Merge branch 'master' of github.com:nschoe/nixpkgs

nixos/modules/services/editors/infinoted.nix

@@ -129,7 +129,7 @@ in {
         serviceConfig = {
           Type = "simple";
           Restart = "always";
-          ExecStart = "${cfg.package}/bin/infinoted-0.6 --config-file=/var/lib/infinoted/infinoted.conf";
+          ExecStart = "${cfg.package}/bin/infinoted-${versions.majorMinor cfg.package.version} --config-file=/var/lib/infinoted/infinoted.conf";
           User = cfg.user;
           Group = cfg.group;
           PermissionsStartOnly = true;

nixos/modules/services/monitoring/prometheus/exporters/varnish.nix

@@ -7,14 +7,80 @@ let
 in
 {
   port = 9131;
+  extraOpts = {
+    noExit = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Do not exit server on Varnish scrape errors.
+      '';
+    };
+    withGoMetrics = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Export go runtime and http handler metrics.
+      '';
+    };
+    verbose = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Enable verbose logging.
+      '';
+    };
+    raw = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Enable raw stdout logging without timestamps.
+      '';
+    };
+    varnishStatPath = mkOption {
+      type = types.str;
+      default = "varnishstat";
+      description = ''
+        Path to varnishstat.
+      '';
+    };
+    instance = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      description = ''
+        varnishstat -n value.
+      '';
+    };
+    healthPath = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      description = ''
+        Path under which to expose healthcheck. Disabled unless configured.
+      '';
+    };
+    telemetryPath = mkOption {
+      type = types.str;
+      default = "/metrics";
+      description = ''
+        Path under which to expose metrics.
+      '';
+    };
+  };
   serviceOpts = {
     path = [ pkgs.varnish ];
     serviceConfig = {
       DynamicUser = true;
       ExecStart = ''
         ${pkgs.prometheus-varnish-exporter}/bin/prometheus_varnish_exporter \
-          -web.listen-address ${cfg.listenAddress}:${toString cfg.port} \
+          --web.listen-address ${cfg.listenAddress}:${toString cfg.port} \
-          ${concatStringsSep " \\\n  " cfg.extraFlags}
+          --web.telemetry-path ${cfg.telemetryPath} \
+          --varnishstat-path ${cfg.varnishStatPath} \
+          ${concatStringsSep " \\\n  " (cfg.extraFlags
+            ++ optional (cfg.healthPath != null) "--web.health-path ${cfg.healthPath}"
+            ++ optional (cfg.instance != null) "-n ${cfg.instance}"
+            ++ optional cfg.noExit "--no-exit"
+            ++ optional cfg.withGoMetrics "--with-go-metrics"
+            ++ optional cfg.verbose "--verbose"
+            ++ optional cfg.raw "--raw")}
       '';
     };
   };

pkgs/applications/audio/spotify/default.nix

@@ -9,7 +9,7 @@ let
   # Latest version number can be found at:
   # http://repository-origin.spotify.com/pool/non-free/s/spotify-client/
   # Be careful not to pick the testing version.
-  version = "1.0.77.338.g758ebd78-41";
+  version = "1.0.79.223.g92622cc2-21";
 
   deps = [
     alsaLib
@@ -54,7 +54,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://repository-origin.spotify.com/pool/non-free/s/spotify-client/spotify-client_${version}_amd64.deb";
-    sha256 = "1971jc0431pl8yixpl37ryl2l0pqdf0xjvkg59nqdwj3vbdx5606";
+    sha256 = "1x1rpprzin4cmz1spzw036b4phd0yk1v7idlrcy4pkv97b4g5dw6";
   };
 
   buildInputs = [ dpkg makeWrapper ];

pkgs/applications/office/gnucash/default.nix

@@ -1,63 +1,81 @@
-{ fetchurl, stdenv, pkgconfig, libxml2, gconf, glib, gtk2, libgnomeui, libofx
+{ fetchurl, stdenv, pkgconfig, makeWrapper, cmake, gtest
-, libgtkhtml, gtkhtml, libgnomeprint, goffice, enchant, gettext, libbonoboui
+, boost, icu, libxml2, libxslt, gettext, swig, isocodes, gtk3, glibcLocales
-, intltool, perl, guile, slibGuile, swig, isocodes, bzip2, makeWrapper, libglade
+, webkit, dconf, hicolor-icon-theme, libofx, aqbanking, gwenhywfar, libdbi
-, libgsf, libart_lgpl, perlPackages, aqbanking, gwenhywfar
+, libdbiDrivers, guile, perl, perlPackages
 }:
 
