Merge branch 'master' into staging

Lots of rebuilds from master; at least some of them due to security.

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

@@ -6,6 +6,7 @@
 , numpydoc
 , isPy3k
 , stdenv
+, pytest
 }:
 
 
@@ -18,14 +19,10 @@ buildPythonPackage rec {
     sha256 = "7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085";
   };
 
-  checkInputs = [ nose sphinx numpydoc ];
+  checkInputs = [ sphinx numpydoc pytest ];
 
-  # Failing test on Python 3.x and Darwin
-  postPatch = '''' + lib.optionalString (isPy3k || stdenv.isDarwin) ''
-    sed -i -e '70,84d' joblib/test/test_format_stack.py
-    # test_nested_parallel_warnings: ValueError: Non-zero return code: -9.
-    # Not sure why but it's nix-specific. Try removing for new joblib releases.
-    rm joblib/test/test_parallel.py
+  checkPhase = ''
+    py.test -k 'not test_disk_used and not test_nested_parallel_warnings' joblib/test
   '';
 
   meta = {
@@ -33,4 +30,4 @@ buildPythonPackage rec {
     homepage = http://pythonhosted.org/joblib/;
     license = lib.licenses.bsd3;
   };
-}
+}

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

@@ -3,7 +3,7 @@
 buildPythonApplication rec {
   pname = "jsbeautifier";
   version = "1.7.4";
-  name = "jsbeautifier-1.6.14";
+  name = "${pname}-${version}";
 
   propagatedBuildInputs = [ six ];
 

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

@@ -0,0 +1,31 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, nose, numpy
+, bottle, pyyaml, redis, six
+, zlib }:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "Jug";
+  version = "1.6.3";
+  buildInputs = [ nose numpy ];
+  propagatedBuildInputs = [
+    bottle
+    pyyaml
+    redis
+    six
+
+    zlib
+  ];
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0dpcwjaf8zzqpdz8w8h0p7vmd6z6bzfz2805a6bdjqs9hhkhrg86";
+  };
+
+  meta = with stdenv.lib; {
+    description = "A Task-Based Parallelization Framework";
+    license = licenses.mit;
+    url = https://jug.readthedocs.io/;
+    maintainers = with maintainers; [ luispedro ];
+  };
+}

pkgs/development/python-modules/pip-tools/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, buildPythonPackage, pip, pytest, click, six, first
-, setuptools_scm, glibcLocales, mock }:
+, setuptools_scm, git, glibcLocales, mock }:
 
 buildPythonPackage rec {
   pname = "pip-tools";
@@ -12,12 +12,18 @@ buildPythonPackage rec {
   };
 
   LC_ALL = "en_US.UTF-8";
-  checkInputs = [ pytest glibcLocales mock ];
+  checkInputs = [ pytest git glibcLocales mock ];
   propagatedBuildInputs = [ pip click six first setuptools_scm ];
 
   checkPhase = ''
-    export HOME=$(mktemp -d)
-    py.test -k "not test_realistic_complex_sub_dependencies" # requires network
+    export HOME=$(mktemp -d) VIRTUAL_ENV=1
+    tests_without_network_access="
+      not test_realistic_complex_sub_dependencies \
+      and not test_editable_package_vcs \
+      and not test_generate_hashes_all_platforms \
+      and not test_generate_hashes_without_interfering_with_each_other \
+    "
+    py.test -k "$tests_without_network_access"
   '';
 
   meta = with stdenv.lib; {

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

@@ -2,14 +2,14 @@
 
 buildPythonPackage rec {
   pname = "podcastparser";
-  version = "0.6.1";
+  version = "0.6.2";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "gpodder";
     repo = "podcastparser";
     rev = version;
-    sha256 = "0q3qc8adykmm692ha0c37xd6wbj830zlq900fyw6vrfan9bgdj5y";
+    sha256 = "1mhg7192d6s1ll9mx1b63yfj6k4cnv4i95jllbnydyjv9ykkv0k1";
   };
 
   propagatedBuildInputs = [ ];

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

@@ -1,13 +1,15 @@
-{ stdenv, buildPythonPackage, fetchPypi, numpy, scipy, cython, networkx, joblib, nose }:
+{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, cython, networkx, joblib, nose }:
 
 buildPythonPackage rec {
   pname = "pomegranate";
-  version = "0.8.0";
+  version = "0.8.1";
   name  = "${pname}-${version}";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "6b03d05bffbe46c674800652cf273a8d338a2e40001b763cd6925aac0b578a43";
+  
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "jmschrei";
+    rev = "v${version}";
+    sha256 = "085nka5bh88bxbd5vl1azyv9cfpp6grz2ngclc85f9kgccac1djr";
   };
 
   propagatedBuildInputs = [ numpy scipy cython networkx joblib ];

pkgs/development/python-modules/pycdio/add-cdtext-toc.patch

@@ -1,52 +0,0 @@
-diff -Nurp pycdio-0.20-orig/test/cdtext.toc pycdio-0.20/test/cdtext.toc
---- pycdio-0.20-orig/test/cdtext.toc	1970-01-01 01:00:00.000000000 +0100
-+++ pycdio-0.20/test/cdtext.toc	2014-11-06 23:36:12.520708320 +0100
-@@ -0,0 +1,48 @@
-+CD_DA
-+
-+// global CD-TEXT data
-+
-+CD_TEXT {
-+
-+  // Mapping from language number (0..7) used in 'LANGUAGE' statements 
-+  // to language code.
-+///  LANGUAGE_MAP {
-+///    0 : EN  // 9 is the code for ENGLISH,
-+///            // I don't know any other language code, yet
-+///  }
-+
-+  // Language number should always start with 0
-+  LANGUAGE 0 {
-+    // Required fields - at least all CD-TEXT CDs I've seen so far have them.
-+    TITLE "CD Title"
-+    PERFORMER "Performer"
-+    DISC_ID "XY12345"
-+    UPC_EAN "" // usually empty
-+
-+    // Further possible items, all of them are optional
-+    ARRANGER ""
-+    SONGWRITER ""
-+    MESSAGE "" 
-+    GENRE "" // I'm not sure if this should be really ascii data
-+  }
-+}
-+
-+
-+TRACK AUDIO
-+// track specific CD-TEXT data
-+CD_TEXT {
-+  LANGUAGE 0 {
-+    // if an item is defined for one track it should be defined for all tracks
-+    TITLE "Track Title"
-+
-+    PERFORMER "Performer"
-+    ISRC "US-XX1-98-01234"
-+
-+    ARRANGER ""
-+    SONGWRITER ""
-+    MESSAGE "" 
-+  }
-+}
-+
-+SILENCE 1:0:0
-+

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

@@ -0,0 +1,28 @@
+{ stdenv, pytest, fetchFromGitHub, buildPythonPackage, appdirs }:
+
+buildPythonPackage rec {
+  pname = "rply";
+  name = "${pname}-${version}";
+  version = "0.7.5";
+
+  src = fetchFromGitHub {
+    owner = "alex";
+    repo = "rply";
+    rev = "v${version}";
+    sha256 = "0v05gdy5dval30wvz96lywvz2jyf000dp0pnrd1lwdx3cyywq659";
+  };
+
+  buildInputs = [ appdirs ];
+
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    HOME=$(mktemp -d) py.test tests
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A python Lex/Yacc that works with RPython";
+    homepage = https://github.com/alex/rply;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ nixy ];
+  };
+}