Merge staging-next into staging

doc/coding-conventions.xml

@@ -56,25 +56,30 @@ foo { arg = ...; }
      or list elements should be aligned:
 <programlisting>
 # A long list.
-list =
+list = [
-  [ elem1
+  elem1
-    elem2
+  elem2
-    elem3
+  elem3
-  ];
+];
 
 # A long attribute set.
-attrs =
-  { attr1 = short_expr;
-    attr2 =
-      if true then big_expr else big_expr;
-  };
-
-# Alternatively:
 attrs = {
   attr1 = short_expr;
   attr2 =
     if true then big_expr else big_expr;
 };
+
+# Combined
+listOfAttrs = [
+  {
+    attr1 = 3;
+    attr2 = "fff";
+  }
+  {
+    attr1 = 5;
+    attr2 = "ggg";
+  }
+];
 </programlisting>
     </para>
    </listitem>

doc/cross-compilation.xml

@@ -385,7 +385,7 @@ nix-build <nixpkgs> --arg crossSystem '(import <nixpkgs/lib>).system
     Eventually we would like to make these platform examples an unnecessary
     convenience so that
 <programlisting>
-nix-build &lt;nixpkgs&gt; --arg crossSystem.config '&lt;arch&gt;-&lt;os&gt;-&lt;vendor&gt;-&lt;abi&gt;' -A whatever</programlisting>
+nix-build &lt;nixpkgs&gt; --arg crossSystem '{ config = "&lt;arch&gt;-&lt;os&gt;-&lt;vendor&gt;-&lt;abi&gt;"; }' -A whatever</programlisting>
     works in the vast majority of cases. The problem today is dependencies on
     other sorts of configuration which aren't given proper defaults. We rely on
     the examples to crudely to set those configuration parameters in some

doc/languages-frameworks/ruby.xml

@@ -50,6 +50,17 @@ bundlerEnv rec {
   future updates can be run easily.
  </para>
 
+ <para>
+  Updating Ruby packages can then be done like this:
+ </para>
+
+<screen>
+<![CDATA[$ cd pkgs/servers/monitoring/sensu
+$ nix-shell -p bundler --run 'bundle lock --update'
+$ nix-shell -p bundix --run 'bundix'
+]]>
+</screen>
+
  <para>
   For tools written in Ruby - i.e. where the desire is to install a package and
   then execute e.g. <command>rake</command> at the command line, there is an

doc/stdenv.xml

@@ -2428,12 +2428,31 @@ addEnvHooks "$hostOffset" myBashFunction
       <para>
        This is a special setup hook which helps in packaging proprietary
        software in that it automatically tries to find missing shared library
-       dependencies of ELF files. All packages within the
+       dependencies of ELF files based on the given
-       <envar>runtimeDependencies</envar> environment variable are
+       <varname>buildInputs</varname> and <varname>nativeBuildInputs</varname>.
-       unconditionally added to executables, which is useful for programs that
+      </para>
-       use <citerefentry>
+      <para>
-       <refentrytitle>dlopen</refentrytitle>
+       You can also specify a <envar>runtimeDependencies</envar> environment
-       <manvolnum>3</manvolnum> </citerefentry> to load libraries at runtime.
+       variable which lists dependencies that are unconditionally added to all
+       executables.
+      </para>
+      <para>
+       This is useful for programs that use <citerefentry>
+        <refentrytitle>dlopen</refentrytitle>
+        <manvolnum>3</manvolnum>
+       </citerefentry> to load libraries at runtime.
+      </para>
+      <para>
+        In certain situations you may want to run the main command
+        (<command>autoPatchelf</command>) of the setup hook on a file or a set
+        of directories instead of unconditionally patching all outputs. This
+        can be done by setting the <envar>dontAutoPatchelf</envar> environment
+        variable to a non-empty value.
+      </para>
+      <para>
+        The <command>autoPatchelf</command> command also recognizes a
+        <parameter class="command">--no-recurse</parameter> command line flag,
+        which prevents it from recursing into subdirectories.
       </para>
      </listitem>
     </varlistentry>
@@ -2455,7 +2474,17 @@ addEnvHooks "$hostOffset" myBashFunction
        use the cntr exec subcommand. Note that <command>cntr</command> also
        needs to be executed on the machine that is doing the build, which might
        be not the case when remote builders are enabled.
-       <command>cntr</command> is only supported on linux based platforms.
+       <command>cntr</command> is only supported on Linux-based platforms. To
+       use it first add <literal>cntr</literal> to your
+       <literal>environment.systemPackages</literal> on NixOS or alternatively to
+       the root user on non-NixOS systems. Then in the package that is supposed
+       to be inspected, add <literal>breakpointHook</literal> to
+       <literal>nativeBuildInputs</literal>.
+<programlisting>
+         nativeBuildInputs = [ breakpointHook ];
+       </programlisting>
+       When a build failure happens there will be an instruction printed that
+       shows how to attach with <literal>cntr</literal> to the build sandbox.
       </para>
      </listitem>
     </varlistentry>

