Merge commit '18aa59b0f26fc707e7313f8467e67159e61600c2' from master into staging

There was one conflict in the NixOS manual; I checked that it still
built after resolving it.

38 files changed, 352 insertions, 87 deletions

diff --git a/pkgs/development/python-modules/Markups/default.nix b/pkgs/development/python-modules/Markups/default.nix
new file mode 100644
index 000000000000..6fe41e404192
--- /dev/null
+++ b/pkgs/development/python-modules/Markups/default.nix
@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python-markdown-math
+, markdown
+, docutils
+, pygments
+}:
+
+buildPythonPackage rec {
+  pname = "Markups";
+  version = "3.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ea19458dfca6a4562044e701aa8698089a0c659fc535689ed260f89a04f8d39";
+  };
+
+  checkInputs = [ markdown docutils pygments ];
+  propagatedBuildInputs = [ python-markdown-math ];
+
+  meta = {
+    description = "A wrapper around various text markup languages.";
+    homepage = https://github.com/retext-project/pymarkups;
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ klntsky ];
+  };
+}
diff --git a/pkgs/development/python-modules/ansible/default.nix b/pkgs/development/python-modules/ansible/default.nix
index 1ec50ef7780b..dff12fcaf92c 100644
--- a/pkgs/development/python-modules/ansible/default.nix
+++ b/pkgs/development/python-modules/ansible/default.nix
@@ -18,11 +18,11 @@
 
 buildPythonPackage rec {
   pname = "ansible";
-  version = "2.7.8";
+  version = "2.7.9";
 
   src = fetchurl {
     url = "https://releases.ansible.com/ansible/${pname}-${version}.tar.gz";
-    sha256 = "11yx7vd0mp5gkq428af141dwnrwf8f9cp3f65243qbs9icjxnrrx";
+    sha256 = "19vyf60zfmnv7frwm96bzqzvia69dysy9apk8bl84vr03ib9vrbf";
   };
 
   prePatch = ''
diff --git a/pkgs/development/python-modules/astropy/default.nix b/pkgs/development/python-modules/astropy/default.nix
index 0ba779ec93e5..90fe66bf4e92 100644
--- a/pkgs/development/python-modules/astropy/default.nix
+++ b/pkgs/development/python-modules/astropy/default.nix
@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "astropy";
-  version = "3.1.1";
+  version = "3.1.2";
 
   disabled = !isPy3k; # according to setup.py
 
@@ -15,7 +15,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0fzm2q922qi68ns5biy807dzmgz1i9gqdh73lcafs0gfk8zyc9v5";
+    sha256 = "1plyx3gcsff02g4yclvhlcdj8bh1lnm98d7h6wdabl36jvnahy2a";
   };
 
   propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires
diff --git a/pkgs/development/python-modules/awkward/default.nix b/pkgs/development/python-modules/awkward/default.nix
index cf619e6021ef..8906b72dcca0 100644
--- a/pkgs/development/python-modules/awkward/default.nix
+++ b/pkgs/development/python-modules/awkward/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "awkward";
-  version = "0.8.4";
+  version = "0.8.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7016dc02d15b8797b59a461ccc8d218f37c335b97fa6b376638c0edd4ffc9de2";
+    sha256 = "0a53c484za2l4yy1i05qhkylvygg8fnh4j1v3n35x2dsi929awdp";
   };
 
   nativeBuildInputs = [ pytestrunner ];
diff --git a/pkgs/development/python-modules/buildbot/default.nix b/pkgs/development/python-modules/buildbot/default.nix
index cd98a8da710a..268c08ced848 100644
--- a/pkgs/development/python-modules/buildbot/default.nix
+++ b/pkgs/development/python-modules/buildbot/default.nix
@@ -1,8 +1,9 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, makeWrapper, isPy3k,
+{ stdenv, lib, buildPythonPackage, /*fetchPypi,*/ fetchFromGitHub, makeWrapper, isPy3k,
   python, twisted, jinja2, zope_interface, future, sqlalchemy,
   sqlalchemy_migrate, dateutil, txaio, autobahn, pyjwt, pyyaml, treq,
   txrequests, txgithub, pyjade, boto3, moto, mock, python-lz4, setuptoolsTrial,
-  isort, pylint, flake8, buildbot-worker, buildbot-pkg, glibcLocales }:
+  isort, pylint, flake8, buildbot-worker, buildbot-pkg, parameterized,
+  glibcLocales }:
 
 let
   withPlugins = plugins: buildPythonPackage {
@@ -24,12 +25,21 @@ let
 
   package = buildPythonPackage rec {
     pname = "buildbot";
-    version = "1.8.1";
+    version = "2.1.0";
 
-    src = fetchPypi {
+    /*src = fetchPypi {
       inherit pname version;
-      sha256 = "1zadmyrlk7p9h1akmbzwa7p90s7jwsxvdx4xn9i54dnda450m3a7";
-    };
+      sha256 = "1745hj9s0c0fcdjv6w05bma76xqg1fv42v0dslmi4d8yz9phf37w";
+    };*/
+    # Temporarily use GitHub source because PyPi archive is missing some files
+    # needed for the tests to pass. This has been fixed upstream.
+    # See: https://github.com/buildbot/buildbot/commit/30f5927cf9a80f98ed909241a149469dec3ce68d
+    src = fetchFromGitHub {
+      owner = "buildbot";
+      repo = "buildbot";
+      rev = "v${version}";
+      sha256 = "022ybhdvp0hp2z0cwgx7n41jyh56bpxj3fwm4z7ppzj1qhm7lb65";
+    } + "/master";
 
     propagatedBuildInputs = [
       # core
@@ -63,6 +73,7 @@ let
       flake8
       buildbot-worker
       buildbot-pkg
+      parameterized
       glibcLocales
     ];
 