-/* If you experience GConf errors when running GnuCash on NixOS, see
+let
- * http://wiki.nixos.org/wiki/Solve_GConf_errors_when_running_GNOME_applications
+
- * for a possible solution.
+  # Enable gnc-fq-* to run in command line.
- */
+  perlWrapper = stdenv.mkDerivation {
+    name = perl.name + "-wrapper-for-gnucash";
+    nativeBuildInputs = [ makeWrapper ];
+    buildInputs = [ perl ] ++ (with perlPackages; [ FinanceQuote DateManip ]);
+    phases = [ "installPhase" ];
+    installPhase = ''
+      mkdir -p $out/bin
+      for script in ${perl}/bin/*; do
+        makeWrapper $script $out''${script#${perl}} \
+          --prefix "PERL5LIB" ":" "$PERL5LIB"
+      done
+    '';
+  };
+
+in
 
 stdenv.mkDerivation rec {
-  name = "gnucash-2.4.15";
+  name = "gnucash-${version}";
+  version = "3.1-1";
 
   src = fetchurl {
     url = "mirror://sourceforge/gnucash/${name}.tar.bz2";
-    sha256 = "058mgfwic6a2g7jq6iip5hv45md1qaxy25dj4lvlzjjr141wm4gx";
+    sha256 = "0qfjpmr6hnr0v7l2fi00rilnlyan4kqiyygyidxlpdxqqg76dvx1";
   };
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ pkgconfig makeWrapper cmake gtest ];
-  buildInputs = [
-    libxml2 gconf glib gtk2 libgnomeui libgtkhtml gtkhtml
-    libgnomeprint goffice enchant gettext intltool perl guile slibGuile
-    swig isocodes bzip2 makeWrapper libofx libglade libgsf libart_lgpl
-    perlPackages.DateManip perlPackages.FinanceQuote aqbanking gwenhywfar
-  ];
-  propagatedUserEnvPkgs = [ gconf ];
 
-  configureFlags = "CFLAGS=-O3 CXXFLAGS=-O3 --disable-dbi --enable-ofx --enable-aqbanking";
+  buildInputs = [
+    boost icu libxml2 libxslt gettext swig isocodes gtk3 glibcLocales
+    webkit dconf hicolor-icon-theme libofx aqbanking gwenhywfar libdbi
+    libdbiDrivers guile perlWrapper
+  ];
+
+  propagatedUserEnvPkgs = [ dconf ];
+
+  postPatch = ''
+    patchShebangs .
+  '';
+
+  makeFlags = [ "GUILE_AUTO_COMPILE=0" ];
 
   postInstall = ''
     # Auto-updaters don't make sense in Nix.
     rm $out/bin/gnc-fq-update
 
-    sed -i $out/bin/update-gnucash-gconf \
+    # Unnecessary in the release build.
-       -e 's|--config-source=[^ ]* --install-schema-file|--makefile-install-rule|'
+    rm $out/bin/gnucash-valgrind
 
-    for prog in $(echo "$out/bin/"*)
+    wrapProgram "$out/bin/gnucash" \
-    do
+      --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH:$out/share/gsettings-schemas/${name}" \
-      # Don't wrap the gnc-fq-* scripts, since gnucash calls them as
+      --prefix XDG_DATA_DIRS : "${hicolor-icon-theme}/share" \
-      # "perl <script>', i.e. they must be Perl scripts.
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules"
-      if [[ $prog =~ gnc-fq ]]; then continue; fi
-      wrapProgram "$prog"                                               \
-        --set SCHEME_LIBRARY_PATH "$SCHEME_LIBRARY_PATH"                \
-        --prefix GUILE_LOAD_PATH ":" "$GUILE_LOAD_PATH"                 \
-        --prefix LD_LIBRARY_PATH ":" "${libgnomeui}/lib/libglade/2.0"   \
-        --prefix LD_LIBRARY_PATH ":" "${libbonoboui}/lib/libglade/2.0"  \
-        --prefix PERL5LIB ":" "$PERL5LIB"                               \
-        --set GCONF_CONFIG_SOURCE 'xml::~/.gconf'                       \
-        --prefix PATH ":" "$out/bin:${stdenv.lib.makeBinPath [ perl gconf ]}"
-    done
-
-    rm $out/share/icons/hicolor/icon-theme.cache
   '';
 
