;
-    maintainers = with maintainers; [ ];
+    maintainers = with maintainers; [ geistesk ];
   };
 }

pkgs/development/python-modules/ansi2html/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi, isPy3k, six, mock, nose, setuptools }:
+
+buildPythonPackage rec {
+  pname = "ansi2html";
+  version = "1.5.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1a9vihsvd03hb0a4dbiklyy686adp9q2ipl79mkxmdr6gfp8bbln";
+  };
+
+  propagatedBuildInputs = [ six setuptools ];
+
+  checkInputs = [ mock nose ];
+
+  meta = with lib; {
+    description = "Convert text with ANSI color codes to HTML";
+    homepage = http://github.com/ralphbean/ansi2html;
+    license = licenses.lgpl3Plus;
+    maintainers = with maintainers; [ davidtwco ];
+    platforms = platforms.all;
+  };
+}

pkgs/development/python-modules/ansible-runner/default.nix

@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "ansible-runner";
-  version = "1.3.4";
+  version = "1.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "087jk00kv0qsqqspyn015nicvbl627wck3fgx2qhqawvrgqk3xb0";
+    sha256 = "1j3jisiy93026ivd28j0c3p2j7ij6zm2k765yjknfx2gg3m5pk14";
   };
 
   checkInputs = [ pytest mock ];

pkgs/development/python-modules/antlr4-python2-runtime/default.nix

@@ -1,18 +1,21 @@
-{ stdenv, fetchPypi, buildPythonPackage, isPy3k }:
+{ lib, buildPythonPackage, isPy3k, python
+, antlr4
+}:
 
 buildPythonPackage rec {
   pname = "antlr4-python2-runtime";
-  version = "4.7.2";
+  inherit (antlr4.runtime.cpp) version src;
   disabled = isPy3k;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "04ljic5wnqpizln8q3c78pqrckz6q5nb433if00j1mlyv2yja22q";
-  };
+  sourceRoot = "source/runtime/Python2";
 
-  meta = {
+  checkPhase = ''
+    ${python.interpreter} tests/TestTokenStreamRewriter.py
+  '';
+
+  meta = with lib; {
     description = "Runtime for ANTLR";
     homepage = "https://www.antlr.org/";
-    license = stdenv.lib.licenses.bsd3;
+    license = licenses.bsd3;
   };
 }

pkgs/development/python-modules/antlr4-python3-runtime/default.nix

@@ -1,18 +1,22 @@
-{ stdenv, fetchPypi, buildPythonPackage, isPy3k }:
+{ lib, buildPythonPackage, isPy3k, python
+, antlr4
+}:
 
 buildPythonPackage rec {
   pname = "antlr4-python3-runtime";
-  version = "4.7.2";
+  inherit (antlr4.runtime.cpp) version src;
   disabled = !isPy3k;
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "02xm7ccsf51vh4xsnhlg6pvchm1x3ckgv9kwm222w5drizndr30n";
-  };
+  sourceRoot = "source/runtime/Python3";
 
-  meta = {
+  checkPhase = ''
+    cd test
+    ${python.interpreter} ctest.py
+  '';
+
+  meta = with lib; {
     description = "Runtime for ANTLR";
     homepage = "https://www.antlr.org/";
-    license = stdenv.lib.licenses.bsd3;
+    license = licenses.bsd3;
   };
 }

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

@@ -9,18 +9,26 @@
 , numpy
 , isPy27
 , astropy
+, setuptools_scm
+, setuptools
 }:
 
 buildPythonPackage rec {
   pname = "asdf";
-  version = "2.3.3";
+  version = "2.4.2";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d02e936a83abd206e7bc65050d94e8848da648344dbec9e49dddc2bdc3bd6870";
+    sha256 = "1wlgx8469wwsczc2gjka9k1a03yzird67zg3va0kg8y6j1qmbwvg";
   };
 
