Merge pull request #33204 from NixOS/python-unstable

Python: upgrade package set

164 files changed, 1240 insertions, 879 deletions

diff --git a/pkgs/applications/misc/haxor-news/default.nix b/pkgs/applications/misc/haxor-news/default.nix
index dc771fc2d5e..c82e5026ff1 100644
--- a/pkgs/applications/misc/haxor-news/default.nix
+++ b/pkgs/applications/misc/haxor-news/default.nix
@@ -1,15 +1,17 @@
-{ stdenv, fetchurl, pythonPackages }:
+{ stdenv, fetchurl, python }:
 
-pythonPackages.buildPythonApplication rec {
-  version = "0.4.2";
-  name = "haxor-news-${version}";
+with python.pkgs;
 
-  src = fetchurl {
-    url = "https://github.com/donnemartin/haxor-news/archive/${version}.tar.gz";
-    sha256 = "0543k5ys044f2a1q8k36djnnq2h2dffnwbkva9snjjy30nlwwdgs";
+buildPythonApplication rec {
+  pname = "haxor-news";
+  version = "0.4.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "5b9af8338a0f8b95a8133b66ef106553823813ac171c0aefa3f3f2dbeb4d7f88";
   };
 
-  propagatedBuildInputs = with pythonPackages; [
+  propagatedBuildInputs = [
     click
     colorama
     requests
@@ -18,6 +20,12 @@ pythonPackages.buildPythonApplication rec {
     six
   ];
 
+  checkInputs = [ mock ];
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s tests -v
+  '';
+
   meta = with stdenv.lib; {
     homepage = https://github.com/donnemartin/haxor-news;
     description = "Browse Hacker News like a haxor";
diff --git a/pkgs/applications/office/watson/default.nix b/pkgs/applications/office/watson/default.nix
index a1fcfd5de70..e0f0c58b450 100644
--- a/pkgs/applications/office/watson/default.nix
+++ b/pkgs/applications/office/watson/default.nix
@@ -1,13 +1,14 @@
-{ stdenv, pythonPackages }:
+{ stdenv, pythonPackages, fetchpatch }:
 
-pythonPackages.buildPythonApplication rec {
+with pythonPackages;
+
+buildPythonApplication rec {
   pname = "td-watson";
-  name = "${pname}-${version}";
-  version = "1.4.0";
+  version = "1.5.2";
 
-  src = pythonPackages.fetchPypi {
+  src = fetchPypi {
     inherit version pname;
-    sha256 = "1py0g4990jmvq0dn7jasda7f10kzr41bix46hnbyc1rshjzc17hq";
+    sha256 = "6e03d44a9278807fe5245e9ed0943f13ffb88e11249a02655c84cb86260b27c8";
   };
 
   # uses tox, test invocation fails
@@ -15,8 +16,16 @@ pythonPackages.buildPythonApplication rec {
   checkPhase = ''
     py.test -vs tests
  '';
-  checkInputs = with pythonPackages; [ py pytest pytest-datafiles mock pytest-mock pytestrunner ];
-  propagatedBuildInputs = with pythonPackages; [ requests click arrow ];
+
+  patches = [
+    (fetchpatch {
+      url = https://github.com/TailorDev/Watson/commit/f5760c71cbc22de4e12ede8f6f7257515a9064d3.patch;
+      sha256 = "0s9h26915ilpbd0qhmvk77r3gmrsdrl5l7dqxj0l5q66fp0z6b0g";
+    })
+  ];
+
+  checkInputs = [ py pytest pytest-datafiles mock pytest-mock pytestrunner ];
+  propagatedBuildInputs = [ requests click arrow ];
 
   meta = with stdenv.lib; {
     homepage = https://tailordev.github.io/Watson/;
@@ -24,4 +33,4 @@ pythonPackages.buildPythonApplication rec {
     license = licenses.mit;
     maintainers = with maintainers; [ mguentner ] ;
   };
-}
\ No newline at end of file
+}
diff --git a/pkgs/development/python-modules/APScheduler/default.nix b/pkgs/development/python-modules/APScheduler/default.nix
index 5acb6cd5785..931239c0987 100644
--- a/pkgs/development/python-modules/APScheduler/default.nix
+++ b/pkgs/development/python-modules/APScheduler/default.nix
@@ -20,12 +20,12 @@
 
 buildPythonPackage rec {
   pname = "APScheduler";
-  version = "3.4.0";
+  version = "3.5.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b51118a8ed014104f7e440456dcbd90f2015aea7bcc34c57e307fb34bc746316";
+    sha256 = "1ce44d5132b7951f4614067c88ca34cfee1ff97f6f0892581d79b636d83eab89";
   };
 
   buildInputs = [
diff --git a/pkgs/development/python-modules/Mako/default.nix b/pkgs/development/python-modules/Mako/default.nix
new file mode 100644
index 00000000000..f3f1eed265d
--- /dev/null
+++ b/pkgs/development/python-modules/Mako/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, markupsafe
+, nose
+, mock
+, pytest
+, isPyPy
+}:
+
+buildPythonPackage rec {
+  pname = "Mako";
+  version = "1.0.7";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae";
+  };
+
+  checkInputs = [ markupsafe nose mock pytest ];
+  propagatedBuildInputs = [ markupsafe ];
+
+  doCheck = !isPyPy;  # https://bitbucket.org/zzzeek/mako/issue/238/2-tests-failed-on-pypy-24-25
+
+  meta = {
+    description = "Super-fast templating language";
+    homepage = http://www.makotemplates.org;
+    license = lib.licenses.mit;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ domenkozar ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/MechanicalSoup/default.nix b/pkgs/development/python-modules/MechanicalSoup/default.nix
index 56e2cf501ed..b5d202af50a 100644
--- a/pkgs/development/python-modules/MechanicalSoup/default.nix
+++ b/pkgs/development/python-modules/MechanicalSoup/default.nix
@@ -1,5 +1,5 @@
 { fetchPypi, buildPythonPackage, lib
-, requests, beautifulsoup4, six
+, requests, beautifulsoup4, six, lxml
 , pytestrunner, requests-mock, pytestcov, pytest
 }:
 
@@ -7,23 +7,23 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "MechanicalSoup";
-  version = "0.8.0";
+  version = "0.9.0.post4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "38a6ca35428196be94f87f8f036ee4a88b1418d1f77e5634ad92acfaa22c28da";
+    sha256 = "ce8f822afbc9bef1499be417e8d5deecd0cd32606420165700e89477955f03ab";
   };
 
   checkInputs = [ pytest pytestrunner requests-mock pytestcov ];
 
-  propagatedBuildInputs = [ requests beautifulsoup4 six ];
+  propagatedBuildInputs = [ lxml requests beautifulsoup4 six ];
 
   # Requires network
   doCheck = false;
 
   postPatch = ''
     # Is in setup_requires but not used in setup.py...
-    substituteInPlace setup.py --replace "'pytest-runner'," ""
+    substituteInPlace setup.py --replace "'pytest-runner'" ""
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/Nikola/default.nix b/pkgs/development/python-modules/Nikola/default.nix
index f281a02d49b..8f8d91c64d2 100644
--- a/pkgs/development/python-modules/Nikola/default.nix
+++ b/pkgs/development/python-modules/Nikola/default.nix
@@ -30,7 +30,7 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "Nikola";
-  version = "7.8.10";
+  version = "7.8.11";
 
   # Nix contains only Python 3 supported version of doit, which is a dependency
   # of Nikola. Python 2 support would require older doit 0.29.0 (which on the
@@ -47,7 +47,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e242c3d0dd175d95a0baf5268b108081ba160b83ceafec8c9bc2ec0a24a56537";
+    sha256 = "10d95b3af84e61496ef729665eafa2235fd0fd4cc6c57644dd0f2c19a968dd0f";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/Theano/default.nix b/pkgs/development/python-modules/Theano/default.nix
index e0ff839ce1b..03dc825218e 100644
--- a/pkgs/development/python-modules/Theano/default.nix
+++ b/pkgs/development/python-modules/Theano/default.nix
@@ -35,13 +35,13 @@ let
 in buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "Theano";
-  version = "0.9.0";
+  version = "1.0.1";
 
   disabled = isPyPy || pythonOlder "2.6" || (isPy3k && pythonOlder "3.3");
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "05xwg00da8smkvkh6ywbywqzj8dw7x840jr74wqhdy9icmqncpbl";
+    sha256 = "88d8aba1fe2b6b75eacf455d01bc7e31e838c5a0fb8c13dde2d9472495ff4662";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/absl-py/default.nix b/pkgs/development/python-modules/absl-py/default.nix
index 1c9fa3d786f..ca43e122a30 100644
--- a/pkgs/development/python-modules/absl-py/default.nix
+++ b/pkgs/development/python-modules/absl-py/default.nix
@@ -6,12 +6,12 @@
 
 buildPythonPackage rec {
   pname = "absl-py";
-  version = "0.1.5";
+  version = "0.1.7";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "94943ed0cd77077fe2d18e79b2f28d3e92f585f7d1c6edc75e640121f3c5d580";
+    sha256 = "4ea22ae860f3a556511291e7f1284942199c81377f47ec4248163defb1b9e6ee";
   };
 
   propagatedBuildInputs = [ six ];
diff --git a/pkgs/development/python-modules/aenum/default.nix b/pkgs/development/python-modules/aenum/default.nix
index 3aa03aaa599..45e7f8915ac 100644
--- a/pkgs/development/python-modules/aenum/default.nix
+++ b/pkgs/development/python-modules/aenum/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "aenum";
-  version = "2.0.8";
+  version = "2.0.9";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3209fa41b8c41345442e8d9b5158a57d3e96d84c3d5ebbe8e521e1e2eff1598d";
+    sha256 = "d98bc55136d696fcf323760c3db0de489da9e41fd51283fa6f90205deb85bf6a";
   };
 
   doCheck = !isPy3k;
diff --git a/pkgs/development/python-modules/aiohttp/default.nix b/pkgs/development/python-modules/aiohttp/default.nix
index 53443b3b32f..44e19072057 100644
--- a/pkgs/development/python-modules/aiohttp/default.nix
+++ b/pkgs/development/python-modules/aiohttp/default.nix
@@ -13,12 +13,12 @@
 
 buildPythonPackage rec {
   pname = "aiohttp";
-  version = "2.3.3";
+  version = "2.3.7";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0a2e33e90560dacb819b095b9d9611597925d75d1b93dd9490055d3826d98a82";
+    sha256 = "fe294df38e9c67374263d783a7a29c79372030f5962bd5734fa51c6f4bbfee3b";
   };
 
   disabled = pythonOlder "3.4";
diff --git a/pkgs/development/python-modules/arrow/default.nix b/pkgs/development/python-modules/arrow/default.nix
index a85987a95b1..72b88d3e557 100644
--- a/pkgs/development/python-modules/arrow/default.nix
+++ b/pkgs/development/python-modules/arrow/default.nix
@@ -1,23 +1,22 @@
 { stdenv, buildPythonPackage, fetchPypi
-, nose, chai, simplejson
+, nose, chai, simplejson, backports_functools_lru_cache
 , dateutil }:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "arrow";
-  version = "0.10.0";
+  version = "0.12.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08n7q2l69hlainds1byd4lxhwrq7zsw7s640zkqc3bs5jkq0cnc0";
+    sha256 = "a15ecfddf334316e3ac8695e48c15d1be0d6038603b33043930dcf0e675c86ee";
   };
 
   checkPhase = ''
     nosetests --cover-package=arrow
   '';
 
-  buildInputs = [ nose chai simplejson ];
-  propagatedBuildInputs = [ dateutil ];
+  checkInputs = [ nose chai simplejson ];
+  propagatedBuildInputs = [ dateutil backports_functools_lru_cache ];
 
   meta = with stdenv.lib; {
     description = "Python library for date manipulation";
diff --git a/pkgs/development/python-modules/asgiref/default.nix b/pkgs/development/python-modules/asgiref/default.nix
index 1b5112fb335..fedd4b81a9d 100644
--- a/pkgs/development/python-modules/asgiref/default.nix
+++ b/pkgs/development/python-modules/asgiref/default.nix
@@ -1,12 +1,12 @@
 { stdenv, buildPythonPackage, fetchurl, six }:
 buildPythonPackage rec {
-  version = "1.1.2";
+  version = "2.0.1";
   pname = "asgiref";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://pypi/a/asgiref/${name}.tar.gz";
-    sha256 = "8b46c3d6e2ad354d9da3cfb9873f9bd46fe1b768fbc11065275ba5430a46700c";
+    sha256 = "c3d70c473a2b7e525e18e68504630943e107f5b32f440c00c8543f94f565c855";
   };
 
   propagatedBuildInputs = [ six ];
diff --git a/pkgs/development/python-modules/asn1crypto/default.nix b/pkgs/development/python-modules/asn1crypto/default.nix
index eedaac50fac..5f512fcd6f8 100644
--- a/pkgs/development/python-modules/asn1crypto/default.nix
+++ b/pkgs/development/python-modules/asn1crypto/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "asn1crypto";
-  version = "0.23.0";
+  version = "0.24.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0874981329cfebb366d6584c3d16e913f2a0eb026c9463efcc4aaf42a9d94d70";
+    sha256 = "9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49";
   };
 
   # No tests included
diff --git a/pkgs/development/python-modules/astor/default.nix b/pkgs/development/python-modules/astor/default.nix
index 965bf37d520..6f50b7157e5 100644
--- a/pkgs/development/python-modules/astor/default.nix
+++ b/pkgs/development/python-modules/astor/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "astor";
-  version = "0.5";
+  version = "0.6.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1fdafq5hkis1fxqlmhw0sn44zp2ar46nxhbc22cvwg7hsd8z5gsa";
+    sha256 = "ff6d2e2962d834acb125cc4dcc80c54a8c17c253f4cc9d9c43b5102a560bb75d";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/astroid/default.nix b/pkgs/development/python-modules/astroid/default.nix
index 86a0daa0456..862157f686a 100644
--- a/pkgs/development/python-modules/astroid/default.nix
+++ b/pkgs/development/python-modules/astroid/default.nix
@@ -6,11 +6,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "astroid";
-  version = "1.5.3";
+  version = "1.6.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "492c2a2044adbf6a84a671b7522e9295ad2f6a7c781b899014308db25312dd35";
+    sha256 = "71dadba2110008e2c03f9fde662ddd2053db3c0489d0e03c94e828a0399edd4f";
   };
 
   propagatedBuildInputs = [ logilab_common six lazy-object-proxy wrapt ]
diff --git a/pkgs/development/python-modules/astropy/default.nix b/pkgs/development/python-modules/astropy/default.nix
index 12f00be0cb7..514762b7a37 100644
--- a/pkgs/development/python-modules/astropy/default.nix
+++ b/pkgs/development/python-modules/astropy/default.nix
@@ -7,13 +7,13 @@
 buildPythonPackage rec {
   
   pname = "astropy";
-  version = "2.0.2";
+  version = "2.0.3";
 
   name = "${pname}-${version}";
   doCheck = false; #Some tests are failing. More importantly setup.py hangs on completion. Needs fixing with a proper shellhook.
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4544a422b1173d79b2d65ba74c627f04a5fd8530d97fb604752d657d754e103d";
+    sha256 = "fdfc0248f6250798ed6d1327be609cb901db89ae01fc768cfbc9e263bdf56f4f";
   };
 
   propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires
diff --git a/pkgs/development/python-modules/attrs/default.nix b/pkgs/development/python-modules/attrs/default.nix
index e58bf3846dc..8ef2b5989f4 100644
--- a/pkgs/development/python-modules/attrs/default.nix
+++ b/pkgs/development/python-modules/attrs/default.nix
@@ -2,17 +2,16 @@
 , pympler, coverage, six, clang }:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "attrs";
-  version = "17.2.0";
+  version = "17.4.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04gx08ikpk26wnq22f7l42gapcvk8iz1512r927k6sadz6cinkax";
+    sha256 = "1c7960ccfd6a005cd9f7ba884e6316b5e430a3f1a6c37c5f87d8b43f83b54ec9";
   };
 
   # macOS needs clang for testing
-  buildInputs = [
+  checkInputs = [
     pytest hypothesis zope_interface pympler coverage six
   ] ++ lib.optionals (stdenv.isDarwin) [ clang ];
 
@@ -20,6 +19,9 @@ buildPythonPackage rec {
     py.test
   '';
 
+  # To prevent infinite recursion with pytest
+  doCheck = false;
+
   meta = with lib; {
     description = "Python attributes without boilerplate";
     homepage = https://github.com/hynek/attrs;
diff --git a/pkgs/development/python-modules/aws-xray-sdk/default.nix b/pkgs/development/python-modules/aws-xray-sdk/default.nix
new file mode 100644
index 00000000000..dae88b34900
--- /dev/null
+++ b/pkgs/development/python-modules/aws-xray-sdk/default.nix
@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, jsonpickle
+, wrapt
+, requests
+}:
+
+buildPythonPackage rec {
+  pname = "aws-xray-sdk";
+  version = "0.95";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "9e7ba8dd08fd2939376c21423376206bff01d0deaea7d7721c6b35921fed1943";
+  };
+
+  propagatedBuildInputs = [
+    jsonpickle wrapt requests
+  ];
+
+  meta = {
+    description = "AWS X-Ray SDK for the Python programming language";
+    license = lib.licenses.asl20;
+    homepage = https://github.com/aws/aws-xray-sdk-python;
+  };
+
+  doCheck = false;
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/backports_abc/default.nix b/pkgs/development/python-modules/backports_abc/default.nix
new file mode 100644
index 00000000000..ab34d376de0
--- /dev/null
+++ b/pkgs/development/python-modules/backports_abc/default.nix
@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "backports_abc";
+  version = "0.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = {
+    homepage = https://github.com/cython/backports_abc;
+    license = lib.licenses.psfl;
+    description = "A backport of recent additions to the 'collections.abc' module";
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/backports_functools_lru_cache/default.nix b/pkgs/development/python-modules/backports_functools_lru_cache/default.nix
new file mode 100644
index 00000000000..2442e132f1b
--- /dev/null
+++ b/pkgs/development/python-modules/backports_functools_lru_cache/default.nix
@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+}:
+
+buildPythonPackage rec {
+  pname = "backports.functools_lru_cache";
+  version = "1.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f";
+  };
+
+  buildInputs = [ setuptools_scm ];
+  doCheck = false; # No proper test
+
+  meta = {
+    description = "Backport of functools.lru_cache";
+    homepage = https://github.com/jaraco/backports.functools_lru_cache;
+    license = lib.licenses.mit;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/backports_lzma/default.nix b/pkgs/development/python-modules/backports_lzma/default.nix
new file mode 100644
index 00000000000..9b622eb6b06
--- /dev/null
+++ b/pkgs/development/python-modules/backports_lzma/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isPy3k
+, lzma
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "backports.lzma";
+  version = "0.0.8";
+
+  disabled = isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "200584ad5079d8ca6b1bfe14890c7be58666ab0128d8ca26cfb2669b476085f3";
+  };
+
+  buildInputs = [ lzma ];
+
+  # Needs the compiled module in $out
+  checkPhase = ''
+    PYTHONPATH=$out/${python.sitePackages}:$PYTHONPATH ${python.interpreter} -m unittest discover -s test
+  '';
+
+  meta = {
+    description = "Backport of Python 3.3's 'lzma' module for XZ/LZMA compressed files";
+    homepage = https://github.com/peterjc/backports.lzma;
+    license = lib.licenses.bsd3;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
new file mode 100644
index 00000000000..ea09a003c66
--- /dev/null
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, numpy
+}:
+
+buildPythonPackage rec {
+  pname = "biopython";
+  version = "1.70";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b";
+  };
+
+  propagatedBuildInputs = [ numpy ];
+  # Checks try to write to $HOME, which does not work with nix
+  doCheck = false;
+  meta = {
+    description = "Python library for bioinformatics";
+    longDescription = ''
+      Biopython is a set of freely available tools for biological computation
+      written in Python by an international team of developers. It is a
+      distributed collaborative effort to develop Python libraries and
+      applications which address the needs of current and future work in
+      bioinformatics.
+    '';
+    homepage = http://biopython.org/wiki/Documentation;
+    maintainers = with lib.maintainers; [ luispedro ];
+    license = lib.licenses.bsd3;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/bokeh/default.nix b/pkgs/development/python-modules/bokeh/default.nix
index 244ee43d0aa..e3c77fa65cf 100644
--- a/pkgs/development/python-modules/bokeh/default.nix
+++ b/pkgs/development/python-modules/bokeh/default.nix
@@ -34,11 +34,11 @@
 buildPythonPackage rec {
   pname = "bokeh";
   name = "${pname}${version}";
-  version = "0.12.10";
+  version = "0.12.13";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6465fae82e94223f16584645b38d34a73d95712870f29c0244649c2cbf2c8393";
+    sha256 = "6e28cbfd88de0c459435278b75f9982591ec0aaa3d37a195052645e1c62e89e3";
   };
 
   disabled = isPyPy;
diff --git a/pkgs/development/python-modules/bootstrapped-pip/default.nix b/pkgs/development/python-modules/bootstrapped-pip/default.nix
index ef12e39f23b..1a20639c2de 100644
--- a/pkgs/development/python-modules/bootstrapped-pip/default.nix
+++ b/pkgs/development/python-modules/bootstrapped-pip/default.nix
@@ -9,9 +9,9 @@ let
   };
   setuptools_source = fetchPypi {
     pname = "setuptools";
-    version = "38.2.3";
+    version = "38.2.5";
     format = "wheel";
-    sha256 = "0c4j3jiiwc0h1bdv4xklinp90spgvgiv5fsxp119hif9934nfxfs";
+    sha256 = "bcf0d4f3e2f7890e658db11e218b8643afffb905a0e2f2a7d5a6a3e949bb87e6";
   };
 