-  # The following settings fix failures in the test suite. It's not required otherwise.
+  # TODO: The following tests FAILED:
-  NIX_LDFLAGS = "-rpath=${guile}/lib -rpath=${glib.out}/lib";
+  #   61 - test-gnc-timezone (Failed)
-  preCheck = "export GNC_DOT_DIR=$PWD/dot-gnucash";
+  #   70 - test-load-c (Failed)
-
+  #   71 - test-modsysver (Failed)
-  doCheck = false;      # https://github.com/NixOS/nixpkgs/issues/11084
+  #   72 - test-incompatdep (Failed)
+  #   73 - test-agedver (Failed)
+  #   77 - test-gnc-module-swigged-c (Failed)
+  #   78 - test-gnc-module-load-deps (Failed)
+  #   80 - test-gnc-module-scm-module (Failed)
+  #   81 - test-gnc-module-scm-multi (Failed)
+  preCheck = ''
+    export LD_LIBRARY_PATH=$PWD/lib:$PWD/lib/gnucash:$PWD/lib/gnucash/test:$LD_LIBRARY_PATH
+    export NIX_CFLAGS_LINK="-lgtest -lgtest_main"
+  '';
+  doCheck = false;
 
   enableParallelBuilding = true;
 

pkgs/applications/science/biology/conglomerate/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, cmake, coreutils, perl, bicpl, libminc, zlib, minc_tools,
+  makeWrapper, GetoptTabular, MNI-Perllib }:
+
+stdenv.mkDerivation rec {
+  pname = "conglomerate";
+  name  = "${pname}-2017-09-10";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "7343238bc6215942c7ecc885a224f24433a291b0";
+    sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr";
+  };
+
+  nativeBuildInputs = [ cmake makeWrapper ];
+  buildInputs = [ libminc zlib bicpl ];
+  propagatedBuildInputs = [ coreutils minc_tools perl GetoptTabular MNI-Perllib ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ];
+
+  postFixup = ''
+    for p in $out/bin/*; do
+      wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}";
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/BIC-MNI/conglomerate;
+    description = "More command-line utilities for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}

pkgs/applications/science/chemistry/jmol/default.nix

@@ -1,9 +1,20 @@
 { stdenv
 , fetchurl
 , unzip
+, makeDesktopItem
 , jre
 }:
 
+let
+  desktopItem = makeDesktopItem {
+    name = "jmol";
+    exec = "jmol";
+    desktopName = "JMol";
+    genericName = "Molecular Modeler";
+    mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
+    categories = "Graphics;Education;Science;Chemistry;";
+  };
+in
 stdenv.mkDerivation rec {
   version = "${baseVersion}.${patchVersion}";
   baseVersion = "14.29";
@@ -16,19 +27,18 @@ stdenv.mkDerivation rec {
     sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
   };
 
-  buildInputs = [
+  patchPhase = ''
-    jre
+    sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
-  ];
+  '';
 
   installPhase = ''
-    mkdir -p "$out/share/jmol"
+    mkdir -p "$out/share/jmol" "$out/bin"
-    mkdir -p "$out/bin"
 
     ${unzip}/bin/unzip jsmol.zip -d "$out/share/"
 
-    sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh
     cp *.jar jmol.sh "$out/share/jmol"
-    ln -s $out/share/jmol/jmol.sh "$out/bin/jmol"
+    cp -r ${desktopItem}/share/applications $out/share
+    cp jmol $out/bin
   '';
 
   enableParallelBuilding = true;
@@ -38,7 +48,6 @@ stdenv.mkDerivation rec {
      homepage = https://sourceforge.net/projects/jmol;
      license = licenses.lgpl2;
      platforms = platforms.all;
-     maintainers = with maintainers; [ timokau ];
+     maintainers = with maintainers; [ timokau mounium ];
   };
 }
-

pkgs/applications/science/chemistry/pymol/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchurl, makeDesktopItem
 , python3, python3Packages
-, glew, freeglut, libpng, libxml2, tk, freetype }:
+, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }:
 
 
 with stdenv.lib;
 
 let
   pname = "pymol";
-  ver_maj = "1.8";
+  ver_maj = "2";
-  ver_min = "4";
+  ver_min = "1";
   version = "${ver_maj}.${ver_min}.0";
   description = "A Python-enhanced molecular graphics tool";
 
@@ -16,7 +16,7 @@ let
     name = "${pname}";
     exec = "${pname}";
     desktopName = "PyMol Molecular Graphics System";
-    genericName = "Molecular Modeller";
+    genericName = "Molecular Modeler";
     comment = description;
     mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;";
     categories = "Graphics;Education;Science;Chemistry;";
@@ -26,10 +26,10 @@ python3Packages.buildPythonApplication {
   name = "pymol-${version}";
   src = fetchurl {
     url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2";
-    sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n";
+    sha256 = "1qpacd5w4r9a0nm5iqmkd92ym3ai00dp7v61cwd6jgakk6wfps3s";
   };
 
