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

lib/maintainers.nix

@@ -98,6 +98,7 @@
   canndrew = "Andrew Cann <shum@canndrew.org>";
   carlsverre = "Carl Sverre <accounts@carlsverre.com>";
   casey = "Casey Rodarmor <casey@rodarmor.net>";
+  catern = "Spencer Baugh <sbaugh@catern.com>";
   caugner = "Claas Augner <nixos@caugner.de>";
   cdepillabout = "Dennis Gosnell <cdep.illabout@gmail.com>";
   cfouche = "Chaddaï Fouché <chaddai.fouche@gmail.com>";

nixos/modules/tasks/filesystems/ext.nix

@@ -5,7 +5,8 @@
 
     system.fsPackages = [ pkgs.e2fsprogs ];
 
-    boot.initrd.availableKernelModules = [ "ext2" "ext3" "ext4" ];
+    # As of kernel 4.3, there is no separate ext3 driver (they're also handled by ext4.ko)
+    boot.initrd.availableKernelModules = [ "ext2" "ext4" ];
 
     boot.initrd.extraUtilsCommands =
       ''

pkgs/data/icons/elementary-icon-theme/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  version = "4.2.0";
+  version = "4.3.0";
 
   package-name = "elementary-icon-theme";
 
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://launchpad.net/elementaryicons/4.x/${version}/+download/${name}.tar.xz";
-    sha256 = "0w1l9hlih4ddkdjpha5lsyf6iagv436nhm4aphak8w8jyycg81bm";
+    sha256 = "1gg7znfgyj4zxsa741psc67nyixi27q9ghjklz0337r4cwmcwn1g";
   };
 
   dontBuild = true;

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 {
+stdenv.mkDerivation rec {
-  name = "ocaml-lablgtk-extras-1.5";
+  version = "1.6";
-  src = fetchurl {
+  name = "ocaml${ocaml.version}-lablgtk-extras-${version}";
-    url = https://forge.ocamlcore.org/frs/download.php/1453/lablgtkextras-1.5.tar.gz;
+  src = fetchFromGitHub {
-    sha256 = "1bgflgadmy2nqnqjf34zja0jy6f9wpqq8x22qcfilj9g8c9wkrmi";
+    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 ];

pkgs/misc/themes/numix/default.nix

@@ -3,14 +3,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "2017-07-26";
+  version = "2.6.7";
   name = "numix-gtk-theme-${version}";
 
   src = fetchFromGitHub {
     repo = "numix-gtk-theme";
     owner = "numixproject";
-    rev = "858e6292c4336302be4d499c9b085a891b4c3b40";
+    rev = version;
-    sha256 = "1z9l13px79yk42874dlh8z6p7chlngwarfnki89win3g2xvclz8q";
+    sha256 = "1fmlc6vi8prvwsq0nxxcd00lp04bwmapzjqf727wb1czqf2lf0dv";
   };
 
   nativeBuildInputs = [ sass glib libxml2 gdk_pixbuf ];

pkgs/misc/urbit/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "urbit-${version}";
-  version = "0.4";
+  version = "0.4.5";
 
   src = fetchFromGitHub {
     owner = "urbit";
     repo = "urbit";
     rev = "v${version}";
-    sha256 = "1ndy58ypilabf9pfkqzzl7wf6x1vr4gpvsbn30sygp2ip908q0xz";
+    sha256 = "1zgxgqbz74nsgfyrvsnjj6xxpb64mrnby7bb5qy733sy04gmzgik";
   };
 
   buildInputs = with stdenv.lib; [

pkgs/os-specific/linux/kernel/common-config.nix

@@ -245,6 +245,9 @@ with stdenv.lib;
   USB_SERIAL_KEYSPAN_USA49W y
   USB_SERIAL_KEYSPAN_USA49WLC y
 
+  # Device mapper (RAID, LVM, etc.)
+  MD y
+
   # Filesystem options - in particular, enable extended attributes and
   # ACLs for all filesystems that support them.
   FANOTIFY y

pkgs/tools/misc/plantuml/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, jre, graphviz }:
 
 stdenv.mkDerivation rec {
-  version = "1.2017.16";
+  version = "1.2017.18";
   name = "plantuml-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/project/plantuml/${version}/plantuml.${version}.jar";
-    sha256 = "a3d319ed54ed78ce3cf7bfcfe76ffc5aa6ed28a72b5aa575fe9125e0c6bd985c";
+    sha256 = "0ssfg6lpk41ydhxhi6y6c9ca3hpql6gg3bxjws8vrx9s3s6r5rb0";
   };
 
   # It's only a .jar file and a shell wrapper

pkgs/tools/networking/mitmproxy/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchpatch, fetchFromGitHub, python3, glibcLocales }:
+{ stdenv, fetchpatch, fetchFromGitHub, fetchurl, python3, glibcLocales }:
 