+  postPatch = ''
+    substituteInPlace setup.cfg \
+      --replace "semantic_version>=2.3.1,<=2.6.0" "semantic_version>=2.3.1" \
+      --replace "doctest_plus = enabled" ""
+  '';
+
   checkInputs = [
     pytest-astropy
     astropy
@@ -32,6 +40,8 @@ buildPythonPackage rec {
     jsonschema
     six
     numpy
+    setuptools_scm
+    setuptools
   ];
 
   checkPhase = ''

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

@@ -14,7 +14,7 @@ buildPythonPackage rec {
   patches = [
     (fetchpatch {
       url = "https://github.com/MagicStack/asyncpg/commit/aaeb7076e5acb045880b46155014c0640624797e.patch";
-      sha256 = "0r6g6pvb39vzci8g67mv9rlrvavqvfz6vlv8988wv53bpz1mss3p";
+      sha256 = "0l420cmk7469wgb1xq2rxinvja1f2brb5cm4smj2s2wqgymbrf6h";
     })
   ];
 

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

@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "awkward";
-  version = "0.12.6";
+  version = "0.12.12";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0xvphwpa1n5q7kim4dw6fmsg9h5kkk7nd51bv9b36i3n4hilmq32";
+    sha256 = "316abd04dd049d56567082670ae8800c265dc3f06b699cf2a953ea6aea7696ce";
   };
 
   nativeBuildInputs = [ pytestrunner ];

pkgs/development/python-modules/azure-mgmt-compute/default.nix

@@ -7,13 +7,13 @@
 }:
 
 buildPythonPackage rec {
-  version = "5.0.0";
+  version = "8.0.0";
   pname = "azure-mgmt-compute";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "1zdypc8f825n60341ai2482rwgsc7l8dpr691j8hqz571l80y85w";
+    sha256 = "06hmf9iq2yqpmmvw7pr9zm4v427q03i436lnin3aczizfndrk76i";
   };
 
   postInstall = if isPy3k then "" else ''

pkgs/development/python-modules/azure-mgmt-containerservice/default.nix

@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "azure-mgmt-containerservice";
-  version = "5.3.0";
+  version = "7.0.0";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "1dhni22n85x76709mvjmby8i8hvginzniq1dna6f5cidfcalc0vs";
+    sha256 = "104w7rxv7hy84yzddbbpkjqha04ghr0zz9qy788n3wl69cj4cv1a";
   };
 
   propagatedBuildInputs = [

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

@@ -7,13 +7,13 @@
 }:
 
 buildPythonPackage rec {
-  version = "4.0.0";
+  version = "4.1.0";
   pname = "azure-mgmt-storage";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "1kxd30s2axn3g4qx3v7q3d5l744a29xlfk3q06ra0rqm1p6prvgv";
+    sha256 = "1src3ki3xd8x0m6vmxig6y4lg7w4mg0sz6vmnsxdk8mxaird03jj";
   };
 
   postInstall = if isPy3k then "" else ''

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

@@ -5,6 +5,7 @@
 , pytestrunner
 , six
 , html5lib
+, setuptools
 }:
 
 buildPythonPackage rec {
@@ -17,7 +18,7 @@ buildPythonPackage rec {
   };
 
   checkInputs = [ pytest pytestrunner ];
-  propagatedBuildInputs = [ six html5lib ];
+  propagatedBuildInputs = [ six html5lib setuptools ];
 
   postPatch = ''
     substituteInPlace setup.py --replace ",<3dev" ""

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

@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "cgen";
-  version = "2017.1";
+  version = "2019.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a04525d51ee975d37d590d6d82bf80a46e77f75187cccfd2248a89616a778795";
+    sha256 = "04gxzfjy2f9qsg3scg1sx4q4rhw5p036dyqngxyfsai0wvj5ya6m";
   };
 
   checkInputs = [ pytest ];