-  buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ];
+  buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype libmsgpack ];
   NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";
 
   installPhase = ''

pkgs/applications/science/machine-learning/labelimg/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, python2Packages, fetchurl }:
+  python2Packages.buildPythonApplication rec {
+    name = "labelImg-${version}";
+    version = "1.6.0";
+    src = fetchurl {
+      url = "https://github.com/tzutalin/labelImg/archive/v${version}.tar.gz";
+      sha256 = "126kc4r7xm9170kh7snqsfkkc868m5bcnswrv7b4cq9ivlrdwbm4";
+    };
+    propagatedBuildInputs = with python2Packages; [
+      pyqt4
+      lxml
+    ];
+    preBuild = ''
+      make qt4py2
+    '';
+    meta = with stdenv.lib; {
+      description = "LabelImg is a graphical image annotation tool and label object bounding boxes in images";
+      homepage = https://github.com/tzutalin/labelImg;
+      license = licenses.mit;
+      platforms = platforms.linux;
+      maintainers = [ maintainers.cmcdragonkai ];
+    };
+  }

pkgs/applications/virtualization/containerd/default.nix

@@ -5,13 +5,13 @@ with lib;
 
 stdenv.mkDerivation rec {
   name = "containerd-${version}";
-  version = "1.0.3";
+  version = "1.1.0";
 
   src = fetchFromGitHub {
     owner = "containerd";
     repo = "containerd";
     rev = "v${version}";
-    sha256 = "0k1zjn0mpd7q3p5srxld2fr4k6ijzbk0r34r6w69sh0d0rd2fvbs";
+    sha256 = "0nknqprmi04jfiivrk158jyddc95q4jggfsm7cg7rpvjamkzn6c8";
   };
 
   hardeningDisable = [ "fortify" ];

pkgs/development/coq-modules/contribs/default.nix

@@ -189,7 +189,7 @@ let mkContrib = repo: revs: param:
     sha256 = "1ddwzg12pbzpnz3njin4zhpph92kscrbsn3bzds26yj8fp76zc33";
   };
 
-  containers = mkContrib "containers" [ "8.6" "8.7" ] {
+  containers = mkContrib "containers" [ "8.6" "8.7" "8.8" ] {
     "8.6" = {
       version = "8.6.0";
       rev = "fa1fec7";
@@ -200,6 +200,11 @@ let mkContrib = repo: revs: param:
       rev = "77ac16366529c9e558f70ba86f0168a76ca76b8f";
       sha256 = "01gp8injb0knaxgqsdc4x9h8714k7qxg7j5w7y6i45dnpd81ndr4";
     };
+    "8.8" = {
+      version = "20180330";
+      rev = "52b86bed1671321b25fe4d7495558f9f221b12aa";
+      sha256 = "0hbnrwdgryr52170cfrlbiymr88jsyxilnpr343vnprqq3zk1xz0";
+    };
   }."${coq.coq-version}";
 
   continuations = mkContrib "continuations" [ ] {

pkgs/development/interpreters/duktape/default.nix

@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   name = "duktape-${version}";
-  version = "2.2.0";
+  version = "2.2.1";
   src = fetchurl {
     url = "http://duktape.org/duktape-${version}.tar.xz";
-    sha256 = "050csp065ll67dck94s0vdad5r5ck4jwsz1fn1y0fcvn88325xv2";
+    sha256 = "1wp7mpkhizknq72ivdbkzps4radi1daqzjcjp1i54c2k4pnjxgis";
   };
 
   buildPhase = ''

pkgs/development/libraries/grib-api/default.nix

@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation rec{
   name = "grib-api-${version}";
-  version = "1.26.0";
+  version = "1.26.1";
 
   src = fetchurl {
     url = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-${version}-Source.tar.gz";
-    sha256 = "00cmmj44bhdlzhqbvwb3bb4xks3bpva669m6g3g6ffjaqm25b90c";
+    sha256 = "1v1apx9421m8zkjmych5yr66mvqjrrygc98bvyl4miasmsb4ndfs";
   };
 
   preConfigure = ''

pkgs/development/libraries/libfm/default.nix

@@ -9,11 +9,11 @@ stdenv.mkDerivation rec {
   name = if extraOnly
     then "libfm-extra-${version}"
     else "libfm-${version}";
-  version = "1.2.5";
+  version = "1.3.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/pcmanfm/libfm-${version}.tar.xz";
-    sha256 = "0nlvfwh09gbq8bkbvwnw6iqr918rrs9gc9ljb9pjspyg408bn1n7";
+    sha256 = "151jyy8ipmp2h829gd9s4s429qafv1zxl7j6zaj1k1gzm9s5rmnb";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/development/libraries/libinfinity/default.nix

@@ -12,7 +12,8 @@ let
 
 in stdenv.mkDerivation rec {
 
-  name = "libinfinity-0.7.1";
+  name = "libinfinity-${version}";
+  version = "0.7.1";
   src = fetchurl {
     url = "http://releases.0x539.de/libinfinity/${name}.tar.gz";
     sha256 = "1jw2fhrcbpyz99bij07iyhy9ffyqdn87vl8cb1qz897y3f2f0vk2";
@@ -36,6 +37,10 @@ in stdenv.mkDerivation rec {
     ${edf avahiSupport "avahi"}
   '';
 