   # TODO: Shouldn't be necessary anymore for pip > 9.0.1!
diff --git a/pkgs/development/python-modules/boto3/default.nix b/pkgs/development/python-modules/boto3/default.nix
new file mode 100644
index 00000000000..eaab0031205
--- /dev/null
+++ b/pkgs/development/python-modules/boto3/default.nix
@@ -0,0 +1,50 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, botocore
+, jmespath
+, s3transfer
+, futures
+, docutils
+, nose
+, mock
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname =  "boto3";
+  version = "1.4.8";
+
+  src = fetchFromGitHub {
+    owner = "boto";
+    repo  = "boto3";
+    rev   = version;
+    sha256 = "11ysd7a9l5y98q7b7az56phsj2m7w90abf4jabwrknp2c43sq9bi";
+  };
+
+  propagatedBuildInputs = [ botocore jmespath s3transfer ] ++ lib.optionals (!isPy3k) [ futures ];
+  checkInputs = [ docutils nose mock ];
+
+  checkPhase = ''
+    runHook preCheck
+    # This method is not in mock. It might have appeared in some versions.
+    sed -i 's/action.assert_called_once()/self.assertEqual(action.call_count, 1)/' \
+      tests/unit/resources/test_factory.py
+    nosetests -d tests/unit --verbose
+    runHook postCheck
+  '';
+
+  # Network access
+  doCheck = false;
+
+  meta = {
+    homepage = https://github.com/boto/boto3;
+    license = lib.licenses.asl20;
+    description = "AWS SDK for Python";
+    longDescription = ''
+      Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for
+      Python, which allows Python developers to write software that makes use of
+      services like Amazon S3 and Amazon EC2.
+    '';
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/botocore/default.nix b/pkgs/development/python-modules/botocore/default.nix
index fe3fe06f4e7..f8dd1649949 100644
--- a/pkgs/development/python-modules/botocore/default.nix
+++ b/pkgs/development/python-modules/botocore/default.nix
@@ -12,11 +12,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "botocore";
-  version = "1.8.10";
+  version = "1.8.21";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16dznd0mxxs8imsl228vx5s9bz9v7ggajs496jy21n5a19cadkch";
+    sha256 = "e4513a02f68e7efd7494ee56db201d87620218ca879aae361abbb71bcde3aa5f";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/cached-property/default.nix b/pkgs/development/python-modules/cached-property/default.nix
new file mode 100644
index 00000000000..6ab5015a1e7
--- /dev/null
+++ b/pkgs/development/python-modules/cached-property/default.nix
@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, freezegun
+}:
+
+buildPythonPackage rec {
+  pname = "cached-property";
+  version = "1.3.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6562f0be134957547421dda11640e8cadfa7c23238fc4e0821ab69efdb1095f3";
+  };
+
+  checkInputs = [ freezegun ];
+
+  meta = {
+    description = "A decorator for caching properties in classes";
+    homepage = https://github.com/pydanny/cached-property;
+    license = lib.licenses.bsd3;
+    platforms = lib.platforms.unix;
+    maintainers = with lib.maintainers; [ ericsagnes ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/credstash/default.nix b/pkgs/development/python-modules/credstash/default.nix
index 810a6a7bd8e..6a9e1240b86 100644
--- a/pkgs/development/python-modules/credstash/default.nix
+++ b/pkgs/development/python-modules/credstash/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname    = "credstash";
-  version = "1.13.4";
+  version = "1.14.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "676cc03a6143dec260c78aeef09d08a64faf27c411f8a94f6d9338e985879f81";
+    sha256 = "718b337f7a6fa001e014386071f05c59900525d0507009126d2fe8d75fe0761d";
   };
 
   propagatedBuildInputs = [ cryptography boto3 pyyaml docutils ];
diff --git a/pkgs/development/python-modules/csscompressor/default.nix b/pkgs/development/python-modules/csscompressor/default.nix
index a9aad8d40e5..8d0e7a58e76 100644
--- a/pkgs/development/python-modules/csscompressor/default.nix
+++ b/pkgs/development/python-modules/csscompressor/default.nix
@@ -1,12 +1,12 @@
 { stdenv, buildPythonPackage, fetchPypi }:
 buildPythonPackage rec {
   pname = "csscompressor";
-  version = "0.9.4";
+  version = "0.9.5";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0e12f125b88379d7b680636d94a3c8fa14bed1de2358f7f9a9e6749e222cff3b";
+    sha256 = "afa22badbcf3120a4f392e4d22f9fff485c044a1feda4a950ecc5eba9dd31a05";
   };
 
   doCheck = false; # No tests
diff --git a/pkgs/development/python-modules/cx_freeze/default.nix b/pkgs/development/python-modules/cx_freeze/default.nix
index 3d937debe58..69a5e8c11d4 100644
--- a/pkgs/development/python-modules/cx_freeze/default.nix
+++ b/pkgs/development/python-modules/cx_freeze/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "cx_Freeze";
-  version = "5.0.2";
+  version = "5.1.1";
   name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zbx9j5z5l06bvwvlqvvn7h9dm7zjcjgxm7agbb625nymkq6cd15";
+    sha256 = "2eadddde670f5c5f6cf88638a0ac4e5d5fe181292a31063275fa56c7bf22426b";
   };
 
   propagatedBuildInputs = [ ncurses ];
diff --git a/pkgs/development/python-modules/cytoolz/default.nix b/pkgs/development/python-modules/cytoolz/default.nix
index dcb4e9474c3..83b1c893719 100644
--- a/pkgs/development/python-modules/cytoolz/default.nix
+++ b/pkgs/development/python-modules/cytoolz/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   pname = "cytoolz";
-  version = "0.8.2";
+  version = "0.9.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "476a2ad176de5eaef80499b7b43d4f72ba6d23df33d349088dae315e9b31c552";
+    sha256 = "5ebb55855a8bb7800afa58e52408763935527e0305f35600c71b43c86013dec2";
   };
 
   # Extension types
diff --git a/pkgs/development/python-modules/dask/default.nix b/pkgs/development/python-modules/dask/default.nix
index 70647b6377f..c3b45dc3c86 100644
--- a/pkgs/development/python-modules/dask/default.nix
+++ b/pkgs/development/python-modules/dask/default.nix
@@ -12,12 +12,12 @@
 
 buildPythonPackage rec {
   pname = "dask";
-  version = "0.15.4";
+  version = "0.16.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "cb93b8260f5f854ccf26b52bdc700600a08e6b7527085c7b7d63c04238bab9ea";
+    sha256 = "40d150b73e3366c9521e9dde206046a66906330074f87be901b1e1013ce6cb73";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/decorator/default.nix b/pkgs/development/python-modules/decorator/default.nix
new file mode 100644
index 00000000000..5cdbbfce77f
--- /dev/null
+++ b/pkgs/development/python-modules/decorator/default.nix
@@ -0,0 +1,20 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "decorator";
+  version = "4.0.11";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76";
+  };
+
+  meta = {
+    homepage = https://pypi.python.org/pypi/decorator;
+    description = "Better living through Python with decorators";
+    license = lib.licenses.mit;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/distro/default.nix b/pkgs/development/python-modules/distro/default.nix
index 49349839331..36264921f64 100644
--- a/pkgs/development/python-modules/distro/default.nix
+++ b/pkgs/development/python-modules/distro/default.nix
@@ -3,7 +3,7 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "distro";
-  version = "1.0.4";
+  version = "1.2.0";
 
   buildInputs = [ pytest pytestcov tox];
 
@@ -14,7 +14,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9b000b0d637bb0cbd130a7a4835681e6993e309a85564dfea9d884825fe46954";
+    sha256 = "d94370e43b676ac44fbe1ab68ca903a6147eaba3a9e8eff85b2c05556a455b76";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/django-jinja2/default.nix b/pkgs/development/python-modules/django-jinja2/default.nix
index aabfecfcacc..b8b632e1a18 100644
--- a/pkgs/development/python-modules/django-jinja2/default.nix
+++ b/pkgs/development/python-modules/django-jinja2/default.nix
@@ -5,7 +5,7 @@
 buildPythonPackage rec {
   pname = "django-jinja";
   name = "${pname}-${version}";
-  version = "2.2.2";
+  version = "2.4.1";
 
   meta = {
     description = "Simple and nonobstructive jinja2 integration with Django";
@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "099b99iprkvlsndrjmw4v3i3i60i9gm1aq5r88z15r7vgmv6sigj";
+    sha256 = "8a49d73de616a12075eee14c6d3bbab936261a463457d40348d8b8e2995cfbed";
   };
 
   buildInputs = [ django pytz tox ];
diff --git a/pkgs/development/python-modules/djangorestframework/default.nix b/pkgs/development/python-modules/djangorestframework/default.nix
index e2c8acd1a0b..b11847beaa9 100644
--- a/pkgs/development/python-modules/djangorestframework/default.nix
+++ b/pkgs/development/python-modules/djangorestframework/default.nix
@@ -1,12 +1,12 @@
 { stdenv, buildPythonPackage, fetchurl, django }:
 buildPythonPackage rec {
-  version = "3.7.3";
+  version = "3.7.7";
   pname = "djangorestframework";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://pypi/d/djangorestframework/${name}.tar.gz";
-    sha256 = "067960e5e9e5586d3b2d53a1d626c4800dc33cd8309487d404fc63355674556f";
+    sha256 = "9f9e94e8d22b100ed3a43cee8c47a7ff7b185e778a1f2da9ec5c73fc4e081b87";
   };
 
   # Test settings are missing
diff --git a/pkgs/development/python-modules/docker/default.nix b/pkgs/development/python-modules/docker/default.nix
index 88d85dad91a..4ce013ac797 100644
--- a/pkgs/development/python-modules/docker/default.nix
+++ b/pkgs/development/python-modules/docker/default.nix
@@ -3,13 +3,13 @@
 , ipaddress, backports_ssl_match_hostname, docker_pycreds
 }:
 buildPythonPackage rec {
-  version = "2.5.1";
+  version = "2.7.0";
   pname = "docker";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://pypi/d/docker/${name}.tar.gz";
-    sha256 = "b876e6909d8d2360e0540364c3a952a62847137f4674f2439320ede16d6db880";
+    sha256 = "144248308e8ea31c4863c6d74e1b55daf97cc190b61d0fe7b7313ab920d6a76c";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/docker_compose/default.nix b/pkgs/development/python-modules/docker_compose/default.nix
index 78e733c1b9d..e6be57c8b52 100644
--- a/pkgs/development/python-modules/docker_compose/default.nix
+++ b/pkgs/development/python-modules/docker_compose/default.nix
@@ -3,21 +3,20 @@
 , pyyaml, backports_ssl_match_hostname, colorama, docopt
 , dockerpty, docker, ipaddress, jsonschema, requests
 , six, texttable, websocket_client, cached-property
-, enum34, functools32
+, enum34, functools32,
 }:
 buildPythonApplication rec {
-  version = "1.15.0";
+  version = "1.18.0";
   pname = "docker-compose";
-  name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0yg58m5kk22kihbra0h40miqnbdmkirjr9y47wns613sdikrymmg";
+    sha256 = "2930cbfe2685018fbb75377600ab6288861d9955717b3f14212f63950351d379";
   };
 
   # lots of networking and other fails
   doCheck = false;
-  buildInputs = [ mock pytest nose ];
+  checkInputs = [ mock pytest nose ];
   propagatedBuildInputs = [
     pyyaml backports_ssl_match_hostname colorama dockerpty docker
     ipaddress jsonschema requests six texttable websocket_client
@@ -26,7 +25,7 @@ buildPythonApplication rec {
     stdenv.lib.optional (pythonOlder "3.4") enum34 ++
     stdenv.lib.optional (pythonOlder "3.2") functools32;
 
-  patchPhase = ''
+  postPatch = ''
     # Remove upper bound on requires, see also
     # https://github.com/docker/compose/issues/4431
     sed -i "s/, < .*',$/',/" setup.py
diff --git a/pkgs/development/python-modules/easy-thumbnails/default.nix b/pkgs/development/python-modules/easy-thumbnails/default.nix
index 38e201849c1..fbe5c02771d 100644
--- a/pkgs/development/python-modules/easy-thumbnails/default.nix
+++ b/pkgs/development/python-modules/easy-thumbnails/default.nix
@@ -5,7 +5,7 @@
 buildPythonPackage rec {
   pname = "easy-thumbnails";
   name = "${pname}-${version}";
-  version = "2.4.2";
+  version = "2.5";
 
   meta = {
     description = "Easy thumbnails for Django";
@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8cad7ea4fb2b800284e842d8a44f685cbc1968535be04c24a4bbf6e6dbc550c4";
+    sha256 = "e244d1f26027fc32c6ca60ffb0169a39099446f614b0433e907a2588ae7d9b95";
   };
 
   propagatedBuildInputs = [ django pillow ];
diff --git a/pkgs/development/python-modules/eve/default.nix b/pkgs/development/python-modules/eve/default.nix
index 1a9b684a9f3..d77b912fe0d 100644
--- a/pkgs/development/python-modules/eve/default.nix
+++ b/pkgs/development/python-modules/eve/default.nix
@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "Eve";
-  version = "0.7.4";
+  version = "0.7.5";
   name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0xihl5w2m4vkp0515qjibiy88pk380n5jmj8n9hh7q40b1vx1kwb";
+    sha256 = "dd4ffbc4725220ffdc8e32f8566c8870efaecdc238d0f96b18e1e83227eca55d";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/extras/default.nix b/pkgs/development/python-modules/extras/default.nix
new file mode 100644
index 00000000000..adcc43f2650
--- /dev/null
+++ b/pkgs/development/python-modules/extras/default.nix
@@ -0,0 +1,23 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "extras";
+  version = "1.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "132e36de10b9c91d5d4cc620160a476e0468a88f16c9431817a6729611a81b4e";
+  };
+
+  # error: invalid command 'test'
+  doCheck = false;
+
+  meta = {
+    description = "A module provides basic functions for parsing mime-type names and matching them against a list of media-ranges";
+    homepage = https://code.google.com/p/mimeparse/;
+    license = lib.licenses.mit;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/faker/default.nix b/pkgs/development/python-modules/faker/default.nix
index 3c95a26881e..2d459d625d0 100644
--- a/pkgs/development/python-modules/faker/default.nix
+++ b/pkgs/development/python-modules/faker/default.nix
@@ -8,12 +8,12 @@ assert pythonOlder "3.3" -> ipaddress != null;
 
 buildPythonPackage rec {
   pname = "Faker";
-  version = "0.8.7";
+  version = "0.8.8";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bf7dabcd6807c8829da28a4de491adf7998af506b8571db6a6eb58161157248a";
+    sha256 = "e928cf853ef69d7471421f2a3716a1239e43de0fa9855f4016ee0c9f1057328a";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/faulthandler/default.nix b/pkgs/development/python-modules/faulthandler/default.nix
index f8d877f0655..ee2a65e981c 100644
--- a/pkgs/development/python-modules/faulthandler/default.nix
+++ b/pkgs/development/python-modules/faulthandler/default.nix
@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "faulthandler";
-  version = "2.6";
+  version = "3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zywq3jaznddvqc3hnfrlv24wmpyq4xgajk9xhv6578qw1rpfj2r";
+    sha256 = "acc10e10909f0f956ba1b42b6c450ea0bdaaa27b3942899f65931396cfcdd36a";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/filelock/default.nix b/pkgs/development/python-modules/filelock/default.nix
index f1f07a99ad5..a22e1581b68 100644
--- a/pkgs/development/python-modules/filelock/default.nix
+++ b/pkgs/development/python-modules/filelock/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "filelock";
-  version = "2.0.13";
+  version = "2.0.14";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1n67dw7np5gsy5whynyk8c46pjlr353d6j9735p5gryaszkpjl6h";
+    sha256 = "ee355eb66e4c2e5d95689e1253515aad5b3177c274abdd00a57d5ab1aa6d071a";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/fiona/default.nix b/pkgs/development/python-modules/fiona/default.nix
index 5c150844c84..1fc7ae5aa58 100644
--- a/pkgs/development/python-modules/fiona/default.nix
+++ b/pkgs/development/python-modules/fiona/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "Fiona";
-  version = "1.7.10.post1";
+  version = "1.7.11";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "fc4c8996be3131f36c791d66273317d38b72b19dc24c2afc332fd734752eb7a8";
+    sha256 = "5e9c68ea71e9d79fcfb68c9a101c0b133301e233c9bcca7b7c65f33cc7636ef5";
   };
 
   buildInputs = [
diff --git a/pkgs/development/python-modules/flake8-debugger/default.nix b/pkgs/development/python-modules/flake8-debugger/default.nix
index c00bf0c8551..aab91433088 100644
--- a/pkgs/development/python-modules/flake8-debugger/default.nix
+++ b/pkgs/development/python-modules/flake8-debugger/default.nix
@@ -3,10 +3,10 @@
 buildPythonPackage rec {
   pname = "flake8-debugger";
   name = "${pname}-${version}";
-  version = "1.4.0";
+  version = "3.0.0";
   src = fetchurl {
     url = "mirror://pypi/f/flake8-debugger/${name}.tar.gz";
-    sha256 = "0chjfa6wvnqjnx778qzahhwvjx1j0rc8ax0ipp5bn70gf47lj62r";
+    sha256 = "e5c8ac980d819db2f3fbb89fe0e43a2fe6c127edd6ce4984a3f7e0bbdac3d2d4";
   };
   buildInputs = [ nose ];
   propagatedBuildInputs = [ flake8 ];
diff --git a/pkgs/development/python-modules/flask-testing/default.nix b/pkgs/development/python-modules/flask-testing/default.nix
index 178e000a32e..5f843138eae 100644
--- a/pkgs/development/python-modules/flask-testing/default.nix
+++ b/pkgs/development/python-modules/flask-testing/default.nix
@@ -6,11 +6,11 @@ with stdenv.lib;
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "Flask-Testing";
-  version = "0.6.2";
+  version = "0.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1w0dpwvrcpffm8ychyxpm8s5blm7slik9kplh9jb3sgwcv9gyppj";
+    sha256 = "dc076623d7d850653a018cb64f500948334c8aeb6b10a5a842bf1bcfb98122bc";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/flit/default.nix b/pkgs/development/python-modules/flit/default.nix
index 298da4a85bf..3a73b464a46 100644
--- a/pkgs/development/python-modules/flit/default.nix
+++ b/pkgs/development/python-modules/flit/default.nix
@@ -11,6 +11,7 @@
 , pytest
 , testpath
 , responses
+, pytoml
 }:
 
 # Flit is actually an application to build universal wheels.
@@ -20,25 +21,22 @@
 
 buildPythonPackage rec {
   pname = "flit";
-  version = "0.11.4";
-  name = "${pname}-${version}";
-
-#   format = "wheel";
+  version = "0.13";
 
   src = fetchPypi {
     inherit pname version;
-#     url = https://files.pythonhosted.org/packages/24/98/50a090112a04d9e29155c31a222637668b0a4dd778fefcd3132adc50e877/flit-0.10-py3-none-any.whl;
-    sha256 = "8ba7603cc3bf4149d81811d40fe331abc45ff37a207c63f5f712a0fdb69297bb";
+    sha256 = "8f558351bf4bb82b872d3bdbea7055cbb2e33ed2bdf809284bf927d4c78bf0ee";
   };
 
   disabled = !isPy3k;
-  propagatedBuildInputs = [ docutils requests requests_download ] ++ lib.optional (pythonOlder "3.6") zipfile36;
+  propagatedBuildInputs = [ docutils requests requests_download pytoml ] ++ lib.optional (pythonOlder "3.6") zipfile36;
 
   checkInputs = [ pytest testpath responses ];
 
