Merge branch 'staging-next'

The failure diff seems good-enough on Hydra now.
NixOS · Sep 1, 2018 · 342d3db · 342d3db
2 parents cdb244a + 355f196
commit 342d3db
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Showing 212 changed files with 1,082 additions and 661 deletions.
diff --git a/pkgs/applications/misc/octoprint/default.nix b/pkgs/applications/misc/octoprint/default.nix
@@ -62,6 +62,14 @@ let
         # No tests included
         doCheck = false;
       };
+
+      pylru = super.pylru.overridePythonAttrs (oldAttrs: rec {
+        version = "1.0.9";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "71376192671f0ad1690b2a7427d39a29b1df994c8469a9b46b03ed7e28c0172c";
+        };
+      });
     };
   };
 

diff --git a/pkgs/applications/networking/newsreaders/pan/default.nix b/pkgs/applications/networking/newsreaders/pan/default.nix
@@ -2,7 +2,7 @@
 , stdenv, fetchurl, pkgconfig, gtk3, gtkspell3 ? null
 , perl, gmime2, gettext, intltool, itstool, libxml2, dbus-glib, libnotify, gnutls
 , makeWrapper, gnupg
-, gnomeSupport ? true, libgnome-keyring3
+, gnomeSupport ? true, gnome3, libsecret
 }:
 
 assert spellChecking -> gtkspell3 != null;
@@ -17,10 +17,10 @@ stdenv.mkDerivation {
     sha256 = "1b4wamv33hprghcjk903bpvnd233yxyrm18qnh13alc8h1553nk8";
   };
 
-  nativeBuildInputs = [ pkgconfig makeWrapper ];
-  buildInputs = [ gtk3 perl gmime2 gettext intltool itstool libxml2 dbus-glib libnotify gnutls ]
+  nativeBuildInputs = [ pkgconfig gettext intltool itstool libxml2 makeWrapper ];
+  buildInputs = [ gtk3 gmime2 libnotify gnutls ]
     ++ stdenv.lib.optional spellChecking gtkspell3
-    ++ stdenv.lib.optional gnomeSupport libgnome-keyring3;
+    ++ stdenv.lib.optionals gnomeSupport [ libsecret gnome3.gcr ];
 
   configureFlags = [
     "--with-dbus"

diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
@@ -21,7 +21,7 @@ let
 
       sagelib = self.callPackage ./sagelib.nix {
         inherit flint ecl arb;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
+        inherit sage-src pynac singular;
         linbox = nixpkgs.linbox.override { withSage = true; };
       };
 
@@ -41,13 +41,13 @@ let
       };
 
       sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
+        inherit sage-src python rWrapper ecl singular palp flint pynac pythonEnv;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
       };
 
       sage-with-env = self.callPackage ./sage-with-env.nix {
         inherit pythonEnv;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
+        inherit sage-src pynac singular;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
         three = nodePackages_8_x.three;
       };
@@ -60,10 +60,6 @@ let
     };
   };
 
-  openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
-  openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
-  openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
-
   sage-src = callPackage ./sage-src.nix {};
 
   pythonRuntimeDeps = with python.pkgs; [

diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix
diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix
@@ -37,7 +37,7 @@
 , lcalc
 , rubiks
 , flintqs
-, openblas-cblas-pc
+, openblasCompat
 , flint
 , gmp
 , mpfr
@@ -98,9 +98,9 @@ writeTextFile rec {
     export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
         # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
         # for it outside of the tests. However since singular and openblas are runtime dependencies anyways
-        # and openblas-cblas-pc is tiny, it doesn't really hurt to include.
+        # it doesn't really hurt to include.
         singular
-        openblas-cblas-pc
+        openblasCompat
       ])
     }'
     export SAGE_ROOT='${sage-src}'

diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix
@@ -4,9 +4,6 @@
 , sage-env
 , sage-src
 , openblasCompat
-, openblas-blas-pc
-, openblas-cblas-pc
-, openblas-lapack-pc
 , pkg-config
 , three
 , singular
@@ -32,9 +29,6 @@ let
     makeWrapper
     pkg-config
     openblasCompat # lots of segfaults with regular (64 bit) openblas
-    openblas-blas-pc
-    openblas-cblas-pc
-    openblas-lapack-pc
     singular
     three
     pynac

diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
@@ -3,9 +3,6 @@
 , buildPythonPackage
 , arb
 , openblasCompat
-, openblas-blas-pc
-, openblas-cblas-pc
-, openblas-lapack-pc
 , brial
 , cliquer
 , cypari2
@@ -59,9 +56,7 @@ buildPythonPackage rec {
   nativeBuildInputs = [
     iml
     perl
-    openblas-blas-pc
-    openblas-cblas-pc
-    openblas-lapack-pc
+    openblasCompat
     jupyter_core
   ];
 

diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix
@@ -1,39 +1,57 @@
-{ stdenv, writeText, fetchurl,
-  libpng, fftw,
-  mpiSupport ? false, mpi ? null
+{ lib
+, bash
+, stdenv
+, writeText
+, fetchFromGitHub
+, libpng
+, gzip
+, fftw
+, openblas
+, mpiSupport ? false, mpi ? null
 }:
 
 assert mpiSupport -> mpi != null;
 
 stdenv.mkDerivation rec {
   # LAMMPS has weird versioning converted to ISO 8601 format
-  version = "2016-02-16";
+  version = "patch_2Aug2018";
   name = "lammps-${version}";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/lammps/lammps-16Feb16.tar.gz";
-    sha256 = "1yzfbkxma3xa1288rnn66h4w0smbmjkwq1fx1y60pjiw0prmk105";
+  lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
+  lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
+
+  src = fetchFromGitHub {
+    owner = "lammps";
+    repo = "lammps";
+    rev = "${version}";
+    sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
   };
 
   passthru = {
     inherit mpi;
   };
 
-  buildInputs = [ fftw libpng ]
+  buildInputs = [ fftw libpng openblas gzip bash ]
   ++ (stdenv.lib.optionals mpiSupport [ mpi ]);
 
   # Must do manual build due to LAMMPS requiring a seperate build for
   # the libraries and executable
   builder = writeText "builder.sh" ''
     source $stdenv/setup
 
-    tar xzf $src
-    cd lammps-*/src
-    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
-    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    mkdir lammps
+    cp -r $src/lib $src/src lammps
+    chmod -R 755 lammps/src/
+    cd lammps/src
+    for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
+    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
 
     mkdir -p $out/bin
-    cp -v lmp_* $out/bin/lammps
+    cp -v lmp_* $out/bin/
+
+    mkdir -p $out/include
+    cp -v *.h $out/include/
 
     mkdir -p $out/lib
     cp -v liblammps* $out/lib/
@@ -51,5 +69,6 @@ stdenv.mkDerivation rec {
     homepage = http://lammps.sandia.gov;
     license = stdenv.lib.licenses.gpl2;
     platforms = stdenv.lib.platforms.linux;
+    maintainers = with lib.maintainers; [ costrouc ];
   };
 }
diff --git a/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix b/pkgs/desktops/gnome-3/core/gnome-desktop/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
+{ stdenv, fetchurl, substituteAll, pkgconfig, libxslt, which, libX11, gnome3, gtk3, glib
 , intltool, libxml2, xkeyboard_config, isocodes, itstool, wayland
 , libseccomp, bubblewrap, gobjectIntrospection, gtk-doc, docbook_xsl }:
 
@@ -30,18 +30,16 @@ stdenv.mkDerivation rec {
   propagatedBuildInputs = [ gnome3.gsettings-desktop-schemas ];
 
   patches = [
-    ./bubblewrap-paths.patch
+    (substituteAll {
+      src = ./bubblewrap-paths.patch;
+      BUBBLEWRAP_BIN = "${bubblewrap}/bin/bwrap";
+    })
   ];
 
   configureFlags = [
     "--enable-gtk-doc"
   ];
 
-  postPatch = ''
-    substituteInPlace libgnome-desktop/gnome-desktop-thumbnail-script.c --subst-var-by \
-      BUBBLEWRAP_BIN "${bubblewrap}/bin/bwrap"
-  '';
-
   passthru = {
     updateScript = gnome3.updateScript {
       packageName = "gnome-desktop";

diff --git a/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix b/pkgs/desktops/gnome-3/core/gnome-keyring/default.nix
@@ -1,6 +1,6 @@
-{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, libtasn1, pam, python2, glib, libxslt
-, intltool, pango, gcr, gdk_pixbuf, atk, p11-kit, openssh, wrapGAppsHook
-, docbook_xsl, docbook_xml_dtd_42, gnome3 }:
+{ stdenv, fetchurl, pkgconfig, dbus, libgcrypt, pam, python2, glib, libxslt
+, gettext, gcr, libcap_ng, libselinux, p11-kit, openssh, wrapGAppsHook
+, docbook_xsl, docbook_xml_dtd_43, gnome3 }:
 
 stdenv.mkDerivation rec {
   name = "gnome-keyring-${version}";
@@ -11,21 +11,15 @@ stdenv.mkDerivation rec {
     sha256 = "0sk4las4ji8wv9nx8mldzqccmpmkvvr9pdwv9imj26r10xyin5w1";
   };
 