pkgs/development/python-modules/chart-studio/default.nix

@@ -0,0 +1,44 @@
+{ lib, buildPythonPackage, fetchFromGitHub
+, mock
+, nose
+, plotly
+, pytest
+, requests
+, retrying
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "chart-studio";
+  version = "1.0.0";
+
+  # chart-studio was split from plotly
+  src = fetchFromGitHub {
+    owner = "plotly";
+    repo = "plotly.py";
+    rev = "${pname}-v${version}";
+    sha256 = "14lyqbjdffnlnkzlfnn60k7yxjd99vx3hfcs23apsiyinzipjlbf";
+  };
+
+  sourceRoot = "source/packages/python/chart-studio";
+
+  propagatedBuildInputs = [
+    plotly
+    requests
+    retrying
+    six
+  ];
+
+  checkInputs = [ mock nose pytest ];
+  # most tests talk to a service
+  checkPhase = ''
+    HOME=$TMPDIR pytest chart_studio/tests/test_core chart_studio/tests/test_plot_ly/test_api
+  '';
+
+  meta = with lib; {
+    description = "Utilities for interfacing with Plotly's Chart Studio service";
+    homepage = "https://github.com/plotly/plotly.py/tree/master/packages/python/chart-studio";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ jonringer ];
+  };
+}

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

@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "colorcet";
-  version = "2.0.1";
+  version = "2.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ab1d16aba97f54af190631c7777c356b04b53de549672ff6b01c66d716eddff3";
+    sha256 = "1vkx00im4s6zhr2m1j9r0a5vmhkl488b4xpzxb1pidbl19wi6j2i";
   };
 
   propagatedBuildInputs = [

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

@@ -1,40 +1,59 @@
-{ buildPythonPackage, stdenv, fetchPypi, fetchpatch
-, numpy, pandas, plotly, six, colorlover
-, ipython, ipywidgets, nose
+{ lib, buildPythonPackage, fetchPypi, fetchpatch
+, chart-studio
+, colorlover
+, ipython
+, ipywidgets
+, nose
+, numpy
+, pandas
+, six
+, statsmodels
 }:
 
 buildPythonPackage rec {
   pname = "cufflinks";
-  version = "0.15";
+  version = "0.16";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "014098a4568199957198c0a7fe3dbeb3b4010b6de8d692a41fe3b3ac107b660e";
+    sha256 = "163lag5g4micpqm3m4qy9b5r06a7pw45nq80x4skxc7dcrly2ygd";
   };
 
   propagatedBuildInputs = [
-    numpy pandas plotly six colorlover
-    ipython ipywidgets
+    chart-studio
+    colorlover
+    ipython
+    ipywidgets
+    numpy
+    pandas
+    six
+    statsmodels
   ];
 
   patches = [
-    # Plotly 3.8 compatibility. Remove with the next release. See https://github.com/santosjorge/cufflinks/pull/178
+    # Plotly 4 compatibility. Remove with next release, assuming it gets merged.
     (fetchpatch {
-      url = "https://github.com/santosjorge/cufflinks/commit/cc4c23c2b45b870f6801d1cb0312948e1f73f424.patch";
-      sha256 = "1psl2h7vscpzvb4idr6s175v8znl2mfhkcyhb1926p4saswmghw1";
+      url = "https://github.com/santosjorge/cufflinks/pull/202/commits/e291dce14181858cb457404adfdaf2624b6d0594.patch";
+      sha256 = "1l0dahwqn3cxg49v3i3amwi80dmx2bi5zrazmgzpwsfargmk2kd1";
     })
   ];
 
+  # in plotly4+, the plotly.plotly module was moved to chart-studio.plotly
+  postPatch = ''
+    substituteInPlace requirements.txt \
+      --replace "plotly>=3.0.0,<4.0.0a0" "chart-studio"
+  '';
+
   checkInputs = [ nose ];
 
   checkPhase = ''
     nosetests -xv tests.py
   '';
 
-  meta = {
-    homepage = https://github.com/santosjorge/cufflinks;
+  meta = with lib; {
     description = "Productivity Tools for Plotly + Pandas";
-    license = stdenv.lib.licenses.mit;
-    maintainers = with stdenv.lib.maintainers; [ globin ];
+    homepage = "https://github.com/santosjorge/cufflinks";
+    license = licenses.mit;
+    maintainers = with maintainers; [ globin ];
   };
 }

