Merge remote-tracking branch 'upstream/master' into staging

Conflicts:
	pkgs/top-level/all-packages.nix

pkgs/development/python-modules/autopep8/default.nix

@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "autopep8";
-  version = "1.3.4";
+  version = "1.3.5";
   name = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "c7be71ab0cb2f50c9c22c82f0c9acaafc6f57492c3fbfee9790c415005c2b9a5";
+    sha256 = "192bvhzi4d0claqxgzymvv7k3qnj627742bc8sgxpzjj42pd9112";
   };
 
   propagatedBuildInputs = [ pycodestyle ];

pkgs/development/python-modules/imbalanced-learn/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, buildPythonPackage, fetchPypi, scikitlearn, pandas, nose, pytest }:
+
+buildPythonPackage rec {
+  pname = "imbalanced-learn";
+  version = "0.3.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1r5js9kw6rvmfvxxkfjlcxv5xn5h19qvg7d41byilxwq9kd515g4";
+  };
+
+  propagatedBuildInputs = [ scikitlearn ];
+  checkInputs = [ nose pytest pandas ];
+  checkPhase = ''
+    export HOME=$PWD
+    # skip some tests that fail because of minimal rounding errors
+    py.test imblearn --ignore=imblearn/metrics/classification.py
+    py.test doc/*.rst
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Library offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance";
+    homepage = https://github.com/scikit-learn-contrib/imbalanced-learn;
+    license = licenses.mit;
+  };
+}

pkgs/development/python-modules/mock-open/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchFromGitHub, pythonOlder, mock }:
+
+buildPythonPackage rec {
+  pname = "mock-open";
+  version = "1.3.1";
+
+  # no tests in PyPI tarball
+  src = fetchFromGitHub {
+    owner = "nivbend";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0ikhrhlkl5c7qbigpsv44jw89ws1z7j06gzyg5dh1ki533ifbjm2";
+  };
+
+  propagatedBuildInputs = lib.optional (pythonOlder "3.3") mock;
+
+  meta = with lib; {
+    homepage = https://github.com/nivbend/mock-open;
+    description = "A better mock for file I/O";
+    license = licenses.mit;
+  };
+}

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

@@ -0,0 +1,28 @@
+{ buildPythonPackage, stdenv, glibcLocales, mock, nose, isPy3k, argparse, jinja2, six
+, fetchPypi, lib
+}:
+
+buildPythonPackage rec {
+  pname = "mrbob";
+  version = "0.1.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "6737eaf98aaeae85e07ebef844ee5156df2f06a8b28d7c3dcb056f811c588121";
+  };
+
+  disabled = isPy3k;
+
+  checkInputs = [ nose glibcLocales mock ];
+  checkPhase = ''
+    LC_ALL="en_US.UTF-8" nosetests
+  '';
+
+  propagatedBuildInputs = [ argparse jinja2 six ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/domenkozar/mr.bob;
+    description = "A tool to generate code skeletons from templates";
+    license = licenses.bsd3;
+  };
+}

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

@@ -21,8 +21,12 @@
 , simplejson
 , traits
 , xvfbwrapper
+, pytestcov
+, codecov
 # other dependencies
 , which
+, bash
+, glibcLocales
 }:
 
 assert !isPy3k -> configparser != null;
@@ -36,9 +40,14 @@ buildPythonPackage rec {
     sha256 = "47f62fda3d6b9a37aa407a6b78c80e91240aa71e61191ed00da68b02839fe258";
   };
 
-  doCheck = false;  # fails with TypeError: None is not callable
-  checkInputs = [ which ];
-  buildInputs = [ pytest mock ];  # required in installPhase
+  # see https://github.com/nipy/nipype/issues/2240
+  patches = [ ./prov-version.patch ];
+
+  postPatch = ''
+    substituteInPlace nipype/interfaces/base/tests/test_core.py \
+      --replace "/usr/bin/env bash" "${bash}/bin/bash"
+  '';
+
   propagatedBuildInputs = [
     click
     dateutil
@@ -59,6 +68,12 @@ buildPythonPackage rec {
     configparser
   ];
 