@@ -84,6 +95,8 @@ let
       export PATH="$out/bin:$PATH"
     '';
 
+    disabled = !isPy3k;
+
     passthru = {
       inherit withPlugins;
     };
diff --git a/pkgs/development/python-modules/buildbot/pkg.nix b/pkgs/development/python-modules/buildbot/pkg.nix
index 480bed2805ee..35524040da99 100644
--- a/pkgs/development/python-modules/buildbot/pkg.nix
+++ b/pkgs/development/python-modules/buildbot/pkg.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "buildbot-pkg";
-  version = "1.8.1";
+  version = "2.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16gjdzkris6475bvsgvb0v6rkn4xb6f55s468q37n0l1r6n8snc3";
+    sha256 = "03lv97q4pp2izjfbwfv4zmf2fyiz7jyp537bi3gc6rhfbrfgib1i";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/buildbot/plugins.nix b/pkgs/development/python-modules/buildbot/plugins.nix
index 4bcaa965d2f3..2f73fbc81a4f 100644
--- a/pkgs/development/python-modules/buildbot/plugins.nix
+++ b/pkgs/development/python-modules/buildbot/plugins.nix
@@ -10,7 +10,8 @@
 
     src = fetchPypi {
       inherit pname version format;
-      sha256 = "03cgjhwpgbm0qgis1cdy9g4vc11hsrya9grcx4j35784rny7lbfl";
+      python = "py3";
+      sha256 = "011sagw8zp1z12vzkxi44w3w2lbxncz5yahkrbxj8hp6iwfzfm5v";
     };
 
     meta = with lib; {
@@ -27,7 +28,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0pfp2n4ys99jglshdrp2f6jm73c4ym3dfwl6qjvbc7y7nsi74824";
+      sha256 = "11gz4ry1law3l64ii383cj5fnbw9409czp2ybzkqafr4xi1qbk9h";
     };
 
     propagatedBuildInputs = [ buildbot-pkg ];
@@ -47,7 +48,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0gnxq9niw64q36dm917lhhcl8zp0wjwaamjp07zidnrb5c3pjbsz";
+      sha256 = "0w4iwpj1rg20fbli0ppqz70l1mc9ilg0crq8g3xrf29f9z8d1w27";
     };
 
     propagatedBuildInputs = [ buildbot-pkg ];
@@ -67,7 +68,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1b06aa8m1pzqq2d8imrq5mazc7llrlbgm7jzi8h6jjd2gahdjgz5";
+      sha256 = "0xyvxamw45qhnfml3x5hfg9nai1jhdwbmq4pm8csf3ad0cw6vqya";
     };
 
     propagatedBuildInputs = [ buildbot-pkg ];
@@ -87,7 +88,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "1v8411bw0cs206vwfnqx1na7dzg77h9aff4wlm11hkbdsy9ayv2d";
+      sha256 = "1szcrx8vslskifzxaq7lrfg2arilaq1w1aqr0nc8pjclj7idp92c";
     };
 
     propagatedBuildInputs = [ buildbot-pkg ];
diff --git a/pkgs/development/python-modules/buildbot/worker.nix b/pkgs/development/python-modules/buildbot/worker.nix
index 8e49d085fbd1..f888448db218 100644
--- a/pkgs/development/python-modules/buildbot/worker.nix
+++ b/pkgs/development/python-modules/buildbot/worker.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage (rec {
   pname = "buildbot-worker";
-  version = "1.8.1";
+  version = "2.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1rh73jbyms4b9wgkkdzcn80xfd18p8rn89rw4rsi2002ydrc7n39";
+    sha256 = "14qimaf513h2hklcpix8vscrawvr1qiyn1vy88ycpsbz9mcqbhps";
   };
 
   propagatedBuildInputs = [ twisted future ];
diff --git a/pkgs/development/python-modules/cartopy/default.nix b/pkgs/development/python-modules/cartopy/default.nix
index 64f649ad28ab..3fc4c3e84ed4 100644
--- a/pkgs/development/python-modules/cartopy/default.nix
+++ b/pkgs/development/python-modules/cartopy/default.nix
@@ -25,12 +25,19 @@ buildPythonPackage rec {
       -k "not test_nightshade_image"
   '';
 
-  buildInputs = [ cython glibcLocales ];
-  LC_ALL = "en_US.UTF-8";
+  nativeBuildInputs = [
+    cython
+    geos # for geos-config
+    proj
+  ];
+
+  buildInputs = [
+    geos proj
+  ];
 
   propagatedBuildInputs = [
     # required
-    six pyshp shapely geos proj numpy
+    six pyshp shapely numpy
 