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

@@ -1,16 +1,21 @@
-{ lib, buildPythonPackage, fetchPypi, requests, py, pytest, pytest-flakes }:
+{ lib, buildPythonPackage, fetchPypi
+, requests
+, py
+, pytest
+, pytest-flake8
+}:
 
 buildPythonPackage rec {
   pname = "devpi-common";
-  version = "3.3.2";
+  version = "3.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2c7a6471c0f5b07ac9257adec3b3c3a89193ee672fdeb0a6f29487dc9d675e0c";
+    sha256 = "1pfl29pnfn120rqv3zwxc22i1hyywwg60rcck9hzxsllbhmfbjqh";
   };
 
   propagatedBuildInputs = [ requests py ];
-  checkInputs = [ pytest pytest-flakes ];
+  checkInputs = [ pytest pytest-flake8 ];
 
   checkPhase = ''
     py.test

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "djangoql";
-  version = "0.12.6";
+  version = "0.13.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mwv1ljznj9mn74ncvcyfmj6ygs8xm2rajpxm88gcac9hhdmk5gs";
+    sha256 = "0hkg0zh8w6f4krbrv4nl66blrx48yixgc8ikf915415ghlqfsbjj";
   };
 
   propagatedBuildInputs = [ ply ];

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "ephem";
-  version = "3.7.6.0";
+  version = "3.7.7.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7a4c82b1def2893e02aec0394f108d24adb17bd7b0ca6f4bc78eb7120c0212ac";
+    sha256 = "0dj4kk325b01s7q1zkwpm9rrzl7n1jf7fr92wcajjhc5kx14hwb0";
   };
 
   patchFlags = "-p0";
@@ -17,11 +17,6 @@ buildPythonPackage rec {
     LC_ALL="en_US.UTF-8" py.test --pyargs ephem.tests -k "not JPLTest"
   '';
 
-  # Unfortunately, the tests are broken for Python 3 in 3.7.6.0. They have been
-  # fixed in https://github.com/brandon-rhodes/pyephem/commit/c8633854e2d251a198b0f701d0528b508baa2411
-  # but there has not been a new release since then.
-  doCheck = !isPy3k;
-
   meta = with stdenv.lib; {
     description = "Compute positions of the planets and stars";
     homepage = https://pypi.python.org/pypi/ephem/;

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "feedgen";
-  version = "0.7.0";
+  version = "0.8.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "82c9e29884e137c3e3e7959a02f142d1f7a46cd387d572e9e40150112a27604f";
+    sha256 = "0551ixbcz2gaala4gi3i8gici3haijj7dhvjsz1a61s050276m96";
   };
 
   propagatedBuildInputs = [ dateutil lxml ];

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "FoxDot";
-  version = "0.8.1";
+  version = "0.8.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "147n2c9rwmrby8rr6xfxlh7mfm12lqk2a7v1gxlzhq1i2jj1j5h4";
+    sha256 = "07ll1rh1bkq1dpb7gxd86jsjhxni73kp9iljiy0d2b86ji8h108p";
   };
 
   propagatedBuildInputs = [ tkinter supercollider ];

pkgs/development/python-modules/git-revise/default.nix

@@ -1,7 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, pythonAtLeast
+, pythonOlder
 , tox
 , pytest
 , pylint
@@ -11,14 +11,14 @@
 
 buildPythonPackage rec {
   pname = "git-revise";
-  version = "0.4.2";
+  version = "0.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mq1fh8m6jxl052d811cgpl378hiq20a8zrhdjn0i3dqmxrcb8vs";
+    sha256 = "16sxmxksb5gjj6zfh1wy2czqj9nm4sd3j4fbrsphs8l065dzzikj";
   };
 
-  disabled = !(pythonAtLeast "3.6");
+  disabled = pythonOlder "3.6";
 
   checkInputs = [ tox pytest pylint mypy black ];
 