nixos/doc/manual/configuration/modularity.xml

@@ -127,4 +127,23 @@ nix-repl> map (x: x.hostName) config.<xref linkend="opt-services.httpd.virtualHo
 [ "example.org" "example.gov" ]
 </screen>
  </para>
+
+ <para>
+   While abstracting your configuration, you may find it useful to generate
+   modules using code, instead of writing files. The example
+   below would have the same effect as importing a file which sets those
+   options.
+   <screen>
+     { config, pkgs, ... }:
+
+     let netConfig = { hostName }: {
+       networking.hostName = hostName;
+       networking.useDHCP = false;
+    };
+
+    in
+
+    { imports = [ (netConfig "nixos.localdomain") ]; }
+  </screen>
+</para>
 </section>

nixos/doc/manual/development/running-nixos-tests-interactively.xml

@@ -19,7 +19,7 @@ starting VDE switch for network 1
 > startAll
 > testScript
 > $machine->succeed("touch /tmp/foo")
-> print($machine->succeed("pwd"), "\n") # Show stdout of command
+> print($machine->succeed("pwd")) # Show stdout of command
 </screen>
   The function <command>testScript</command> executes the entire test script
   and drops you back into the test driver command line upon its completion.

nixos/doc/manual/development/writing-nixos-tests.xml

@@ -108,7 +108,7 @@ xlink:href="https://github.com/NixOS/nixpkgs/blob/master/nixos/modules/virtualis
 <programlisting>
 $machine->start;
 $machine->waitForUnit("default.target");
-die unless $machine->succeed("uname") =~ /Linux/;
+$machine->succeed("uname") =~ /Linux/ or die;
 </programlisting>
   The first line is actually unnecessary; machines are implicitly started when
   you first execute an action on them (such as <literal>waitForUnit</literal>

nixos/doc/manual/release-notes/rl-1903.xml

@@ -111,6 +111,16 @@
       without Syncthing resetting the permission on every start.
     </para>
    </listitem>
+   <listitem>
+    <para>
+      The <literal>ntp</literal> module now has sane default restrictions.
+      If you're relying on the previous defaults, which permitted all queries
+      and commands from all firewall-permitted sources, you can set
+      <varname>services.ntp.restrictDefault</varname> and
+      <varname>services.ntp.restrictSource</varname> to
+      <literal>[]</literal>.
+    </para>
+   </listitem>
    <listitem>
     <para>
      Package <varname>rabbitmq_server</varname> is renamed to

nixos/lib/make-system-tarball.nix

@@ -1,4 +1,4 @@
-{ stdenv, perl, pixz, pathsFromGraph
+{ stdenv, closureInfo, pixz
 
 , # The file name of the resulting tarball
   fileName ? "nixos-system-${stdenv.hostPlatform.system}"
@@ -29,24 +29,28 @@
 , extraInputs ? [ pixz ]
 }:
 
+let
+  symlinks = map (x: x.symlink) storeContents;
+  objects = map (x: x.object) storeContents;
+in
+
 stdenv.mkDerivation {
   name = "tarball";
   builder = ./make-system-tarball.sh;
-  buildInputs = [ perl ] ++ extraInputs;
+  buildInputs = extraInputs;
 
-  inherit fileName pathsFromGraph extraArgs extraCommands compressCommand;
+  inherit fileName extraArgs extraCommands compressCommand;
 
   # !!! should use XML.
   sources = map (x: x.source) contents;
   targets = map (x: x.target) contents;
 
   # !!! should use XML.
-  objects = map (x: x.object) storeContents;
+  inherit symlinks objects;
-  symlinks = map (x: x.symlink) storeContents;
 
-  # For obtaining the closure of `storeContents'.
+  closureInfo = closureInfo {
-  exportReferencesGraph =
+    rootPaths = objects;
-    map (x: [("closure-" + baseNameOf x.object) x.object]) storeContents;
+  };
 
   extension = compressionExtension;
 }

nixos/lib/make-system-tarball.sh

@@ -3,7 +3,6 @@ source $stdenv/setup
 sources_=($sources)
 targets_=($targets)
 
-echo $objects
 objects=($objects)
 symlinks=($symlinks)
 
@@ -14,8 +13,6 @@ stripSlash() {
     if test "${res:0:1}" = /; then res=${res:1}; fi
 }
 
-touch pathlist
-
 # Add the individual files.
 for ((i = 0; i < ${#targets_[@]}; i++)); do
     stripSlash "${targets_[$i]}"
@@ -25,9 +22,9 @@ done
 