     # optional
     gdal pillow matplotlib pyepsg pykdtree scipy fiona owslib
diff --git a/pkgs/development/python-modules/cssselect2/default.nix b/pkgs/development/python-modules/cssselect2/default.nix
index 381c114b44e4..45a9920dbe2e 100644
--- a/pkgs/development/python-modules/cssselect2/default.nix
+++ b/pkgs/development/python-modules/cssselect2/default.nix
@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, tinycss2, pytest, pytestrunner, pytestcov, pytest-flake8, pytest-isort, glibcLocales }:
+{ lib, buildPythonPackage, fetchPypi, tinycss2, pytest, pytestrunner }:
 
 buildPythonPackage rec {
   pname = "cssselect2";
@@ -9,11 +9,21 @@ buildPythonPackage rec {
     sha256 = "505d2ce3d3a1d390ddb52f7d0864b7efeb115a5b852a91861b498b92424503ab";
   };
 
-  propagatedBuildInputs = [ tinycss2 ];
+  # We're not interested in code quality tests
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "pytest-cov" "" \
+      --replace "pytest-flake8" "" \
+      --replace "pytest-isort" ""
+    substituteInPlace setup.cfg \
+      --replace "--cov=cssselect2" "" \
+      --replace "--flake8" "" \
+      --replace "--isort" ""
+  '';
 
-  checkInputs = [ pytest pytestrunner pytestcov pytest-flake8 pytest-isort glibcLocales ];
+  propagatedBuildInputs = [ tinycss2 ];
 
-  LC_ALL = "en_US.UTF-8";
+  checkInputs = [ pytest pytestrunner ];
 
   meta = with lib; {
     description = "CSS selectors for Python ElementTree";
diff --git a/pkgs/development/python-modules/djangorestframework/default.nix b/pkgs/development/python-modules/djangorestframework/default.nix
index f227ed99bc9a..0f4c559bd16b 100644
--- a/pkgs/development/python-modules/djangorestframework/default.nix
+++ b/pkgs/development/python-modules/djangorestframework/default.nix
@@ -1,11 +1,11 @@
 { stdenv, buildPythonPackage, fetchPypi, django }:
 buildPythonPackage rec {
-  version = "3.9.1";
+  version = "3.9.2";
   pname = "djangorestframework";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "79c6efbb2514bc50cf25906d7c0a5cfead714c7af667ff4bd110312cd380ae66";
+    sha256 = "05sam4z69mypxk8fv415zvs8mp09jqsagmslrbs1qvk51lk6d8pp";
   };
 
   # Test settings are missing
diff --git a/pkgs/development/python-modules/dnslib/default.nix b/pkgs/development/python-modules/dnslib/default.nix
new file mode 100644
index 000000000000..15c771ebaf52
--- /dev/null
+++ b/pkgs/development/python-modules/dnslib/default.nix
@@ -0,0 +1,20 @@
+{ lib, python, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "dnslib";
+  version = "0.9.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0w8spp4fnw63xx9zj77zvgk1qabd97ifrj6gap2j36gydnarr42c";
+  };
+
+  checkPhase = "VERSIONS=${python.interpreter} ./run_tests.sh";
+
+  meta = with lib; {
+    description = "Simple library to encode/decode DNS wire-format packets";
+    license = licenses.bsd2;
+    homepage = https://bitbucket.org/paulc/dnslib/;
+    maintainers = with maintainers; [ delroth ];
+  };
+}
diff --git a/pkgs/development/python-modules/flake8-import-order/default.nix b/pkgs/development/python-modules/flake8-import-order/default.nix
index 5709b17c524a..8099f3318e86 100644
--- a/pkgs/development/python-modules/flake8-import-order/default.nix
+++ b/pkgs/development/python-modules/flake8-import-order/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "flake8-import-order";
-  version = "0.18";
+  version = "0.18.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "9be5ca10d791d458eaa833dd6890ab2db37be80384707b0f76286ddd13c16cbf";
+    sha256 = "14kfvsagqc6lrplvf3x58ia6x744bk8fj91wmk0hcipa8naw73d2";
   };
 
   propagatedBuildInputs = [ pycodestyle ] ++ lib.optional (!isPy3k) enum34;
diff --git a/pkgs/development/python-modules/gym/default.nix b/pkgs/development/python-modules/gym/default.nix
index fe4cf01a8dfe..b207e7ca239e 100644
--- a/pkgs/development/python-modules/gym/default.nix
+++ b/pkgs/development/python-modules/gym/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "gym";
-  version = "0.11.0";
+  version = "0.12.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f9c79fc295b8b20cfda5ab0a671e72c95615dc77517ae414f8f8b10e9375f155";
+    sha256 = "0ggac8a8qk06wplwg5xsisn9id3lis9qslri7m9rz22khlyl7z4j";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/irc/default.nix b/pkgs/development/python-modules/irc/default.nix
index 672704249dc9..b422b368ffb6 100644
--- a/pkgs/development/python-modules/irc/default.nix
+++ b/pkgs/development/python-modules/irc/default.nix
@@ -1,6 +1,7 @@
 { buildPythonPackage, fetchPypi, isPy3k
 , six, jaraco_logging, jaraco_text, jaraco_stream, pytz, jaraco_itertools
-, setuptools_scm }:
+, setuptools_scm, jaraco_collections
+}:
 
 buildPythonPackage rec {
   pname = "irc";
@@ -23,5 +24,6 @@ buildPythonPackage rec {
     jaraco_stream
     pytz
     jaraco_itertools
+    jaraco_collections
   ];
 }
diff --git a/pkgs/development/python-modules/isort/default.nix b/pkgs/development/python-modules/isort/default.nix
index 5a7e50d43322..bb9958a6fef1 100644
--- a/pkgs/development/python-modules/isort/default.nix
+++ b/pkgs/development/python-modules/isort/default.nix
@@ -1,22 +1,24 @@
-{ lib, buildPythonPackage, fetchPypi, isPy27, futures, mock, pytest }:
+{ lib, buildPythonPackage, fetchPypi, isPy27, futures, backports_functools_lru_cache, mock, pytest }:
 
