Merge staging-next into staging

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

@@ -7,13 +7,13 @@
 }:
 
 buildPythonPackage rec {
-  version = "5.0.0";
+  version = "6.0.0";
   pname = "azure-mgmt-storage";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "dd27ffc8c763932100dff1cda3d5a72dc2348686093732747f68396b1dd3fabf";
+    sha256 = "0pgmxr8shz6rmgbacfy1xb99y9ja38ck1lap0n58m6jjy1mgxk2w";
   };
 
   postInstall = if isPy3k then "" else ''

pkgs/development/python-modules/boolean-py/default.nix

@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "boolean.py";
-  version = "3.6";
+  version = "3.7";
 
   src = fetchFromGitHub {
     owner = "bastikr";
     repo = "boolean.py";
     rev = "v${version}";
-    sha256 = "1wc89y73va58cj7dsx6c199zpxsy9q53dsffsdj6zmc90inqz6qs";
+    sha256 = "1q9ji2jq07qr6vgp9yv6y8lx6h0zyi07fqjga3yi3vpfk46h2jn1";
   };
 
   meta = with lib; {

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Cerberus";
-  version = "1.3.1";
+  version = "1.3.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0be48fc0dc84f83202a5309c0aa17cd5393e70731a1698a50d118b762fbe6875";
+    sha256 = "12cm547hpypqd7bwcl4wr4w6varibc1dagzicg5qbp86yaa6cbih";
   };
 
   checkInputs = [ pytestrunner pytest ];

pkgs/development/python-modules/check-manifest/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi }:
+{ stdenv, buildPythonPackage, fetchPypi, toml }:
 
 buildPythonPackage rec {
   pname = "check-manifest";
@@ -9,6 +9,8 @@ buildPythonPackage rec {
     sha256 = "42de6eaab4ed149e60c9b367ada54f01a3b1e4d6846784f9b9710e770ff5572c";
   };
 
+  propagatedBuildInputs = [ toml ];
+
   doCheck = false;
 
   meta = with stdenv.lib; {

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

@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "django-extensions";
-  version = "2.2.3";
+  version = "2.2.5";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = version;
-    sha256 = "19bln9z25dmz1waqcxivlwg20dlm033c7f4z3h3mkhzkbk928y71";
+    sha256 = "0053yqq4vq3mwy7zkfs5vfm3g8j9sfy3vrc6xby83qlj9wz43ipi";
   };
 
   postPatch = ''

pkgs/development/python-modules/dogpile.cache/default.nix

@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "dogpile.cache";
-  version = "0.8.0";
+  version = "0.9.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "70f5eae4aec908f76188a2c287e07105f60c05d879bb9a4efcc5ba44563d8de6";
+    sha256 = "0sr1fn6b4k5bh0cscd9yi8csqxvj4ngzildav58x5p694mc86j5k";
   };
 
   # Disable concurrency tests that often fail,

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

@@ -1,14 +1,14 @@
 { lib, buildPythonPackage, fetchFromGitHub }:
 
 buildPythonPackage rec {
-  version = "1.3.0";
+  version = "1.3.1";
   pname = "elementpath";
 
   src = fetchFromGitHub {
     owner = "sissaschool";
     repo = "elementpath";
     rev = "v${version}";
-    sha256 = "0ahqqqpcf3fd6xcdhiwwscincyj6h5xyjaacnqxwph1y1b8mnzyw";
+    sha256 = "0060cd49m0q25k7anzyiz76360hag2f9j5hvqhbmscivf1ssckzq";
   };
 
   # avoid circular dependency with xmlschema which directly depends on this

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "emcee";
-  version = "3.0.0";
+  version = "3.0.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "353c26d8a8b09553532cd93662ddbedcd1a77feecefda5e46ea7e38829dede89";
+    sha256 = "01mx1w4a7j5p29a3r7ilh9la9n6gnlgwb46m439vrnfgvbvjjy9c";
   };
 
   propagatedBuildInputs = [ numpy ];

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

@@ -10,9 +10,15 @@ buildPythonPackage rec {
     sha256 = "05id72xwvhni23yasdvpdd8vsf3v4j6gzbqqff2g04j6xcih85vj";
   };
 