+  passthru = {
+    inherit version;
+  };
+
   meta = {
     homepage = http://gobby.0x539.de/;
     description = "An implementation of the Infinote protocol written in GObject-based C";

pkgs/development/libraries/libraw/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "libraw-${version}";
-  version = "0.18.8";
+  version = "0.18.9";
 
   src = fetchurl {
     url = "http://www.libraw.org/data/LibRaw-${version}.tar.gz";
-    sha256 = "1qi0fkw2zmd0yplrf79z7lgpz0hxl45dj5rdgpaj7283jzys9b2n";
+    sha256 = "0kmjfdr409k9q9n17k9ywims5z4kqc16s81ba7y09n7669q1gvyj";
   };
 
   outputs = [ "out" "lib" "dev" "doc" ];

pkgs/development/tools/gron/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "gron-${version}";
-  version = "0.5.1";
+  version = "0.5.2";
 
   owner = "tomnomnom";
   repo = "gron";
@@ -11,7 +11,7 @@ buildGoPackage rec {
   src = fetchFromGitHub {
     inherit owner repo;
     rev = "v${version}";
-    sha256 = "1s688ynjddchviwbiggnfbw28s4wsff2941f4b1q1j7mfak7iym2";
+    sha256 = "0nxcvih8n5a4f0a53dxaipab5ckqxgnsznzymhfw5kv4inr9v6j6";
   };
 
   goDeps = ./deps.nix;

pkgs/misc/source-and-tags/default.nix

@@ -1,4 +1,4 @@
-args: with args; {
+{ stdenv, lib, glibcLocales, unzip, hasktags, ctags } : {
   # optional srcDir
   annotatedWithSourceAndTagInfo = x : (x ? passthru && x.passthru ? sourceWithTags 
                                       || x ? meta && x.meta ? sourceWithTags );
@@ -59,7 +59,7 @@ args: with args; {
                     # without this creating tag files for lifted-base fails
                     export LC_ALL=en_US.UTF-8
                     export LANG=en_US.UTF-8
-                    ${if args.stdenv.isLinux then "export LOCALE_ARCHIVE=${args.pkgs.glibcLocales}/lib/locale/locale-archive;" else ""}
+                    ${if stdenv.isLinux then "export LOCALE_ARCHIVE=${glibcLocales}/lib/locale/locale-archive;" else ""}
 
                     ${toString hasktags}/bin/hasktags --ignore-close-implementation --ctags .
                     mv tags \$TAG_FILE

pkgs/os-specific/linux/kernel/linux-copperhead-lts.nix

@@ -3,9 +3,9 @@
 with stdenv.lib;
 
 let
-  version = "4.14.37";
+  version = "4.14.38";
   revision = "a";
-  sha256 = "0dwi17hx13kkccqc2315dnb8sfdc0jgv9v4b1xd10v2pnq7qb0x8";
+  sha256 = "0cad9fp1h96blbgqlgxyv8wc0jg88mildc1ayljz0zpa5dxdfzh4";
 
   # modVersion needs to be x.y.z, will automatically add .0 if needed
   modVersion = concatStrings (intersperse "." (take 3 (splitString "." "${version}.0")));

pkgs/os-specific/linux/kernel/linux-copperhead-stable.nix

@@ -3,9 +3,9 @@
 with stdenv.lib;
 
 let
-  version = "4.16.5";
+  version = "4.16.6";
   revision = "a";
-  sha256 = "150cwq51x3cnnvnd7izizi93jmiqs0na15p8ip4vkm5frspmnks7";
+  sha256 = "0lkycpb837svrvyy04a8n2ix1rrzfl87ah5293mgf9jgy4kmaa2l";
 
   # modVersion needs to be x.y.z, will automatically add .0 if needed
   modVersion = concatStrings (intersperse "." (take 3 (splitString "." "${version}.0")));

pkgs/servers/monitoring/prometheus/varnish-exporter.nix

@@ -1,26 +1,34 @@
 # This file was generated by go2nix.
-{ stdenv, buildGoPackage, fetchFromGitHub, lib }:
+{ stdenv, lib, buildGoPackage, fetchFromGitHub, makeWrapper, varnish }:
 
 buildGoPackage rec {
   name = "prometheus_varnish_exporter-${version}";
-  version = "1.2";
+  version = "1.4";
-  rev = "0f0e3e2";
 
   goPackagePath = "github.com/jonnenauha/prometheus_varnish_exporter";
 
   src = fetchFromGitHub {
-    inherit rev;
     owner = "jonnenauha";
     repo = "prometheus_varnish_exporter";
-    sha256 = "15vw3jqzm2nad81j14spib5v7q2jpibclzrnkd688003vkizlwyn";
+    rev = version;
+    sha256 = "12gd09858zlhn8gkkchfwxv0ca2r72s18wrsz0agfr8pd1gxqh6j";
   };
 
   goDeps = ./varnish-exporter_deps.nix;
 
