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

pkgs/development/ocaml-modules/lablgtk-extras/default.nix

@@ -1,12 +1,15 @@
-{ stdenv, fetchurl, ocaml, findlib, camlp4, config-file, lablgtk, xmlm }:
+{ stdenv, fetchFromGitHub, ocaml, findlib, camlp4, config-file, lablgtk, xmlm }:
 
 assert stdenv.lib.versionAtLeast (stdenv.lib.getVersion ocaml) "4.02";
 
-stdenv.mkDerivation {
-  name = "ocaml-lablgtk-extras-1.5";
-  src = fetchurl {
-    url = https://forge.ocamlcore.org/frs/download.php/1453/lablgtkextras-1.5.tar.gz;
-    sha256 = "1bgflgadmy2nqnqjf34zja0jy6f9wpqq8x22qcfilj9g8c9wkrmi";
+stdenv.mkDerivation rec {
+  version = "1.6";
+  name = "ocaml${ocaml.version}-lablgtk-extras-${version}";
+  src = fetchFromGitHub {
+    owner = "zoggy";
+    repo = "lablgtk-extras";
+    rev = "release-${version}";
+    sha256 = "1bbdp5j18s582mmyd7qiaq1p08g2ag4gl7x65pmzahbhg719hjda";
   };
 
   buildInputs = [ ocaml findlib camlp4 ];

pkgs/development/ocaml-modules/xmlm/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, ocaml, findlib, ocamlbuild, opam }:
+{ stdenv, fetchurl, ocaml, findlib, ocamlbuild, opam, topkg }:
 let
   pname = "xmlm";
   webpage = "http://erratique.ch/software/${pname}";
@@ -6,22 +6,37 @@ in
 
 assert stdenv.lib.versionAtLeast ocaml.version "3.12";
 
+let param =
+  if stdenv.lib.versionAtLeast ocaml.version "4.02"
+  then {
+    version = "1.3.0";
+    sha256 = "1rrdxg5kh9zaqmgapy9bhdqyxbbvxxib3bdfg1vhw4rrkp1z0x8n";
+    buildInputs = [ topkg ];
+    inherit (topkg) buildPhase;
+  } else {
+    version = "1.2.0";
+    sha256 = "1jywcrwn5z3gkgvicr004cxmdaqfmq8wh72f81jqz56iyn5024nh";
+    buildInputs = [];
+    buildPhase = "./pkg/build true";
+  };
+in
+
 stdenv.mkDerivation rec {
   name = "ocaml-${pname}-${version}";
-  version = "1.2.0";
+  inherit (param) version;
 
   src = fetchurl {
     url = "${webpage}/releases/${pname}-${version}.tbz";
-    sha256 = "1jywcrwn5z3gkgvicr004cxmdaqfmq8wh72f81jqz56iyn5024nh";
+    inherit (param) sha256;
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild opam ];
+  buildInputs = [ ocaml findlib ocamlbuild opam ] ++ param.buildInputs;
 
   createFindlibDestdir = true;
 
   unpackCmd = "tar xjf $src";
 
-  buildPhase = "./pkg/build true";
+  inherit (param) buildPhase;
 
   installPhase = ''
     opam-installer --script --prefix=$out ${pname}.install > install.sh

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

@@ -34,11 +34,11 @@
 buildPythonPackage rec {
   pname = "bokeh";
   name = "${pname}${version}";
-  version = "0.12.7";
+  version = "0.12.9";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "2c42c95bf1a418c758dbff8446b4f5e5fc72ac10ea5da4e6b5010067396d0880";
+    sha256 = "00jx3yycy6fziihz45hwj1dsh520h3vmypp28mw0877rxpxl2yxg";
   };
 
   disabled = isPyPy;
@@ -79,4 +79,4 @@ buildPythonPackage rec {
     homepage = "http://github.com/bokeh/bokeh";
     license = lib.licenses.bsd3;
   };
-}
+}