-  buildInputs = [ nose ];
+  checkInputs = [ nose ];
   propagatedBuildInputs = [ flask six ];
 
+  # Exclude test_acl_uncaught_exception_500 test case because is not compatible
+  # with Flask>=1.1.0. See: https://github.com/corydolphin/flask-cors/issues/253
+  checkPhase = ''
+    nosetests --exclude test_acl_uncaught_exception_500
+  '';
+
   meta = with stdenv.lib; {
     description = "A Flask extension adding a decorator for CORS support";
     homepage = https://github.com/corydolphin/flask-cors;

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

@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "Flask-JWT-Extended";
-  version = "3.24.0";
+  version = "3.24.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1znqjp780nrp94hjcrcx0945izzl3zsrqkmdac44d2fmlnbdp2by";
+    sha256 = "1p8rwcsscyjw2m7dbybiaflqk4z1r2d1kp9r9qqyjfzblxpyxa0a";
   };
 
   propagatedBuildInputs = [ dateutil flask pyjwt werkzeug ];

pkgs/development/python-modules/ipython/5.nix

@@ -0,0 +1,62 @@
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+# Build dependencies
+, glibcLocales
+# Test dependencies
+, nose
+, pygments
+, testpath
+, isPy27
+, mock
+# Runtime dependencies
+, backports_shutil_get_terminal_size
+, decorator
+, pathlib2
+, pickleshare
+, requests
+, simplegeneric
+, traitlets
+, prompt_toolkit
+, pexpect
+, appnope
+}:
+
+buildPythonPackage rec {
+  pname = "ipython";
+  version = "5.8.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906";
+  };
+
+  prePatch = stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace setup.py --replace "'gnureadline'" " "
+  '';
+
+  buildInputs = [ glibcLocales ];
+
+  checkInputs = [ nose pygments testpath ] ++ lib.optional isPy27 mock;
+
+  propagatedBuildInputs = [
+    backports_shutil_get_terminal_size decorator pickleshare prompt_toolkit
+    simplegeneric traitlets requests pathlib2 pexpect
+  ] ++ lib.optionals stdenv.isDarwin [ appnope ];
+
+  LC_ALL="en_US.UTF-8";
+
+  doCheck = false; # Circular dependency with ipykernel
+
+  checkPhase = ''
+    nosetests
+  '';
+
+  meta = {
+    description = "IPython: Productive Interactive Computing";
+    homepage = http://ipython.org/;
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ bjornfor orivej lnl7 ];
+  };
+}

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

@@ -25,11 +25,11 @@
 
 buildPythonPackage rec {
   pname = "notebook";
-  version = "6.0.1";
+  version = "5.7.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "660976fe4fe45c7aa55e04bf4bccb9f9566749ff637e9020af3422f9921f9a5d";
+    sha256 = "573e0ae650c5d76b18b6e564ba6d21bf321d00847de1d215b418acb64f056eb8";
   };
 
   LC_ALL = "en_US.utf8";

pkgs/development/python-modules/paho-mqtt/default.nix

@@ -3,14 +3,14 @@
 
 buildPythonPackage rec {
   pname = "paho-mqtt";
-  version = "1.4.0";
+  version = "1.5.0";
 
   # No tests in PyPI tarball
   src = fetchFromGitHub {
     owner = "eclipse";
     repo = "paho.mqtt.python";
     rev = "v${version}";
-    sha256 = "1xg9ppz2lqacd9prsrx93q2wfkjjyla03xlfw74aj1alz9ki5hrs";
+    sha256 = "1fq5z53g2k18iiqnz5qq87vzjpppfza072nx0dwllmhimm2dskh5";
   };
 
   postPatch = ''

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

@@ -5,7 +5,7 @@
 
 buildPythonPackage rec {
   pname = "plumbum";
-  version = "1.6.7";
+  version = "1.6.8";
 
   checkInputs = [ pytest ];
 