-buildPythonPackage rec {
+let
+  skipTests = lib.optional isPy27 "test_standard_library_deprecates_user_issue_778";
+  testOpts = lib.concatMapStringsSep " " (t: "--deselect test_isort.py::${t}") skipTests;
+in buildPythonPackage rec {
   pname = "isort";
-  version = "4.3.4";
+  version = "4.3.16"; # Note 4.x is the last version that supports Python2
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1y0yfv56cqyh9wyg7kxxv9y5wmfgcq18n7a49mp7xmzka2bhxi5r";
+    sha256 = "1v6lapqhc33rxr9698lqjyb49fis27i42p3ymngrw95py3qf7y08";
   };
 
-  propagatedBuildInputs = lib.optional isPy27 futures;
+  propagatedBuildInputs = lib.optionals isPy27 [ futures backports_functools_lru_cache ];
 
   checkInputs = [ mock pytest ];
 
+  # isort excludes paths that contain /build/, so test fixtures don't work with TMPDIR=/build/
   checkPhase = ''
-    py.test test_isort.py -k "not test_long_line_comments \
-                          and not test_import_case_produces_inconsistent_results_issue_472 \
-                          and not test_no_extra_lines_issue_557"
+    PATH=$out/bin:$PATH TMPDIR=/tmp/ pytest ${testOpts}
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/jaraco_collections/default.nix b/pkgs/development/python-modules/jaraco_collections/default.nix
index c0b30edb9ad4..8fde41e9b499 100644
--- a/pkgs/development/python-modules/jaraco_collections/default.nix
+++ b/pkgs/development/python-modules/jaraco_collections/default.nix
@@ -1,5 +1,6 @@
 { buildPythonPackage, fetchPypi, setuptools_scm
-, six, jaraco_classes }:
+, six, jaraco_classes, jaraco_text
+}:
 
 buildPythonPackage rec {
   pname = "jaraco.collections";
@@ -11,7 +12,7 @@ buildPythonPackage rec {
 
   doCheck = false;
   buildInputs = [ setuptools_scm ];
-  propagatedBuildInputs = [ six jaraco_classes ];
+  propagatedBuildInputs = [ six jaraco_classes jaraco_text ];
 
   # break dependency cycle
   patchPhase = ''
diff --git a/pkgs/development/python-modules/jaraco_itertools/0001-Don-t-run-flake8-checks-during-the-build.patch b/pkgs/development/python-modules/jaraco_itertools/0001-Don-t-run-flake8-checks-during-the-build.patch
new file mode 100644
index 000000000000..43530fcc3285
--- /dev/null
+++ b/pkgs/development/python-modules/jaraco_itertools/0001-Don-t-run-flake8-checks-during-the-build.patch
@@ -0,0 +1,38 @@
+From fcffcc61e432e5250e7fbfb1ecbe0f1cac3006cf Mon Sep 17 00:00:00 2001
+From: Maximilian Bosch <maximilian@mbosch.me>
+Date: Sun, 10 Mar 2019 13:10:18 +0100
+Subject: [PATCH] Don't run flake8 checks during the build
+
+If the code simply violates their code style, the Nix package shouldn't fail.
+---
+ pytest.ini | 2 +-
+ setup.cfg  | 1 -
+ 2 files changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/pytest.ini b/pytest.ini
+index d165e5e..d8e4694 100644
+--- a/pytest.ini
++++ b/pytest.ini
+@@ -1,6 +1,6 @@
+ [pytest]
+ norecursedirs=dist build .tox .eggs
+-addopts=--doctest-modules --flake8
++addopts=--doctest-modules
+ doctest_optionflags=ALLOW_UNICODE ELLIPSIS ALLOW_BYTES
+ filterwarnings=
+ 	ignore:Possible nested set::pycodestyle:113
+diff --git a/setup.cfg b/setup.cfg
+index 9f3517f..c9033ec 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -30,7 +30,6 @@ setup_requires = setuptools_scm >= 1.15.0
+ testing = 
+ 	pytest >= 3.5, !=3.7.3
+ 	pytest-checkdocs
+-	pytest-flake8
+ docs = 
+ 	sphinx
+ 	jaraco.packaging >= 3.2
+-- 
+2.18.1
+
diff --git a/pkgs/development/python-modules/jaraco_itertools/default.nix b/pkgs/development/python-modules/jaraco_itertools/default.nix
index 4057d7ad2758..cbf966785e17 100644
--- a/pkgs/development/python-modules/jaraco_itertools/default.nix
+++ b/pkgs/development/python-modules/jaraco_itertools/default.nix
@@ -1,5 +1,6 @@
 { lib, buildPythonPackage, fetchPypi, setuptools_scm
-, inflect, more-itertools, six, pytest, pytest-flake8 }:
+, inflect, more-itertools, six, pytest
+}:
 
 buildPythonPackage rec {
   pname = "jaraco.itertools";
@@ -10,9 +11,11 @@ buildPythonPackage rec {
     sha256 = "d1380ed961c9a4724f0bcca85d2bffebaa2507adfde535d5ee717441c9105fae";
   };
 