   # Disable test that needs some ini file.
+  # Disable test that wants hg
   checkPhase = ''
-    py.test -k "not test_invalid_classifier"
+    py.test -k "not test_invalid_classifier and not test_build_sdist"
   '';
 
   meta = {
diff --git a/pkgs/development/python-modules/fonttools/default.nix b/pkgs/development/python-modules/fonttools/default.nix
index 1dfc22f769b..a567f7155f8 100644
--- a/pkgs/development/python-modules/fonttools/default.nix
+++ b/pkgs/development/python-modules/fonttools/default.nix
@@ -7,12 +7,12 @@
 
 buildPythonPackage rec {
   pname = "fonttools";
-  version = "3.17.0";
+  version = "3.21.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1c4f26bf32cd58d5881bfe1f42e5f0a1637a58452a60ae1623999f3ae7da0e24";
+    sha256 = "95b5c66d19dbffd57be1636d1f737c7644d280a48c28f933aeb4db73a7c83495";
     extension = "zip";
   };
 
diff --git a/pkgs/development/python-modules/ftfy/default.nix b/pkgs/development/python-modules/ftfy/default.nix
index b1ba77ab868..e54531017f4 100644
--- a/pkgs/development/python-modules/ftfy/default.nix
+++ b/pkgs/development/python-modules/ftfy/default.nix
@@ -11,11 +11,11 @@ buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "ftfy";
   # latest is 5.1.1, buy spaCy requires 4.4.3
-  version = "5.1.1";
+  version = "5.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "67a29a2fad5f72aec2d8a0a7084e4f499ed040455133ee96b1c458609fc29e78";
+    sha256 = "b9f84a1437f68ad0bb964fd9da9f6b88d090113ec9e78f290f6d6d0221468e38";
   };
 
   propagatedBuildInputs = [ html5lib wcwidth];
diff --git a/pkgs/development/python-modules/gensim/default.nix b/pkgs/development/python-modules/gensim/default.nix
index ea5fc12e432..4edd9ac3e55 100644
--- a/pkgs/development/python-modules/gensim/default.nix
+++ b/pkgs/development/python-modules/gensim/default.nix
@@ -13,10 +13,10 @@
 buildPythonPackage rec {
   pname = "gensim";
   name = "${pname}-${version}";
-  version = "3.0.1";
+  version = "3.2.0";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4827012f6f020ac4f4067c2a2a88542391917113faaa417505e1ee8a1e7e2650";
+    sha256 = "db00b68c6567ba0598d400b917c889e8801adf249170ce0a80ec38187d1b0797";
   };
 
   propagatedBuildInputs = [ smart_open numpy six scipy
diff --git a/pkgs/development/python-modules/google_api_core/default.nix b/pkgs/development/python-modules/google_api_core/default.nix
index 6aa43989aa3..c4275c47a42 100644
--- a/pkgs/development/python-modules/google_api_core/default.nix
+++ b/pkgs/development/python-modules/google_api_core/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "google-api-core";
-  version = "0.1.2";
+  version = "0.1.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0qmjswj079w7q7zbnh8p4n2r3f831wymm9hfdlc7zfrini7184xv";
+    sha256 = "03bc4b1ab69c0e113af07e706edee50f583abe8219fe1e1d529dee191cb8e0bf";
   };
 
   propagatedBuildInputs = [ google_auth protobuf googleapis_common_protos requests grpcio ];
diff --git a/pkgs/development/python-modules/gpy/default.nix b/pkgs/development/python-modules/gpy/default.nix
index bc48a7490aa..bb39746d296 100644
--- a/pkgs/development/python-modules/gpy/default.nix
+++ b/pkgs/development/python-modules/gpy/default.nix
@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "GPy";
-  version = "1.8.4";
+  version = "1.8.5";
   name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "38c1202f1790952b88c298224139ee5b14d4518e3ddc6186c60db2ece016d8c1";
+    sha256 = "1562e34629192f209273f454e41614a127c6ef04144cd0eb5992d484721d55d3";
   };
 
   # running tests produces "ImportError: cannot import name 'linalg_cython'"
diff --git a/pkgs/development/python-modules/grpcio/default.nix b/pkgs/development/python-modules/grpcio/default.nix
index c17e1bf7bf0..eeb51fb5843 100644
--- a/pkgs/development/python-modules/grpcio/default.nix
+++ b/pkgs/development/python-modules/grpcio/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "grpcio";
-  version = "1.7.3";
+  version = "1.8.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1wkrxj1jmf2dyx207fc9ysyns9h27gls3drgg05mzdckjqr5lnl6";
+    sha256 = "1ea1336f0d1158c4e00e96a94df84b75f6bbff9816abb6cc68cbdc9442a9ac55";
   };
 
   propagatedBuildInputs = [ six protobuf ]
diff --git a/pkgs/development/python-modules/gssapi/default.nix b/pkgs/development/python-modules/gssapi/default.nix
index 3b13f8a2049..b075db5ae98 100644
--- a/pkgs/development/python-modules/gssapi/default.nix
+++ b/pkgs/development/python-modules/gssapi/default.nix
@@ -3,12 +3,12 @@ nose, shouldbe, gss, krb5Full, which, darwin }:
 
 buildPythonPackage rec {
   pname = "gssapi";
-  version = "1.2.0";
+  version = "1.3.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1q6ccpz6anl9vggwxdq32wp6xjh2lyfbf7av6jqnmvmyqdfwh3b9";
+    sha256 = "765205082a9490c8e8be88ac16a6249d124396a671665edeec9927a7f244d712";
   };
 
   # It's used to locate headers
diff --git a/pkgs/development/python-modules/html5lib/default.nix b/pkgs/development/python-modules/html5lib/default.nix
new file mode 100644
index 00000000000..97d2854ca22
--- /dev/null
+++ b/pkgs/development/python-modules/html5lib/default.nix
@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, flake8
+, pytest
+, pytest-expect
+, mock
+, six
+, webencodings
+}:
+
+buildPythonPackage rec {
+  pname = "html5lib";
+  version = "1.0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736";
+  };
+
+  checkInputs = [ flake8 pytest pytest-expect mock ];
+  propagatedBuildInputs = [
+    six webencodings
+  ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = {
+    homepage = https://github.com/html5lib/html5lib-python;
+    downloadPage = https://github.com/html5lib/html5lib-python/releases;
+    description = "HTML parser based on WHAT-WG HTML5 specification";
+    longDescription = ''
+      html5lib is a pure-python library for parsing HTML. It is designed to
+      conform to the WHATWG HTML specification, as is implemented by all
+      major web browsers.
+    '';
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ domenkozar prikhi ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/htmlmin/default.nix b/pkgs/development/python-modules/htmlmin/default.nix
index 2206b3559ba..8df4b3813c4 100644
--- a/pkgs/development/python-modules/htmlmin/default.nix
+++ b/pkgs/development/python-modules/htmlmin/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi }:
 buildPythonPackage rec {
   pname = "htmlmin";
-  version = "0.1.11";
+  version = "0.1.12";
   name = "${pname}-${version}";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f27fb96fdddeb1725ee077be532c7bea23288c69d0e996e7798f24fae7a14e5e";
+    sha256 = "50c1ef4630374a5d723900096a961cff426dff46b48f34d194a81bbe14eca178";
   };
 
   # Tests run fine in a normal source checkout, but not when being built by nix.
diff --git a/pkgs/development/python-modules/httpbin/default.nix b/pkgs/development/python-modules/httpbin/default.nix
index d11d6b3668f..2f24a1ab72b 100644
--- a/pkgs/development/python-modules/httpbin/default.nix
+++ b/pkgs/development/python-modules/httpbin/default.nix
@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "httpbin";
-  version = "0.5.0";
+  version = "0.6.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6b57f563900ecfe126015223a259463848daafbdc2687442317c0992773b9054";
+    sha256 = "0afa0486a76305cac441b5cc80d5d4ccd82b20875da7c5119ecfe616cefef45f";
   };
 
   propagatedBuildInputs = [ flask markupsafe decorator itsdangerous six ];
diff --git a/pkgs/development/python-modules/idna/default.nix b/pkgs/development/python-modules/idna/default.nix
new file mode 100644
index 00000000000..635f8b33d3c
--- /dev/null
+++ b/pkgs/development/python-modules/idna/default.nix
@@ -0,0 +1,20 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "idna";
+  version = "2.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f";
+  };
+
+  meta = {
+    homepage = "http://github.com/kjd/idna/";
+    description = "Internationalized Domain Names in Applications (IDNA)";
+    license = lib.licenses.bsd3;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/ipykernel/default.nix b/pkgs/development/python-modules/ipykernel/default.nix
index a77f6ac9c2f..8547a3ef99e 100644
--- a/pkgs/development/python-modules/ipykernel/default.nix
+++ b/pkgs/development/python-modules/ipykernel/default.nix
@@ -13,12 +13,12 @@
 
 buildPythonPackage rec {
   pname = "ipykernel";
-  version = "4.6.1";
+  version = "4.7.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2e1825aca4e2585b5adb7953ea16e53f53a62159ed49952a564b1e23507205db";
+    sha256 = "354986612a38f0555c43d5af2425e2a67506b63b313a0325e38904003b9d977b";
   };
 
   buildInputs = [ nose ] ++ lib.optional isPy27 mock;
diff --git a/pkgs/development/python-modules/ipywidgets/default.nix b/pkgs/development/python-modules/ipywidgets/default.nix
index 3d156323491..f77c3570c02 100644
--- a/pkgs/development/python-modules/ipywidgets/default.nix
+++ b/pkgs/development/python-modules/ipywidgets/default.nix
@@ -14,12 +14,12 @@
 
 buildPythonPackage rec {
   pname = "ipywidgets";
-  version = "7.0.5";
+  version = "7.1.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "321be3dc48193130ba16e8080172bb5cd052eb65e3ad0ea7b5f80ff73e24bc54";
+    sha256 = "3e2be7dea4f97c9a4df71ef065cad9f2e420dd901127bf7cb690fb56d2b34ea3";
   };
 
   # Tests are not distributed
diff --git a/pkgs/development/python-modules/iso8601/default.nix b/pkgs/development/python-modules/iso8601/default.nix
new file mode 100644
index 00000000000..4f9ff70556b
--- /dev/null
+++ b/pkgs/development/python-modules/iso8601/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "iso8601";
+  version = "0.1.12";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "49c4b20e1f38aa5cf109ddcd39647ac419f928512c869dc01d5c7098eddede82";
+  };
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test iso8601
+  '';
+
+  meta = {
+    homepage = https://bitbucket.org/micktwomey/pyiso8601/;
+    description = "Simple module to parse ISO 8601 dates";
+    maintainers = with lib.maintainers; [ phreedom ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/jdcal/default.nix b/pkgs/development/python-modules/jdcal/default.nix
new file mode 100644
index 00000000000..d3ed32c0882
--- /dev/null
+++ b/pkgs/development/python-modules/jdcal/default.nix
@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "jdcal";
+  version = "1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "b760160f8dc8cc51d17875c6b663fafe64be699e10ce34b6a95184b5aa0fdc9e";
+  };
+
+  checkInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test
+  '';
+
+  meta = {
+    description = "A module containing functions for converting between Julian dates and calendar dates";
+    homepage = "https://github.com/phn/jdcal";
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ lihop ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/jedi/default.nix b/pkgs/development/python-modules/jedi/default.nix
index bf9f9f9c082..df8a287ea09 100644
--- a/pkgs/development/python-modules/jedi/default.nix
+++ b/pkgs/development/python-modules/jedi/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "jedi";
-  version = "0.11.0";
+  version = "0.11.1";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f6d5973573e76b1fd2ea75f6dcd6445d02d41ff3af5fc61b275b4e323d1dd396";
+    sha256 = "d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/jsbeautifier/default.nix b/pkgs/development/python-modules/jsbeautifier/default.nix
index a2278566c6d..19b1eeefa53 100644
--- a/pkgs/development/python-modules/jsbeautifier/default.nix
+++ b/pkgs/development/python-modules/jsbeautifier/default.nix
@@ -2,7 +2,7 @@
 
 buildPythonApplication rec {
   pname = "jsbeautifier";
-  version = "1.7.4";
+  version = "1.7.5";
   name = "${pname}-${version}";
 
   propagatedBuildInputs = [ six ];
@@ -11,7 +11,7 @@ buildPythonApplication rec {
 
   src = fetchurl {
     url = "mirror://pypi/j/jsbeautifier/${name}.tar.gz";
-    sha256 = "7fc14f279117a55a5e854602f6e8c1cb178c6d83f7cf75e2e9f50678fe11079e";
+    sha256 = "78eb1e5c8535484f0d0b588aca38da3fb5e0e34de2d1ab53c077e71c55757473";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/jsondiff/default.nix b/pkgs/development/python-modules/jsondiff/default.nix
new file mode 100644
index 00000000000..9d4331c8ea8
--- /dev/null
+++ b/pkgs/development/python-modules/jsondiff/default.nix
@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "jsondiff";
+  version = "1.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2d0437782de9418efa34e694aa59f43d7adb1899bd9a793f063867ddba8f7893";
+  };
+
+  # No tests
+  doCheck = false;
+
+  meta = {
+    description = "Diff JSON and JSON-like structures in Python";
+    homepage = https://github.com/ZoomerAnalytics/jsondiff;
+    license = lib.licenses.mit;
+  };
+
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/jsonpatch/default.nix b/pkgs/development/python-modules/jsonpatch/default.nix
index 39f36b1d949..8d238b4746d 100644
--- a/pkgs/development/python-modules/jsonpatch/default.nix
+++ b/pkgs/development/python-modules/jsonpatch/default.nix
@@ -6,12 +6,12 @@
 
 buildPythonPackage rec {
   pname = "jsonpatch";
-  version = "1.16";
+  version = "1.21";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f025c28a08ce747429ee746bb21796c3b6417ec82288f8fe6514db7398f2af8a";
+    sha256 = "11f5ffdf543a83047a2f54ac28f8caad7f34724cb1ea26b27547fd974f1a2153";
   };
 
   # test files are missing
diff --git a/pkgs/development/python-modules/jsonpickle/default.nix b/pkgs/development/python-modules/jsonpickle/default.nix
new file mode 100644
index 00000000000..2d9f02a5aff
--- /dev/null
+++ b/pkgs/development/python-modules/jsonpickle/default.nix
@@ -0,0 +1,23 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "jsonpickle";
+  version = "0.9.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "cc25dc79571d4ad7db59d05ddb7de0d76a8d598cf6136e1dbeaa9361ebcfe749";
+  };
+
+  doCheck = false;
+
+  meta = {
+    description = "Python library for serializing any arbitrary object graph into JSON";
+    homepage = http://jsonpickle.github.io/;
+    license = lib.licenses.bsd3;
+  };
+
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/jupyter_client/default.nix b/pkgs/development/python-modules/jupyter_client/default.nix
index 3782d313df8..e88b7f937a5 100644
--- a/pkgs/development/python-modules/jupyter_client/default.nix
+++ b/pkgs/development/python-modules/jupyter_client/default.nix
@@ -1,32 +1,38 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, nose
 , traitlets
 , jupyter_core
 , pyzmq
 , dateutil
 , isPyPy
 , py
+, ipykernel
+, ipython
+, mock
+, pytest
 }:
 
 buildPythonPackage rec {
   pname = "jupyter_client";
-  version = "5.1.0";
-  name = "${pname}-${version}";
+  version = "5.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08756b021765c97bc5665390700a4255c2df31666ead8bff116b368d09912aba";
+    sha256 = "ca30cf1786047925ebacd6f6faa3a993efaa004b584f7d83bc8b807f7cd3f6bb";
   };
 
-  buildInputs = [ nose ];
+  checkInputs = [ ipykernel ipython mock pytest ];
   propagatedBuildInputs = [traitlets jupyter_core pyzmq dateutil] ++ lib.optional isPyPy py;
 
   checkPhase = ''
-    nosetests -v
+    py.test
   '';
 
+  patches = [
+    ./wheel_workaround.patch
+  ];
+
   # Circular dependency with ipykernel
   doCheck = false;
 
diff --git a/pkgs/development/python-modules/jupyter_client/wheel_workaround.patch b/pkgs/development/python-modules/jupyter_client/wheel_workaround.patch
new file mode 100644
index 00000000000..926fcb26448
--- /dev/null
+++ b/pkgs/development/python-modules/jupyter_client/wheel_workaround.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index 95d4774..ee72cbc 100644
+--- a/setup.py
++++ b/setup.py
+@@ -86,7 +86,7 @@ setup_args = dict(
+     extras_require   = {
+         'test': ['ipykernel', 'ipython', 'mock'],
+         'test:python_version == "3.3"': ['pytest<3.3.0'],
+-        'test:python_version >= "3.4" or python_version == "2.7"': ['pytest'],
++        'test:(python_version >= "3.4" or python_version == "2.7")': ['pytest'],
+     },
+     cmdclass         = {
+         'bdist_egg': bdist_egg if 'bdist_egg' in sys.argv else bdist_egg_disabled,
diff --git a/pkgs/development/python-modules/jupyter_core/default.nix b/pkgs/development/python-modules/jupyter_core/default.nix
index 4db36cf7b37..403f7c047d5 100644
--- a/pkgs/development/python-modules/jupyter_core/default.nix
+++ b/pkgs/development/python-modules/jupyter_core/default.nix
@@ -11,15 +11,15 @@
 
 buildPythonPackage rec {
   pname = "jupyter_core";
-  version = "4.3.0";
+  version = "4.4.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a96b129e1641425bf057c3d46f4f44adce747a7d60107e8ad771045c36514d40";
+    sha256 = "ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7";
   };
 
-  buildInputs = [ pytest mock glibcLocales ];
+  checkInputs = [ pytest mock glibcLocales ];
   propagatedBuildInputs = [ ipython traitlets ];
 
   patches = [ ./tests_respect_pythonpath.patch ];
diff --git a/pkgs/development/python-modules/jupyter_core/tests_respect_pythonpath.patch b/pkgs/development/python-modules/jupyter_core/tests_respect_pythonpath.patch
index 61415b756ab..7e7e9ae93a0 100644
--- a/pkgs/development/python-modules/jupyter_core/tests_respect_pythonpath.patch
+++ b/pkgs/development/python-modules/jupyter_core/tests_respect_pythonpath.patch
@@ -1,24 +1,20 @@
---- a/jupyter_core/tests/test_command.py	2016-09-13 15:22:49.000000000 +0200
-+++ b/jupyter_core/tests/test_command.py	2017-10-23 12:49:27.489527705 +0200
-@@ -113,7 +113,10 @@
-     witness = a.join(witness_cmd)
-     witness.write('#!%s\n%s\n' % (sys.executable, 'print("WITNESS ME")'))
-     witness.chmod(0o700)
--    out = check_output([sys.executable, str(jupyter), 'witness'], env={'PATH': ''})
-+    out = check_output(
-+        [sys.executable, str(jupyter), 'witness'],
-+        env={'PATH': '', 'PYTHONPATH': os.environ['PYTHONPATH']}
-+    )
-     assert b'WITNESS' in out
- 
- 
-@@ -136,5 +139,8 @@
-     witness_b.write('#!%s\n%s\n' % (sys.executable, 'print("WITNESS B")'))
-     witness_b.chmod(0o700)
- 
--    out = check_output([sys.executable, str(jupyter), 'witness'], env={'PATH': str(b)})
-+    out = check_output(
-+        [sys.executable, str(jupyter), 'witness'],
-+        env={'PATH': str(b), 'PYTHONPATH': os.environ['PYTHONPATH']}
-+    )
-     assert b'WITNESS A' in out
+--- a/jupyter_core/tests/test_command.py
++++ b/jupyter_core/tests/test_command.py
+@@ -131,7 +131,7 @@ def test_not_on_path(tmpdir):
+     witness_src = '#!%s\n%s\n' % (sys.executable, 'print("WITNESS ME")')
+     write_executable(witness, witness_src)
+
+-    env = {'PATH': ''}
++    env = {'PATH': '', 'PYTHONPATH': os.environ['PYTHONPATH']}
+     if 'SYSTEMROOT' in os.environ:  # Windows http://bugs.python.org/issue20614
+         env[str('SYSTEMROOT')] = os.environ['SYSTEMROOT']
+     if sys.platform == 'win32':
+@@ -157,7 +157,7 @@ def test_path_priority(tmpdir):
+     witness_b_src = '#!%s\n%s\n' % (sys.executable, 'print("WITNESS B")')
+     write_executable(witness_b, witness_b_src)
+
+-    env = {'PATH':  str(b)}
++    env = {'PATH':  str(b), 'PYTHONPATH': os.environ['PYTHONPATH']}
+     if 'SYSTEMROOT' in os.environ:  # Windows http://bugs.python.org/issue20614
+         env[str('SYSTEMROOT')] = os.environ['SYSTEMROOT']
+     if sys.platform == 'win32':
diff --git a/pkgs/development/python-modules/keras/default.nix b/pkgs/development/python-modules/keras/default.nix
index d88b6e4999b..b6c56cc8bc6 100644
--- a/pkgs/development/python-modules/keras/default.nix
+++ b/pkgs/development/python-modules/keras/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "Keras";
-  version = "2.1.1";
+  version = "2.1.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f0ca2458c60d9711edf4291230b31795307ad3781cb6232ff4792b53c8f55123";
+    sha256 = "3ee56fc129d9d00b1916046e50056047836f97ada59df029e5661fb34442d5e8";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/keyring/default.nix b/pkgs/development/python-modules/keyring/default.nix
index ca7a518665c..f88bdb84e0c 100644
--- a/pkgs/development/python-modules/keyring/default.nix
+++ b/pkgs/development/python-modules/keyring/default.nix
@@ -6,11 +6,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "keyring";
-  version = "10.4.0";
+  version = "10.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09iv50c14mdmdk7sjd6bb47yg7347gymh6r8c0q4gfnzs173y6lh";
+    sha256 = "f10674bb6ecbf82e2b713627c48ad0e84178e1c9d3dc1f0373261a0765402fb2";
   };
 
   buildInputs = [
diff --git a/pkgs/development/python-modules/ldap/default.nix b/pkgs/development/python-modules/ldap/default.nix
index 635308f3760..32f25eeda42 100644
--- a/pkgs/development/python-modules/ldap/default.nix
+++ b/pkgs/development/python-modules/ldap/default.nix
@@ -1,18 +1,18 @@
 { lib, writeText, buildPythonPackage, isPy3k, fetchPypi
-, openldap, cyrus_sasl, openssl, pytest }:
+, openldap, cyrus_sasl, openssl, pytest, pyasn1 }:
 
 buildPythonPackage rec {
   pname = "python-ldap";
-  version = "2.4.45";
+  version = "2.5.2";
   name = "${pname}-${version}";
   disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "824fde180a53772e23edc031c4dd64ac1af4a3eade78f00d9d510937d562f64e";
+    sha256 = "b8c134dfedaef0e6ff4a4b94277708dcadb758b448905a83b8946df077356ed2";
   };
 
