Merge branch 'master' into staging

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

@@ -31,12 +31,13 @@ buildPythonPackage rec {
     export PATH="$out/bin:$PATH"
   '';
 
-  buildInputs = lib.optionals pariSupport [
-    pari
-  ];
-
   propagatedBuildInputs = [
     cython
+  ] ++ lib.optionals pariSupport [
+    # When cysignals is built with pari, including cysignals into the
+    # buildInputs of another python package will cause cython to link against
+    # pari.
+    pari
   ];
 
   enableParallelBuilding = true;

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

@@ -17,7 +17,7 @@ buildPythonPackage rec {
 
   # Only Darwin needs LANG, but we could set it in general.
   # It's done here conditionally to prevent mass-rebuilds.
-  checkPhase = lib.optionalString (isPy3k && stdenv.isDarwin) ''LANG="en_US.UTF-8" '' + (if isPy3k then ''
+  checkPhase = lib.optionalString (isPy3k && stdenv.isDarwin) ''LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" '' + (if isPy3k then ''
     ${python.interpreter} test3/alltests.py
   '' else ''
     ${python.interpreter} test/alltests.py

pkgs/development/python-modules/gmpy2/default.nix

@@ -1,8 +1,15 @@
-{ stdenv, buildPythonPackage, fetchurl, isPyPy, gmp, mpfr, libmpc } :
+{ stdenv
+, buildPythonPackage
+, fetchFromGitHub
+, isPyPy
+, gmp
+, mpfr
+, libmpc
+}:
 
 let
   pname = "gmpy2";
-  version = "2.0.8";
+  version = "2.1a4";
 in
 
 buildPythonPackage {
@@ -10,9 +17,11 @@ buildPythonPackage {
 
   disabled = isPyPy;
 
-  src = fetchurl {
-    url = "mirror://pypi/g/gmpy2/${pname}-${version}.zip";
-    sha256 = "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx";
+  src = fetchFromGitHub {
+    owner = "aleaxit";
+    repo = "gmpy";
+    rev = "gmpy2-${version}";
+    sha256 = "1wg4w4q2l7n26ksrdh4rwqmifgfm32n7x29cgdvmmbv5lmilb5hz";
   };
 
   buildInputs = [ gmp mpfr libmpc ];

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

@@ -1,25 +1,48 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, pythonAtLeast
 , numpy
 , decorator
 , imageio
+, imageio-ffmpeg
 , isPy3k
+, proglog
+, requests
 , tqdm
+# Advanced image processing (triples size of output)
+, advancedProcessing ? false
+, opencv ? null
+, scikitimage ? null
+, scikitlearn ? null
+, scipy ? null
+, matplotlib ? null
+, youtube-dl ? null
 }:
 
+assert advancedProcessing -> (
+  opencv != null && scikitimage != null && scikitlearn != null
+  && scipy != null && matplotlib != null && youtube-dl != null);
+
 buildPythonPackage rec {
   pname = "moviepy";
   version = "1.0.0";
 
+  disabled = !(pythonAtLeast "3.4");
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "16c7ffca23d90c76dd7b163f648c8166dfd589b7c180b8ff75aa327ae0a2fc6d";
   };
 
-  # No tests
+  # No tests, require network connection
   doCheck = false;
-  propagatedBuildInputs = [ numpy decorator imageio tqdm ];
+
+  propagatedBuildInputs = [
+    numpy decorator imageio imageio-ffmpeg tqdm requests proglog
+  ] ++ (stdenv.lib.optionals advancedProcessing [
+    opencv scikitimage scikitlearn scipy matplotlib youtube-dl
+  ]);
 
   meta = with stdenv.lib; {
     description = "Video editing with Python";

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

@@ -3,11 +3,11 @@
 }:
 buildPythonPackage rec {
   pname = "parse";
-  version = "1.11.1";
+  version = "1.12.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "870dd675c1ee8951db3e29b81ebe44fd131e3eb8c03a79483a58ea574f3145c2";
+    sha256 = "0hkic57kaxd5s56ylbwslmngqnpab864mjj8c0ayawfk6is6as0v";
   };
 
   checkPhase = ''