+  patches = [ ./0001-Don-t-run-flake8-checks-during-the-build.patch ];
+
   buildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ inflect more-itertools six ];
-  checkInputs = [ pytest pytest-flake8 ];
+  checkInputs = [ pytest ];
 
   checkPhase = ''
     pytest
diff --git a/pkgs/development/python-modules/jaraco_logging/0001-Don-t-run-flake8-checks-during-the-build.patch b/pkgs/development/python-modules/jaraco_logging/0001-Don-t-run-flake8-checks-during-the-build.patch
new file mode 100644
index 000000000000..aab9604b9ce8
--- /dev/null
+++ b/pkgs/development/python-modules/jaraco_logging/0001-Don-t-run-flake8-checks-during-the-build.patch
@@ -0,0 +1,38 @@
+From 4b9801d9bbe535fd6719933b96278915573e3595 Mon Sep 17 00:00:00 2001
+From: Maximilian Bosch <maximilian@mbosch.me>
+Date: Sun, 10 Mar 2019 16:42:21 +0100
+Subject: [PATCH] Don't run flake8 checks during the build
+
+If the code simply violates their code style, the Nix package shouldn't fail.
+---
+ pytest.ini | 2 +-
+ setup.cfg  | 1 -
+ 2 files changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/pytest.ini b/pytest.ini
+index 9b3c1ec..a5189c1 100644
+--- a/pytest.ini
++++ b/pytest.ini
+@@ -1,6 +1,6 @@
+ [pytest]
+ norecursedirs=dist build .tox .eggs
+-addopts=--doctest-modules --flake8
++addopts=--doctest-modules
+ doctest_optionflags=ALLOW_UNICODE ELLIPSIS
+ filterwarnings=
+ 	ignore:Possible nested set::pycodestyle:113
+diff --git a/setup.cfg b/setup.cfg
+index 3e7bbed..5cac7a2 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -29,7 +29,6 @@ setup_requires = setuptools_scm >= 1.15.0
+ testing = 
+ 	pytest >= 3.5, !=3.7.3
+ 	pytest-checkdocs
+-	pytest-flake8
+ docs = 
+ 	sphinx
+ 	jaraco.packaging >= 3.2
+-- 
+2.18.1
+
diff --git a/pkgs/development/python-modules/jaraco_logging/default.nix b/pkgs/development/python-modules/jaraco_logging/default.nix
index 68fba6bfb5fb..ae05a76da1d5 100644
--- a/pkgs/development/python-modules/jaraco_logging/default.nix
+++ b/pkgs/development/python-modules/jaraco_logging/default.nix
@@ -1,5 +1,6 @@
 { lib, buildPythonPackage, fetchPypi, setuptools_scm
-, tempora, six, pytest, pytest-flake8 }:
+, tempora, six, pytest
+}:
 
 buildPythonPackage rec {
   pname = "jaraco.logging";
@@ -10,9 +11,11 @@ buildPythonPackage rec {
     sha256 = "1lb846j7qs1hgqwkyifv51nhl3f8jimbc4lk8yn9nkaynw0vyzcg";
   };
 
+  patches = [ ./0001-Don-t-run-flake8-checks-during-the-build.patch ];
+
   buildInputs = [ setuptools_scm ];
   propagatedBuildInputs = [ tempora six ];
-  checkInputs = [ pytest pytest-flake8 ];
+  checkInputs = [ pytest ];
 
   checkPhase = ''
     PYTHONPATH=".:$PYTHONPATH" pytest
diff --git a/pkgs/development/python-modules/jaraco_text/default.nix b/pkgs/development/python-modules/jaraco_text/default.nix
index 222a92e60fb6..6087258a289b 100644
--- a/pkgs/development/python-modules/jaraco_text/default.nix
+++ b/pkgs/development/python-modules/jaraco_text/default.nix
@@ -1,14 +1,15 @@
 { buildPythonPackage, fetchPypi, setuptools_scm
-, jaraco_functools, jaraco_collections }:
+, jaraco_functools
+}:
 
 buildPythonPackage rec {
   pname = "jaraco.text";
-  version = "2.0";
+  version = "3.0";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3660678d395073626e72a455b24bacf07c064138a4cc6c1dae63e616f22478aa";
+    sha256 = "1l5hq2jvz9xj05aayc42f85v8wx8rpi16lxph8blw51wgnvymsyx";
   };
   doCheck = false;
   buildInputs =[ setuptools_scm ];
-  propagatedBuildInputs = [ jaraco_functools jaraco_collections ];
+  propagatedBuildInputs = [ jaraco_functools ];
 }
diff --git a/pkgs/development/python-modules/joblib/default.nix b/pkgs/development/python-modules/joblib/default.nix
index d96752ba05f3..f9f5ba23eac9 100644
--- a/pkgs/development/python-modules/joblib/default.nix
+++ b/pkgs/development/python-modules/joblib/default.nix
@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
-, fetchFromGitHub
+, fetchPypi
+, fetchpatch
 , sphinx
 , numpydoc
 , pytest
@@ -10,16 +11,30 @@
 
 buildPythonPackage rec {
   pname = "joblib";
-  version = "0.12.4";
+  version = "0.13.2";
 