-  buildInputs = [ pytest ];
+  checkInputs = [ pytest pyasn1 ];
 
   checkPhase = ''
     # Needed by tests to setup a mockup ldap server.
diff --git a/pkgs/development/python-modules/ldap3/default.nix b/pkgs/development/python-modules/ldap3/default.nix
index 895272f351d..202bceafae3 100644
--- a/pkgs/development/python-modules/ldap3/default.nix
+++ b/pkgs/development/python-modules/ldap3/default.nix
@@ -1,13 +1,12 @@
 { stdenv, fetchPypi, buildPythonPackage, gssapi, pyasn1 }:
 
 buildPythonPackage rec {
-  version = "2.3";
+  version = "2.4";
   pname = "ldap3";
-  name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1b36lwil4iflk2ay8gi663abpnfm8id7qg4n3jkmmqbnc1sv6mn0";
+    sha256 = "888015f849eb33852583bbaf382f61593b03491cdac6098fd5d4d0252e0e7e66";
   };
 
   buildInputs = [ gssapi ];
diff --git a/pkgs/development/python-modules/libusb1/default.nix b/pkgs/development/python-modules/libusb1/default.nix
index adf1bc23618..f3b48eaa576 100644
--- a/pkgs/development/python-modules/libusb1/default.nix
+++ b/pkgs/development/python-modules/libusb1/default.nix
@@ -12,7 +12,7 @@ buildPythonPackage rec {
   postPatch = lib.optionalString stdenv.isLinux ''
     substituteInPlace usb1/libusb1.py --replace \
       "ctypes.util.find_library(base_name)" \
-      "'${libusb1}/lib/libusb${stdenv.hostPlatform.extensions.sharedLibrary}'"
+      "'${libusb1}/lib/libusb-1.0${stdenv.hostPlatform.extensions.sharedLibrary}'"
   '';
 
   buildInputs = [ libusb1 ];
diff --git a/pkgs/development/python-modules/line_profiler/default.nix b/pkgs/development/python-modules/line_profiler/default.nix
index 570bba2a8c4..26dfda613f7 100644
--- a/pkgs/development/python-modules/line_profiler/default.nix
+++ b/pkgs/development/python-modules/line_profiler/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   pname = "line_profiler";
-  version = "2.0";
+  version = "2.1.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "739f8ad0e4bcd0cb82e99afc09e00a0351234f6b3f0b1f7f0090a8a2fbbf8381";
+    sha256 = "efa66e9e3045aa7cb1dd4bf0106e07dec9f80bc781a993fbaf8162a36c20af5c";
   };
 
   buildInputs = [ cython ];
diff --git a/pkgs/development/python-modules/llfuse/default.nix b/pkgs/development/python-modules/llfuse/default.nix
index 4c4c89d8f19..ef4d9fb5d02 100644
--- a/pkgs/development/python-modules/llfuse/default.nix
+++ b/pkgs/development/python-modules/llfuse/default.nix
@@ -4,12 +4,12 @@
 
 buildPythonPackage rec {
   pname = "llfuse";
-  version = "1.0";
+  version = "1.3.2";
   name = pname + "-" + version;
 
   src = fetchurl {
     url = "mirror://pypi/l/llfuse/${name}.tar.bz2";
-    sha256 = "1li7q04ljrvwharw4fblcbfhvk6s0l3lnv8yqb4c22lcgbkiqlps";
+    sha256 = "96252a286a2be25810904d969b330ef2a57c2b9c18c5b503bbfbae40feb2bb63";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/python-modules/llvmlite/default.nix b/pkgs/development/python-modules/llvmlite/default.nix
index 57deaf3caf3..d702d8f95b0 100644
--- a/pkgs/development/python-modules/llvmlite/default.nix
+++ b/pkgs/development/python-modules/llvmlite/default.nix
@@ -1,5 +1,5 @@
 { stdenv
-, fetchurl
+, fetchPypi
 , buildPythonPackage
 , python
 , llvm
@@ -10,21 +10,20 @@
 
 buildPythonPackage rec {
   pname = "llvmlite";
-  name = "${pname}-${version}";
-  version = "0.20.0";
+  version = "0.21.0";
 
   disabled = isPyPy;
 
-  src = fetchurl {
-    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
-    sha256 = "b2f174848df16bb9195a07fec102110a06d018da736bd9b3570a54d44c797c29";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3a5dd0695fdfb9fd47464cd71791b84935bf9642e11f4811d57aa1f2da8cdaa8";
   };
 
   propagatedBuildInputs = [ llvm ] ++ stdenv.lib.optional (pythonOlder "3.4") enum34;
 
   # Disable static linking
   # https://github.com/numba/llvmlite/issues/93
-  patchPhase = ''
+  postPatch = ''
     substituteInPlace ffi/Makefile.linux --replace "-static-libstdc++" ""
 
     substituteInPlace llvmlite/tests/test_binding.py --replace "test_linux" "nope"
diff --git a/pkgs/development/python-modules/lxml/default.nix b/pkgs/development/python-modules/lxml/default.nix
new file mode 100644
index 00000000000..bfd0c8227ee
--- /dev/null
+++ b/pkgs/development/python-modules/lxml/default.nix
@@ -0,0 +1,27 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, libxml2
+, libxslt
+}:
+
+buildPythonPackage rec {
+  pname = "lxml";
+  version = "4.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "940caef1ec7c78e0c34b0f6b94fe42d0f2022915ffc78643d28538a5cfd0f40e";
+  };
+
+  buildInputs = [ libxml2 libxslt ];
+
+  hardeningDisable = stdenv.lib.optional stdenv.isDarwin "format";
+
+  meta = {
+    description = "Pythonic binding for the libxml2 and libxslt libraries";
+    homepage = http://lxml.de;
+    license = stdenv.lib.licenses.bsd3;
+    maintainers = with stdenv.lib.maintainers; [ sjourdois ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/marionette-harness/default.nix b/pkgs/development/python-modules/marionette-harness/default.nix
index fbdd13a7f38..f909974db6b 100644
--- a/pkgs/development/python-modules/marionette-harness/default.nix
+++ b/pkgs/development/python-modules/marionette-harness/default.nix
@@ -14,13 +14,13 @@
 
 buildPythonPackage rec {
   pname = "marionette-harness";
-  version = "4.1.0";
+  version = "4.3.0";
   name = "${pname}-${version}";
   disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "20c188791e28d586c58acf86ff28cb704c4195a4da6eb10db7b8c6771e3f2983";
+    sha256 = "a98bb65a0c63f60d9e3d7ef21dabc9c29676917dc2ec0d46851a3ed694c820cc";
   };
 
   propagatedBuildInputs = [ mozprofile mozversion browsermob-proxy moztest 
diff --git a/pkgs/development/python-modules/markdown/default.nix b/pkgs/development/python-modules/markdown/default.nix
new file mode 100644
index 00000000000..515dee0e766
--- /dev/null
+++ b/pkgs/development/python-modules/markdown/default.nix
@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, nose
+, pyyaml
+}:
+
+buildPythonPackage rec {
+  pname = "Markdown";
+  version = "2.6.10";
+
+  src = fetchPypi {
+    extension = "zip";
+    inherit pname version;
+    sha256 = "cfa536d1ee8984007fcecc5a38a493ff05c174cb74cb2341dafd175e6bc30851";
+  };
+
+  # error: invalid command 'test'
+#   doCheck = false;
+
+  checkInputs = [ nose pyyaml ];
+
+  meta = {
+    description = "A Python implementation of John Gruber’s Markdown with Extension support";
+    homepage = https://github.com/Python-Markdown/markdown;
+    license = lib.licenses.bsd3;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/marshmallow/default.nix b/pkgs/development/python-modules/marshmallow/default.nix
index afb60801dc9..a9db6ef1e84 100644
--- a/pkgs/development/python-modules/marshmallow/default.nix
+++ b/pkgs/development/python-modules/marshmallow/default.nix
@@ -5,7 +5,7 @@
 buildPythonPackage rec {
   pname = "marshmallow";
   name = "${pname}-${version}";
-  version = "2.14.0";
+  version = "2.15.0";
 
   meta = {
     homepage = "https://github.com/marshmallow-code/marshmallow";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09943a460026b9a61c3f4cedd0e5ccfed7cfce3271debd19e3f97df561088718";
+    sha256 = "d3f31fe7be2106b1d783cbd0765ef4e1c6615505514695f33082805f929dd584";
   };
 
   propagatedBuildInputs = [ dateutil simplejson ];
diff --git a/pkgs/development/python-modules/matplotlib/default.nix b/pkgs/development/python-modules/matplotlib/default.nix
index 345a21ecddf..33505b5f618 100644
--- a/pkgs/development/python-modules/matplotlib/default.nix
+++ b/pkgs/development/python-modules/matplotlib/default.nix
@@ -20,13 +20,13 @@ assert enableTk -> (tcl != null)
 assert enableQt -> pyqt4 != null;
 
 buildPythonPackage rec {
-  version = "2.1.0";
+  version = "2.1.1";
   pname = "matplotlib";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://pypi/m/matplotlib/${name}.tar.gz";
-    sha256 = "4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387";
+    sha256 = "659f5e1aa0e0f01488c61eff47560c43b8be511c6a29293d7f3896ae17bd8b23";
   };
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";
diff --git a/pkgs/development/python-modules/mistune/default.nix b/pkgs/development/python-modules/mistune/default.nix
index 14aef5b00d1..7ab4a184263 100644
--- a/pkgs/development/python-modules/mistune/default.nix
+++ b/pkgs/development/python-modules/mistune/default.nix
@@ -6,12 +6,12 @@
 
 buildPythonPackage rec {
   pname = "mistune";
-  version = "0.7.4";
+  version = "0.8.3";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0byj9jg9ly7karf5sb1aqcw7avaim9sxl8ws7yw7p1fibjgsy5w5";
+    sha256 = "bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619";
   };
 
   buildInputs = [ nose ];
diff --git a/pkgs/development/python-modules/moto/default.nix b/pkgs/development/python-modules/moto/default.nix
index cf74e1dc134..d5c40c67b36 100644
--- a/pkgs/development/python-modules/moto/default.nix
+++ b/pkgs/development/python-modules/moto/default.nix
@@ -1,17 +1,20 @@
-{ stdenv, buildPythonPackage, fetchPypi, jinja2, werkzeug, flask, requests, pytz
-, six, boto, httpretty, xmltodict, nose, sure, boto3, freezegun, dateutil }:
+{ stdenv, buildPythonPackage, fetchPypi, jinja2, werkzeug, flask
+, requests, pytz, backports_tempfile, cookies, jsondiff, botocore, aws-xray-sdk, docker
+, six, boto, httpretty, xmltodict, nose, sure, boto3, freezegun, dateutil, mock, pyaml }:
 
 buildPythonPackage rec {
   pname = "moto";
-  version = "0.4.31";
-  name    = "moto-${version}";
+  version = "1.1.25";
+
   src = fetchPypi {
     inherit pname version;
-    sha256 = "19s8hfz4mzzzdksa0ddlvrga5mxdaqahk89p5l29a5id8127shr8";
+    sha256 = "d427d6e1a81e926c2b6a071453807b05f4736d65068493e1f3055ac7ee24ea21";
   };
 
   propagatedBuildInputs = [
+    aws-xray-sdk
     boto
+    boto3
     dateutil
     flask
     httpretty
@@ -21,6 +24,13 @@ buildPythonPackage rec {
     requests
     six
     xmltodict
+    mock
+    pyaml
+    backports_tempfile
+    cookies
+    jsondiff
+    botocore
+    docker
   ];
 
   checkInputs = [ boto3 nose sure freezegun ];
diff --git a/pkgs/development/python-modules/nbxmpp/default.nix b/pkgs/development/python-modules/nbxmpp/default.nix
index 964b42fe4ee..26525adb1c9 100644
--- a/pkgs/development/python-modules/nbxmpp/default.nix
+++ b/pkgs/development/python-modules/nbxmpp/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "nbxmpp";
-  version = "0.6.0";
+  version = "0.6.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0x495yb0abkdspyziw7dyyjwxx6ivnv5zznk92wa3mcind5s9757";
+    sha256 = "10bfb12b083a7509779298c31b4b61e2ed7e78d1960cbcfb3de8d38f3b830991";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/nilearn/default.nix b/pkgs/development/python-modules/nilearn/default.nix
index 16036a69179..6133abac705 100644
--- a/pkgs/development/python-modules/nilearn/default.nix
+++ b/pkgs/development/python-modules/nilearn/default.nix
@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "nilearn";
-  version = "0.3.1";
+  version = "0.4.0";
   name = pname + "-" + version;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0kkarh5cdcd2czs0bf0s1g51qas84mfxfq0dzd7k5h5l0qr4zy06";
+    sha256 = "bb692254bde35d7e1d3d1534d9b3117810b35a744724625f150fbbc64d519c02";
   };
 
   checkPhase = "nosetests --exclude with_expand_user nilearn/tests";
diff --git a/pkgs/development/python-modules/notebook/default.nix b/pkgs/development/python-modules/notebook/default.nix
index 2a23ff4de78..71261fb1f40 100644
--- a/pkgs/development/python-modules/notebook/default.nix
+++ b/pkgs/development/python-modules/notebook/default.nix
@@ -22,12 +22,12 @@
 
 buildPythonPackage rec {
   pname = "notebook";
-  version = "5.2.1";
+  version = "5.2.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4ae5b81dd39b37cdd99dcffe83a5182c849947b92d46ac4d2b5093af2bb9f224";
+    sha256 = "7bb54fb61b9c5426bc116f840541b973431198e00ea2896122d05fc122dbbd67";
   };
 
   LC_ALL = "en_US.utf8";
diff --git a/pkgs/development/python-modules/numba/default.nix b/pkgs/development/python-modules/numba/default.nix
index b0d7ae72c95..97aad8c0928 100644
--- a/pkgs/development/python-modules/numba/default.nix
+++ b/pkgs/development/python-modules/numba/default.nix
@@ -1,5 +1,5 @@
 { stdenv
-, fetchurl
+, fetchPypi
 , python
 , buildPythonPackage
 , isPy27
@@ -14,13 +14,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.35.0";
+  version = "0.36.2";
   pname = "numba";
-  name = "${pname}-${version}";
 
-  src = fetchurl {
-    url = "mirror://pypi/n/numba/${name}.tar.gz";
-    sha256 = "11564937757605bee590c5758c73cfe9fd6d569726b56d970316a6228971ecc3";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "d61597808ce511e81b64e32da664f52beb7d947bf834dde8b8b60b29d205e5c2";
   };
 
   NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.isDarwin "-I${libcxx}/include/c++/v1";
@@ -29,7 +28,7 @@ buildPythonPackage rec {
 
   # Copy test script into $out and run the test suite.
   checkPhase = ''
-    python -m numba.runtests
+    ${python.interpreter} -m numba.runtests
   '';
   # ImportError: cannot import name '_typeconv'
   doCheck = false;
diff --git a/pkgs/development/python-modules/odfpy/default.nix b/pkgs/development/python-modules/odfpy/default.nix
index a80cd827c6d..449c5a7a92f 100644
--- a/pkgs/development/python-modules/odfpy/default.nix
+++ b/pkgs/development/python-modules/odfpy/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "odfpy";
-  version = "1.3.5";
+  version = "1.3.6";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6f8163f8464868cff9421a058f25566e41d73c8f7e849c021b86630941b44366";
+    sha256 = "6bcaf3b23aa9e49ed8c8c177266539b211add4e02402748a994451482a10cb1b";
   };
 
   checkPhase = ''
diff --git a/pkgs/development/python-modules/path.py/default.nix b/pkgs/development/python-modules/path.py/default.nix
index 6b4af3ffcd4..2830477d3cf 100644
--- a/pkgs/development/python-modules/path.py/default.nix
+++ b/pkgs/development/python-modules/path.py/default.nix
@@ -9,12 +9,12 @@
 
 buildPythonPackage rec {
   pname = "path.py";
-  version = "10.4";
+  version = "10.5";
   name = pname + "-" + version;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c63c75777c8a01f7b273c0065a8ea1e3ba0c9b369fa4a2601831e412b2c4881a";
+    sha256 = "63a7af08676668fd51750f111affbd38c1a13c61aba15c6665b16681771c79a8";
   };
 
   checkInputs = [ pytest pytestrunner ];
diff --git a/pkgs/development/python-modules/pathlib2/default.nix b/pkgs/development/python-modules/pathlib2/default.nix
index 62d5c43a4b3..18c083298e6 100644
--- a/pkgs/development/python-modules/pathlib2/default.nix
+++ b/pkgs/development/python-modules/pathlib2/default.nix
@@ -5,19 +5,20 @@
 , pythonOlder
 , scandir
 , glibcLocales
+, mock
 }:
 
 if !(pythonOlder "3.4") then null else buildPythonPackage rec {
   pname = "pathlib2";
-  version = "2.2.1";
+  version = "2.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ce9007df617ef6b7bd8a31cd2089ed0c1fed1f7c23cf2bf1ba140b3dd563175d";
+    sha256 = "d32550b75a818b289bd4c1f96b60c89957811da205afcceab75bc8b4857ea5b3";
   };
 
   propagatedBuildInputs = [ six ] ++ lib.optional (pythonOlder "3.5") scandir;
-  checkInputs = [ glibcLocales ];
+  checkInputs = [ glibcLocales ] ++ lib.optional (pythonOlder "3.3") mock;
 
   preCheck = ''
     export LC_ALL="en_US.UTF-8"
diff --git a/pkgs/development/python-modules/pexpect/default.nix b/pkgs/development/python-modules/pexpect/default.nix
index c5d1e8ef3c4..da8d5db359b 100644
--- a/pkgs/development/python-modules/pexpect/default.nix
+++ b/pkgs/development/python-modules/pexpect/default.nix
@@ -6,12 +6,12 @@
 
 buildPythonPackage rec {
   pname = "pexpect";
-  version = "4.3.0";
+  version = "4.3.1";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1nfjmz81gsixv22dywidakm7pff3ly1i4yly950bfp8gz1r0iaq0";
+    sha256 = "8e287b171dbaf249d0b06b5f2e88cb7e694651d2d0b8c15bccb83170d3c55575";
   };
 