@@ -29,6 +29,7 @@ buildPythonPackage rec {
   meta = with lib; {
     description = "Efficiently update, split, and rearrange git commits";
     homepage = https://github.com/mystor/git-revise;
+    changelog = "https://github.com/mystor/git-revise/blob/${version}/CHANGELOG.md";
     license = licenses.mit;
     maintainers = with maintainers; [ emily ];
   };

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

@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "goobook";
-  version = "3.3";
+  version = "3.4";
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0sanlki1rcqvhbds7a049v2kzglgpm761i728115mdracw0s6i3h";
+    sha256 = "089a95s6g9izsy1fzpz48p6pz0wpngcbbrvsillm1n53492gfhjg";
   };
 
   propagatedBuildInputs = [ google_api_python_client simplejson oauth2client ];

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

@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, future
+, requests
+, python-dateutil
+, flake8
+, isort
+, mock
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "hcloud";
+  version = "1.6.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1skqq36k1dm7mngfg9c93pb1rdvmbapc0cv8zj00hnm63r67hmrj";
+  };
+
+  propagatedBuildInputs = [ future requests python-dateutil ];
+
+  checkInputs = [ flake8 isort mock pytest ];
+
+  # Skip integration tests since they require a separate external fake API endpoint.
+  checkPhase = ''
+    pytest --ignore=tests/integration
+  '';
+
+  meta = with lib; {
+    description = "Official Hetzner Cloud python library";
+    homepage = "https://github.com/hetznercloud/hcloud-python";
+    license = licenses.mit;
+    platforms = platforms.all;
+    maintainers = with maintainers; [ liff ];
+  };
+}

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

@@ -1,8 +1,9 @@
-{ stdenv, buildPythonPackage, fetchPypi, scikitlearn }:
+{ stdenv, isPy27, buildPythonPackage, fetchPypi, scikitlearn }:
 
 buildPythonPackage rec {
   pname = "mlrose";
   version = "1.2.0";
+  disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;

pkgs/development/python-modules/nixpkgs-pytools/default.nix

@@ -3,22 +3,24 @@
 , fetchPypi
 , jinja2
 , setuptools
+, rope
 , isPy27
 }:
 
 buildPythonPackage rec {
   pname = "nixpkgs-pytools";
-  version = "1.0.1";
+  version = "1.3.0";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0796c6e95daeb3d7e61c9c53126d95ba6a48f84b995b12b60f45619caf28a574";
+    sha256 = "11skcbi1lf9qcv9j5ikifb4pakhbbygqpcmv3390j7gxsa85cn19";
   };
 
   propagatedBuildInputs = [
     jinja2
     setuptools
+    rope
   ];
 
   # tests require network ..

pkgs/development/python-modules/openrazer/daemon.nix

@@ -1,4 +1,5 @@
 { buildPythonApplication
+, isPy3k
 , daemonize
 , dbus-python
 , fetchFromGitHub
@@ -21,6 +22,8 @@ buildPythonApplication (common // rec {
 
   sourceRoot = "source/daemon";
 
+  disabled = !isPy3k;
+
   outputs = [ "out" "man" ];
 
   nativeBuildInputs = [ makeWrapper wrapGAppsHook ];

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

@@ -30,11 +30,11 @@ let
 
 in buildPythonPackage rec {
   pname = "pandas";
-  version = "0.25.0";
+  version = "0.25.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "914341ad2d5b1ea522798efa4016430b66107d05781dbfe7cf05eba8f37df995";
+    sha256 = "1xm9dmbngsq46vj836csnb5j0bs88b1d713b0b5vx1q6gdxijbnb";
   };
 
   checkInputs = [ pytest glibcLocales moto hypothesis ];