 
 # Add the closures of the top-level store objects.
+chmod +w .
 mkdir -p nix/store
-storePaths=$(perl $pathsFromGraph closure-*)
+for i in $(< $closureInfo/store-paths); do
-for i in $storePaths; do
     cp -a "$i" "${i:1}"
 done
 
@@ -35,7 +32,7 @@ done
 # TODO tar ruxo
 # Also include a manifest of the closures in a format suitable for
 # nix-store --load-db.
-printRegistration=1 perl $pathsFromGraph closure-* > nix-path-registration
+cp $closureInfo/registration nix-path-registration
 
 # Add symlinks to the top-level store objects.
 for ((n = 0; n < ${#objects[*]}; n++)); do

nixos/lib/testing.nix

@@ -1,5 +1,5 @@
 { system
-, pkgs
+, pkgs ? import ../.. { inherit system config; }
   # Use a minimal kernel?
 , minimal ? false
   # Ignored

nixos/maintainers/scripts/gce/create-gce.sh

@@ -7,9 +7,9 @@ BUCKET_NAME="${BUCKET_NAME:-nixos-cloud-images}"
 TIMESTAMP="$(date +%Y%m%d%H%M)"
 export TIMESTAMP
 
-nix-build '<nixpkgs/nixos>' \
+nix-build '<nixpkgs/nixos/lib/eval-config.nix>' \
    -A config.system.build.googleComputeImage \
-   --arg configuration "{ imports = [ <nixpkgs/nixos/modules/virtualisation/google-compute-image.nix> ]; }" \
+   --arg modules "[ <nixpkgs/nixos/modules/virtualisation/google-compute-image.nix> ]" \
    --argstr system x86_64-linux \
    -o gce \
    -j 10

nixos/modules/hardware/raid/hpsa.nix

@@ -8,7 +8,7 @@ let
     version = "2.40-13.0";
 
     src = pkgs.fetchurl {
-      url = "http://downloads.linux.hpe.com/SDR/downloads/MCP/Ubuntu/pool/non-free/${name}_amd64.deb";
+      url = "https://downloads.linux.hpe.com/SDR/downloads/MCP/Ubuntu/pool/non-free/${name}_amd64.deb";
       sha256 = "11w7fwk93lmfw0yya4jpjwdmgjimqxx6412sqa166g1pz4jil4sw";
     };
 
@@ -34,7 +34,7 @@ let
 
     meta = with lib; {
       description = "HP Smart Array CLI";
-      homepage = http://downloads.linux.hpe.com/SDR/downloads/MCP/Ubuntu/pool/non-free/;
+      homepage = https://downloads.linux.hpe.com/SDR/downloads/MCP/Ubuntu/pool/non-free/;
       license = licenses.unfreeRedistributable;
       platforms = [ "x86_64-linux" ];
       maintainers = with maintainers; [ volth ];

nixos/modules/installer/cd-dvd/sd-image.nix

@@ -134,7 +134,9 @@ in
         ${config.sdImage.populateBootCommands}
 
         # Copy the populated /boot into the SD image
-        (cd boot; mcopy -bpsvm -i ../bootpart.img ./* ::)
+        (cd boot; mcopy -psvm -i ../bootpart.img ./* ::)
+        # Verify the FAT partition before copying it.
+        fsck.vfat -vn bootpart.img
         dd conv=notrunc if=bootpart.img of=$img seek=$START count=$SECTORS
       '';
     }) {};

nixos/modules/misc/ids.nix

@@ -175,7 +175,7 @@
       dnsmasq = 141;
       uhub = 142;
       yandexdisk = 143;
-      #collectd = 144; #unused
+      mxisd = 144; # was once collectd
       consul = 145;
       mailpile = 146;
       redmine = 147;
@@ -484,7 +484,7 @@
       #dnsmasq = 141; # unused
       uhub = 142;
       #yandexdisk = 143; # unused
-      #collectd = 144; # unused
+      mxisd = 144; # was once collectd
       #consul = 145; # unused
       mailpile = 146;
       redmine = 147;

nixos/modules/module-list.nix

@@ -560,6 +560,7 @@
   ./services/networking/miredo.nix
   ./services/networking/mstpd.nix
   ./services/networking/murmur.nix
+  ./services/networking/mxisd.nix
   ./services/networking/namecoind.nix
   ./services/networking/nat.nix
   ./services/networking/ndppd.nix

nixos/modules/profiles/docker-container.nix

@@ -15,15 +15,19 @@ in {
 
   # Create the tarball
   system.build.tarball = pkgs.callPackage ../../lib/make-system-tarball.nix {
-    contents = [];
+    contents = [
+      {
+        source = "${config.system.build.toplevel}/.";
+        target = "./";
+      }
+    ];
     extraArgs = "--owner=0";
 