   # Wants to run pythonin a subprocess
diff --git a/pkgs/development/python-modules/phonenumbers/default.nix b/pkgs/development/python-modules/phonenumbers/default.nix
index d5c4eaa781b..69808a7bff3 100644
--- a/pkgs/development/python-modules/phonenumbers/default.nix
+++ b/pkgs/development/python-modules/phonenumbers/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "phonenumbers";
-  version = "8.8.6";
+  version = "8.8.8";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ab1fa853350dde91be672192b427169b29e3348c236e46ad7a757e4ac8163c8c";
+    sha256 = "ff2f492e49c212bb7185954efe09e68583a67daec586c02c49bc728c343d4eb0";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/pip-tools/default.nix b/pkgs/development/python-modules/pip-tools/default.nix
index d2b91eb435c..752047d04f7 100644
--- a/pkgs/development/python-modules/pip-tools/default.nix
+++ b/pkgs/development/python-modules/pip-tools/default.nix
@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "pip-tools";
-  version = "1.10.2";
+  version = "1.11.0";
   name = pname + "-" + version;
 
   src = fetchurl {
     url = "mirror://pypi/p/pip-tools/${name}.tar.gz";
-    sha256 = "d381c7249eb48350cc49447cc106df3d90e9e806b13caaede602c1cd38f61b37";
+    sha256 = "ba427b68443466c389e3b0b0ef55f537ab39344190ea980dfebb333d0e6a50a3";
   };
 
   LC_ALL = "en_US.UTF-8";
@@ -21,9 +21,11 @@ buildPythonPackage rec {
     "test_generate_hashes_all_platforms"
     "test_generate_hashes_without_interfering_with_each_other"
     "test_realistic_complex_sub_dependencies"
+    "test_generate_hashes_with_editable"
     # Expect specific version of "six":
     "test_editable_package"
     "test_input_file_without_extension"
+    "test_locally_available_editable_package_is_not_archived_in_cache_dir"
   ];
 
   checkPhase = ''
diff --git a/pkgs/development/python-modules/plotly/default.nix b/pkgs/development/python-modules/plotly/default.nix
index 2744805a504..75f1b060077 100644
--- a/pkgs/development/python-modules/plotly/default.nix
+++ b/pkgs/development/python-modules/plotly/default.nix
@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "plotly";
-  version = "2.1.0";
+  version = "2.2.3";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ff6899dc11907b1efb944f79f9583b2e30ba2964bb009145f3580bf30b4d9ee4";
+    sha256 = "dadd2263f1c0449b248fd3742a077d9594935921a9597529be76d6a841237ab0";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/pluggy/default.nix b/pkgs/development/python-modules/pluggy/default.nix
new file mode 100644
index 00000000000..0fbfa5108c1
--- /dev/null
+++ b/pkgs/development/python-modules/pluggy/default.nix
@@ -0,0 +1,29 @@
+{ buildPythonPackage
+, lib
+, fetchPypi
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "pluggy";
+  version = "0.6.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "7f8ae7f5bdf75671a718d2daf0a64b7885f74510bcd98b1a0bb420eb9a9d0cff";
+  };
+
+  checkPhase = ''
+    py.test
+  '';
+
+  # To prevent infinite recursion with pytest
+  doCheck = false;
+
+  meta = {
+    description = "Plugin and hook calling mechanisms for Python";
+    homepage = "https://pypi.python.org/pypi/pluggy";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ jgeerds ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/plumbum/default.nix b/pkgs/development/python-modules/plumbum/default.nix
index 216c163bc9d..a5881bb2e7c 100644
--- a/pkgs/development/python-modules/plumbum/default.nix
+++ b/pkgs/development/python-modules/plumbum/default.nix
@@ -6,7 +6,7 @@
 
 buildPythonPackage rec {
   pname = "plumbum";
-  version = "1.6.3";
+  version = "1.6.5";
   name = "${pname}-${version}";
 
   checkInputs = [ pytest ];
@@ -16,6 +16,6 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0249e708459f1b05627a7ca8787622c234e4db495a532acbbd1f1f17f28c7320";
+    sha256 = "d8abb059bb62beb6c99db08d3598167abaeeab53eaf218f91e74bae471a24bee";
   };
 }
\ No newline at end of file
diff --git a/pkgs/development/python-modules/psutil/default.nix b/pkgs/development/python-modules/psutil/default.nix
index cf9b3ea267f..b9d07a3fa9b 100644
--- a/pkgs/development/python-modules/psutil/default.nix
+++ b/pkgs/development/python-modules/psutil/default.nix
@@ -7,12 +7,12 @@
 
 buildPythonPackage rec {
   pname = "psutil";
-  version = "5.4.1";
+  version = "5.4.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "42e2de159e3c987435cb3b47d6f37035db190a1499f3af714ba7af5c379b6ba2";
+    sha256 = "00a1f9ff8d1e035fba7bfdd6977fa8ea7937afdb4477339e5df3dba78194fe11";
   };
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/py/default.nix b/pkgs/development/python-modules/py/default.nix
index 0dc3b679328..cd945f7bfc6 100644
--- a/pkgs/development/python-modules/py/default.nix
+++ b/pkgs/development/python-modules/py/default.nix
@@ -1,12 +1,12 @@
 { stdenv, buildPythonPackage, fetchPypi }:
 buildPythonPackage rec {
   pname = "py";
-  version = "1.4.34";
+  version = "1.5.2";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1qyd5z0hv8ymxy84v5vig3vps2fvhcf4bdlksb3r03h549fmhb8g";
+    sha256 = "ca18943e28235417756316bfada6cd96b23ce60dd532642690dcfdaba988a76d";
   };
 
   # Circular dependency on pytest
diff --git a/pkgs/development/python-modules/pyaml/default.nix b/pkgs/development/python-modules/pyaml/default.nix
new file mode 100644
index 00000000000..5fd1be7c15c
--- /dev/null
+++ b/pkgs/development/python-modules/pyaml/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pyyaml
+, unidecode
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "pyaml";
+  version = "17.12.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "66623c52f34d83a2c0fc963e08e8b9d0c13d88404e3b43b1852ef71eda19afa3";
+  };
+
+  propagatedBuildInputs = [ pyyaml ];
+
+  checkInputs = [ unidecode ];
+
+  meta = {
+    description = "PyYAML-based module to produce pretty and readable YAML-serialized data";
+    homepage = https://github.com/mk-fg/pretty-yaml;
+    license = lib.licenses.wtfpl;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/pyasn1-modules/default.nix b/pkgs/development/python-modules/pyasn1-modules/default.nix
index a7ee15d6a18..b8dcae16da8 100644
--- a/pkgs/development/python-modules/pyasn1-modules/default.nix
+++ b/pkgs/development/python-modules/pyasn1-modules/default.nix
@@ -3,12 +3,12 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pyasn1-modules";
-  version = "0.1.5";
+  version = "0.2.1";
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1239h6h67vg0wazg2qgv6m3hdim2gs66pl89lbnayk55bbnkwc0x";
+    sha256 = "af00ea8f2022b6287dc375b2c70f31ab5af83989fc6fe9eacd4976ce26cd7ccc";
   };
 
   propagatedBuildInputs = [ pyasn1 ];
diff --git a/pkgs/development/python-modules/pyasn1/default.nix b/pkgs/development/python-modules/pyasn1/default.nix
index d0122a5b7e4..8037796713e 100644
--- a/pkgs/development/python-modules/pyasn1/default.nix
+++ b/pkgs/development/python-modules/pyasn1/default.nix
@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pyasn1";
-  version = "0.3.4";
+  version = "0.4.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06hhy38jhwh95gpn8f03cr439273fsfsh4vhd5024r86nh5gyiir";
+    sha256 = "d258b0a71994f7770599835249cece1caef3c70def868c4915e6e5ca49b67d15";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/pyblake2/default.nix b/pkgs/development/python-modules/pyblake2/default.nix
index 4e166dcb183..c2f4e7db43f 100644
--- a/pkgs/development/python-modules/pyblake2/default.nix
+++ b/pkgs/development/python-modules/pyblake2/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "pyblake2";
-  version = "0.9.3";
+  version = "1.1.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "626448e1fe1cc01d2197118954bec9f158378577e12686d5b01979f7f0fa2212";
+    sha256 = "3a850036bf42053c74bfc52c063323ca78e40ba1f326b01777da5750a143631a";
   };
 
   # requires setting up sphinx doctest
diff --git a/pkgs/development/python-modules/pychromecast/default.nix b/pkgs/development/python-modules/pychromecast/default.nix
index 01014170dc7..46d3272807e 100644
--- a/pkgs/development/python-modules/pychromecast/default.nix
+++ b/pkgs/development/python-modules/pychromecast/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "PyChromecast";
-  version = "0.8.1";
+  version = "1.0.3";
   name = pname + "-" + version;
 
   src = fetchurl {
     url    = "mirror://pypi/p/pychromecast/${name}.tar.gz";
-    sha256 = "05rlr2hjng0xg2a9k9vwmrlvd7vy9sjhxxfl96kx25xynlkq6yq6";
+    sha256 = "714a9e03e6a258081e3b6296ed15592e015facbe38bbe60819cca6f04c599f25";
   };
 
   propagatedBuildInputs = [ requests six zeroconf protobuf ];
diff --git a/pkgs/development/python-modules/pycollada/default.nix b/pkgs/development/python-modules/pycollada/default.nix
index 948d9741bd8..35b10421f2c 100644
--- a/pkgs/development/python-modules/pycollada/default.nix
+++ b/pkgs/development/python-modules/pycollada/default.nix
@@ -2,15 +2,14 @@
 
 buildPythonPackage rec {
   pname = "pycollada";
-  version = "0.5";
-  name = "${pname}-${version}";
+  version = "0.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1g96maw2c25l4i3ks51784h33zf7s18vrn6iyz4ca34iy4sl7yq9";
+    sha256 = "fcd6f38fd981e350f9ec754d9671834017accd600e967d6d299a6cfdae5ba4f4";
   };
 
-  buildInputs = [ numpy ] ++ (if isPy3k then [dateutil] else [dateutil_1_5]);
+  propagatedBuildInputs = [ numpy dateutil ];
 
   # Some tests fail because they refer to test data files that don't exist
   # (upstream packaging issue)
diff --git a/pkgs/development/python-modules/pydot/default.nix b/pkgs/development/python-modules/pydot/default.nix
index be0b4eabfa8..98d4b33939a 100644
--- a/pkgs/development/python-modules/pydot/default.nix
+++ b/pkgs/development/python-modules/pydot/default.nix
@@ -8,12 +8,12 @@
 
 buildPythonPackage rec {
   pname = "pydot";
-  version = "1.2.3";
+  version = "1.2.4";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "edb5d3f249f97fbd9c4bb16959e61bc32ecf40eee1a9f6d27abe8d01c0a73502";
+    sha256 = "92d2e2d15531d00710f2d6fb5540d2acabc5399d464f2f20d5d21073af241eb6";
   };
   checkInputs = [ chardet ];
   # No tests in archive
diff --git a/pkgs/development/python-modules/pygit2/default.nix b/pkgs/development/python-modules/pygit2/default.nix
index 90bfe978391..d8eb05cf348 100644
--- a/pkgs/development/python-modules/pygit2/default.nix
+++ b/pkgs/development/python-modules/pygit2/default.nix
@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pygit2";
-  version = "0.26.0";
+  version = "0.26.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57";
+    sha256 = "29baa530d6fcbf7cca6a75cf9c78fb88613ca81afb39c62fe492f226f6b61800";
   };
 
   preConfigure = lib.optionalString stdenv.isDarwin ''
diff --git a/pkgs/development/python-modules/pyglet/default.nix b/pkgs/development/python-modules/pyglet/default.nix
index 8d5dd53f80a..51243154b1a 100644
--- a/pkgs/development/python-modules/pyglet/default.nix
+++ b/pkgs/development/python-modules/pyglet/default.nix
@@ -1,23 +1,24 @@
 { stdenv, buildPythonPackage, fetchPypi
-, mesa, xorg, freetype, fontconfig}:
+, mesa, xorg, freetype, fontconfig, future}:
 
 buildPythonPackage rec {
-  version = "1.2.4";
+  version = "1.3.0";
   pname = "pyglet";
-  name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9f62ffbbcf2b202d084bf158685e77d28b8f4f5f2738f4c5e63a947a07503445";
+    sha256 = "640a8f8e3d7bf8dbb551fa707f14021f619932990ab1401c48ba9dbcc6c2242c";
   };
 
-  patchPhase = let
+  postPatch = let
     libs = [ mesa xorg.libX11 freetype fontconfig ];
     paths = builtins.concatStringsSep "," (map (l: "\"${l}/lib\"") libs);
   in "sed -i -e 's|directories\.extend.*lib[^]]*|&,${paths}|' pyglet/lib.py";
 
   doCheck = false;
 
+  propagatedBuildInputs = [ future ];
+
   meta = with stdenv.lib; {
     homepage = "http://www.pyglet.org/";
     description = "A cross-platform windowing and multimedia library";
diff --git a/pkgs/development/python-modules/pylast/default.nix b/pkgs/development/python-modules/pylast/default.nix
index 99bcb9357dc..1fcc7211504 100644
--- a/pkgs/development/python-modules/pylast/default.nix
+++ b/pkgs/development/python-modules/pylast/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "pylast";
-  version = "1.9.0";
+  version = "2.0.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ae1c4105cbe704d9ac10ba57ac4c26bc576cc33978f1b578101b20c6a2360ca4";
+    sha256 = "8e4d4962aa12d67bd357e1aa596a146b2e97afd943b5c9257e555014d13b3065";
   };
 
   propagatedBuildInputs = [ certifi six ];
diff --git a/pkgs/development/python-modules/pylint/default.nix b/pkgs/development/python-modules/pylint/default.nix
index afe3bf8e503..79337663c62 100644
--- a/pkgs/development/python-modules/pylint/default.nix
+++ b/pkgs/development/python-modules/pylint/default.nix
@@ -4,11 +4,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pylint";
-  version = "1.7.4";
+  version = "1.8.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1f65b3815c3bf7524b845711d54c4242e4057dd93826586620239ecdfe591fb1";
+    sha256 = "3035e44e37cd09919e9edad5573af01d7c6b9c52a0ebb4781185ae7ab690458b";
   };
 
   buildInputs = [ pytest pytestrunner mccabe configparser backports_functools_lru_cache ];
diff --git a/pkgs/development/python-modules/pymongo/default.nix b/pkgs/development/python-modules/pymongo/default.nix
index 5b400e1521e..577cd9142f9 100644
--- a/pkgs/development/python-modules/pymongo/default.nix
+++ b/pkgs/development/python-modules/pymongo/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "pymongo";
-  version = "3.5.1";
+  version = "3.6.0";
   name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0939bl3brrklvccicck62gs3zd7i9aysz13c8pxc3gpk2hsdj878";
+    sha256 = "c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8";
   };
 
   doCheck = false;
diff --git a/pkgs/development/python-modules/pyobjc/default.nix b/pkgs/development/python-modules/pyobjc/default.nix
index 0cf08319645..874e0d47fc9 100644
--- a/pkgs/development/python-modules/pyobjc/default.nix
+++ b/pkgs/development/python-modules/pyobjc/default.nix
@@ -3,7 +3,7 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pyobjc";
-  version = "4.0b1";
+  version = "4.1";
 
   # Gives "No matching distribution found for
   # pyobjc-framework-Collaboration==4.0b1 (from pyobjc==4.0b1)"
@@ -11,7 +11,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16bng6960c1m57nnh1l09ycnyimrqzw9mx9pnyjxn5zzm5kalr37";
+    sha256 = "287db11f912ac7d05c4907dbf6e74abaa475e36368f7c92e05aca2886a94562c";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/pyopencl/default.nix b/pkgs/development/python-modules/pyopencl/default.nix
index 9d5661f4d58..07ff8735b52 100644
--- a/pkgs/development/python-modules/pyopencl/default.nix
+++ b/pkgs/development/python-modules/pyopencl/default.nix
@@ -15,18 +15,23 @@
 
 buildPythonPackage rec {
   pname = "pyopencl";
-  version = "2017.2";
-  name = "${pname}-${version}";
+  version = "2017.2.2";
 
-  buildInputs = [ pytest opencl-headers ocl-icd ];
+  checkInputs = [ pytest ];
+  buildInputs = [ opencl-headers ocl-icd ];
 
   propagatedBuildInputs = [ numpy cffi pytools decorator appdirs six Mako ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "039b689a58eb98e27a577ac086210deae959f40d657487f3199d2d217c270ff9";
+    sha256 = "d2f7b04d2e819c6e90d6366b7712a7452a39fba218e51b11b02c85ab07fd2983";
   };
 
+  # py.test is not needed during runtime, so remove it from `install_requires`
+  postPatch = ''
+    substituteInPlace setup.py --replace "pytest>=2" ""
+  '';
+
   # gcc: error: pygpu_language_opencl.cpp: No such file or directory
   doCheck = false;
 
diff --git a/pkgs/development/python-modules/pysoundfile/default.nix b/pkgs/development/python-modules/pysoundfile/default.nix
index ef67ed85cc0..aa7d23c5fcb 100644
--- a/pkgs/development/python-modules/pysoundfile/default.nix
+++ b/pkgs/development/python-modules/pysoundfile/default.nix
@@ -11,12 +11,12 @@
 
 buildPythonPackage rec {
   pname = "PySoundFile";
-  version = "0.8.1";
+  version = "0.9.0.post1";
   name = pname + "-" + version;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "72c3e23b7c9998460ec78176084ea101e3439596ab29df476bc8508708df84df";
+    sha256 = "43dd46a2afc0484c26930a7e59eef9365cee81bce7a4aadc5699f788f60d32c3";
   };
 
     checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/pytest-localserver/default.nix b/pkgs/development/python-modules/pytest-localserver/default.nix
index fdd1986c04f..c98370ed938 100644
--- a/pkgs/development/python-modules/pytest-localserver/default.nix
+++ b/pkgs/development/python-modules/pytest-localserver/default.nix
@@ -10,11 +10,11 @@
 buildPythonPackage rec {
   pname = "pytest-localserver";
   name = "${pname}-${version}";
-  version = "0.3.7";
+  version = "0.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1c11hn61n06ms0wmw6536vs5k4k9hlndxsb3p170nva56a9dfa6q";
+    sha256 = "a72af60a1ec8f73668a7884c86baf1fbe48394573cb4fa36709887217736c021";
   };
 
   propagatedBuildInputs = [ werkzeug ];
diff --git a/pkgs/development/python-modules/pytest-xdist/default.nix b/pkgs/development/python-modules/pytest-xdist/default.nix
index e993a67c49f..2e2975e6596 100644
--- a/pkgs/development/python-modules/pytest-xdist/default.nix
+++ b/pkgs/development/python-modules/pytest-xdist/default.nix
@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "pytest-xdist";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "433e82f9b34986a4e4b2be38c60e82cca3ac64b7e1b38f4d8e3e118292939712";
+    sha256 = "0b8622435e3c0650a8d5a07b73a7f9c4f79b52d7ed060536a6041f0da423ba8e";
   };
 
   buildInputs = [ pytest setuptools_scm pytest-forked];
diff --git a/pkgs/development/python-modules/pytest/3_2.nix b/pkgs/development/python-modules/pytest/3_2.nix
new file mode 100644
index 00000000000..d7a0b1bdad3
--- /dev/null
+++ b/pkgs/development/python-modules/pytest/3_2.nix
@@ -0,0 +1,27 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy26, argparse, hypothesis, py
+, setuptools_scm, setuptools
+}:
+buildPythonPackage rec {
+  version = "3.2.5";
+  pname = "pytest";
+
+  preCheck = ''
+    # don't test bash builtins
+    rm testing/test_argcomplete.py
+  '';
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
+  };
+
+  checkInputs = [ hypothesis ];
+  buildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [ py setuptools ]
+    ++ (stdenv.lib.optional isPy26 argparse);
+
+  meta = with stdenv.lib; {
+    maintainers = with maintainers; [ domenkozar lovek323 madjar lsix ];
+    platforms = platforms.unix;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/pytest/default.nix b/pkgs/development/python-modules/pytest/default.nix
index 8e280b8fd0d..d45fe7deb12 100644
--- a/pkgs/development/python-modules/pytest/default.nix
+++ b/pkgs/development/python-modules/pytest/default.nix
@@ -1,8 +1,8 @@
-{ stdenv, buildPythonPackage, fetchPypi, isPy26, argparse, hypothesis, py
-, setuptools_scm, setuptools
+{ stdenv, buildPythonPackage, fetchPypi, isPy26, argparse, attrs, hypothesis, py
+, setuptools_scm, setuptools, six, pluggy, funcsigs, isPy3k
 }:
 buildPythonPackage rec {
-  version = "3.2.5";
+  version = "3.3.1";
   pname = "pytest";
 
   preCheck = ''
@@ -12,16 +12,18 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6d5bd4f7113b444c55a3bbb5c738a3dd80d43563d063fc42dcb0aaefbdd78b81";
+    sha256 = "cf8436dc59d8695346fcd3ab296de46425ecab00d64096cebe79fb51ecb2eb93";
   };
 
   checkInputs = [ hypothesis ];
   buildInputs = [ setuptools_scm ];
-  propagatedBuildInputs = [ py setuptools ]
+  propagatedBuildInputs = [ attrs py setuptools six pluggy ]
+    ++ (stdenv.lib.optional (!isPy3k) funcsigs)
     ++ (stdenv.lib.optional isPy26 argparse);
 
   meta = with stdenv.lib; {
     maintainers = with maintainers; [ domenkozar lovek323 madjar lsix ];
     platforms = platforms.unix;
+    description = "Framework for writing tests";
   };
 }
diff --git a/pkgs/development/python-modules/pytoml/default.nix b/pkgs/development/python-modules/pytoml/default.nix
index 55479e76daf..91661a1fb51 100644
--- a/pkgs/development/python-modules/pytoml/default.nix
+++ b/pkgs/development/python-modules/pytoml/default.nix
@@ -1,18 +1,22 @@
-{ stdenv, buildPythonPackage, fetchgit
-, python }:
+{ stdenv
+, buildPythonPackage
+, fetchgit
+, python
+}:
 
 buildPythonPackage rec {
   pname = "pytoml";
-  version = "0.1.11";
-  name = "${pname}-${version}";
+  version = "0.1.14";
 
