Merge master into staging-next

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

@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "aioamqp";
-  version = "0.11.0";
+  version = "0.12.0";
 
   meta = {
     homepage = https://github.com/polyconseil/aioamqp;
@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7f1eb9e0f1b7c7e21a3a6ca498c3daafdfc3e95b4a1a0633fd8d6ba2dfcab777";
+    sha256 = "17vrl6jajr81bql7kjgq0zkxy225px97z4g9wmbhbbnvzn1p92c0";
   };
 
   buildInputs = lib.optionals isPy33 [ asyncio ];

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

@@ -3,6 +3,13 @@
 , fetchPypi
 , dateutil
 , sigtools
+, six
+, attrs
+, od
+, docutils
+, repeated_test
+, unittest2
+, pygments
 }:
 
 buildPythonPackage rec {
@@ -14,8 +21,20 @@ buildPythonPackage rec {
     sha256 = "dbcfba5571dc30aaf90dc98fc279e2aab69d0f8f3665fc0394fbc10a87a2be60";
   };
 
-  buildInputs = [ dateutil ];
-  propagatedBuildInputs = [ sigtools ];
+  checkInputs = [ 
+    dateutil
+    pygments
+    repeated_test
+    unittest2
+  ];
+  
+  propagatedBuildInputs = [ 
+    attrs
+    docutils
+    od
+    sigtools
+    six
+  ];
 
   meta = with stdenv.lib; {
     description = "Command-line argument parsing for Python";

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

@@ -9,11 +9,11 @@ assert pariSupport -> pari != null;
 
 buildPythonPackage rec {
   pname = "cysignals";
-  version = "1.8.0";
+  version = "1.8.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1yh4lyrinhxxra42p0k4hiyjdrqjmifg4gnmf4bky5wa0mqnyai6";
+    sha256 = "1hnkcrrxgh6g8a197v2yw61xz43iyv81jbl6jpy19ql3k66w81zx";
   };
 
   # explicit check:
@@ -22,9 +22,9 @@ buildPythonPackage rec {
     "fortify"
   ];
 
-  # currently fails, probably because of formatting changes in gdb 8.0
-  # https://trac.sagemath.org/ticket/24692
+  # known failure: https://github.com/sagemath/cysignals/blob/582dbf6a7b0f9ade0abe7a7b8720b7fb32435c3c/testgdb.py#L5
   doCheck = false;
+  checkTarget = "check-install";
 
   preCheck = ''
     # Make sure cysignals-CSI is in PATH

pkgs/development/python-modules/dependency-injector/default.nix

@@ -1,19 +1,26 @@
-{ stdenv, buildPythonPackage, fetchPypi, six, unittest2 }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, six, unittest2 }:
+
+let
+  testPath =
+    if isPy3k
+    then "test_*_py3.py"
+    else "test_*_py2_py3.py";
+in
 
 buildPythonPackage rec {
   pname = "dependency-injector";
-  version = "3.14.2";
+  version = "3.14.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f478a26e9bf3111ce98bbfb8502af274643947f87a7e12a6481a35eaa693062b";
+    sha256 = "07366palyav9bawyq2b1gi76iamjkq6r5akzzbqv8s930sxq6yim";
   };
 
   propagatedBuildInputs = [ six ];
   checkInputs = [ unittest2 ];
 
   checkPhase = ''
-    unit2 discover tests/unit
+    unit2 discover -s tests/unit -p "${testPath}"
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/flask-jwt-extended/default.nix

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Flask-JWT-Extended";
-  version = "3.13.1";
+  version = "3.14.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "10qz3ljr2kpd93al2km6iijxp23z33kvvwd0y5bc840f86b4mra8";
+    sha256 = "133s9js7j1b2m6vv56a2xd9in0rmx5zrdp4r005qwbvr5qxld39s";
   };
 
   propagatedBuildInputs = [ flask pyjwt werkzeug ];

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

@@ -1,39 +1,24 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, isPy3k
-, oauth2client
-, gdata
-, google_api_python_client
-, simplejson
-, httplib2
-, keyring
-, six
-, rsa
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, google_api_python_client, simplejson, oauth2client
 }:
 
 buildPythonPackage rec {
   pname = "goobook";
-  version = "3.1";
-  disabled = isPy3k;
+  version = "3.3";
+  disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "139a98d646d5c5963670944d5cfcc1a107677ee11fa98329221bd600457fda6d";
+    sha256 = "0sanlki1rcqvhbds7a049v2kzglgpm761i728115mdracw0s6i3h";
   };
 