     # Add init script to image
-    storeContents = [
+    storeContents = pkgs2storeContents [
-      { object = config.system.build.toplevel + "/init";
+      config.system.build.toplevel
-        symlink = "/init";
+      pkgs.stdenv
-      }
+    ];
-    ] ++ (pkgs2storeContents [ pkgs.stdenv ]);
 
     # Some container managers like lxc need these
     extraCommands = "mkdir -p proc sys dev";

nixos/modules/profiles/hardened.nix

@@ -12,6 +12,8 @@ with lib;
 
   boot.kernelPackages = mkDefault pkgs.linuxPackages_hardened;
 
+  nix.allowedUsers = mkDefault [ "@users" ];
+
   security.hideProcessInformation = mkDefault true;
 
   security.lockKernelModules = mkDefault true;

nixos/modules/programs/sway-beta.nix

@@ -8,7 +8,7 @@ let
 
   swayWrapped = pkgs.writeShellScriptBin "sway" ''
     ${cfg.extraSessionCommands}
-    exec ${pkgs.dbus.dbus-launch} --exit-with-session ${swayPackage}/bin/sway
+    exec ${pkgs.dbus.dbus-launch} --exit-with-session ${swayPackage}/bin/sway "$@"
   '';
   swayJoined = pkgs.symlinkJoin {
     name = "sway-joined";

nixos/modules/services/cluster/kubernetes/default.nix

@@ -784,7 +784,7 @@ in {
     clusterCidr = mkOption {
       description = "Kubernetes controller manager and proxy CIDR Range for Pods in cluster.";
       default = "10.1.0.0/16";
-      type = types.str;
+      type = types.nullOr types.str;
     };
 
     flannel.enable = mkOption {
@@ -1018,9 +1018,9 @@ in {
             ${if (cfg.controllerManager.rootCaFile!=null)
               then "--root-ca-file=${cfg.controllerManager.rootCaFile}"
               else "--root-ca-file=/var/run/kubernetes/apiserver.crt"} \
-            ${optionalString (cfg.clusterCidr!=null)
+            ${if (cfg.clusterCidr!=null)
-              "--cluster-cidr=${cfg.clusterCidr}"} \
+              then "--cluster-cidr=${cfg.clusterCidr} --allocate-node-cidrs=true"
-            --allocate-node-cidrs=true \
+              else "--allocate-node-cidrs=false"} \
             ${optionalString (cfg.controllerManager.featureGates != [])
               "--feature-gates=${concatMapStringsSep "," (feature: "${feature}=true") cfg.controllerManager.featureGates}"} \
             ${optionalString cfg.verbose "--v=6"} \

nixos/modules/services/databases/postgresql.nix

@@ -238,6 +238,9 @@ in
             User = "postgres";
             Group = "postgres";
             PermissionsStartOnly = true;
+            Type = if lib.versionAtLeast cfg.package.version "9.6"
+                   then "notify"
+                   else "simple";
 
             # Shut down Postgres using SIGINT ("Fast Shutdown mode").  See
             # http://www.postgresql.org/docs/current/static/server-shutdown.html

nixos/modules/services/mail/rspamd.nix

@@ -45,7 +45,9 @@ let
       else "${config.socket}${maybeOption "mode"}${maybeOption "owner"}${maybeOption "group"}";
   };
 
-  workerOpts = { name, ... }: {
+  traceWarning = w: x: builtins.trace "warning: ${w}" x;
+
+  workerOpts = { name, options, ... }: {
     options = {
       enable = mkOption {
         type = types.nullOr types.bool;
@@ -59,9 +61,18 @@ let
       };
       type = mkOption {
         type = types.nullOr (types.enum [
-          "normal" "controller" "fuzzy_storage" "rspamd_proxy" "lua"
+          "normal" "controller" "fuzzy_storage" "rspamd_proxy" "lua" "proxy"
         ]);
-        description = "The type of this worker";
+        description = ''
+          The type of this worker. The type <literal>proxy</literal> is
+          deprecated and only kept for backwards compatibility and should be
+          replaced with <literal>rspamd_proxy</literal>.
+        '';
+        apply = let
+            from = "services.rspamd.workers.\”${name}\".type";
+            files = options.type.files;
+            warning = "The option `${from}` defined in ${showFiles files} has enum value `proxy` which has been renamed to `rspamd_proxy`";
+          in x: if x == "proxy" then traceWarning warning "rspamd_proxy" else x;
       };
       bindSockets = mkOption {
         type = types.listOf (types.either types.str (types.submodule bindSocketOpts));

nixos/modules/services/monitoring/apcupsd.nix

@@ -180,7 +180,7 @@ in
       serviceConfig = {
         Type = "oneshot";
         ExecStart = "${pkgs.apcupsd}/bin/apcupsd --killpower -f ${configFile}";
-        TimeoutSec = 0;
+        TimeoutSec = "infinity";
         StandardOutput = "tty";
         RemainAfterExit = "yes";
       };