-  # get full repository inorder to run tests
-  src = fetchFromGitHub {
-    owner = "joblib";
-    repo = pname;
-    rev = version;
-    sha256 = "06zszgp7wpa4jr554wkk6kkigp4k9n5ad5h08i6w9qih963rlimb";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524";
   };
 
+  # python-lz4 compatibility
+  # https://github.com/joblib/joblib/pull/847
+  patches = [
+    (fetchpatch {
+      url = https://github.com/joblib/joblib/commit/d3235fd601f40c91e074d48a411d7380329fe155.patch;
+      sha256 = "1hg1vfbba7mfilrpvmd97s68v03vs4bhlp1c1dj9lizi51mj2q2h";
+    })
+    (fetchpatch {
+      url = https://github.com/joblib/joblib/commit/884c92cd2aa5c2c1975ab48786da75556d779833.patch;
+      sha256 = "11kvpkvi428dq13ayy7vfyrib8isvcrdw8cd5hxkp5axr7sl12ba";
+    })
+    (fetchpatch {
+      url = https://github.com/joblib/joblib/commit/f1e177d781cc0d64420ec964a0b17d8268cb42a0.patch;
+      sha256 = "1sq6wcw4bhaq8cqwcd43fdws3467qy342xx3pgv62hp2nn75a21d";
+    })
+  ];
+
   checkInputs = [ sphinx numpydoc pytest ];
   propagatedBuildInputs = [ python-lz4 ];
 
diff --git a/pkgs/development/python-modules/pivy/default.nix b/pkgs/development/python-modules/pivy/default.nix
index 4619400b6e35..37c999e86b4c 100644
--- a/pkgs/development/python-modules/pivy/default.nix
+++ b/pkgs/development/python-modules/pivy/default.nix
@@ -16,8 +16,13 @@ buildPythonPackage rec {
     sha256 = "18n14ha2d3j3ghg2f2aqnf2mks94nn7ma9ii7vkiwcay93zm82cf";
   };
 
+  nativeBuildInputs = with pkgs; [
+    swig1 coin3d soqt
+  ];
+
   buildInputs = with pkgs; with xorg; [
-    swig1 coin3d soqt libGLU_combined
+    coin3d soqt
+    libGLU_combined
     libXi libXext libSM libICE libX11
   ];
 
diff --git a/pkgs/development/python-modules/py3status/default.nix b/pkgs/development/python-modules/py3status/default.nix
index 5f43ae32ea23..d8f3c01bbd48 100644
--- a/pkgs/development/python-modules/py3status/default.nix
+++ b/pkgs/development/python-modules/py3status/default.nix
@@ -5,6 +5,10 @@
 , requests
 , pytz
 , tzlocal
+, i3ipc
+, pydbus
+, pygobject3
+, pyserial
 
 , file
 , acpi
@@ -20,14 +24,14 @@
 buildPythonPackage rec {
   pname = "py3status";
   version = "3.16";
-  
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "1xrfph277bgjln3jbpzpgkhxad04fjvj7s3xfil42q1sxi4s3q3g";
   };
 
   doCheck = false;
-  propagatedBuildInputs = [ pytz requests tzlocal ];
+  propagatedBuildInputs = [ pytz requests tzlocal i3ipc pydbus pygobject3 pyserial ];
   buildInputs = [ file ];
   prePatch = ''
     sed -i -e "s|'file|'${file}/bin/file|" py3status/parse_config.py
diff --git a/pkgs/development/python-modules/pyarrow/default.nix b/pkgs/development/python-modules/pyarrow/default.nix
index 899b18eecbed..32c5f38b66d0 100644
--- a/pkgs/development/python-modules/pyarrow/default.nix
+++ b/pkgs/development/python-modules/pyarrow/default.nix
@@ -16,6 +16,7 @@ buildPythonPackage rec {
   checkInputs = [ hypothesis pandas pytest ];
 
   PYARROW_BUILD_TYPE = "release";
+  PYARROW_WITH_PARQUET = true;
   PYARROW_CMAKE_OPTIONS = [
     "-DCMAKE_INSTALL_RPATH=${ARROW_HOME}/lib"
 
@@ -24,6 +25,10 @@ buildPythonPackage rec {
     "-DCMAKE_POLICY_DEFAULT_CMP0025=NEW"
   ];
 
+  preBuild = ''
+    export PYARROW_PARALLEL=$NIX_BUILD_CORES
+  '';
+
   preCheck = ''
     rm pyarrow/tests/test_jvm.py
     rm pyarrow/tests/test_hdfs.py
@@ -43,13 +48,15 @@ buildPythonPackage rec {
     # when it is not intended to be imported at all
     rm pyarrow/tests/deserialize_buffer.py
     substituteInPlace pyarrow/tests/test_feather.py --replace "test_deserialize_buffer_in_different_process" "_disabled"
+
+    # Fails to bind a socket
+    # "PermissionError: [Errno 1] Operation not permitted"
+    substituteInPlace pyarrow/tests/test_ipc.py --replace "test_socket_" "_disabled"
   '';
 