+  nativeBuildInputs = [ makeWrapper ];
+
+  postInstall = ''
+    wrapProgram $bin/bin/prometheus_varnish_exporter \
+      --prefix PATH : "${varnish}/bin"
+  '';
+
+  doCheck = true;
+
   meta = {
     homepage = https://github.com/jonnenauha/prometheus_varnish_exporter;
     description = "Varnish exporter for Prometheus";
     license = lib.licenses.mit;
-    maintainers = with lib.maintainers; [ MostAwesomeDude ];
+    maintainers = with lib.maintainers; [ MostAwesomeDude willibutz ];
   };
 }

pkgs/servers/monitoring/prometheus/varnish-exporter_deps.nix

@@ -1,12 +1,11 @@
-# This file was generated by go2nix.
 [
   {
     goPackagePath = "github.com/beorn7/perks";
     fetch = {
       type = "git";
       url = "https://github.com/beorn7/perks";
-      rev = "4c0e84591b9aa9e6dcfdf3e020114cd81f89d5f9";
+      rev = "3a771d992973f24aa725d07868b467d1ddfceafb";
-      sha256 = "1hrybsql68xw57brzj805xx2mghydpdiysv3gbhr7f5wlxj2514y";
+      sha256 = "1l2lns4f5jabp61201sh88zf3b0q793w4zdgp9nll7mmfcxxjif3";
     };
   }
   {
@@ -14,8 +13,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/golang/protobuf";
-      rev = "8ee79997227bf9b34611aee7946ae64735e6fd93";
+      rev = "b4deda0973fb4c70b50d226b1af49f3da59f5265";
-      sha256 = "0qm1lpdhf97k2hxgivq2cpjgawhlmmz39y230kgxijhm96xijxb8";
+      sha256 = "0ya4ha7m20bw048m1159ppqzlvda4x0vdprlbk5sdgmy74h3xcdq";
     };
   }
   {
@@ -32,8 +31,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/prometheus/client_golang";
-      rev = "575f371f7862609249a1be4c9145f429fe065e32";
+      rev = "82f5ff156b29e276022b1a958f7d385870fb9814";
-      sha256 = "0hyvszjv5m6i40k2fn21c3bjr8jhlfdqavk1r6g2v5dybyj47vps";
+      sha256 = "111j329yrlgvh73dm80gawwxsh9dgjkw74254kyj5c2rfmra7znz";
     };
   }
   {
@@ -41,8 +40,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/prometheus/client_model";
-      rev = "fa8ad6fec33561be4280a8f0514318c79d7f6cb6";
+      rev = "99fa1f4be8e564e8a6b613da7fa6f46c9edafc6c";
-      sha256 = "11a7v1fjzhhwsl128znjcf5v7v6129xjgkdpym2lial4lac1dhm9";
+      sha256 = "19y4ywsivhpxj7ikf2j0gm9k3cmyw37qcbfi78n526jxcc7kw998";
     };
   }
   {
@@ -50,8 +49,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/prometheus/common";
-      rev = "0d5de9d6d8629cb8bee6d4674da4127cd8b615a3";
+      rev = "d811d2e9bf898806ecfb6ef6296774b13ffc314c";
-      sha256 = "1zlvvgw67p66fz9nswkydq15j4a5z5kkiskl0jxps8i27ya1baq0";
+      sha256 = "0r4067r4ysmljksqw3awcxx5qplqhykahc5igdzgkky7i4bvaik1";
     };
   }
   {
@@ -59,8 +58,8 @@
     fetch = {
       type = "git";
       url = "https://github.com/prometheus/procfs";
-      rev = "abf152e5f3e97f2fafac028d2cc06c1feb87ffa5";
+      rev = "8b1c2da0d56deffdbb9e48d4414b4e674bd8083e";
-      sha256 = "0cp8lznv1b4zhi3wnbjkfxwzhkqd3wbmiy6mwgjanip8l9l3ykws";
+      sha256 = "0x128p15h35mgwqxkigfkk1lfrcz9g697ahl8v6xp9kwvcqvjrrf";
     };
   }
 ]

pkgs/servers/unifi/default.nix

@@ -1,53 +1,61 @@
-{ stdenv
+{ stdenv, dpkg, fetchurl }:
-, dpkg
-, fetchurl
-, unzip
-, useLTS ? false
-}:
-
 