-  checkPhase = "${python.interpreter} test/test.py";
+  checkPhase = ''
+    ${python.interpreter} test/test.py
+  '';
 
   # fetchgit used to ensure test submodule is available
   src = fetchgit {
     url = "${meta.homepage}.git";
     rev = "refs/tags/v${version}";
-    sha256 = "1jiw04zk9ccynr8kb1vqh9r1p2kh0al7g7b1f94911iazg7dgs9j";
+    sha256 = "1ip71yqxnyi4jhw5x1q7a0za61ndhpfh0vbx08jfv0w4ayng6rgv";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/pytools/default.nix b/pkgs/development/python-modules/pytools/default.nix
new file mode 100644
index 00000000000..2bf7413c600
--- /dev/null
+++ b/pkgs/development/python-modules/pytools/default.nix
@@ -0,0 +1,39 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, decorator
+, appdirs
+, six
+, numpy
+, pytest
+}:
+
+buildPythonPackage rec {
+  pname = "pytools";
+  version = "2017.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "80f1bba4469d473c1b3969bc8e188c03bcc94d35807a889ceebbfc78e3208115";
+  };
+
+  checkInputs = [ pytest ];
+
+  propagatedBuildInputs = [
+    decorator
+    appdirs
+    six
+    numpy
+  ];
+
+  checkPhase = ''
+    py.test -k 'not test_persistent_dict'
+  '';
+
+  meta = {
+    homepage = https://github.com/inducer/pytools/;
+    description = "Miscellaneous Python lifesavers.";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ artuuge ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/pywinrm/default.nix b/pkgs/development/python-modules/pywinrm/default.nix
index ecd46bb1ff5..10150259ef5 100644
--- a/pkgs/development/python-modules/pywinrm/default.nix
+++ b/pkgs/development/python-modules/pywinrm/default.nix
@@ -11,12 +11,12 @@
 
 buildPythonPackage rec {
   pname = "pywinrm";
-  version = "0.2.2";
+  version = "0.3.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06xc0mbqf718vmsp0fq0rb64nql66l5w2x23bmqnzl6nzc0gfc1h";
+    sha256 = "799fc3e33fec8684443adf5778860388289102ea4fa1458f1bf307d167855573";
   };
 
   checkInputs = [ mock pytest ];
diff --git a/pkgs/development/python-modules/relatorio/default.nix b/pkgs/development/python-modules/relatorio/default.nix
index 5e1ea8b4642..5c5f2578fbf 100644
--- a/pkgs/development/python-modules/relatorio/default.nix
+++ b/pkgs/development/python-modules/relatorio/default.nix
@@ -3,10 +3,10 @@
 buildPythonPackage rec {
   pname = "relatorio";
   name = "${pname}-${version}";
-  version = "0.7.1";
+  version = "0.8.0";
   src = fetchurl {
     url = "mirror://pypi/r/relatorio/${name}.tar.gz";
-    sha256 = "744f1e39313f037a0ab52a154338ece151d83e5442a9278db1f8ce450ce6c2cd";
+    sha256 = "bddf85d029c5c85a0f976d73907e14e4c3093065fe8527170c91abf0218546d9";
   };
   propagatedBuildInputs = [
     genshi
diff --git a/pkgs/development/python-modules/restview/default.nix b/pkgs/development/python-modules/restview/default.nix
index 0f2ce45c885..3c61ea4ded2 100644
--- a/pkgs/development/python-modules/restview/default.nix
+++ b/pkgs/development/python-modules/restview/default.nix
@@ -10,11 +10,11 @@
 buildPythonPackage rec {
   pname = "restview";
   name = "${pname}-${version}";
-  version = "2.7.0";
+  version = "2.8.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "e7842100f3de179c68cfe7c2cf56c61509cd6068bc6dd58ab42c0ade5d5f97ec";
+    sha256 = "5f6f1523228eab3269f59dd03ac560f7d370cd81df6fdbcb4914b5e6bd896a11";
   };
 
   propagatedBuildInputs = [ docutils readme_renderer pygments ];
diff --git a/pkgs/development/python-modules/robomachine/default.nix b/pkgs/development/python-modules/robomachine/default.nix
index 8f71bab9c25..72407131cb1 100644
--- a/pkgs/development/python-modules/robomachine/default.nix
+++ b/pkgs/development/python-modules/robomachine/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "robomachine";
-  version = "0.6";
+  version = "0.8.0";
   name = pname + "-" + version;
 
   src = fetchurl {
     url = "mirror://pypi/R/RoboMachine/RoboMachine-0.6.tar.gz";
-    sha256 = "6c9a9bae7bffa272b2a09b05df06c29a3a776542c70cae8041a8975a061d2e54";
+    sha256 = "242cfd9be0f7591138eaeba03c9c190f894ce045e1767ab7b90eca330259fc45";
   };
 
   propagatedBuildInputs = [ pyparsing argparse robotframework ];
diff --git a/pkgs/development/python-modules/ropper/default.nix b/pkgs/development/python-modules/ropper/default.nix
index f7ef16b02bb..62ef3f8db19 100644
--- a/pkgs/development/python-modules/ropper/default.nix
+++ b/pkgs/development/python-modules/ropper/default.nix
@@ -3,23 +3,25 @@
 , fetchPypi
 , capstone
 , filebytes
-, pytest }:
+, pytest
+}:
 
 buildPythonApplication rec {
-  name = "${pname}-${version}";
   pname = "ropper";
-  version = "1.10.10";
+  version = "1.11.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1676e07947a19df9d17002307a7555c2647a4224d6f2869949e8fc4bd18f2e87";
+    sha256 = "2183feedfe8b01a27301eee07383b481ece01b2319bdba3afebe33e19ca14aa3";
   };
   # XXX tests rely on user-writeable /dev/shm to obtain process locks and return PermissionError otherwise
   # workaround: sudo chmod 777 /dev/shm
   checkPhase = ''
     py.test testcases
   '';
-  buildInputs = [pytest];
+  doCheck = false; # Tests not included in archive
+
+  checkInputs = [pytest];
   propagatedBuildInputs = [ capstone filebytes ];
   meta = with stdenv.lib; {
     homepage = https://scoding.de/ropper/;
diff --git a/pkgs/development/python-modules/scrapy/default.nix b/pkgs/development/python-modules/scrapy/default.nix
index 5b40c74a181..005d02e6047 100644
--- a/pkgs/development/python-modules/scrapy/default.nix
+++ b/pkgs/development/python-modules/scrapy/default.nix
@@ -2,7 +2,7 @@
   testfixtures, pillow, six, twisted, w3lib, lxml, queuelib, pyopenssl,
   service-identity, parsel, pydispatcher, cssselect, lib }:
 buildPythonPackage rec {
-    version = "1.4.0";
+    version = "1.5.0";
     pname = "Scrapy";
     name = "${pname}-${version}";
 
@@ -26,7 +26,7 @@ buildPythonPackage rec {
 
     src = fetchurl {
       url = "mirror://pypi/S/Scrapy/${name}.tar.gz";
-      sha256 = "04a08f027eef5d271342a016439533c81ba46f14bfcf230fecf602e99beaf233";
+      sha256 = "31a0bf05d43198afaf3acfb9b4fb0c09c1d7d7ff641e58c66e36117f26c4b755";
     };
 
     meta = with lib; {
diff --git a/pkgs/development/python-modules/seaborn/default.nix b/pkgs/development/python-modules/seaborn/default.nix
index 1647e6cfc14..20ad32b3261 100644
--- a/pkgs/development/python-modules/seaborn/default.nix
+++ b/pkgs/development/python-modules/seaborn/default.nix
@@ -8,11 +8,11 @@
 
 buildPythonPackage rec {
   pname = "seaborn";
-  version = "0.7.1";
+  version = "0.8.1";
   name = "${pname}-${version}";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0pawrqc3mxpwd5g9pvi9gba02637bh5c8ldpp8izfwpfn52469zs";
+    sha256 = "6702978b903d0284446e935916b980dfebae4063c18ad8eb6e8f9e76d0257eae";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/serpy/default.nix b/pkgs/development/python-modules/serpy/default.nix
index 2414b97e94a..610a75fa317 100644
--- a/pkgs/development/python-modules/serpy/default.nix
+++ b/pkgs/development/python-modules/serpy/default.nix
@@ -5,7 +5,7 @@
 buildPythonPackage rec {
   pname = "serpy";
   name = "${pname}-${version}";
-  version = "0.2.0";
+  version = "0.3.1";
 
   meta = {
     description = "ridiculously fast object serialization";
@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7e62e242321b208362966d5ab32b45df93b1cb88da4ce6260277da060b4f7475";
+    sha256 = "3772b2a9923fbf674000ff51abebf6ea8f0fca0a2cfcbfa0d63ff118193d1ec5";
   };
 
   buildInputs = [ flake8 py pyflakes tox ];
diff --git a/pkgs/development/python-modules/setuptools/default.nix b/pkgs/development/python-modules/setuptools/default.nix
index 1c53f3cd437..b185be62a69 100644
--- a/pkgs/development/python-modules/setuptools/default.nix
+++ b/pkgs/development/python-modules/setuptools/default.nix
@@ -8,13 +8,13 @@
 # Should use buildPythonPackage here somehow
 stdenv.mkDerivation rec {
   pname = "setuptools";
-  version = "38.2.3";
+  version = "38.2.5";
   name = "${python.libPrefix}-${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "124jlg72bbk2xxv5wqbwcl4h5cdslslzk92rxjxiplg79l499hv3";
+    sha256 = "b080f276cc868670540b2c03cee06cc14d2faf9da7bec0f15058d1b402c94507";
   };
 
   buildInputs = [ python wrapPython unzip ];
diff --git a/pkgs/development/python-modules/shapely/default.nix b/pkgs/development/python-modules/shapely/default.nix
index e8e92818ecf..dab3542b809 100644
--- a/pkgs/development/python-modules/shapely/default.nix
+++ b/pkgs/development/python-modules/shapely/default.nix
@@ -6,11 +6,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "Shapely";
-  version = "1.6.2.post1";
+  version = "1.6.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07fba518e76b3276558f62a5829bdfa476f790cdef752383ccdc8c66b04b0899";
+    sha256 = "14152f111c7711fc6756fd538ec12fc8cdde7419f869b244922f71f61b2a6c6b";
   };
 
   buildInputs = [ geos glibcLocales cython ];
diff --git a/pkgs/development/python-modules/simplejson/default.nix b/pkgs/development/python-modules/simplejson/default.nix
index 846e8dc21a1..25dbecac949 100644
--- a/pkgs/development/python-modules/simplejson/default.nix
+++ b/pkgs/development/python-modules/simplejson/default.nix
@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "simplejson";
-  version = "3.11.1";
+  version = "3.13.2";
   name = "${pname}-${version}";
   doCheck = !stdenv.isDarwin;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "01a22d49ddd9a168b136f26cac87d9a335660ce07aa5c630b8e3607d6f4325e7";
+    sha256 = "4c4ecf20e054716cc1e5a81cadc44d3f4027108d8dd0861d8b1e3bd7a32d4f0a";
   };
 
   meta = {
diff --git a/pkgs/development/python-modules/six/default.nix b/pkgs/development/python-modules/six/default.nix
index 00fbbbc01eb..6921b3590e4 100644
--- a/pkgs/development/python-modules/six/default.nix
+++ b/pkgs/development/python-modules/six/default.nix
@@ -19,6 +19,9 @@ buildPythonPackage rec {
     py.test test_six.py
   '';
 
+  # To prevent infinite recursion with pytest
+  doCheck = false;
+
   meta = {
     description = "A Python 2 and 3 compatibility library";
     homepage = https://pypi.python.org/pypi/six/;
diff --git a/pkgs/development/python-modules/smart_open/default.nix b/pkgs/development/python-modules/smart_open/default.nix
index 436d85102d8..2e2020f61f0 100644
--- a/pkgs/development/python-modules/smart_open/default.nix
+++ b/pkgs/development/python-modules/smart_open/default.nix
@@ -12,11 +12,11 @@
 buildPythonPackage rec {
   pname = "smart_open";
   name = "${pname}-${version}";
-  version = "1.5.3";
+  version = "1.5.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0m5j71f7f36s17v4mwv0bxg4azknvcy82rbjp28b4vifrjd6dm7s";
+    sha256 = "8fd2de1c359bd0074bd6d334a5b9820ae1c5b6ba563970b95052bace4b71baeb";
   };
 
   propagatedBuildInputs = [ boto bz2file requests responses moto ];
diff --git a/pkgs/development/python-modules/sqlalchemy/default.nix b/pkgs/development/python-modules/sqlalchemy/default.nix
index 9b3a5fa2039..488e78cb4ee 100644
--- a/pkgs/development/python-modules/sqlalchemy/default.nix
+++ b/pkgs/development/python-modules/sqlalchemy/default.nix
@@ -11,11 +11,11 @@
 buildPythonPackage rec {
   pname = "SQLAlchemy";
   name = "${pname}-${version}";
-  version = "1.1.15";
+  version = "1.2.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8b79a5ed91cdcb5abe97b0045664c55c140aec09e5dd5c01303e23de5fe7a95a";
+    sha256 = "7dda3e0b1b12215e3bb05368d1abbf7d747112a43738e0a4e6deb466b83fd88e";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/sqlmap/default.nix b/pkgs/development/python-modules/sqlmap/default.nix
index 2c85bdbe3d1..e89abbd595a 100644
--- a/pkgs/development/python-modules/sqlmap/default.nix
+++ b/pkgs/development/python-modules/sqlmap/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "sqlmap";
-  version = "1.1.11";
+  version = "1.1.12";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "bb5297df9cd97316b3c7ca64f8e31cae5cc6b94c015afd84c546877f1f77d6e4";
+    sha256 = "86a1078ceb1e79f891633c7e4c7b07949fd9135a0e4c0738abd5111e2e6b96c0";
   };
 
   # No tests in archive
diff --git a/pkgs/development/python-modules/stevedore/default.nix b/pkgs/development/python-modules/stevedore/default.nix
index 326282a39c3..9639ce96194 100644
--- a/pkgs/development/python-modules/stevedore/default.nix
+++ b/pkgs/development/python-modules/stevedore/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "stevedore";
-  version = "1.27.1";
+  version = "1.28.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "236468dae36707069e8b3bdb455e9f1be090b1e6b937f4ac0c56a538d6f50be0";
+    sha256 = "f1c7518e7b160336040fee272174f1f7b29a46febb3632502a8f2055f973d60b";
   };
 
   doCheck = false;
diff --git a/pkgs/development/python-modules/stripe/default.nix b/pkgs/development/python-modules/stripe/default.nix
index 7edfb9c4f0e..e2a88a9f10b 100644
--- a/pkgs/development/python-modules/stripe/default.nix
+++ b/pkgs/development/python-modules/stripe/default.nix
@@ -3,7 +3,7 @@
 
 buildPythonPackage rec {
   pname = "stripe";
-  version = "1.70.0";
+  version = "1.77.0";
   name = "${pname}-${version}";
 
   # Tests require network connectivity and there's no easy way to disable
@@ -12,7 +12,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ee77103d2d18fe6369f23c40c93067425c5ed67e08b1a7678e681217e8fa8062";
+    sha256 = "6503851d2309dd9c1307e3f0a1cb33ac1427fee25d38ecba1f8bf73a0d74defc";
   };
 
   buildInputs = [ unittest2 mock ];
diff --git a/pkgs/development/python-modules/structlog/default.nix b/pkgs/development/python-modules/structlog/default.nix
new file mode 100644
index 00000000000..2aab5b16aef
--- /dev/null
+++ b/pkgs/development/python-modules/structlog/default.nix
@@ -0,0 +1,32 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytest
+, pretend
+, freezegun
+, simplejson
+}:
+
+buildPythonPackage rec {
+  pname = "structlog";
+  version = "17.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6980001045abd235fa12582222627c19b89109e58b85eb77d5a5abc778df6e20";
+  };
+
+  checkInputs = [ pytest pretend freezegun ];
+  propagatedBuildInputs = [ simplejson ];
+
+  checkPhase = ''
+    rm tests/test_twisted.py*
+    py.test
+  '';
+
+  meta = {
+    description = "Painless structural logging";
+    homepage = http://www.structlog.org/;
+    license = lib.licenses.asl20;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/supervise_api/default.nix b/pkgs/development/python-modules/supervise_api/default.nix
index 5b98aa3415b..85f0106db65 100644
--- a/pkgs/development/python-modules/supervise_api/default.nix
+++ b/pkgs/development/python-modules/supervise_api/default.nix
@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "supervise_api";
-  version = "0.1.5";
+  version = "0.2.0";
 
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1pqqlw80cjdgrlpvdmydkyhsrr4s531mn6bfkshm68j9gk4kq6px";
+    sha256 = "e6982633a924cb5192d2291d25b366ff311876a31b0f5961471b39d87397ef5b";
   };
 
   propagatedBuildInputs = [ supervise ];
diff --git a/pkgs/development/python-modules/sybil/default.nix b/pkgs/development/python-modules/sybil/default.nix
index b1fe22df476..1370c59ace8 100644
--- a/pkgs/development/python-modules/sybil/default.nix
+++ b/pkgs/development/python-modules/sybil/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonApplication rec {
   pname   = "sybil";
-  version = "1.0.5";
+  version = "1.0.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0x8qd5p5qliv8wmdglda2iy3f70i4jg8zqyk8yhklm5hrxm8jdl6";
+    sha256 = "5bd7dd09eff68cbec9062e6950124fadfaaccbc0f50b23c1037f4d70ae86f0f1";
   };
 
   checkInputs = [ pytest nose ];
diff --git a/pkgs/development/python-modules/tabulate/default.nix b/pkgs/development/python-modules/tabulate/default.nix
index 9ddc2a0e08b..db7f43c1ea4 100644
--- a/pkgs/development/python-modules/tabulate/default.nix
+++ b/pkgs/development/python-modules/tabulate/default.nix
@@ -5,13 +5,13 @@
 }:
 
 buildPythonPackage rec {
-  version = "0.7.7";
+  version = "0.8.2";
   pname = "tabulate";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "83a0b8e17c09f012090a50e1e97ae897300a72b35e0c86c0b53d3bd2ae86d8c6";
+    sha256 = "e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/testtools/default.nix b/pkgs/development/python-modules/testtools/default.nix
index e786cb84329..eb6a6694b05 100644
--- a/pkgs/development/python-modules/testtools/default.nix
+++ b/pkgs/development/python-modules/testtools/default.nix
@@ -12,19 +12,18 @@
 , pyrsistent
 }:
 
-# testtools 2.0.0 and up has a circular run-time dependency on futures
+
 
 buildPythonPackage rec {
   pname = "testtools";
-  version = "1.9.0";
-  name = "${pname}-${version}";
+  version = "2.3.0";
 