   ARROW_HOME = _arrow-cpp;
   PARQUET_HOME = _arrow-cpp;
 
-  setupPyBuildFlags = ["--with-parquet" ];
-
   checkPhase = ''
     mv pyarrow/tests tests
     rm -rf pyarrow
diff --git a/pkgs/development/python-modules/pyhocon/default.nix b/pkgs/development/python-modules/pyhocon/default.nix
new file mode 100644
index 000000000000..ac4af42851cd
--- /dev/null
+++ b/pkgs/development/python-modules/pyhocon/default.nix
@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+# Runtime inputs:
+, pyparsing
+# Check inputs:
+, pytest
+, mock
+}:
+
+buildPythonPackage rec {
+  pname = "pyhocon";
+  version = "0.3.51";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "10l014br012fa583rnj3wqf6g9gmljamcwpw4snqwwg15i0dmkll";
+  };
+
+  propagatedBuildInputs = [ pyparsing ];
+
+  checkInputs = [ pytest mock ];
+
+  # Tests fail because necessary data files aren't packaged for PyPi yet.
+  # See https://github.com/chimpler/pyhocon/pull/203
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/chimpler/pyhocon/;
+    description = "HOCON parser for Python";
+    # Long description copied from
+    # https://github.com/chimpler/pyhocon/blob/55a9ea3ebeeac5764bdebebfbeacbf099f64db26/setup.py
+    # (the tip of master as of 2019-03-24).
+    longDescription = ''
+      A HOCON parser for Python. It additionally provides a tool
+      (pyhocon) to convert any HOCON content into json, yaml and properties
+      format
+    '';
+    license = licenses.asl20;
+    maintainers = [ maintainers.chreekat ];
+  };
+}
diff --git a/pkgs/development/python-modules/pyshp/default.nix b/pkgs/development/python-modules/pyshp/default.nix
index b58e1f48bb80..17d60f7507d3 100644
--- a/pkgs/development/python-modules/pyshp/default.nix
+++ b/pkgs/development/python-modules/pyshp/default.nix
@@ -2,12 +2,12 @@
 , setuptools }:
 
 buildPythonPackage rec {
-  version = "2.0.1";
+  version = "2.1.0";
   pname = "pyshp";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "049xj760s75nkvs7rhz710a6x3lvvfajddknmfz1vkf2p3f2l2as";
+    sha256 = "1h75a5fisqqj48m6wq7jhdxv6arjg3mvnr5q404pvfbjscj7yp76";
   };
 
   buildInputs = [ setuptools ];
diff --git a/pkgs/development/python-modules/pyside/tools.nix b/pkgs/development/python-modules/pyside/tools.nix
index abb0bdebd5da..e23e63525183 100644
--- a/pkgs/development/python-modules/pyside/tools.nix
+++ b/pkgs/development/python-modules/pyside/tools.nix
@@ -13,7 +13,11 @@ buildPythonPackage rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [ cmake pyside qt4 pysideShiboken ];
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ qt4 ];
+
+  propagatedBuildInputs = [ pyside pysideShiboken ];
 
   meta = {
     description = "Tools for pyside, the LGPL-licensed Python bindings for the Qt cross-platform application and UI framework";
diff --git a/pkgs/development/python-modules/pytest-faulthandler/default.nix b/pkgs/development/python-modules/pytest-faulthandler/default.nix
index 852de1fd49cd..f9e6846367c3 100644
--- a/pkgs/development/python-modules/pytest-faulthandler/default.nix
+++ b/pkgs/development/python-modules/pytest-faulthandler/default.nix
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     sha256 = "bf8634c3fd6309ef786ec03b913a5366163fdb094ebcfdebc35626400d790e0d";
   };
 
-  buildInputs = [ setuptools_scm pytest ];
+  nativeBuildInputs = [ setuptools_scm pytest ];
   checkInputs = [ pytest-mock ];
   propagatedBuildInputs = lib.optional (pythonOlder "3.0") faulthandler;
 
diff --git a/pkgs/development/python-modules/pytest-mock/default.nix b/pkgs/development/python-modules/pytest-mock/default.nix
index 6a70b6e8ce97..4fd0570a50dc 100644
--- a/pkgs/development/python-modules/pytest-mock/default.nix
+++ b/pkgs/development/python-modules/pytest-mock/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pytest-mock";
-  version = "1.10.1";
+  version = "1.10.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "4d0d06d173eecf172703219a71dbd4ade0e13904e6bbce1ce660e2e0dc78b5c4";
+    sha256 = "cbec53e7cb0f2b57275220cb4f2822093ac89e486095555105ffe1a4e2f11df4";
   };
 