-  passthru = {
-    updateScript = gnome3.updateScript { packageName = "gnome-keyring"; attrPath = "gnome3.gnome-keyring"; };
-  };
-
   outputs = [ "out" "dev" ];
 
-  buildInputs = with gnome3; [
-    dbus libgcrypt pam gtk3 libgnome-keyring openssh
-    pango gcr gdk_pixbuf atk p11-kit
+  buildInputs = [
+    glib libgcrypt pam openssh libcap_ng libselinux
+    gcr p11-kit
   ];
 
-  propagatedBuildInputs = [ glib libtasn1 libxslt ];
-
   nativeBuildInputs = [
-    pkgconfig intltool docbook_xsl docbook_xml_dtd_42 wrapGAppsHook
+    pkgconfig gettext libxslt docbook_xsl docbook_xml_dtd_43 wrapGAppsHook
   ];
 
   configureFlags = [
@@ -48,6 +42,13 @@ stdenv.mkDerivation rec {
       make check
   '';
 
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = "gnome-keyring";
+      attrPath = "gnome3.gnome-keyring";
+    };
+  };
+
   meta = with stdenv.lib; {
     description = "Collection of components in GNOME that store secrets, passwords, keys, certificates and make them available to applications";
     homepage = https://wiki.gnome.org/Projects/GnomeKeyring;

diff --git a/pkgs/desktops/gnome-3/core/gnome-shell/default.nix b/pkgs/desktops/gnome-3/core/gnome-shell/default.nix
@@ -2,7 +2,7 @@
 , python3Packages, libsoup, polkit, clutter, networkmanager, docbook_xsl , docbook_xsl_ns, at-spi2-core
 , libstartup_notification, telepathy-glib, telepathy-logger, libXtst, unzip, glibcLocales, shared-mime-info
 , libgweather, libcanberra-gtk3, librsvg, geoclue2, perl, docbook_xml_dtd_42, desktop-file-utils
-, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook
+, libpulseaudio, libical, gobjectIntrospection, gstreamer, wrapGAppsHook, libxslt
 , accountsservice, gdk_pixbuf, gdm, upower, ibus, networkmanagerapplet
 , sassc, systemd, gst_all_1 }:
 
@@ -27,7 +27,7 @@ in stdenv.mkDerivation rec {
 
   nativeBuildInputs = [
     meson ninja pkgconfig gettext docbook_xsl docbook_xsl_ns docbook_xml_dtd_42 perl wrapGAppsHook glibcLocales
-    sassc desktop-file-utils
+    sassc desktop-file-utils libxslt.bin
   ];
   buildInputs = with gnome3; [
     systemd caribou

diff --git a/pkgs/desktops/xfce4-13/xfce4-settings/default.nix b/pkgs/desktops/xfce4-13/xfce4-settings/default.nix
@@ -1,4 +1,4 @@
-{ mkXfceDerivation, automakeAddFlags, dbus-glib, exo, garcon, gtk3
+{ mkXfceDerivation, automakeAddFlags, exo, garcon, gtk3
 , libnotify ? null, libxfce4ui, libxfce4util, libxklavier ? null
 , upower ? null, xfconf, xf86inputlibinput ? null }:
 
@@ -19,7 +19,6 @@ mkXfceDerivation rec {
   nativeBuildInputs = [ automakeAddFlags ];
 
   buildInputs = [
-    dbus-glib
     exo
     garcon
     gtk3

diff --git a/pkgs/development/libraries/mesa/default.nix b/pkgs/development/libraries/mesa/default.nix
@@ -63,7 +63,7 @@ let
 in
 
 let
-  version = "18.1.5";
+  version = "18.1.7";
   branch  = head (splitString "." version);
 in
 
@@ -77,7 +77,7 @@ let self = stdenv.mkDerivation {
       "ftp://ftp.freedesktop.org/pub/mesa/older-versions/${branch}.x/${version}/mesa-${version}.tar.xz"
       "https://mesa.freedesktop.org/archive/mesa-${version}.tar.xz"
     ];
-    sha256 = "69dbe6f1a6660386f5beb85d4fcf003ee23023ed7b9a603de84e9a37e8d98dea";
+    sha256 = "655e3b32ce3bdddd5e6e8768596e5d4bdef82d0dd37067c324cc4b2daa207306";
   };
 
   prePatch = "patchShebangs .";
@@ -100,6 +100,7 @@ let self = stdenv.mkDerivation {
     "--with-dri-driverdir=$(drivers)/lib/dri"
     "--with-dri-searchpath=${libglvnd.driverLink}/lib/dri"
     "--with-platforms=x11,wayland,drm"
+    "--enable-texture-float"
   ]
   ++ (optional (galliumDrivers != [])
       ("--with-gallium-drivers=" +