 let
-  versions = {
+  generic = { version, sha256, suffix ? "" }:
-    stable = {
+  stdenv.mkDerivation rec {
-      version = "5.7.20";
+    name = "unifi-controller-${version}";
-      sha256 = "1ylj4i5mcv6z9n32275ccdf1rqk74zilqsih3r6xzhm30pxrd8dd";
+
+    src = fetchurl {
+      url = "https://dl.ubnt.com/unifi/${version}${suffix}/unifi_sysvinit_all.deb";
+      inherit sha256;
     };
-    lts = {
+
-      version = "5.6.36";
+    nativeBuildInputs = [ dpkg ];
-      sha256 = "075q7vm56fdsjwh72y2cb1pirl2pxdkvqnhvd3bf1c2n64mvp6bi";
+
+    unpackPhase = ''
+      runHook preUnpack
+      dpkg-deb -x $src ./
+      runHook postUnpack
+    '';
+
+    doConfigure = false;
+
+    installPhase = ''
+      runHook preInstall
+
+      mkdir -p $out
+      cd ./usr/lib/unifi
+      cp -ar dl lib webapps $out
+
+      runHook postInstall
+    '';
+
+    meta = with stdenv.lib; {
+      homepage = http://www.ubnt.com/;
+      description = "Controller for Ubiquiti UniFi access points";
+      license = licenses.unfree;
+      platforms = platforms.unix;
+      maintainers = with maintainers; [ wkennington ];
     };
   };
-  selectedVersion =
-    let attr = if useLTS then "lts" else "stable";
-    in versions."${attr}";
-in
 
-stdenv.mkDerivation {
+in rec {
-  name = "unifi-controller-${selectedVersion.version}";
+
-  src = with selectedVersion; fetchurl {
+  # https://help.ubnt.com/hc/en-us/articles/115000441548-UniFi-Current-Controller-Versions
-    url = "https://dl.ubnt.com/unifi/${version}/unifi_sysvinit_all.deb";
+
-    inherit sha256;
+  unifiLTS = generic {
+    version = "5.6.37";
+    sha256  = "0kiksqsbmmfva1blbpg2wl4c3w7j6dzzqmwp6028g7bh303c47qa";
   };
 
-  buildInputs = [ dpkg ];
+  unifiStable = generic {
+    version = "5.7.23";
+    sha256  = "14jkhp9jl341zsyk5adh3g98mhqwfbd42c7wahzc31bxq8a0idp7";
+  };
 
-  unpackPhase = ''
+  unifiTesting = generic {
-    dpkg-deb -x $src ./
+    version = "5.8.14";
-  '';
+    suffix  = "-7ef9535d1b";
-
+    sha256  = "09gr7zkck6npjhhmd27c9ymyna6anwj3w9v9zjicz9skbrddkccq";
-  doConfigure = false;
-
-  installPhase = ''
-    mkdir -p $out
-    cd ./usr/lib/unifi
-    cp -ar dl lib webapps $out
-  '';
-
-  meta = with stdenv.lib; {
-    homepage = http://www.ubnt.com/;
-    description = "Controller for Ubiquiti UniFi accesspoints";
-    license = licenses.unfree;
-    platforms = platforms.unix;
-    maintainers = with maintainers; [ wkennington ];
   };
 }

pkgs/tools/misc/bat/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, pkgs, rustPlatform, fetchFromGitHub }:
+
+rustPlatform.buildRustPackage rec {
+  name    = "bat-${version}";
+  version = "0.2.0";
+
+  src = fetchFromGitHub {
+    owner  = "sharkdp";
+    repo   = "bat";
+    rev    = "v${version}";
+    sha256 = "0qbjkrakcpvnzzljifykw88g0qmmk60id23sjvhp4md54h4xg29p";
+  };
+
+  cargoSha256 = "07r10wwxv8svrw94djl092zj512868izlxldsiljfj34230abl02";
+
+  buildInputs = with pkgs; [ openssl pkgconfig cmake zlib file perl curl ];
+
+  meta = with stdenv.lib; {
+    description = "A cat(1) clone with syntax highlighting and Git integration";
+    homepage    = https://github.com/sharkdp/bat;
+    license     = licenses.mit;
+    maintainers = [];
+    platforms   = platforms.linux;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -288,7 +288,7 @@ with pkgs;
     ... # For hash agility
   }@args: fetchzip ({
     inherit name;
-    url = "https://gitlab.com/${owner}/${repo}/-/archive/${rev}/${repo}-${rev}.tar.gz";
+    url = "https://gitlab.com/api/v4/projects/${owner}%2F${repo}/repository/archive.tar.gz?sha=${rev}";
     meta.homepage = "https://gitlab.com/${owner}/${repo}/";
   } // removeAttrs args [ "owner" "repo" "rev" ]) // { inherit rev; };
 
@@ -785,6 +785,8 @@ with pkgs;
 
   bashmount = callPackage ../tools/filesystems/bashmount {};
 
+  bat = callPackage ../tools/misc/bat { };
+
   bc = callPackage ../tools/misc/bc { };
 
   bdf2psf = callPackage ../tools/misc/bdf2psf { };
@@ -2780,8 +2782,6 @@ with pkgs;
 
   gvolicon = callPackage ../tools/audio/gvolicon {};
 