nixos/modules/services/monitoring/osquery.nix

@@ -78,7 +78,7 @@ in
         mkdir -p "$(dirname ${escapeShellArg cfg.databasePath})"
       '';
       serviceConfig = {
-        TimeoutStartSec = 0;
+        TimeoutStartSec = "infinity";
         ExecStart = "${pkgs.osquery}/bin/osqueryd --logger_path ${escapeShellArg cfg.loggerPath} --pidfile ${escapeShellArg cfg.pidfile} --database_path ${escapeShellArg cfg.databasePath}";
         KillMode = "process";
         KillSignal = "SIGTERM";

nixos/modules/services/monitoring/systemhealth.nix

@@ -8,7 +8,7 @@ let
   systemhealth = with pkgs; stdenv.mkDerivation {
     name = "systemhealth-1.0";
     src = fetchurl {
-      url = "http://www.brianlane.com/static/downloads/systemhealth/systemhealth-1.0.tar.bz2";
+      url = "https://www.brianlane.com/downloads/systemhealth/systemhealth-1.0.tar.bz2";
       sha256 = "1q69lz7hmpbdpbz36zb06nzfkj651413n9icx0njmyr3xzq1j9qy";
     };
     buildInputs = [ python ];

nixos/modules/services/networking/consul.nix

@@ -185,7 +185,7 @@ in
           PermissionsStartOnly = true;
           User = if cfg.dropPrivileges then "consul" else null;
           Restart = "on-failure";
-          TimeoutStartSec = "0";
+          TimeoutStartSec = "infinity";
         } // (optionalAttrs (cfg.leaveOnStop) {
           ExecStop = "${cfg.package.bin}/bin/consul leave";
         });

nixos/modules/services/networking/flashpolicyd.nix

@@ -11,7 +11,7 @@ let
 
     src = pkgs.fetchurl {
       name = "flashpolicyd_v0.6.zip";
-      url = "http://www.adobe.com/content/dotcom/en/devnet/flashplayer/articles/socket_policy_files/_jcr_content/articlePrerequistes/multiplefiles/node_1277808777771/file.res/flashpolicyd_v0.6%5B1%5D.zip";
+      url = "https://download.adobe.com/pub/adobe/devnet/flashplayer/articles/socket_policy_files/flashpolicyd_v0.6.zip";
       sha256 = "16zk237233npwfq1m4ksy4g5lzy1z9fp95w7pz0cdlpmv0fv9sm3";
     };
 
@@ -35,9 +35,9 @@ in
   ###### interface
 
   options = {
-  
+
     services.flashpolicyd = {
-    
+
       enable = mkOption {
         default = false;
         description =
@@ -47,13 +47,13 @@ in
             connections to your server.
           '';
       };
-      
+
       policy = mkOption {
         default =
           ''
             <?xml version="1.0"?>
             <!DOCTYPE cross-domain-policy SYSTEM "/xml/dtds/cross-domain-policy.dtd">
-            <cross-domain-policy> 
+            <cross-domain-policy>
               <site-control permitted-cross-domain-policies="master-only"/>
               <allow-access-from domain="*" to-ports="*" />
             </cross-domain-policy>