-  propagatedBuildInputs = [ oauth2client gdata google_api_python_client simplejson httplib2 keyring six rsa ];
-
-  preConfigure = ''
-    sed -i '/distribute/d' setup.py
-  '';
+  propagatedBuildInputs = [ google_api_python_client simplejson oauth2client ];
 
   meta = with stdenv.lib; {
     description = "Search your google contacts from the command-line or mutt";
     homepage    = https://pypi.python.org/pypi/goobook;
     license     = licenses.gpl3;
-    maintainers = with maintainers; [ lovek323 hbunke ];
+    maintainers = with maintainers; [ primeos ];
     platforms   = platforms.unix;
   };
-
 }

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

@@ -2,12 +2,12 @@
 , python, pytest, sortedcontainers }:
 
 buildPythonPackage rec {
-  version = "2.1.0";
+  version = "3.0.2";
   pname = "intervaltree";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc";
+    sha256 = "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb";
   };
 
   buildInputs = [ pytest ];

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

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi, unittest2, repeated_test }:
+
+buildPythonPackage rec {
+  pname = "od";
+  version = "1.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1az30snc3w6s4k1pi7mspcv8y0kp3ihf3ly44z517nszmz9lrjfi";
+  };
+
+  checkInputs = [
+    repeated_test
+    unittest2
+  ];
+
+  meta = with lib; {
+    description = "Shorthand syntax for building OrderedDicts";
+    homepage = https://github.com/epsy/od;
+    license = licenses.mit;
+  };
+
+}

pkgs/development/python-modules/opt-einsum/default.nix

@@ -0,0 +1,31 @@
+{ buildPythonPackage, fetchPypi, lib, numpy, pytest, pytestpep8, pytestcov }:
+buildPythonPackage rec {
+  version = "2.3.2";
+  pname = "opt_einsum";
+
+  src = fetchPypi {
+    inherit version pname;
+    sha256 = "0ny3v8x83mzpwmqjdzqhzy2pzwyy4wx01r1h9i29xw3yvas69m6k";
+  };
+
+  checkInputs = [
+    pytest
+    pytestpep8
+    pytestcov
+  ];
+
+  checkPhase = ''
+    pytest
+  '';
+
+  propagatedBuildInputs = [
+    numpy
+  ];
+
+  meta = {
+    description = "Optimizing NumPy's einsum function with order optimization and GPU support.";
+    homepage = http://optimized-einsum.readthedocs.io;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ teh ];
+  };
+}

pkgs/development/python-modules/pyqt/5.x.nix

@@ -1,30 +1,21 @@
 { lib, fetchurl, fetchpatch, pythonPackages, pkgconfig
-, qmake, lndir, qtbase, qtsvg, qtwebkit, qtwebengine, dbus
-, withWebSockets ? false, qtwebsockets
+, qmake, lndir, qtbase, qtsvg, qtwebengine, dbus
 , withConnectivity ? false, qtconnectivity
+, withWebKit ? false, qtwebkit
+, withWebSockets ? false, qtwebsockets
 }:
 
 let
-  pname = "PyQt";
-  version = "5.11.3";
 
   inherit (pythonPackages) buildPythonPackage python isPy3k dbus-python enum34;
 
   sip = pythonPackages.sip.override { sip-module = "PyQt5.sip"; };
 
-in buildPythonPackage {
-  pname = pname;
-  version = version;
+in buildPythonPackage rec {
+  pname = "PyQt";
+  version = "5.11.3";
   format = "other";
 
-  meta = with lib; {
-    description = "Python bindings for Qt5";
-    homepage    = http://www.riverbankcomputing.co.uk;
-    license     = licenses.gpl3;
-    platforms   = platforms.mesaPlatforms;
-    maintainers = with maintainers; [ sander ];
-  };
-
   src = fetchurl {
     url = "mirror://sourceforge/pyqt/PyQt5/PyQt-${version}/PyQt5_gpl-${version}.tar.gz";
     sha256 = "0wqh4srqkcc03rvkwrcshaa028psrq58xkys6npnyhqxc0apvdf9";
@@ -36,9 +27,11 @@ in buildPythonPackage {
 
   buildInputs = [ dbus sip ];
 
-  propagatedBuildInputs = [
-    qtbase qtsvg qtwebkit qtwebengine
-  ] ++ lib.optional (!isPy3k) enum34 ++ lib.optional withWebSockets qtwebsockets ++ lib.optional withConnectivity qtconnectivity;
+  propagatedBuildInputs = [ qtbase qtsvg qtwebengine ]
+    ++ lib.optional (!isPy3k) enum34
+    ++ lib.optional withConnectivity qtconnectivity
+    ++ lib.optional withWebKit qtwebkit
+    ++ lib.optional withWebSockets qtwebsockets;
 
   configurePhase = ''
     runHook preConfigure
@@ -49,10 +42,6 @@ in buildPythonPackage {
 