+  checkInputs = [ pytest mock pytestcov codecov which glibcLocales ];
+
+  checkPhase = ''
+    LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype
+  '';
+
   meta = with stdenv.lib; {
     homepage = http://nipy.org/nipype/;
     description = "Neuroimaging in Python: Pipelines and Interfaces";

pkgs/development/python-modules/nipype/prov-version.patch

@@ -0,0 +1,21 @@
+diff --git a/nipype/info.py b/nipype/info.py
+index 1daa382e2..da338d0ea 100644
+--- a/nipype/info.py
++++ b/nipype/info.py
+@@ -108,7 +108,6 @@ DATEUTIL_MIN_VERSION = '2.2'
+ PYTEST_MIN_VERSION = '3.0'
+ FUTURE_MIN_VERSION = '0.16.0'
+ SIMPLEJSON_MIN_VERSION = '3.8.0'
+-PROV_VERSION = '1.5.0'
+ CLICK_MIN_VERSION = '6.6.0'
+ PYDOT_MIN_VERSION = '1.2.3'
+ 
+@@ -140,7 +139,7 @@ REQUIRES = [
+     'traits>=%s' % TRAITS_MIN_VERSION,
+     'future>=%s' % FUTURE_MIN_VERSION,
+     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
+-    'prov==%s' % PROV_VERSION,
++    'prov<2',
+     'click>=%s' % CLICK_MIN_VERSION,
+     'funcsigs',
+     'pytest>=%s' % PYTEST_MIN_VERSION,

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

@@ -0,0 +1,42 @@
+{ buildPythonPackage, fetchPypi, stdenv, sip, qtbase, pyqt5, poppler, pkgconfig, fetchpatch
+, python, substituteAll
+}:
+
+buildPythonPackage rec {
+  pname = "python-poppler-qt5";
+  version = "0.24.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0l69llw1fzwz8y90q0qp9q5pifbrqjjbwii7di54dwghw5fc6w1r";
+  };
+
+  patches = [
+    (substituteAll {
+      src = ./poppler-include-dir.patch;
+      poppler_include_dir = "${poppler.dev}/include/poppler";
+    })
+    (fetchpatch {
+      url = "https://github.com/wbsoft/python-poppler-qt5/commit/faf4d1308f89560b0d849671226e3080dfc72e79.patch";
+      sha256 = "18krhh6wzsnpxzlzv02nginb1vralla8ai24zqk10nc4mj6fkj86";
+    })
+  ];
+
+  setupPyBuildFlags = [
+    "--pyqt-sip-dir ${pyqt5}/share/sip/PyQt5"
+    "--qt-include-dir ${qtbase.dev}/include"
+  ];
+
+  buildInputs = [ qtbase.dev poppler ];
+  nativeBuildInputs = [ pkgconfig ];
+  propagatedBuildInputs = [ sip pyqt5.dev ];
+
+  # no tests, just bindings for `poppler_qt5`
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/wbsoft/python-poppler-qt5;
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ ma27 ];
+  };
+}

pkgs/development/python-modules/poppler-qt5/poppler-include-dir.patch

@@ -0,0 +1,12 @@
+diff --git a/setup.py b/setup.py
+index 59a75b0..0a73268 100644
+--- a/setup.py
++++ b/setup.py
+@@ -169,6 +169,7 @@ class build_ext(build_ext_base):
+                              'Please specify via --pyqt-sip-flags=')
+ 
+         self.include_dirs += (self.qt_include_dir,
++                              '@poppler_include_dir@',
+                               os.path.join(self.qt_include_dir, 'QtCore'),
+                               os.path.join(self.qt_include_dir, 'QtGui'),
+                               os.path.join(self.qt_include_dir, 'QtXml'))

pkgs/development/python-modules/pytest-flake8/default.nix

@@ -1,9 +1,8 @@
 {lib, buildPythonPackage, fetchPypi, fetchpatch, pytest, flake8}:
 
 buildPythonPackage rec {
-  name = "${pname}-${version}";
   pname = "pytest-flake8";
-  version = "0.9.1";
+  version = "1.0.0";
 