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

@@ -0,0 +1,64 @@
+{ lib
+, python
+, fetchPypi
+, buildPythonPackage
+, gmp
+, mpfr
+, libmpc
+, ppl
+, pari
+, cython
+, cysignals
+, gmpy2
+, sphinx
+}:
+
+buildPythonPackage rec {
+  pname = "pplpy";
+  version = "0.8.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0dk8l5r3f2jbkkasddvxwvhlq35pjsiirh801lrapv8lb16r2qmr";
+  };
+
+  buildInputs = [
+    gmp
+    mpfr
+    libmpc
+    ppl
+  ];
+
+  nativeBuildInputs = [
+    sphinx # docbuild, called by make
+  ];
+
+  propagatedBuildInputs = [
+    cython
+    cysignals
+    gmpy2
+  ];
+
+  outputs = [ "out" "doc" ];
+
+  postBuild = ''
+    # Find the build result in order to put it into PYTHONPATH. The doc
+    # build needs to import pplpy.
+    build_result="$PWD/$( find build/ -type d -name 'lib.*' | head -n1 )"
+
+    echo "Building documentation"
+    PYTHONPATH="$build_result:$PYTHONPATH" make -C docs html
+  '';
+
+  postInstall = ''
+    mkdir -p "$doc/share/doc"
+    mv docs/build/html "$doc/share/doc/pplpy"
+  '';
+
+  meta = with lib; {
+    description = "A Python wrapper for ppl";
+    homepage = https://gitlab.com/videlec/pplpy;
+    maintainers = with maintainers; [ timokau ];
+    license = licenses.gpl3;
+  };
+}

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

@@ -0,0 +1,19 @@
+{ stdenv, fetchPypi, buildPythonPackage, tqdm }:
+
+buildPythonPackage rec {
+  pname = "proglog";
+  version = "0.1.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "13diln950wk6nnn4rpmzx37rvrnpa7f803gwygiwbq1q46zwri6q";
+  };
+
+  propagatedBuildInputs = [ tqdm ];
+
+  meta = with stdenv.lib; {
+    description = "Logs and progress bars manager for Python";
+    homepage = https://github.com/Edinburgh-Genome-Foundry/Proglog;
+    license = licenses.mit;
+  };
+}

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

@@ -23,8 +23,8 @@ buildPythonPackage rec {
     patchShebangs .
   '';
 
-  nativeBuildInputs = [ pkgs.pkgconfig ];
-  buildInputs = [ setuptools nose pkgs.swig pkgs.libcdio ]
+  nativeBuildInputs = [ nose pkgs.pkgconfig pkgs.swig ];
+  buildInputs = [ setuptools pkgs.libcdio ]
     ++ stdenv.lib.optional stdenv.isDarwin pkgs.libiconv;
 
   # Run tests using nosetests but first need to install the binaries

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

@@ -16,6 +16,11 @@ buildPythonPackage rec {
     sha256 = "d176792a50eb015d7865b44bd9b24a7bd0489fa9a5cebbd17b9e05048cef9017";
   };
 
+  patches = [
+    # https://github.com/Pylons/pyramid_chameleon/pull/25
+    ./test-renderers-pyramid-import.patch
+  ];
+
   propagatedBuildInputs = [ chameleon pyramid zope_interface setuptools ];
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/pyramid_chameleon/test-renderers-pyramid-import.patch

@@ -0,0 +1,11 @@
+--- a/pyramid_chameleon/tests/test_renderers.py
++++ b/pyramid_chameleon/tests/test_renderers.py
+@@ -258,7 +258,7 @@ class TestChameleonRendererLookup(unittest.TestCase):
+         self.assertRaises(ValueError, lookup.__call__, info)
+ 
+     def test___call__spec_alreadyregistered(self):
+-        from pyramid import tests
++        from pyramid_chameleon import tests
+         module_name = tests.__name__
+         relpath = 'test_renderers.py'
+         spec = '%s:%s' % (module_name, relpath)