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, murmurhash
 , pytest
 , cython
 , cymem
@@ -8,27 +9,23 @@
 }:
 buildPythonPackage rec {
   pname = "preshed";
-  version = "2.0.1";
+  version = "3.0.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1rd943zp4gyspajqm5qxzndxziyh51grx0zcw23w8r9r65s1rq6s";
+    sha256 = "1jrnci1pw9yv7j1a9b2q6c955l3gb8fv1q4d0id6s7bwr5l39mv1";
   };
 
   propagatedBuildInputs = [
    cython
    cymem
+   murmurhash
   ];
 
-  buildInputs = [
+  checkInputs = [
     pytest
   ];
 
-  prePatch = ''
-    substituteInPlace setup.py \
-      --replace "wheel>=0.32.0,<0.33.0" "wheel>=0.31.0"
-  '';
-
   checkPhase = ''
     ${python.interpreter} setup.py test
   '';

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "psycopg2";
-  version = "2.7.7";
+  version = "2.8.3";
 
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f4526d078aedd5187d0508aa5f9a01eae6a48a470ed678406da94b4cd6524b7e";
+    sha256 = "0ms4kx0p5n281l89awccix4d05ybmdngnjjpi9jbzd0rhf1nwyl9";
   };
 
   buildInputs = lib.optional stdenv.isDarwin openssl;

pkgs/development/python-modules/pykde4/default.nix

@@ -37,6 +37,7 @@ in stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     platforms = platforms.linux;
+    hydraPlatforms = platforms.none;
     description = "Python bindings for KDE";
     license = with licenses; [ gpl2 lgpl2 ];
     homepage = https://api.kde.org/pykde-4.3-api/;

pkgs/development/python-modules/pykde4/kdelibs.nix

@@ -1,5 +1,5 @@
 {
-  stdenv, fetchurl,
+  stdenv, fetchurl, fetchpatch,
   automoc4, cmake_2_8, libxslt, perl, pkgconfig, shared-mime-info,
   attica, docbook_xml_dtd_42, docbook_xsl, giflib,
   libdbusmenu_qt, libjpeg, phonon, qt4, openssl
@@ -12,6 +12,14 @@ stdenv.mkDerivation rec {
     url = "mirror://kde/stable/applications/17.08.3/src/${pname}-${version}.tar.xz";
     sha256 = "1zn3yb09sd22bm54is0rn98amj0398zybl550dp406419sil7z9p";
   };
+  patches = [
+    # https://phabricator.kde.org/D22989
+    (fetchpatch {
+      url = "https://cgit.kde.org/kdelibs.git/patch/?id=2c3762feddf7e66cf6b64d9058f625a715694a00";
+      sha256 = "1wbzywh8lcc66n6y3pxs18h7cwkq6g216faz27san33jpl8ra1i9";
+      name = "CVE-2019-14744.patch";
+    })
+  ];
 
   enableParallelBuilding = true;
 
@@ -32,7 +40,9 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     platforms = platforms.linux;
+    hydraPlatforms = platforms.none;
     homepage = http://www.kde.org;
     license = with licenses; [ gpl2 fdl12 lgpl21 ];
+    maintainers = with maintainers; [ gnidorah ];
   };
 }

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

@@ -14,7 +14,7 @@
 
 buildPythonPackage rec {
   pname   = "pysam";
-  version = "0.15.2";
+  version = "0.15.3";
 
   # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
   # missing some files which cause test failures.
@@ -23,7 +23,7 @@ buildPythonPackage rec {
     owner = "pysam-developers";
     repo = "pysam";
     rev = "v${version}";
-    sha256 = "03aczbzx6gmvgy60fhswpwkry7a8zb5q1pbp55v5gx8hk15n40k1";
+    sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb";
   };
 
   buildInputs = [ bzip2 curl cython lzma zlib ];

pkgs/development/python-modules/qscintilla-qt5/default.nix

@@ -15,6 +15,13 @@ buildPythonPackage {
   buildInputs = [ qscintilla ];
   propagatedBuildInputs = [ pyqt5 ];
 