 let
   p = python3.override {
@@ -19,6 +19,19 @@ let
           sha256 = "00daa04c9870345f56605d91d7d4897bc1b16f6fff7c74cb602b08ef16c0fb43";
         };
       });
+      pyopenssl = super.pyopenssl.overridePythonAttrs (oldAttrs: rec {
+        version = "17.0.0";
+        name = "${oldAttrs.pname}-${version}";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "1pdg1gpmkzj8yasg6cmkhcivxcdp4c12nif88y4qvsxq5ffzxas8";
+        };
+        patches = fetchpatch {
+          url = "https://github.com/pyca/pyopenssl/commit/"
+              + "a40898b5f1d472f9449a344f703fa7f90cddc21d.patch";
+          sha256 = "0bdfrhfvdfxhfknn46s4db23i3hww6ami2r1l5rfrri0pn8b8mh7";
+        };
+      });
     };
   };
 in p.pkgs.buildPythonPackage rec {
@@ -70,6 +83,6 @@ in p.pkgs.buildPythonPackage rec {
     description = "Man-in-the-middle proxy";
     homepage = http://mitmproxy.org/;
     license = licenses.mit;
-    maintainers = with maintainers; [ fpletz ];
+    maintainers = with maintainers; [ fpletz kamilchm ];
   };
 }

pkgs/tools/system/supervise/default.nix

@@ -0,0 +1,27 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+
+  name = "supervise-${version}";
+  version = "1.0.0";
+
+  src = fetchFromGitHub {
+    owner = "catern";
+    repo = "supervise";
+    rev = "v${version}";
+    sha256 = "1cjdxgns3gh2ir4kcmjdmc480w8sm49inws0ihhjmnisjy4100lg";
+  };
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp supervise unlinkwait -t $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/catern/supervise;
+    description = "A minimal unprivileged process supervisor making use of modern Linux features";
+    platforms = platforms.linux;
+    license = licenses.gpl3;
+    maintainers = with stdenv.lib.maintainers; [ catern ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -11842,6 +11842,8 @@ with pkgs;
 
   s6-rc = callPackage ../tools/system/s6-rc { };
 
+  supervise = callPackage ../tools/system/supervise { };
+
   spamassassin = callPackage ../servers/mail/spamassassin {
     inherit (perlPackages) HTMLParser NetDNS NetAddrIP DBFile
       HTTPDate MailDKIM LWP IOSocketSSL;

pkgs/top-level/python-packages.nix

@@ -291,6 +291,8 @@ in {
 
   sip = callPackage ../development/python-modules/sip { };
 
+  supervise_api = callPackage ../development/python-modules/supervise_api { };
+
   tables = callPackage ../development/python-modules/tables {
     hdf5 = pkgs.hdf5.override { zlib = pkgs.zlib; };
   };
@@ -14994,59 +14996,6 @@ in {
 
   pandas = callPackage ../development/python-modules/pandas { };
 
-  pandas_17 = let
-    inherit (pkgs.stdenv.lib) optional optionalString;
-    inherit (pkgs.stdenv) isDarwin;
-  in buildPythonPackage rec {
-    name = "pandas-${version}";
-    version = "0.17.1";
-
-    src = pkgs.fetchurl {
-      url = "https://pypi.python.org/packages/source/p/pandas/${name}.tar.gz";
-      sha256 = "cfd7214a7223703fe6999fbe34837749540efee1c985e6aee9933f30e3f72837";
-    };
-
-    buildInputs = with self; [ nose ] ++ optional isDarwin pkgs.libcxx;
-    propagatedBuildInputs = with self; [
-      dateutil
-      scipy_0_17
-      numexpr
-      pytz
-      xlrd
-      bottleneck
-      sqlalchemy
-      lxml
-      html5lib
-#      modules.sqlite3
-      beautifulsoup4
-    ] ++ optional isDarwin pkgs.darwin.locale; # provides the locale command
-
-    # For OSX, we need to add a dependency on libcxx, which provides
-    # `complex.h` and other libraries that pandas depends on to build.
-    patchPhase = optionalString isDarwin ''
-      cpp_sdk="${pkgs.libcxx}/include/c++/v1";
-      echo "Adding $cpp_sdk to the setup.py common_include variable"
-      substituteInPlace setup.py \
-        --replace "['pandas/src/klib', 'pandas/src']" \
-                  "['pandas/src/klib', 'pandas/src', '$cpp_sdk']"
-
-      # disable clipboard tests since pbcopy/pbpaste are not open source
-      substituteInPlace pandas/io/tests/test_clipboard.py \
-        --replace pandas.util.clipboard no_such_module \
-        --replace OSError ImportError
-    '';
-
-    doCheck = false;
-
-    meta = {
-      homepage = "http://pandas.pydata.org/";
-      description = "Python Data Analysis Library";
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ raskin fridh ];
-      platforms = platforms.unix;
-    };
-  };
-
   xlrd = buildPythonPackage rec {
     name = "xlrd-${version}";
 
@@ -17797,11 +17746,12 @@ in {
   };
 
   pyopenssl = buildPythonPackage rec {
-    name = "pyopenssl-${version}";
+    pname = "pyOpenSSL";
+    name = "${pname}-${version}";
     version = "17.2.0";
 
-    src = pkgs.fetchurl {
+    src = self.fetchPypi {
-      url = "mirror://pypi/p/pyOpenSSL/pyOpenSSL-${version}.tar.gz";
+      inherit pname version;
       sha256 = "0d283g4zi0hr9papd24mjl70mi15gyzq6fx618rizi87dgipqqax";
     };
 
@@ -19407,8 +19357,6 @@ in {
 
   scipy = callPackage ../development/python-modules/scipy { };
 
-  scipy_0_17 = callPackage ../development/python-modules/scipy/0.17.1.nix { };
-
   scikitimage = buildPythonPackage rec {
     name = "scikit-image-${version}";
     version = "0.12.3";