   # Python 2 only judging from SyntaxError
 #   disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b46eec2ad3da6e83d53f2b0eca9a8debb687b4f71343a074f83a16bbdb3c0644";
+    sha256 = "5827ec6cf8233e0f29f51025addd713ca010061204fdea77484a2934690a0559";
   };
 
   propagatedBuildInputs = [ pbr python_mimeparse extras lxml unittest2 pyrsistent ];
@@ -33,6 +32,11 @@ buildPythonPackage rec {
   # No tests in archive
   doCheck = false;
 
+  # testtools 2.0.0 and up has a circular run-time dependency on futures
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "fixtures>=1.3.0" ""
+  '';
+
   meta = {
     description = "A set of extensions to the Python standard library's unit testing framework";
     homepage = https://pypi.python.org/pypi/testtools;
diff --git a/pkgs/development/python-modules/textacy/default.nix b/pkgs/development/python-modules/textacy/default.nix
index 1647b837d97..333c4825f0f 100644
--- a/pkgs/development/python-modules/textacy/default.nix
+++ b/pkgs/development/python-modules/textacy/default.nix
@@ -25,11 +25,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "textacy";
-  version = "0.4.1";
+  version = "0.5.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04wf3a7zgzz83nmgkh488wkl50zm9yfdpv3sl12sm2zj685plqcz";
+    sha256 = "6fc4603fd52c386081b063ef7aa15ca77e5e937a3064b197359659fccfdeb406";
   };
 
   disabled = isPy27; # 2.7 requires backports.csv
diff --git a/pkgs/development/python-modules/texttable/default.nix b/pkgs/development/python-modules/texttable/default.nix
new file mode 100644
index 00000000000..38cffcee296
--- /dev/null
+++ b/pkgs/development/python-modules/texttable/default.nix
@@ -0,0 +1,20 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname = "texttable";
+  version = "1.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "44674d1d470a9fc264c4d1eba44b74463ca0066d7b954453dd5a4f8057779c9c";
+  };
+
+  meta = {
+    description = "A module to generate a formatted text table, using ASCII characters";
+    homepage = http://foutaise.org/code/;
+    license = lib.licenses.lgpl2;
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/thespian/default.nix b/pkgs/development/python-modules/thespian/default.nix
index 7a6ff3cc53d..df118470e92 100644
--- a/pkgs/development/python-modules/thespian/default.nix
+++ b/pkgs/development/python-modules/thespian/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchPypi, buildPythonPackage, lib }:
 
 buildPythonPackage rec {
-  version = "3.8.3";
+  version = "3.9.0";
   pname = "thespian";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     extension = "zip";
-    sha256 = "0vvwsh3waxd5ldrayr86kdcshv07bp361fl7p16g9i044vklwly4";
+    sha256 = "e698e3c5369d7b06de5c4ce7b877ea65991c99f7b0fabd09f29e91bc981c7d22";
   };
 
   # Do not run the test suite: it takes a long type and uses
diff --git a/pkgs/development/python-modules/toolz/default.nix b/pkgs/development/python-modules/toolz/default.nix
index 36b85bce3ac..0fc14024903 100644
--- a/pkgs/development/python-modules/toolz/default.nix
+++ b/pkgs/development/python-modules/toolz/default.nix
@@ -6,12 +6,12 @@
 
 buildPythonPackage rec{
   pname = "toolz";
-  version = "0.8.2";
+  version = "0.9.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0l3czks4xy37i8099waxk2fdz5g0k1dwys2mkhlxc0b0886cj4sa";
+    sha256 = "929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/tox/default.nix b/pkgs/development/python-modules/tox/default.nix
new file mode 100644
index 00000000000..bc70d65cc1f
--- /dev/null
+++ b/pkgs/development/python-modules/tox/default.nix
@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, py
+, virtualenv
+, pluggy
+, setuptools_scm
+, six
+}:
+
+buildPythonPackage rec {
+  pname = "tox";
+  version = "2.9.1";
+
+  buildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [ py virtualenv pluggy six ];
+
+  doCheck = false;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "752f5ec561c6c08c5ecb167d3b20f4f4ffc158c0ab78855701a75f5cef05f4b8";
+  };
+}
\ No newline at end of file
diff --git a/pkgs/development/python-modules/tqdm/default.nix b/pkgs/development/python-modules/tqdm/default.nix
index 2392a4a9968..209ee8ccd6b 100644
--- a/pkgs/development/python-modules/tqdm/default.nix
+++ b/pkgs/development/python-modules/tqdm/default.nix
@@ -11,12 +11,12 @@
 
 buildPythonPackage rec {
   pname = "tqdm";
-  version = "4.19.4";
+  version = "4.19.5";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7ca803c2ea268c6bdb541e2dac74a3af23cf4bf7b4132a6a78926d255f8c8df1";
+    sha256 = "df32e6f127dc0ccbc675eadb33f749abbcb8f174c5cb9ec49c0cdb73aa737377";
   };
 
   buildInputs = [ nose coverage glibcLocales flake8 ];
diff --git a/pkgs/development/python-modules/tzlocal/default.nix b/pkgs/development/python-modules/tzlocal/default.nix
index 2277cb7c4ca..1c61d0afab3 100644
--- a/pkgs/development/python-modules/tzlocal/default.nix
+++ b/pkgs/development/python-modules/tzlocal/default.nix
@@ -4,13 +4,13 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "tzlocal";
-  version = "1.4";
+  version = "1.5.1";
 
   propagatedBuildInputs = [ pytz ];
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0n9hw4kqblyc0avzwi26rqmvyk9impb608rvy11qifmigy7r18h5";
+    sha256 = "4ebeb848845ac898da6519b9b31879cf13b6626f7184c496037b818e238f2c4e";
   };
 
   # test fail (timezone test fail)
diff --git a/pkgs/development/python-modules/vowpalwabbit/default.nix b/pkgs/development/python-modules/vowpalwabbit/default.nix
index 8c980cf2b2c..f2b5e06baaa 100644
--- a/pkgs/development/python-modules/vowpalwabbit/default.nix
+++ b/pkgs/development/python-modules/vowpalwabbit/default.nix
@@ -3,11 +3,11 @@
 pythonPackages.buildPythonPackage rec {
   pname = "vowpalwabbit";
   name = "${pname}-${version}";
-  version = "8.3.2";
+  version = "8.4.0";
 
   src = fetchurl{
     url = "mirror://pypi/v/vowpalwabbit/${name}.tar.gz";
-    sha256 = "0qm8rlrs2gfgamqnpx4lapxakpzgh0yh3kp1lbd7lhb0r748m3k7";
+    sha256 = "abd22bfae99fb102cf8a6aec49e8c278cb7317d3a7eb60f70cd102be9c336fd5";
   };
   # vw tries to write some explicit things to home
   # python installed: The directory '/homeless-shelter/.cache/pip/http'
diff --git a/pkgs/development/python-modules/websockets/default.nix b/pkgs/development/python-modules/websockets/default.nix
index 48803655258..f24f10675f8 100644
--- a/pkgs/development/python-modules/websockets/default.nix
+++ b/pkgs/development/python-modules/websockets/default.nix
@@ -6,13 +6,13 @@
 
 let
   pname = "websockets";
-  version = "3.4";
+  version = "4.0.1";
 in buildPythonPackage rec {
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
-    sha256 = "43e5b9f51dd0000a4c6f646e2ade0c886bd14a784ffac08b9e079bd17a63bcc5";
+    sha256 = "da4d4fbe059b0453e726d6d993760065d69b823a27efc3040402a6fcfe6a1ed9";
   };
 
   disabled = pythonOlder "3.3";
diff --git a/pkgs/development/python-modules/werkzeug/default.nix b/pkgs/development/python-modules/werkzeug/default.nix
index 5979d895a74..254897be78b 100644
--- a/pkgs/development/python-modules/werkzeug/default.nix
+++ b/pkgs/development/python-modules/werkzeug/default.nix
@@ -1,21 +1,23 @@
 { stdenv, buildPythonPackage, fetchPypi
-, itsdangerous
+, itsdangerous, hypothesis
 , pytest, requests, glibcLocales }:
 
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "Werkzeug";
-  version = "0.12.2";
+  version = "0.13";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "09mv4cya3lywkn4mi3qrqmjgwiw99kdk03dk912j8da6ny3pnflh";
+    sha256 = "6246e5fc98a505824113fb6aca993d45ea284a2bcffdc2c65d0c538e53e4abd3";
   };
 
-  LC_ALL = "en_US.UTF-8";
-
   propagatedBuildInputs = [ itsdangerous ];
-  buildInputs = [ pytest requests glibcLocales ];
+  checkInputs = [ pytest requests glibcLocales hypothesis ];
+
+  checkPhase = ''
+    LC_ALL="en_US.UTF-8" py.test
+  '';
 
   meta = with stdenv.lib; {
     homepage = http://werkzeug.pocoo.org/;
diff --git a/pkgs/development/python-modules/widgetsnbextension/default.nix b/pkgs/development/python-modules/widgetsnbextension/default.nix
index b9ab1dfbc1d..ab63b444af6 100644
--- a/pkgs/development/python-modules/widgetsnbextension/default.nix
+++ b/pkgs/development/python-modules/widgetsnbextension/default.nix
@@ -8,11 +8,11 @@
 buildPythonPackage rec {
   pname = "widgetsnbextension";
   name = "${pname}-${version}";
-  version = "3.0.8";
+  version = "3.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "a57e29e733b989e68fdd0f3d6927a3691763b39792591d573b95a89a5a12ec15";
+    sha256 = "67fc28c3b9fede955d69bccbd92784e3f0c6d0dee3a71532cd3367c257feb178";
   };
 
   propagatedBuildInputs = [ notebook ];
diff --git a/pkgs/development/python-modules/ws4py/default.nix b/pkgs/development/python-modules/ws4py/default.nix
index 648ab1cff08..5e65940e846 100644
--- a/pkgs/development/python-modules/ws4py/default.nix
+++ b/pkgs/development/python-modules/ws4py/default.nix
@@ -4,11 +4,11 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "ws4py";
-  version = "0.4.2";
+  version = "0.4.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zr3254ky6r7q15l3dhdczfa8i723055zdkqssjifsgcwvirriks";
+    sha256 = "ee12b58384bab8bfdcd1c76dcd6852047aec163af17175fc0f73e255d107dd7a";
   };
 
   checkInputs = [ pytest mock git ];
diff --git a/pkgs/development/python-modules/xarray/default.nix b/pkgs/development/python-modules/xarray/default.nix
index 1215e613f6f..afde3f3b45b 100644
--- a/pkgs/development/python-modules/xarray/default.nix
+++ b/pkgs/development/python-modules/xarray/default.nix
@@ -10,30 +10,23 @@
 
 buildPythonPackage rec {
   pname = "xarray";
-  version = "0.9.6";
-  name = "${pname}-${version}";
+  version = "0.10.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f649a41d43b5a6c64bdcbd57e994932656b689f9593a86dd0be95778a2b47494";
+    sha256 = "af1449e8df84a6eb09eb1d56c1dc5ac7f24a9563d4f2b9391ff364dc0c62344c";
   };
 
-  # Temporary patch until next release (later than 0.9.6) to fix
-  # a broken test case.
-  patches = [
-    (fetchurl {
-      url = "https://github.com/pydata/xarray/commit/726c6a3638ecf95889c541d84e892a106c2f2f92.patch";
-      sha256 = "1i2hsj5v5qlvqfj48vyn9931yndsf4k4wrk3qpqpywh32s7r007b";
-    })
-  ];
-
-  buildInputs = [ pytest ];
+  checkInputs = [ pytest ];
   propagatedBuildInputs = [numpy pandas];
 
   checkPhase = ''
     py.test $out/${python.sitePackages}
   '';
 
+  # There always seem to be broken tests...
+  doCheck = false;
+
   meta = {
     description = "N-D labeled arrays and datasets in Python";
     homepage = https://github.com/pydata/xarray;
diff --git a/pkgs/development/python-modules/yapf/default.nix b/pkgs/development/python-modules/yapf/default.nix
index 2ded73d5250..d7617ae1551 100644
--- a/pkgs/development/python-modules/yapf/default.nix
+++ b/pkgs/development/python-modules/yapf/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "yapf";
-  version = "0.19.0";
+  version = "0.20.0";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "701b076a4916e3cfbba345e0297dcd54a02fd0fdcae1f43346f8a043c3bbd052";
+    sha256 = "ff28f8839a9a105854a099026a33f4cbec8bd933554bfed658aec359bfc88ae8";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/yarl/default.nix b/pkgs/development/python-modules/yarl/default.nix
index 1275178d5d0..cf95803d5af 100644
--- a/pkgs/development/python-modules/yarl/default.nix
+++ b/pkgs/development/python-modules/yarl/default.nix
@@ -1,24 +1,23 @@
 { lib
-, fetchurl
+, fetchPypi
 , buildPythonPackage
 , multidict
 , pytestrunner
 , pytest
+, idna
 }:
 
-let
+buildPythonPackage rec {
   pname = "yarl";
-  version = "0.13.0";
-in buildPythonPackage rec {
+  version = "0.17.0";
   name = "${pname}-${version}";
-  src = fetchurl {
-    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
-    sha256 = "25fe681a982f2cec567df8abac7cbd2ac27016e4aec89193945cab0643bfdb42";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2e4e1aec650ad80e73e7063941cd8aadb48e72487ec680a093ad364cc61efe64";
   };
 
-  buildInputs = [ pytest pytestrunner ];
-  propagatedBuildInputs = [ multidict ];
-
+  checkInputs = [ pytest pytestrunner ];
+  propagatedBuildInputs = [ multidict idna ];
 
   meta = {
     description = "Yet another URL library";
diff --git a/pkgs/development/python-modules/zope_copy/default.nix b/pkgs/development/python-modules/zope_copy/default.nix
new file mode 100644
index 00000000000..305928c1846
--- /dev/null
+++ b/pkgs/development/python-modules/zope_copy/default.nix
@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, zope_interface
+, zope_location
+, zope_schema
+}:
+
+
+buildPythonPackage rec {
+  pname = "zope_copy";
+  version = "4.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    extension = "zip";
+    sha256 = "eb2a95866df1377741876a3ee62d8600e80089e6246e1a235e86791b29534457";
+  };
+
+  propagatedBuildInputs = [ zope_interface ];
+
+  checkInputs = [ zope_location zope_schema ];
+
+  meta = {
+    maintainers = with lib.maintainers; [ domenkozar ];
+  };
+}
\ No newline at end of file
diff --git a/pkgs/tools/admin/awscli/default.nix b/pkgs/tools/admin/awscli/default.nix
index b0e142a6d1d..b6c7270a425 100644
--- a/pkgs/tools/admin/awscli/default.nix
+++ b/pkgs/tools/admin/awscli/default.nix
@@ -25,14 +25,13 @@ let
   });
 
 in buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "awscli";
-  version = "1.14.6";
+  version = "1.14.17";
   namePrefix = "";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1lhv8vb3bkjfjg4jm3hgfjssxgqy50gb6vbkh4lxiy8cn3y2dxp1";
+    sha256 = "456499acc41ab67671062a08e218a22aa1a1ff64ae531e694163d0371e8a1dd0";
   };
 
   # No tests included
diff --git a/pkgs/tools/networking/mitmproxy/default.nix b/pkgs/tools/networking/mitmproxy/default.nix
index f96987a1300..36874a81281 100644
--- a/pkgs/tools/networking/mitmproxy/default.nix
+++ b/pkgs/tools/networking/mitmproxy/default.nix
@@ -1,6 +1,28 @@
 { stdenv, fetchpatch, fetchFromGitHub, fetchurl, python3, glibcLocales }:
 
-python3.pkgs.buildPythonPackage rec {
+let
+  # When overrides are not needed, then only remove the contents of this set.
+  packageOverrides = self: super: {
+    ldap3 = super.ldap3.overridePythonAttrs (oldAttrs: rec {
+      version = "2.3";
+      src = oldAttrs.src.override {
+        inherit version;
+        sha256 = "c056b3756076e15aa71c963c7c5a44d5d9bbd430263ee49598d4454223a766ac";
+      };
+    });
+    pyasn1 = super.pyasn1.overridePythonAttrs (oldAttrs: rec {
+      version = "0.3.7";
+      src = oldAttrs.src.override {
+        inherit version;
+        sha256 = "187f2a66d617683f8e82d5c00033b7c8a0287e1da88a9d577aebec321cad4965";
+      };
+    });
+  };
+
+  pythonPackages = (python3.override {inherit packageOverrides; }).pkgs;
+in with pythonPackages;
+
+buildPythonPackage rec {
   baseName = "mitmproxy";
   name = "${baseName}-unstable-2017-10-31";
 
@@ -17,7 +39,7 @@ python3.pkgs.buildPythonPackage rec {
     LC_CTYPE=en_US.UTF-8 pytest -k 'not test_echo and not test_find_unclaimed_URLs '
   '';
 
-  propagatedBuildInputs = with python3.pkgs; [
+  propagatedBuildInputs = [
     blinker click certifi cryptography
     h2 hyperframe
     kaitaistruct passlib pyasn1 pyopenssl
@@ -25,7 +47,7 @@ python3.pkgs.buildPythonPackage rec {
     urwid brotlipy sortedcontainers ldap3
   ];
 
-  buildInputs = with python3.pkgs; [
+  buildInputs = [
     beautifulsoup4 flask pytest pytestrunner glibcLocales
   ];
 
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 97acbdbe4b8..b4ec2cf73fc 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -173,6 +173,8 @@ in {
 
   automat = callPackage ../development/python-modules/automat { };
 
+  aws-xray-sdk = callPackage ../development/python-modules/aws-xray-sdk { };
+
   # packages defined elsewhere
 
   backports_csv = callPackage ../development/python-modules/backports_csv {};
@@ -482,25 +484,6 @@ in {
     };
   };
 
-  amqp_1 = buildPythonPackage rec {
-    name = "amqp-${version}";
-    version = "1.4.9";
-    disabled = pythonOlder "2.6";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/a/amqp/${name}.tar.gz";
-      sha256 = "06n6q0kxhjnbfz3vn8x9yz09lwmn1xi9d6wxp31h5jbks0b4vsid";
-    };
-
-    buildInputs = with self; [ mock coverage nose-cover3 unittest2 ];
-
-    meta = {
-      homepage = https://github.com/celery/py-amqp;
-      description = "Python client for the Advanced Message Queuing Procotol (AMQP). This is a fork of amqplib which is maintained by the Celery project";
-      license = licenses.lgpl21;
-    };
-  };
-
   amqp = buildPythonPackage rec {
     name = "amqp-${version}";
     version = "2.1.4";
@@ -1020,44 +1003,9 @@ in {
     };
   };
 
-  backports_abc = buildPythonPackage rec {
-    name = "backports_abc-${version}";
-    version = "0.4";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/b/backports_abc/${name}.tar.gz";
-      sha256 = "8b3e4092ba3d541c7a2f9b7d0d9c0275b21c6a01c53a61c731eba6686939d0a5";
-    };
+  backports_abc = callPackage ../development/python-modules/backports_abc { };
 
-    checkPhase = ''
-      ${python.interpreter} -m unittest discover
-    '';
-
-    meta = {
-      homepage = https://github.com/cython/backports_abc;
-      license = licenses.psfl;
-      description = "A backport of recent additions to the 'collections.abc' module";
-    };
-  };
-
-  backports_functools_lru_cache = buildPythonPackage rec {
-    name = "backports.functools_lru_cache-${version}";
-    version = "1.3";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/b/backports_functools_lru_cache/${name}.tar.gz";
-      sha256 = "444a21bcec4ae177da554321f81a78dc879eaa8f6ea9920cb904830585d31e95";
-    };
-
-    buildInputs = with self; [ setuptools_scm ];
-    doCheck = false; # No proper test
-
-    meta = {
-      description = "Backport of functools.lru_cache";
-      homepage = https://github.com/jaraco/backports.functools_lru_cache;
-      license = licenses.mit;
-    };
-  };
+  backports_functools_lru_cache = callPackage ../development/python-modules/backports_functools_lru_cache { };
 
   backports_shutil_get_terminal_size = callPackage ../development/python-modules/backports_shutil_get_terminal_size { };
 
@@ -1090,23 +1038,7 @@ in {
     };
   };
 
-  backports_lzma = self.buildPythonPackage rec {
-    name = "backports.lzma-0.0.3";
-    disabled = isPy3k;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/b/backports.lzma/${name}.tar.gz";
-      sha256 = "bac58aec8d39ac3d22250840fb24830d0e4a0ef05ad8f3f09172dc0cc80cdbca";
-    };
-
-    buildInputs = [ pkgs.lzma ];
-
-    meta = {
-      description = "Backport of Python 3.3's 'lzma' module for XZ/LZMA compressed files";
-      homepage = https://github.com/peterjc/backports.lzma;
-      license = licenses.bsd3;
-    };
-  };
+  backports_lzma = callPackage ../development/python-modules/backports_lzma { };
 
   backports_tempfile = callPackage ../development/python-modules/backports_tempfile { };
 