pkgs/development/python-modules/scipy/0.17.1.nix

@@ -1,56 +0,0 @@
-{lib, fetchurl, python, buildPythonPackage, isPyPy, gfortran, nose, numpy}:
-
-buildPythonPackage rec {
-  pname = "scipy";
-  version = "0.17.1";
-  name = "${pname}-${version}";
-
-  src = fetchurl {
-    url = "mirror://pypi/s/scipy/scipy-${version}.tar.gz";
-    sha256 = "1b1qpfz2j2rvmlplsjbnznnxnqr9ckbmis506110ii1w07wd4k4w";
-  };
-
-  buildInputs = [ gfortran nose numpy.blas ];
-  propagatedBuildInputs = [ numpy ];
-
-  # Remove tests because of broken wrapper
-  prePatch = ''
-    rm scipy/linalg/tests/test_lapack.py
-  '';
-
-  preConfigure = ''
-    sed -i '0,/from numpy.distutils.core/s//import setuptools;from numpy.distutils.core/' setup.py
-    export NPY_NUM_BUILD_JOBS=$NIX_BUILD_CORES
-  '';
-
-  preBuild = ''
-    echo "Creating site.cfg file..."
-    cat << EOF > site.cfg
-    [openblas]
-    include_dirs = ${numpy.blas}/include
-    library_dirs = ${numpy.blas}/lib
-    EOF
-  '';
-
-  enableParallelBuilding = true;
-
-  checkPhase = ''
-    runHook preCheck
-    pushd dist
-    ${python.interpreter} -c 'import scipy; scipy.test("fast", verbose=10)'
-    popd
-    runHook postCheck
-  '';
-
-  passthru = {
-    blas = numpy.blas;
-  };
-
-  setupPyBuildFlags = [ "--fcompiler='gnu95'" ];
-
-  meta = {
-    description = "SciPy (pronounced 'Sigh Pie') is open-source software for mathematics, science, and engineering. ";
-    homepage = http://www.scipy.org/;
-    maintainers = with lib.maintainers; [ fridh ];
-  };
-}

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

@@ -0,0 +1,29 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, supervise
+}:
+
+buildPythonPackage rec {
+  pname = "supervise_api";
+  version = "0.1.5";
+
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1pqqlw80cjdgrlpvdmydkyhsrr4s531mn6bfkshm68j9gk4kq6px";
+  };
+
+  propagatedBuildInputs = [ supervise ];
+
+  # no tests
+  doCheck = false;
+
+  meta = {
+    description = "An API for running processes safely and securely";
+    homepage = https://github.com/catern/supervise;
+    license = lib.licenses.lgpl3;
+    maintainers = with lib.maintainers; [ catern ];
+  };
+}

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

@@ -5,6 +5,7 @@
 , numpy
 , pandas
 , python
+, fetchurl
 }:
 
 buildPythonPackage rec {
@@ -17,6 +18,15 @@ buildPythonPackage rec {
     sha256 = "f649a41d43b5a6c64bdcbd57e994932656b689f9593a86dd0be95778a2b47494";
   };
 
+  # 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 ];
   propagatedBuildInputs = [numpy pandas];
 

pkgs/development/qtcreator/default.nix

@@ -7,7 +7,7 @@ with stdenv.lib;
 
 let
   baseVersion = "4.4";
-  revision = "0";
+  revision = "1";
 in
 
 stdenv.mkDerivation rec {
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "http://download.qt-project.org/official_releases/qtcreator/${baseVersion}/${version}/qt-creator-opensource-src-${version}.tar.xz";
-    sha256 = "00k2bb2pamqlq0i619wz8chii8yp884qnrjngzzxrdffk05d95wc";
+    sha256 = "0kn1k2zvc93xin4kdp2fpiz21i5j0qymyx6jjzkqp7r3x8yxwr06";
   };
 
   buildInputs = [ qtbase qtscript qtquickcontrols qtdeclarative ];

pkgs/development/tools/continuous-integration/gitlab-runner/default.nix

@@ -1,16 +1,16 @@
 { lib, buildGoPackage, fetchFromGitLab, fetchurl, go-bindata }:
 
 let
-  version = "10.0.0";
+  version = "10.0.2";
   # Gitlab runner embeds some docker images these are prebuilt for arm and x86_64
   docker_x86_64 = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-x86_64.tar.xz";
-    sha256 = "13rfpyzrld20pjhkjzx78qfdmi4w86v6nhq3460bcjpi4kwyd24w";
+    sha256 = "14lrc9frigym93ppphmdhwnbhk7xz5drpai3d29gyi1z4xsm1jaq";
   };
 
   docker_arm = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-arm.tar.xz";
-    sha256 = "19z3rmkmv6z6g27bsjkqkfj8xwpyf9v1fhk2vb81xj5fisjzhmlw";
+    sha256 = "013bly0xswzkf2kwi2pr2ryd880h63n8pya2ccv4z77hxs80cfmp";
   };
 in
 buildGoPackage rec {
@@ -29,7 +29,7 @@ buildGoPackage rec {
     owner = "gitlab-org";
     repo = "gitlab-runner";
     rev = "v${version}";
-    sha256 = "11gp6l5kqcz4spxq552hsnw480vdhp70zmqlgjr906px3r31j7h3";
+    sha256 = "0hr964r7bcff74sna0b8w3d2ip0hs441ijlhplh2xzqnzpbvx2jq";
   };
 
   patches = [ ./fix-shell-path.patch ];