+  postPatch = ''
+    substituteInPlace Python/configure.py \
+      --replace \
+      "target_config.py_module_dir" \
+      "'$out/${python.sitePackages}'"
+  '';
+
   preConfigure = ''
     mkdir -p $out
     lndir ${pyqt5} $out
@@ -26,6 +33,7 @@ buildPythonPackage {
       --stubsdir=$out/${python.sitePackages}/PyQt5 \
       --apidir=$out/api/${python.libPrefix} \
       --qsci-incdir=${qscintilla}/include \
+      --qsci-featuresdir=${qscintilla}/mkspecs/features \
       --qsci-libdir=${qscintilla}/lib \
       --pyqt-sipdir=${pyqt5}/share/sip/PyQt5 \
       --qsci-sipdir=$out/share/sip/PyQt5 \

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

@@ -26,18 +26,16 @@
 
 buildPythonPackage rec {
   pname = "spacy";
-  version = "2.1.8";
+  version = "2.2.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1dja0crbai2n1l19m0hkv2fkj9r6zzy5ijd6dffp60v7lrch8lcw";
+    sha256 = "1a833dx8i4s106fk42x4dnayaq5p3qxaxnc012xij991i09v2pxn";
   };
 
   prePatch = ''
-    substituteInPlace setup.py \
-      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6" \
-      --replace "thinc>=7.0.8,<7.1.0" "thinc>=7.0.8" \
-      --replace "blis>=0.2.2,<0.3.0" "blis>=0.2.2"
+    substituteInPlace setup.cfg \
+      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6"
   '';
 