     export PYTHONPATH=$PYTHONPATH:$out/${python.sitePackages}
 
-    substituteInPlace configure.py \
-      --replace 'install_dir=pydbusmoddir' "install_dir='$out/${python.sitePackages}/dbus/mainloop'" \
-      --replace "ModuleMetadata(qmake_QT=['webkitwidgets'])" "ModuleMetadata(qmake_QT=['webkitwidgets', 'printsupport'])"
-
     ${python.executable} configure.py  -w \
       --confirm-license \
       --dbus=${dbus.dev}/include/dbus-1.0 \
@@ -74,4 +63,12 @@ in buildPythonPackage {
   '';
 
   enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "Python bindings for Qt5";
+    homepage    = http://www.riverbankcomputing.co.uk;
+    license     = licenses.gpl3;
+    platforms   = platforms.mesaPlatforms;
+    maintainers = with maintainers; [ sander ];
+  };
 }

pkgs/development/python-modules/pyro-ppl/default.nix

@@ -0,0 +1,38 @@
+{ buildPythonPackage, fetchPypi, lib, pytorch, contextlib2
+, graphviz, networkx, six, opt-einsum, tqdm }:
+buildPythonPackage rec {
+  version = "0.3.0";
+  pname = "pyro-ppl";
+
+  src = fetchPypi {
+    inherit version pname;
+    sha256 = "0shsnc5bia9k1fzmqnwwbm1x5qvac3zrq4lvyhg27rjgpcamvb9l";
+  };
+
+  propagatedBuildInputs = [
+    pytorch
+    contextlib2
+    # TODO(tom): graphviz pulls in a lot of dependencies - make
+    # optional when some time to figure out how.
+    graphviz
+    networkx
+    six
+    opt-einsum
+    tqdm
+  ];
+
+  # pyro not shipping tests do simple smoke test instead
+  checkPhase = ''
+    python -c "import pyro"
+    python -c "import pyro.distributions"
+    python -c "import pyro.infer"
+    python -c "import pyro.optim"
+  '';
+
+  meta = {
+    description = "A Python library for probabilistic modeling and inference";
+    homepage = http://pyro.ai;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ teh ];
+  };
+}

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

@@ -31,7 +31,7 @@ buildPythonPackage rec {
     description = "Jupyter Qt console";
     homepage = http://jupyter.org/;
     license = lib.licenses.bsd3;
-    platforms = lib.platforms.linux; # fails on Darwin
+    platforms = lib.platforms.unix;
     maintainers = with lib.maintainers; [ fridh ];
   };
 }

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

@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   pname = "shippai";
   # Please make sure that vdirsyncer still builds if you update this package.
-  version = "0.2.4";
+  version = "0.3.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "87cc9899212d917031853becd7cb14808181289c3c329b1418e9b4b6aae93c80";
+    sha256 = "0r6iwvmay8ygn2m15pyjrk9am4mfpk7rkf0lcbcb15pnabixlyzj";
   };
 
   meta = with stdenv.lib; {

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

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "unidiff";
+  version = "0.5.5";
+
+  # PyPI tarball doesn't ship tests
+  src = fetchFromGitHub {
+    owner = "matiasb";
+    repo = "python-unidiff";
+    rev = "v${version}";
+    sha256 = "1nvi7s1nn5p7j6aql1nkn2kiadnfby98yla5m3jq8xwsx0aplwdm";
+  };
+
+  meta = with lib; {
+    description = "Unified diff python parsing/metadata extraction library";
+    homepage = https://github.com/matiasb/python-unidiff;
+    license = licenses.mit;
+    maintainers = [ maintainers.marsam ];
+  };
+}

pkgs/development/python-modules/update-copyright/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi, isPy3k }:
+
+buildPythonPackage rec {
+  pname = "update-copyright";
+  version = "0.6.2";
+
+  disabled = !isPy3k;
+
+  # Has no tests
+  doCheck = false;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17ybdgbdc62yqhda4kfy1vcs1yzp78d91qfhj5zbvz1afvmvdk7z";
+  };
+
+  meta = with lib; {
+    description = "An automatic copyright update tool";
+    homepage = http://blog.tremily.us/posts/update-copyright;
+    license = licenses.gpl3;
+  };
+}

pkgs/development/python-modules/x256/default.nix

@@ -0,0 +1,22 @@
+{ stdenv, buildPythonPackage, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "x256";
+  version = "0.0.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "00g02b9a6jsl377xb5fmxvkjff3lalw21n430a4zalqyv76dnmgq";
+  };
+
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Find the nearest xterm 256 color index for an RGB";
+    homepage = https://github.com/magarcia/python-x256;
+    license = licenses.mit;
+    maintainers = with maintainers; [ Scriptkiddi ];
+  };
+}
+

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "zc.lockfile";
-  version = "1.3.0";
+  version = "1.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "96cb13769e042988ea25d23d44cf09342ea0f887083d0f9736968f3617665853";
+    sha256 = "0lrj2zdr06sff7i151710jbbnnhx4phdc0qpns8jkarpd62f7a4m";
   };
 
   buildInputs = [ mock ];