-  gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
-
   gzip = callPackage ../tools/compression/gzip { };
 
   gzrt = callPackage ../tools/compression/gzrt { };
@@ -3124,8 +3124,6 @@ with pkgs;
 
   jmespath = callPackage ../development/tools/jmespath { };
 
-  jmol = callPackage ../applications/science/chemistry/jmol { };
-
   jmtpfs = callPackage ../tools/filesystems/jmtpfs { };
 
   jnettop = callPackage ../tools/networking/jnettop { };
@@ -3754,8 +3752,6 @@ with pkgs;
 
   modsecurity_standalone = callPackage ../tools/security/modsecurity { };
 
-  molden = callPackage ../applications/science/chemistry/molden { };
-
   molly-guard = callPackage ../os-specific/linux/molly-guard { };
 
   moneyplex = callPackage ../applications/office/moneyplex { };
@@ -7167,8 +7163,6 @@ with pkgs;
 
   ocropus = callPackage ../applications/misc/ocropus { };
 
-  octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
-
   inherit (callPackages ../development/interpreters/perl {}) perl perl522 perl524 perl526;
 
   pachyderm = callPackage ../applications/networking/cluster/pachyderm { };
@@ -12451,6 +12445,8 @@ with pkgs;
 
   lwan = callPackage ../servers/http/lwan { };
 
+  labelImg = callPackage ../applications/science/machine-learning/labelimg { };
+
   mailman = callPackage ../servers/mail/mailman { };
 
   mattermost = callPackage ../servers/mattermost { };
@@ -12927,8 +12923,11 @@ with pkgs;
 
   axis2 = callPackage ../servers/http/tomcat/axis2 { };
 
-  unifi = callPackage ../servers/unifi { };
+  inherit (callPackages ../servers/unifi { })
-  unifiLTS = callPackage ../servers/unifi { useLTS=true; };
+    unifiLTS
+    unifiStable
+    unifiTesting;
+  unifi = unifiStable;
 
   virtuoso6 = callPackage ../servers/sql/virtuoso/6.x.nix { };
 
@@ -14857,10 +14856,6 @@ with pkgs;
 
   avidemux = libsForQt5.callPackage ../applications/video/avidemux { };
 
-  avogadro = callPackage ../applications/science/chemistry/avogadro {
-    eigen = eigen2;
-  };
-
   avrdudess = callPackage ../applications/misc/avrdudess { };
 
   avxsynth = callPackage ../applications/video/avxsynth {
@@ -15967,11 +15962,7 @@ with pkgs;
   gmrun = callPackage ../applications/misc/gmrun {};
 
   gnucash = callPackage ../applications/office/gnucash {
-    inherit (gnome2) libgnomeui libgtkhtml gtkhtml libbonoboui libgnomeprint libglade libart_lgpl;
+    inherit (gnome3) dconf;
-    gconf = gnome2.GConf;
-    guile = guile_1_8;
-    slibGuile = slibGuile.override { scheme = guile_1_8; };
-    goffice = goffice_0_8;
   };
 
   gnucash26 = lowPrio (callPackage ../applications/office/gnucash/2.6.nix {
@@ -17421,8 +17412,6 @@ with pkgs;
 
   puremapping = callPackage ../applications/audio/pd-plugins/puremapping { };
 
-  pymol = callPackage ../applications/science/chemistry/pymol { };
-
   pybitmessage = callPackage ../applications/networking/instant-messengers/pybitmessage { };
 
   pythonmagick = callPackage ../applications/graphics/PythonMagick { };
@@ -19753,6 +19742,22 @@ with pkgs;
 
   ### SCIENCE
 
+  ### SCIENCE/CHEMISTY
+
+  avogadro = callPackage ../applications/science/chemistry/avogadro {
+    eigen = eigen2;
+  };
+
+  gwyddion = callPackage ../applications/science/chemistry/gwyddion {};
+
+  jmol = callPackage ../applications/science/chemistry/jmol { };
+
+  molden = callPackage ../applications/science/chemistry/molden { };
+
+  octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };
+
+  pymol = callPackage ../applications/science/chemistry/pymol { };
+
   ### SCIENCE/GEOMETRY
 
   drgeo = callPackage ../applications/science/geometry/drgeo {
@@ -19777,6 +19782,10 @@ with pkgs;
 
   bcftools = callPackage ../applications/science/biology/bcftools { };
 
+  conglomerate = callPackage ../applications/science/biology/conglomerate {
+    inherit (perlPackages) GetoptTabular MNI-Perllib;
+  };
+
   dcm2niix = callPackage ../applications/science/biology/dcm2niix { };
 
   diamond = callPackage ../applications/science/biology/diamond { };