nixos/modules/services/networking/mxisd.nix

@@ -0,0 +1,125 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.services.mxisd;
+
+  server = optionalAttrs (cfg.server.name != null) { inherit (cfg.server) name; }
+        // optionalAttrs (cfg.server.port != null) { inherit (cfg.server) port; };
+
+  baseConfig = {
+    matrix.domain = cfg.matrix.domain;
+    key.path = "${cfg.dataDir}/signing.key";
+    storage = {
+      provider.sqlite.database = "${cfg.dataDir}/mxisd.db";
+    };
+  } // optionalAttrs (server != {}) { inherit server; };
+
+  # merges baseConfig and extraConfig into a single file
+  fullConfig = recursiveUpdate baseConfig cfg.extraConfig;
+
+  configFile = pkgs.writeText "mxisd-config.yaml" (builtins.toJSON fullConfig);
+
+in {
+  options = {
+    services.mxisd = {
+      enable = mkEnableOption "mxisd matrix federated identity server";
+
+      package = mkOption {
+        type = types.package;
+        default = pkgs.mxisd;
+        defaultText = "pkgs.mxisd";
+        description = "The mxisd package to use";
+      };
+
+      dataDir = mkOption {
+        type = types.str;
+        default = "/var/lib/mxisd";
+        description = "Where data mxisd uses resides";
+      };
+
+      extraConfig = mkOption {
+        type = types.attrs;
+        default = {};
+        description = "Extra options merged into the mxisd configuration";
+      };
+
+      matrix = {
+
+        domain = mkOption {
+          type = types.str;
+          description = ''
+            the domain of the matrix homeserver
+          '';
+        };
+
+      };
+
+      server = {
+
+        name = mkOption {
+          type = types.nullOr types.str;
+          default = null;
+          description = ''
+            Public hostname of mxisd, if different from the Matrix domain.
+          '';
+        };
+
+        port = mkOption {
+          type = types.nullOr types.int;
+          default = null;
+          description = ''
+            HTTP port to listen on (unencrypted)
+          '';
+        };
+
+      };
+
+    };
+  };
+
+  config = mkIf cfg.enable {
+    users.users = [
+      {
+        name = "mxisd";
+        group = "mxisd";
+        home = cfg.dataDir;
+        createHome = true;
+        shell = "${pkgs.bash}/bin/bash";
+        uid = config.ids.uids.mxisd;
+      }
+    ];
+
+    users.groups = [
+      {
+        name = "mxisd";
+        gid = config.ids.gids.mxisd;
+      }
+    ];
+
+    systemd.services.mxisd = {
+      description = "a federated identity server for the matrix ecosystem";
+      after = [ "network.target" ];
+      wantedBy = [ "multi-user.target" ];
+
+      # mxisd / spring.boot needs the configuration to be named "application.yaml"
+      preStart = ''
+        config=${cfg.dataDir}/application.yaml
+        cp ${configFile} $config
+        chmod 444 $config
+      '';
+
+      serviceConfig = {
+        Type = "simple";
+        User = "mxisd";
+        Group = "mxisd";
+        ExecStart = "${cfg.package}/bin/mxisd --spring.config.location=${cfg.dataDir}/ --spring.profiles.active=systemd --java.security.egd=file:/dev/./urandom";
+        WorkingDirectory = cfg.dataDir;
+        PermissionsStartOnly = true;
+        SuccessExitStatus = 143;
+        Restart = "on-failure";
+      };
+    };
+  };
+}

nixos/modules/services/networking/ntpd.nix

@@ -15,6 +15,10 @@ let
   configFile = pkgs.writeText "ntp.conf" ''
     driftfile ${stateDir}/ntp.drift
 
+    restrict default ${toString cfg.restrictDefault}
+    restrict -6 default ${toString cfg.restrictDefault}
+    restrict source ${toString cfg.restrictSource}
+
     restrict 127.0.0.1
     restrict -6 ::1
 
@@ -36,11 +40,40 @@ in
       enable = mkOption {
         default = false;
         description = ''
-          Whether to synchronise your machine's time using the NTP
+          Whether to synchronise your machine's time using ntpd, as a peer in
-          protocol.
+          the NTP network.
+          </para>
+          <para>
+          Disables <literal>systemd.timesyncd</literal> if enabled.
         '';
       };
 
+      restrictDefault = mkOption {
+        type = types.listOf types.str;
+        description = ''
+          The restriction flags to be set by default.
+          </para>
+          <para>
+          The default flags prevent external hosts from using ntpd as a DDoS
+          reflector, setting system time, and querying OS/ntpd version. As
+          recommended in section 6.5.1.1.3, answer "No" of
+          http://support.ntp.org/bin/view/Support/AccessRestrictions
+        '';
+        default = [ "limited" "kod" "nomodify" "notrap" "noquery" "nopeer" ];
+      };
+
+      restrictSource = mkOption {
+        type = types.listOf types.str;
+        description = ''
+          The restriction flags to be set on source.
+          </para>
+          <para>
+          The default flags allow peers to be added by ntpd from configured
+          pool(s), but not by other means.
+        '';
+        default = [ "limited" "kod" "nomodify" "notrap" "noquery" ];
+      };
+
       servers = mkOption {
         default = config.networking.timeServers;
         description = ''
@@ -51,6 +84,7 @@ in
       extraFlags = mkOption {
         type = types.listOf types.str;
         description = "Extra flags passed to the ntpd command.";
+        example = literalExample ''[ "--interface=eth0" ]'';
         default = [];
       };
 

nixos/modules/services/security/tor.nix

@@ -92,6 +92,7 @@ let
   # Hidden services
   + concatStrings (flip mapAttrsToList cfg.hiddenServices (n: v: ''
     HiddenServiceDir ${torDirectory}/onion/${v.name}
+    ${optionalString (v.version != null) "HiddenServiceVersion ${toString v.version}"}
     ${flip concatMapStrings v.map (p: ''
       HiddenServicePort ${toString p.port} ${p.destination}
     '')}
@@ -667,6 +668,12 @@ in
                  };
                }));
              };
+
+             version = mkOption {
+               default = null;
+               description = "Rendezvous service descriptor version to publish for the hidden service. Currently, versions 2 and 3 are supported. (Default: 2)";
+               type = types.nullOr (types.enum [ 2 3 ]);
+             };
           };
 