   propagatedBuildInputs = lib.optional (!isPy3k) mock;
diff --git a/pkgs/development/python-modules/python-markdown-math/default.nix b/pkgs/development/python-modules/python-markdown-math/default.nix
new file mode 100644
index 000000000000..053b4897e833
--- /dev/null
+++ b/pkgs/development/python-modules/python-markdown-math/default.nix
@@ -0,0 +1,24 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, markdown
+}:
+
+buildPythonPackage rec {
+  pname = "python-markdown-math";
+  version = "0.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "c68d8cb9695cb7b435484403dc18941d1bad0ff148e4166d9417046a0d5d3022";
+  };
+
+  checkInputs = [ markdown ];
+
+  meta = {
+    description = "Math extension for Python-Markdown";
+    homepage = https://github.com/mitya57/python-markdown-math;
+    license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ klntsky ];
+  };
+}
diff --git a/pkgs/development/python-modules/quandl/default.nix b/pkgs/development/python-modules/quandl/default.nix
index 598767e6ca9b..fc4c192968f2 100644
--- a/pkgs/development/python-modules/quandl/default.nix
+++ b/pkgs/development/python-modules/quandl/default.nix
@@ -10,12 +10,12 @@
 
 buildPythonPackage rec {
   pname = "quandl";
-  version = "3.4.5";
+  version = "3.4.6";
 
   src = fetchPypi {
     inherit version;
     pname = "Quandl";
-    sha256 = "1rflyc6q3wa5ghc5v81yw79yg7lkpgd2c22mgbb0cvza724k53ys";
+    sha256 = "15b58nj45bdax0aha6kwjz5pxj3bz8bs6ajwxqp9r89j13xxn94g";
   };
 
   doCheck = true;
diff --git a/pkgs/development/python-modules/restructuredtext_lint/default.nix b/pkgs/development/python-modules/restructuredtext_lint/default.nix
index eeed42892308..4522c7623283 100644
--- a/pkgs/development/python-modules/restructuredtext_lint/default.nix
+++ b/pkgs/development/python-modules/restructuredtext_lint/default.nix
@@ -9,14 +9,11 @@
 
 buildPythonPackage rec {
   pname = "restructuredtext_lint";
-  version = "1.2.2";
-
-  # https://github.com/twolfson/restructuredtext-lint/pull/47
-  disabled = isPy37;
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "82880a8de8a41bfc84f533744091b1ead8e2ab9ad6c0a3f60f4750ef6c802350";
+    sha256 = "97b3da356d5b3a8514d8f1f9098febd8b41463bed6a1d9f126cf0a048b6fd908";
   };
 
   checkInputs = [ nose testtools ];
diff --git a/pkgs/development/python-modules/shellingham/default.nix b/pkgs/development/python-modules/shellingham/default.nix
index b2c63ea97e3b..c1791db9fbc9 100644
--- a/pkgs/development/python-modules/shellingham/default.nix
+++ b/pkgs/development/python-modules/shellingham/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "shellingham";
-  version = "1.2.8";
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "115k1z2klgsvyzg4q5ip0iqxyb565pkchhf2fsr846k68gqcgrjn";
+    sha256 = "116r78nhw74rh857kv9l614xjr6k89919s6l8b14hlvy8fz8rg51";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/shodan/default.nix b/pkgs/development/python-modules/shodan/default.nix
index 0fde898ca04f..bf57b9846ee5 100644
--- a/pkgs/development/python-modules/shodan/default.nix
+++ b/pkgs/development/python-modules/shodan/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "shodan";
-  version = "1.10.4";
+  version = "1.11.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "13966vqxww7v2b5hf2kjismdzvqyjvxlcdvpkzpbsrpxy9pvn2n4";
+    sha256 = "0kjcyw3xmps3maf4vzn1pypc6i60q8b67xj78v4gbv4yx2cp2fzr";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/snakeviz/default.nix b/pkgs/development/python-modules/snakeviz/default.nix
index 2b0ff6e443a7..b41633da4d39 100644
--- a/pkgs/development/python-modules/snakeviz/default.nix
+++ b/pkgs/development/python-modules/snakeviz/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "snakeviz";
-  version = "1.0.0";
+  version = "2.0.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "5fe23667708a4ed04047abfbf209675a8488ea6ea8c038d7de06d8a083fb3531";
+    sha256 = "0hvfc7c25cz6p3m3p3klm3njiysp7lkrs9sxm4p40spldl0jlfpa";
   };
 
   # Upstream doesn't run tests from setup.py
diff --git a/pkgs/development/python-modules/xdot/default.nix b/pkgs/development/python-modules/xdot/default.nix
index 68d097d71d6a..79f0fb13d70d 100644
--- a/pkgs/development/python-modules/xdot/default.nix
+++ b/pkgs/development/python-modules/xdot/default.nix
@@ -1,5 +1,5 @@
 { lib, buildPythonPackage, fetchPypi, isPy3k
-, wrapGAppsHook, gobject-introspection, pygobject3, graphviz, gnome3 }:
+, wrapGAppsHook, gobject-introspection, pygobject3, graphviz, gnome3, gtk3 }:
 
 buildPythonPackage rec {
   pname = "xdot";
@@ -13,7 +13,7 @@ buildPythonPackage rec {
   disabled = !isPy3k;
 
   nativeBuildInputs = [ wrapGAppsHook ];
-  propagatedBuildInputs = [ gobject-introspection pygobject3 graphviz gnome3.gtk ];
+  propagatedBuildInputs = [ gobject-introspection pygobject3 graphviz gtk3 ];
 
   meta = with lib; {
     description = "xdot.py is an interactive viewer for graphs written in Graphviz's dot";