@@ -14,6 +14,6 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d143f079bfb60b11e9bec09a49695ce2e55ce5ca0246877bdb0818ab7c7fc312";
+    sha256 = "14mbyvc1y25lr72n1zh9ym5ngify7zdr57lxahidq03ycpwz4wc5";
   };
 }

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

@@ -3,7 +3,7 @@
 }:
 buildPythonPackage rec {
   pname = "pypillowfight";
-  version = "0.2.4";
+  version = "0.3.0";
 
   src = fetchFromGitLab {
     domain = "gitlab.gnome.org";
@@ -11,7 +11,7 @@ buildPythonPackage rec {
     owner = "OpenPaperwork";
     repo = "libpillowfight";
     rev = version;
-    sha256 = "0wbzfhbzim61fmkm7p7f2rwslacla1x00a6xp50haawjh9zfwc4y";
+    sha256 = "096242v425mlqqj5g1giy59p7grxp05g78w6bk37vzph98jrgv3w";
   };
 
   prePatch = ''

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

@@ -15,6 +15,8 @@ buildPythonPackage rec {
     sha256 = "1acbfvpbr45i137s00mbhh21p71ywjfw3r8z0ybcmjjqz7rbwg8c";
   };
 
+  patches = [ ./setup.py-Fix-the-setuptools-version-check.patch ];
+
   # NameError: name 'mibBuilder' is not defined
   doCheck = false;
 

pkgs/development/python-modules/pysnmp/setup.py-Fix-the-setuptools-version-check.patch

@@ -0,0 +1,27 @@
+From 5f843f7c8554e2feab7f57d8718231408196fd80 Mon Sep 17 00:00:00 2001
+From: Michael Weiss <dev.primeos@gmail.com>
+Date: Fri, 1 Nov 2019 18:47:14 +0100
+Subject: [PATCH] setup.py: Fix the setuptools version check
+
+This broke the Nix build after setuptools.__version__ changed from
+"41.2.0" to "41.4.0.post20191022".
+---
+ setup.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 0d987d5c..4f625d7c 100644
+--- a/setup.py
++++ b/setup.py
+@@ -63,7 +63,7 @@ try:
+ 
+     setup, Command = setuptools.setup, setuptools.Command
+ 
+-    observed_version = [int(x) for x in setuptools.__version__.split('.')]
++    observed_version = [int(x) for x in setuptools.__version__.split('.')[0:3]]
+     required_version = [36, 2, 0]
+ 
+     # NOTE(etingof): require fresh setuptools to build proper wheels
+-- 
+2.23.0
+

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

@@ -12,6 +12,7 @@
 , dask
 , cloudpickle
 , pytest
+, imageio
 }:
 
 buildPythonPackage rec {
@@ -25,7 +26,7 @@ buildPythonPackage rec {
 
   buildInputs = [ cython ];
 
-  propagatedBuildInputs = [ numpy scipy matplotlib networkx six pillow pywavelets dask cloudpickle ];
+  propagatedBuildInputs = [ numpy scipy matplotlib networkx six pillow pywavelets dask cloudpickle imageio ];
 
   checkInputs = [ pytest ];
 
@@ -37,4 +38,4 @@ buildPythonPackage rec {
     homepage = http://scikit-image.org;
     license = lib.licenses.bsd3;
   };
-}
+}

pkgs/development/python-modules/sentry-sdk/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, urllib3, certifi, django, flask, tornado, sanic, aiohttp, bottle, rq, falcon, pyramid, celery }:
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, urllib3, certifi, django, flask, tornado, bottle, rq, falcon, celery, pyramid, sanic, aiohttp }:
 
 buildPythonPackage rec {
   pname = "sentry-sdk";
@@ -9,7 +9,8 @@ buildPythonPackage rec {
     sha256 = "ff14935cc3053de0650128f124c36f34a4be120b8cc522c149f5cba342c1fd05";
   };
 
-  checkInputs = [ django flask tornado sanic aiohttp bottle rq falcon pyramid celery ];
+  checkInputs = [ django flask tornado bottle rq falcon ]
+  ++ stdenv.lib.optionals isPy3k [ celery pyramid sanic aiohttp ];
 
   propagatedBuildInputs = [ urllib3 certifi ];