           config = {

nixos/modules/services/system/cloud-init.nix

@@ -119,7 +119,7 @@ in
           { Type = "oneshot";
             ExecStart = "${pkgs.cloud-init}/bin/cloud-init init --local";
             RemainAfterExit = "yes";
-            TimeoutSec = "0";
+            TimeoutSec = "infinity";
             StandardOutput = "journal+console";
           };
       };
@@ -137,7 +137,7 @@ in
           { Type = "oneshot";
             ExecStart = "${pkgs.cloud-init}/bin/cloud-init init";
             RemainAfterExit = "yes";
-            TimeoutSec = "0";
+            TimeoutSec = "infinity";
             StandardOutput = "journal+console";
           };
       };
@@ -153,7 +153,7 @@ in
           { Type = "oneshot";
             ExecStart = "${pkgs.cloud-init}/bin/cloud-init modules --mode=config";
             RemainAfterExit = "yes";
-            TimeoutSec = "0";
+            TimeoutSec = "infinity";
             StandardOutput = "journal+console";
           };
       };
@@ -169,7 +169,7 @@ in
           { Type = "oneshot";
             ExecStart = "${pkgs.cloud-init}/bin/cloud-init modules --mode=final";
             RemainAfterExit = "yes";
-            TimeoutSec = "0";
+            TimeoutSec = "infinity";
             StandardOutput = "journal+console";
           };
       };

nixos/modules/services/web-servers/apache-httpd/mediawiki.nix

@@ -86,7 +86,7 @@ let
     name= "mediawiki-1.29.1";
 
     src = pkgs.fetchurl {
-      url = "http://download.wikimedia.org/mediawiki/1.29/${name}.tar.gz";
+      url = "https://releases.wikimedia.org/mediawiki/1.29/${name}.tar.gz";
       sha256 = "03mpazbxvb011s2nmlw5p6dc43yjgl5yrsilmj1imyykm57bwb3m";
     };
 
@@ -311,7 +311,7 @@ in
       description = ''
         Any additional text to be appended to MediaWiki's
         configuration file.  This is a PHP script.  For configuration
-        settings, see <link xlink:href='http://www.mediawiki.org/wiki/Manual:Configuration_settings'/>.
+        settings, see <link xlink:href='https://www.mediawiki.org/wiki/Manual:Configuration_settings'/>.
       '';
     };
 

nixos/modules/services/x11/urxvtd.nix

@@ -18,27 +18,17 @@ in {
   };
 
   config = mkIf cfg.enable {
-    systemd.user = {
+    systemd.user.services.urxvtd = {
-      sockets.urxvtd = {
+      description = "urxvt terminal daemon";
-        description = "socket for urxvtd, the urxvt terminal daemon";
+      wantedBy = [ "graphical-session.target" ];
-        wantedBy = [ "graphical-session.target" ];
+      partOf = [ "graphical-session.target" ];
-        partOf = [ "graphical-session.target" ];
+      path = [ pkgs.xsel ];
-        socketConfig = {
+      serviceConfig = {
-          ListenStream = "%t/urxvtd-socket";
+        ExecStart = "${pkgs.rxvt_unicode-with-plugins}/bin/urxvtd -o";
-        };
+        Environment = "RXVT_SOCKET=%t/urxvtd-socket";
+        Restart = "on-failure";
+        RestartSec = "5s";
       };
-
-      services.urxvtd = {
-        description = "urxvt terminal daemon";
-        path = [ pkgs.xsel ];
-        serviceConfig = {
-          ExecStart = "${pkgs.rxvt_unicode-with-plugins}/bin/urxvtd -o";
-          Environment = "RXVT_SOCKET=%t/urxvtd-socket";
-          Restart = "on-failure";
-          RestartSec = "5s";
-        };
-      };
-
     };
 
     environment.systemPackages = [ pkgs.rxvt_unicode-with-plugins ];

nixos/modules/system/boot/systemd-nspawn.nix

@@ -112,7 +112,7 @@ in {
 
       environment.etc."systemd/nspawn".source = generateUnits "nspawn" units [] [];
 
-      systemd.targets."multi-user".wants = [ "machines.target "];
+      systemd.targets."multi-user".wants = [ "machines.target" ];
   };
 
 }

nixos/modules/virtualisation/container-config.nix

@@ -22,12 +22,8 @@ with lib;
     # Not supported in systemd-nspawn containers.
     security.audit.enable = false;
 
-    # Make sure that root user in container will talk to host nix-daemon
+    # Use the host's nix-daemon.
-    environment.etc."profile".text = ''
+    environment.variables.NIX_REMOTE = "daemon";
-    export NIX_REMOTE=daemon
-    '';
-
-
 