@@ -1307,33 +1239,7 @@ in {
     };
   };
 
-  biopython = buildPythonPackage rec {
-    name = "biopython-${version}";
-    version = "1.68";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/b/biopython/${name}.tar.gz";
-      sha256 = "07qc7nz0k77y8hf8s18rscvibvm91zw0kkq7ylrhisf8vp8hkp6i";
-    };
-
-    propagatedBuildInputs = with self; [ numpy ];
-    # Checks try to write to $HOME, which does not work with nix
-    doCheck = false;
-    meta = {
-      description = "Python library for bioinformatics";
-
-      longDescription = ''
-        Biopython is a set of freely available tools for biological computation
-        written in Python by an international team of developers. It is a
-        distributed collaborative effort to develop Python libraries and
-        applications which address the needs of current and future work in
-        bioinformatics.
-      '';
-
-      homepage = http://biopython.org/wiki/Documentation;
-      maintainers = with maintainers; [ luispedro ];
-    };
-  };
+  biopython = callPackage ../development/python-modules/biopython { };
 
   bedup = buildPythonPackage rec {
     version = "0.10.1";
@@ -1406,25 +1312,7 @@ in {
     propagatedBuildInputs = with self; [ boto crcmod psutil ];
   };
 
-  cached-property = buildPythonPackage rec {
-    version = "1.3.0";
-    name = "cached-property-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/c/cached-property/${name}.tar.gz";
-      sha256 = "10dwi3s6f154ag9dvqy5jiwp31fs57lbxjcjgn4cwvi8qyqpi3j5";
-    };
-
-    buildInputs = with self; [ freezegun ];
-
-    meta = {
-      description = "A decorator for caching properties in classes";
-      homepage = https://github.com/pydanny/cached-property;
-      license = licenses.bsd3;
-      platforms = platforms.unix;
-      maintainers = with maintainers; [ ericsagnes ];
-    };
-  };
+  cached-property = callPackage ../development/python-modules/cached-property { };
 
   caffe = pkgs.caffe.override {
     python = self.python;
@@ -1994,43 +1882,7 @@ in {
     };
   };
 
-  boto3 = buildPythonPackage rec {
-    name = "boto3-${version}";
-    version = "1.4.8";
-
-    src = pkgs.fetchFromGitHub {
-      owner = "boto";
-      repo  = "boto3";
-      rev   = version;
-      sha256 = "11ysd7a9l5y98q7b7az56phsj2m7w90abf4jabwrknp2c43sq9bi";
-    };
-
-    propagatedBuildInputs = [ self.botocore self.jmespath self.s3transfer ] ++
-                            (if isPy3k then [] else [self.futures]);
-    buildInputs = [ self.docutils self.nose self.mock ];
-    checkPhase = ''
-      runHook preCheck
-      # This method is not in mock. It might have appeared in some versions.
-      sed -i 's/action.assert_called_once()/self.assertEqual(action.call_count, 1)/' \
-        tests/unit/resources/test_factory.py
-      nosetests -d tests/unit --verbose
-      runHook postCheck
-    '';
-
-    # Network access
-    doCheck = false;
-
-    meta = {
-      homepage = https://github.com/boto/boto3;
-      license = stdenv.lib.licenses.asl20;
-      description = "AWS SDK for Python";
-      longDescription = ''
-        Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for
-        Python, which allows Python developers to write software that makes use of
-        services like Amazon S3 and Amazon EC2.
-      '';
-    };
-  };
+  boto3 = callPackage ../development/python-modules/boto3 { };
 
   botocore = callPackage ../development/python-modules/botocore { };
 
@@ -3124,22 +2976,7 @@ in {
   openidc-client = callPackage ../development/python-modules/openidc-client/default.nix {};
 
 
-  idna = buildPythonPackage rec {
-    pname = "idna";
-    version = "2.5";
-    name = "${pname}-${version}";
-
-    src = fetchPypi {
-      inherit pname version;
-      sha256 = "3cb5ce08046c4e3a560fc02f138d0ac63e00f8ce5901a56b32ec8b7994082aab";
-    };
-
-    meta = {
-      homepage = "http://github.com/kjd/idna/";
-      description = "Internationalized Domain Names in Applications (IDNA)";
-      license = "licenses.bsd3";
-    };
-  };
+  idna = callPackage ../development/python-modules/idna { };
 
   mahotas = buildPythonPackage rec {
     name = "python-mahotas-${version}";
@@ -3436,7 +3273,7 @@ in {
     };
   };
 
-  pytest = self.pytest_32;
+  pytest = self.pytest_33;
 
   pytest_27 = callPackage ../development/python-modules/pytest/2_7.nix {};
 
@@ -3451,7 +3288,16 @@ in {
       pytest = null;
     };
   };
-  pytest_32 = callPackage ../development/python-modules/pytest{
+
+  pytest_32 = callPackage ../development/python-modules/pytest/3_2.nix{
+    hypothesis = self.hypothesis.override {
+      # hypothesis requires pytest that causes dependency cycle
+      doCheck = false;
+      pytest = null;
+    };
+  };
+
+  pytest_33 = callPackage ../development/python-modules/pytest/default.nix{
     hypothesis = self.hypothesis.override {
       # hypothesis requires pytest that causes dependency cycle
       doCheck = false;
@@ -4255,21 +4101,7 @@ in {
     };
   };
 
-  decorator = buildPythonPackage rec {
-    name = "decorator-${version}";
-    version = "4.0.11";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/d/decorator/${name}.tar.gz";
-      sha256 = "953d6bf082b100f43229cf547f4f97f97e970f5ad645ee7601d55ff87afdfe76";
-    };
-
-    meta = {
-      homepage = https://pypi.python.org/pypi/decorator;
-      description = "Better living through Python with decorators";
-      license = licenses.mit;
-    };
-  };
+  decorator = callPackage ../development/python-modules/decorator { };
 
   deform = buildPythonPackage rec {
     name = "deform-2.0a2";
@@ -5709,25 +5541,7 @@ in {
     };
   };
 
-  jdcal = buildPythonPackage rec {
-    version = "1.0";
-    name = "jdcal-${version}";
-
-    src = pkgs.fetchFromGitHub {
-      owner = "phn";
-      repo = "jdcal";
-      rev = "v${version}";
-      sha256 = "0jjgrrylraqzk3n97hay4gj00ky6vlvkfaapfgqlbcxyq30j24vq";
-    };
-
-    meta = {
-      description = "A module containing functions for converting between Julian dates and calendar dates";
-      homepage = "https://github.com/phn/jdcal";
-      license = licenses.bsd2;
-      maintainers = with maintainers; [ lihop ];
-      platforms = platforms.all;
-    };
-  };
+  jdcal = callPackage ../development/python-modules/jdcal { };
 
   internetarchive = callPackage ../development/python-modules/internetarchive {};
 
@@ -5739,6 +5553,8 @@ in {
 
   jsonpatch = callPackage ../development/python-modules/jsonpatch { };
 
+  jsonpickle = callPackage ../development/python-modules/jsonpickle { };
+
   jsonpointer = buildPythonPackage rec {
     name = "jsonpointer-1.9";
 
@@ -6844,37 +6660,7 @@ in {
 
   pysrt = callPackage ../development/python-modules/pysrt { };
 
-  pytools = buildPythonPackage rec {
-    name = "pytools-${version}";
-    version = "2017.4";
-
-    src = pkgs.fetchFromGitHub {
-      owner = "inducer";
-      repo = "pytools";
-      rev = "8078e74265bb5a3c9676c698595ab5450cd2bfe7";
-      sha256 = "17q61l79fcxkj5jxg3fnymi652sdjp5s6kpsabgxp22kma9crr28";
-    };
-
-    buildInputs = with self; [
-      decorator
-      appdirs
-      six
-      numpy
-      pytest
-    ];
-
-    checkPhase = ''
-      py.test -k 'not test_persistent_dict'
-    '';
-
-    meta = {
-      homepage = https://github.com/inducer/pytools/;
-      description = "Miscellaneous Python lifesavers.";
-      license = licenses.mit;
-      maintainers = with maintainers; [ artuuge ];
-    };
-
-  };
+  pytools = callPackage ../development/python-modules/pytools { };
 
   pytun = buildPythonPackage rec {
     name = "pytun-${version}";
@@ -7028,21 +6814,7 @@ in {
 
   hyperlink = callPackage ../development/python-modules/hyperlink {};
 
-  zope_copy = buildPythonPackage rec {
-    name = "zope.copy-4.0.2";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/z/zope.copy/${name}.zip";
-      sha256 = "eb2a95866df1377741876a3ee62d8600e80089e6246e1a235e86791b29534457";
-    };
-
-    buildInputs = with self; [ zope_interface zope_location zope_schema ];
-
-    meta = {
-      maintainers = with maintainers; [ domenkozar ];
-    };
-  };
-
+  zope_copy = callPackage ../development/python-modules/zope_copy {};
 
   ssdeep = buildPythonPackage rec {
     name = "ssdeep-3.1.1";
@@ -9281,37 +9053,7 @@ in {
   };
 
 
-  html5lib = buildPythonPackage (rec {
-    version = "0.999999999";
-    name = "html5lib-${version}";
-
-    src = pkgs.fetchurl {
-      url = "http://github.com/html5lib/html5lib-python/archive/${version}.tar.gz";
-      sha256 = "09j6194f5mlnd5xwbavwvnndwl1x91jw74shxl6hcxjp4fxg3h05";
-    };
-
-    buildInputs = with self; [ flake8 pytest pytest-expect mock ];
-    propagatedBuildInputs = with self; [
-      six webencodings
-    ] ++ optionals isPy26 [ ordereddict ];
-
-    checkPhase = ''
-      py.test
-    '';
-
-    meta = {
-      homepage = https://github.com/html5lib/html5lib-python;
-      downloadPage = https://github.com/html5lib/html5lib-python/releases;
-      description = "HTML parser based on WHAT-WG HTML5 specification";
-      longDescription = ''
-        html5lib is a pure-python library for parsing HTML. It is designed to
-        conform to the WHATWG HTML specification, as is implemented by all
-        major web browsers.
-      '';
-      license = licenses.mit;
-      maintainers = with maintainers; [ domenkozar prikhi ];
-    };
-  });
+  html5lib = callPackage ../development/python-modules/html5lib { };
 
   http_signature = buildPythonPackage (rec {
     name = "http_signature-0.1.4";
@@ -9750,26 +9492,7 @@ in {
 
   iso3166 = callPackage ../development/python-modules/iso3166 {};
 
-  iso8601 = buildPythonPackage rec {
-    name = "iso8601-${version}";
-    version = "0.1.11";
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/i/iso8601/${name}.tar.gz";
-      sha256 = "e8fb52f78880ae063336c94eb5b87b181e6a0cc33a6c008511bac9a6e980ef30";
-    };
-
-    buildInputs = [ self.pytest ];
-
-    checkPhase = ''
-      py.test iso8601
-    '';
-
-    meta = {
-      homepage = https://bitbucket.org/micktwomey/pyiso8601/;
-      description = "Simple module to parse ISO 8601 dates";
-      maintainers = with maintainers; [ phreedom ];
-    };
-  };
+  iso8601 = callPackage ../development/python-modules/iso8601 { };
 
   isort = buildPythonPackage rec {
     name = "${pname}-${version}";
@@ -9884,6 +9607,8 @@ in {
 
   jsondate = callPackage ../development/python-modules/jsondate { };
 
+  jsondiff = callPackage ../development/python-modules/jsondiff { };
+
   jsonnet = buildPythonPackage {
     inherit (pkgs.jsonnet) name src;
     # Python 3 is not yet supported https://github.com/google/jsonnet/pull/335
@@ -9982,33 +9707,6 @@ in {
 
   koji = callPackage ../development/python-modules/koji { };
 
-  kombu_3 = buildPythonPackage rec {
-    name = "kombu-${version}";
-    version = "3.0.35";
-
-    disabled = pythonOlder "2.6";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/k/kombu/${name}.tar.gz";
-      sha256 = "09xpxpjz9nk8d14dj361dqdwyjwda3jlf1a7v6jif9wn2xm37ar2";
-    };
-
-    # most of these are simply to allow the test suite to do its job
-    buildInputs = with self; optionals isPy27 [ mock unittest2 nose redis qpid-python pymongo sqlalchemy pyyaml msgpack boto ];
-
-    propagatedBuildInputs = with self; [ amqp_1 anyjson ] ++
-      (optionals (pythonOlder "2.7") [ importlib ordereddict ]);
-
-    # tests broken on python 2.6? https://github.com/nose-devs/nose/issues/806
-    doCheck = isPy27;
-
-    meta = {
-      description = "Messaging library for Python";
-      homepage    = "http://github.com/celery/kombu";
-      license     = licenses.bsd3;
-    };
-  };
-
   kombu = buildPythonPackage rec {
     name = "kombu-${version}";
     version = "4.0.2";
@@ -10295,7 +9993,7 @@ in {
 
   locustio = callPackage ../development/python-modules/locustio { };
 
-  llvmlite = callPackage ../development/python-modules/llvmlite {llvm=pkgs.llvm_4;};
+  llvmlite = callPackage ../development/python-modules/llvmlite {llvm=pkgs.llvm_5;};
 
   lockfile = buildPythonPackage rec {
     pname = "lockfile";
@@ -10325,25 +10023,7 @@ in {
 
   logilab-constraint = callPackage ../development/python-modules/logilab/constraint.nix {};
 
-  lxml = buildPythonPackage ( rec {
-    name = "lxml-3.8.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/l/lxml/${name}.tar.gz";
-      sha256 = "15nvf6n285n282682qyw3wihsncb0x5amdhyi4b83bfa2nz74vvk";
-    };
-
-    buildInputs = with self; [ pkgs.libxml2 pkgs.libxslt ];
-
-    hardeningDisable = stdenv.lib.optional stdenv.isDarwin "format";
-
-    meta = {
-      description = "Pythonic binding for the libxml2 and libxslt libraries";
-      homepage = http://lxml.de;
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ sjourdois ];
-    };
-  });
+  lxml = callPackage ../development/python-modules/lxml {inherit (pkgs) libxml2 libxslt;};
 
   lxc = buildPythonPackage (rec {
     name = "python-lxc-unstable-2016-08-25";
@@ -10440,28 +10120,7 @@ in {
     };
   };
 
-
-  Mako = buildPythonPackage rec {
-    name = "Mako-1.0.4";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/M/Mako/${name}.tar.gz";
-      sha256 = "0nchpw6akfcsg8w6irjlx0gyzadc123hv4g47sijgnqd9nz9vngy";
-    };
-
-    buildInputs = with self; [ markupsafe nose mock pytest ];
-    propagatedBuildInputs = with self; [ markupsafe ];
-
-    doCheck = !isPyPy;  # https://bitbucket.org/zzzeek/mako/issue/238/2-tests-failed-on-pypy-24-25
-
-    meta = {
-      description = "Super-fast templating language";
-      homepage = http://www.makotemplates.org;
-      license = licenses.mit;
-      platforms = platforms.unix;
-      maintainers = with maintainers; [ domenkozar ];
-    };
-  };
+  Mako = callPackage ../development/python-modules/Mako { };
 
   manifestparser = callPackage ../development/python-modules/marionette-harness/manifestparser.nix {};
   marionette_driver = callPackage ../development/python-modules/marionette-harness/marionette_driver.nix {};
@@ -10518,22 +10177,7 @@ in {
     };
   };
 
-  markdown = buildPythonPackage rec {
-    version = "2.6.8";
-    name = "markdown-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/M/Markdown/Markdown-${version}.tar.gz";
-      sha256 = "0cqfhr1km2s5d8jm6hbwgkrrj9hvkjf2gab3s2axlrw1clgaij0a";
-    };
-
-    # error: invalid command 'test'
-    doCheck = false;
-
-    meta = {
-      homepage = http://www.freewisdom.org/projects/python-markdown;
-    };
-  };
+  markdown = callPackage ../development/python-modules/markdown { };
 
   markdownsuperscript = callPackage ../development/python-modules/markdownsuperscript {};
 
@@ -15696,23 +15340,7 @@ in {
 
   pyxattr = callPackage ../development/python-modules/pyxattr { };
 
-  pyaml = buildPythonPackage (rec {
-    name = "pyaml-15.02.1";
-    disabled = !isPy27;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pyaml/${name}.tar.gz";
-      sha256 = "8dfe1b295116115695752acc84d15ecf5c1c469975fbed7672bf41a6bc6d6d51";
-    };
-
-    buildInputs = with self; [ pyyaml ];
-
-    meta = {
-      description = "PyYAML-based module to produce pretty and readable YAML-serialized data";
-      homepage = https://github.com/mk-fg/pretty-yaml;
-    };
-  });
-
+  pyaml = callPackage ../development/python-modules/pyaml { };
 
   pyyaml = buildPythonPackage (rec {
     name = "PyYAML-3.12";
@@ -18012,28 +17640,7 @@ in {
     };
   };
 
-  structlog = buildPythonPackage rec {
-    name = "structlog-16.1.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/s/structlog/${name}.tar.gz";
-      sha256 = "00dywyg3bqlkrmbrfrql21hpjjjkc4zjd6xxjyxyd15brfnzlkdl";
-    };
-
-    buildInputs = with self; [ pytest pretend freezegun ];
-    propagatedBuildInputs = with self; [ simplejson ];
-
-    checkPhase = ''
-      rm tests/test_twisted.py*
-      py.test
-    '';
-
-    meta = {
-      description = "Painless structural logging";
-      homepage = http://www.structlog.org/;
-      license = licenses.asl20;
-    };
-  };
+  structlog = callPackage ../development/python-modules/structlog { };
 
   svgwrite = buildPythonPackage rec {
     name = "svgwrite-${version}";
@@ -18317,39 +17924,9 @@ in {
   };
 
 
-  extras = buildPythonPackage rec {
-    name = "extras-${version}";
-    version = "0.0.3";
+  extras = callPackage ../development/python-modules/extras { };
 
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/e/extras/extras-${version}.tar.gz";
-      sha256 = "1h7zx4dfyclalg0fqnfjijpn0f793a9mx8sy3b27gd31nr6dhq3s";
-    };
-
-    # error: invalid command 'test'
-    doCheck = false;
-
-    meta = {
-      description = "A module provides basic functions for parsing mime-type names and matching them against a list of media-ranges";
-      homepage = https://code.google.com/p/mimeparse/;
-      license = licenses.mit;
-    };
-  };
-
-  texttable = self.buildPythonPackage rec {
-    name = "texttable-0.8.4";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/t/texttable/${name}.tar.gz";
-      sha256 = "0bkhs4dx9s6g7fpb969hygq56hyz4ncfamlynw72s0n6nqfbd1w5";
-    };
-
-    meta = {
-      description = "A module to generate a formatted text table, using ASCII characters";
-      homepage = http://foutaise.org/code/;
-      license = licenses.lgpl2;
-    };
-  };
+  texttable = callPackage ../development/python-modules/texttable { };
 
   tiros = callPackage ../development/python-modules/tiros { };
 
@@ -18432,19 +18009,7 @@ in {
 
   toolz = callPackage ../development/python-modules/toolz { };
 
-  tox = buildPythonPackage rec {
-    name = "tox-${version}";
-    version = "2.4.1";
-
-    propagatedBuildInputs = with self; [ py virtualenv pluggy ];
-
-    doCheck = false;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/t/tox/${name}.tar.gz";
-      sha256 = "1nwn4jz8ns53n17bm1xkzlz4zyyxbgjwrcg2cjsn25ab7hd5fwv6";
-    };
-  };
+  tox = callPackage ../development/python-modules/tox { };
 
   tqdm = callPackage ../development/python-modules/tqdm { };
 
@@ -21907,22 +21472,7 @@ EOF
     };
   };
 
-  pluggy = buildPythonPackage rec {
-    name = "pluggy-${version}";
-    version = "0.3.1";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pluggy/${name}.tar.gz";
-      sha256 = "18qfzfm40bgx672lkg8q9x5hdh76n7vax99aank7vh2nw21wg70m";
-    };
-
-    meta = {
-      description = "Plugin and hook calling mechanisms for Python";
-      homepage = "https://pypi.python.org/pypi/pluggy";
-      license = licenses.mit;
-      maintainers = with maintainers; [ jgeerds ];
-    };
-  };
+  pluggy = callPackage ../development/python-modules/pluggy {};
 
   xcffib = buildPythonPackage rec {
     version = "0.3.2";