   # although pytest is a runtime dependency, do not add it as
   # propagatedBuildInputs in order to allow packages depend on another version
@@ -13,7 +12,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0032l4x2i5qn7ikaaw0kjs9f4ccpas21j564spyxwmx50wnhf5p7";
+    sha256 = "01driw4sc6nfi3m3ii7d074pxi3h1h4mbiyad9crg5i1l5jxx5ir";
   };
 
   checkPhase = ''

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

@@ -3,11 +3,11 @@
 buildPythonPackage rec {
   name    = "${pname}-${version}";
   pname   = "python-gnupg";
-  version = "0.4.1";
+  version = "0.4.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06hfw9cmiw5306fyisp3kzg1hww260qzip829g7y7pj1mwpb0izg";
+    sha256 = "0wzvx8y4ii1y1vch28a0m6f2y4px9r7qd8fpimsx6y5z4pfscm2s";
   };
 
   propagatedBuildInputs = [ gnupg1 ];

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

@@ -0,0 +1,21 @@
+{ buildPythonPackage, fetchPypi, stdenv }:
+
+buildPythonPackage rec {
+  pname = "python-ly";
+  version = "0.9.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0x98dv7p8mg26p4816yy8hz4f34zf6hpnnfmr56msgh9jnsm2qfl";
+  };
+
+  # tests not shipped on `pypi` and
+  # seem to be broken ATM: https://github.com/wbsoft/python-ly/issues/70
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Tool and library for manipulating LilyPond files";
+    license = licenses.gpl2;
+    maintainers = with maintainers; [ ma27 ];
+  };
+}

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

@@ -1,4 +1,4 @@
-{ lib, fetchPypi, isPy3k, buildPythonPackage, numpy, root }:
+{ lib, fetchPypi, isPy3k, buildPythonPackage, numpy, root, nose }:
 
 buildPythonPackage rec {
   pname = "root_numpy";
@@ -11,6 +11,11 @@ buildPythonPackage rec {
   };
 
   disabled = isPy3k; # blocked by #27649
+  checkInputs = [ nose ];
+  checkPhase = ''
+    python setup.py install_lib -d .
+    nosetests -s -v root_numpy
+  '';
 
   propagatedBuildInputs = [ numpy root ];
 

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

@@ -3,7 +3,9 @@
 , isPy3k
 , fetchPypi
 , boto
+, boto3
 , bz2file
+, mock
 , moto
 , requests
 , responses
@@ -12,14 +14,26 @@
 buildPythonPackage rec {
   pname = "smart_open";
   name = "${pname}-${version}";
-  version = "1.5.6";
+  version = "1.5.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8fd2de1c359bd0074bd6d334a5b9820ae1c5b6ba563970b95052bace4b71baeb";
+    sha256 = "0y1c29pdxxgxkymr7g2n59siqqaq351zbx9vz8433dxvzy4qgd7p";
   };
 
-  propagatedBuildInputs = [ boto bz2file requests responses moto ];
+  # nixpkgs version of moto is >=1.2.0, remove version pin to fix build
+  postPatch = ''
+    substituteInPlace ./setup.py --replace "moto==0.4.31" "moto"
+  '';
+
+  # moto>=1.0.0 is backwards-incompatible and some tests fail with it,
+  # so disable tests for now
+  doCheck = false;
+
+  checkInputs = [ mock moto responses ];
+
+  # upstream code requires both boto and boto3
+  propagatedBuildInputs = [ boto boto3 bz2file requests ];
   meta = {
     license = lib.licenses.mit;
     description = "smart_open is a Python 2 & Python 3 library for efficient streaming of very large file";