   propagatedBuildInputs = [

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

@@ -1,43 +1,43 @@
 [{
   "pname": "de_core_news_md",
-  "version": "2.1.0",
-  "sha256": "0q1flyrp2n8ja11kdlw6x1k0gll0r096pxy8ba4xv15hjng2zay1",
+  "version": "2.2.0",
+  "sha256": "1n61jg0mxpl5mqpydclq9d2xds14v0blnb0plmnf7qhzzfhrmxq9",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "de_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "0fj4dqa915i6niyskxmw2318fxzjhgdjhjx79h9cpp4mxw719w95",
+  "version": "2.2.0",
+  "sha256": "06g2snm57k64il3plgn20l27a00dsr9dcxkyyqj6pq5ih91mfycb",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "el_core_news_md",
-  "version": "2.1.0",
-  "sha256": "1rgy9hlb92amhlbwkd91yh87xssqj2a1ign0wm59aai69rb79q3s",
+  "version": "2.2.0",
+  "sha256": "0xgyh5wj9mpbl2mdrk60i3m8wmgaxbf5qviy78qk8zb1jvnxzc2n",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "el_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "07n7qg0nnzg5gjq7vs72j9qc6z4zjx65qsrrj0hjhiihk3ps378z",
+  "version": "2.2.0",
+  "sha256": "0qbf16g6s1xfm2clnmrwr3m3vgmvvsziyhy6jbm6axh8c0fy0j8p",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "en_core_web_lg",
-  "version": "2.1.0",
-  "sha256": "0ywcczd9nsxmpfwknxa7z54h566bwi7chq0jzx3sqk2a6lva4q52",
+  "version": "2.2.0",
+  "sha256": "1dxy43kf3vbz4jxc7jkr315hyzmi44v41lf09rax53f3s1jghsbh",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "en_core_web_md",
-  "version": "2.1.0",
-  "sha256": "10vgq1xd6dpdl7xdssgf0kywbq7xpxp79yqc2vcnl3c4axfpwk5q",
+  "version": "2.2.0",
+  "sha256": "13fvr8z7fjhyzc9mm55ah6c2snpj27lrrc0rzgyb0hcg7ghd6v58",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "en_core_web_sm",
-  "version": "2.1.0",
-  "sha256": "1wg5a7nxq82sfmnc3j5xfr8il65rprmcx2h36va5dvydm1h6icad",
+  "version": "2.2.0",
+  "sha256": "197afra99lhh84yi6wxvxdxibd1ikaybqfsq2nsmm7ahsw9s3kk5",
   "license": "cc-by-sa-40"
 },
 {
@@ -48,49 +48,49 @@
 },
 {
   "pname": "es_core_news_md",
-  "version": "2.1.0",
-  "sha256": "02v7hm711r9ma8p5yk057z7hm2pcvpfjgnjszc697d0ymfn4avby",
+  "version": "2.2.0",
+  "sha256": "0sdps0cdmsd2l3irsg63d874sba9vpn0san0n89rk8h3pa49dpab",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "es_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "1smyyb1gqp090sailqdqp5v5ww4kf99a3hcd9d9rdhn1wgsv28dh",
+  "version": "2.2.0",
+  "sha256": "073dgna796lk4rm7f25gyyl2ml7dfsb4azd4jkk03kxkcy6ypnag",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "fr_core_news_md",
-  "version": "2.1.0",
-  "sha256": "0n94ja7y4jbvz0k0x5bij2dypy11ikvgpd9dav0m0hw1wpqgls1i",
+  "version": "2.2.0",
+  "sha256": "0061hnw03189z3ya1gb6506bq8yxrg17v9cywg7zbk6izakxcasr",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "fr_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "1czr40y5sqs0n2dd4s37kc2xawkh2nsj41wvmsx48bw0aksb1n75",
+  "version": "2.2.0",
+  "sha256": "0kj31kx4q9mm7ms622ph2i6pkl1ifm8s5ng3f3khf9ia0vr31vbq",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "it_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "1i8dm703mf1l39jwis3mn5mb9azpx6bsimh66iriax94612x64mb",
+  "version": "2.2.0",
+  "sha256": "0gxmknd68kajak8jr443799bfd69pp5j0jnmcbnyx5abzyq6wkzx",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "nl_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "0ywyn7jprsfr10bvwnm3qk270raxm9s9rvzyp1cp7ca037ab633y",
+  "version": "2.2.1",
+  "sha256": "0gw9a1j3v4f15cxcz7zr7dz7mqi2a3541b04q6kj74gg397li4ny",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "pt_core_news_sm",
-  "version": "2.1.0",
-  "sha256": "0vigc9x7158sdqxjgcxgvp6458k5936jlmlp2qdmlmzxr5wmfrbc",
+  "version": "2.2.0",
+  "sha256": "1fi4wick1x96sj46idic1ad26l9zd2p5smi4v7mkry71xp7d9s13",
   "license": "cc-by-sa-40"
 },
 {
   "pname": "xx_ent_wiki_sm",
-  "version": "2.1.0",
-  "sha256": "19sfsxwjqdzlfm43gb4hbyj0hgqcfhcfxwdib4g5i1pcfx1v3pf4",
+  "version": "2.2.0",
+  "sha256": "0niwnd1mdaji92yp2dqsbmr0w420gpaybb1ppbqr1rmk6bwgyhsb",
   "license": "cc-by-sa-40"
 }]

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "sqlparse";
-  version = "0.2.4";
+  version = "0.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ce028444cfab83be538752a2ffdb56bc417b7784ff35bb9a3062413717807dec";
+    sha256 = "0wxqrm9fpn4phz6rqm7kfd1wwkwzx376gs27nnalwx12q0lwlgbw";
   };
 
   checkInputs = [ pytest ];

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

@@ -28,11 +28,11 @@
 
 buildPythonPackage rec {
   pname = "thinc";
-  version = "7.1.0";
+  version = "7.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0j2nfzz154j9331gzwa5rmc2f5ljjan728rhgsx6c7jwg323mmsa";
+    sha256 = "0gkz4q53ps3vzz0ww154y0dv6nri5sli8yflh7c26maawvz8wiv8";
   };
 
   buildInputs = lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [

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

@@ -45,6 +45,7 @@ buildPythonPackage rec {
     pytest trackpy --ignore trackpy/tests/test_motion.py \
                    --ignore trackpy/tests/test_feature_saving.py \
                    --ignore trackpy/tests/test_feature.py \
+                   --ignore trackpy/tests/test_plots.py \
                    --ignore trackpy/tests/test_legacy_linking.py
   '';