   };
 

nixos/modules/virtualisation/docker-image.nix

@@ -17,3 +17,41 @@
   # Socket activated ssh presents problem in Docker.
   services.openssh.startWhenNeeded = false;
 }
+
+# Example usage:
+#
+## default.nix
+# let
+#   nixos = import <nixpkgs/nixos> {
+#     configuration = ./configuration.nix;
+#     system = "x86_64-linux";
+#   };
+# in
+# nixos.config.system.build.tarball
+#
+## configuration.nix
+# { pkgs, config, lib, ... }:
+# {
+#   imports = [
+#     <nixpkgs/nixos/modules/virtualisation/docker-image.nix>
+#     <nixpkgs/nixos/modules/installer/cd-dvd/channel.nix>
+#   ];
+#
+#   documentation.doc.enable = false;
+#
+#   environment.systemPackages = with pkgs; [
+#     bashInteractive
+#     cacert
+#     nix
+#   ];
+# }
+#
+## Run
+# Build the tarball:
+# $ nix-build default.nix
+# Load into docker:
+# $ docker import result/tarball/nixos-system-*.tar.xz nixos-docker
+# Boots into systemd
+# $ docker run --privileged -it nixos-docker /init
+# Log into the container
+# $ docker exec -it <container-name> /run/current-system/sw/bin/bash

nixos/modules/virtualisation/google-compute-config.nix

@@ -1,5 +1,261 @@
-{ ... }:
+{ config, lib, pkgs, ... }:
-
+with lib;
+let
+  gce = pkgs.google-compute-engine;
+  cfg = config.virtualisation.googleComputeImage;
+in
 {
-  imports = [ <nixpkgs/nixos/modules/virtualisation/google-compute-image.nix> ];
+  imports = [
+    ../profiles/headless.nix
+    ../profiles/qemu-guest.nix
+  ];
+
+
+  fileSystems."/" = {
+    device = "/dev/disk/by-label/nixos";
+    autoResize = true;
+  };
+
+  boot.growPartition = true;
+  boot.kernelParams = [ "console=ttyS0" "panic=1" "boot.panic_on_fail" ];
+  boot.initrd.kernelModules = [ "virtio_scsi" ];
+  boot.kernelModules = [ "virtio_pci" "virtio_net" ];
+
+  # Generate a GRUB menu.  Amazon's pv-grub uses this to boot our kernel/initrd.
+  boot.loader.grub.device = "/dev/sda";
+  boot.loader.timeout = 0;
+
+  # Don't put old configurations in the GRUB menu.  The user has no
+  # way to select them anyway.
+  boot.loader.grub.configurationLimit = 0;
+
+  # Allow root logins only using the SSH key that the user specified
+  # at instance creation time.
+  services.openssh.enable = true;
+  services.openssh.permitRootLogin = "prohibit-password";
+  services.openssh.passwordAuthentication = mkDefault false;
+
+  # Use GCE udev rules for dynamic disk volumes
+  services.udev.packages = [ gce ];
+
+  # Force getting the hostname from Google Compute.
+  networking.hostName = mkDefault "";
+
+  # Always include cryptsetup so that NixOps can use it.
+  environment.systemPackages = [ pkgs.cryptsetup ];
+
+  # Make sure GCE image does not replace host key that NixOps sets
+  environment.etc."default/instance_configs.cfg".text = lib.mkDefault ''
+    [InstanceSetup]
+    set_host_keys = false
+  '';
+
+  # Rely on GCP's firewall instead
+  networking.firewall.enable = mkDefault false;
+
+  # Configure default metadata hostnames
+  networking.extraHosts = ''
+    169.254.169.254 metadata.google.internal metadata
+  '';
+
+  networking.timeServers = [ "metadata.google.internal" ];
+
+  networking.usePredictableInterfaceNames = false;
+
+  # GC has 1460 MTU
+  networking.interfaces.eth0.mtu = 1460;
+
+  # allow the google-accounts-daemon to manage users
+  users.mutableUsers = true;
+  # and allow users to sudo without password
+  security.sudo.enable = true;
+  security.sudo.extraConfig = ''
+  %google-sudoers ALL=(ALL:ALL) NOPASSWD:ALL
+  '';
+
+  # NOTE: google-accounts tries to write to /etc/sudoers.d but the folder doesn't exist
+  # FIXME: not such file or directory on dynamic SSH provisioning
+  systemd.services.google-accounts-daemon = {
+    description = "Google Compute Engine Accounts Daemon";
+    # This daemon creates dynamic users
+    enable = config.users.mutableUsers;
+    after = [
+      "network.target"
+      "google-instance-setup.service"
+      "google-network-setup.service"
+    ];
+    requires = ["network.target"];
+    wantedBy = ["multi-user.target"];
+    path = with pkgs; [ shadow ];
+    serviceConfig = {
+      Type = "simple";
+      ExecStart = "${gce}/bin/google_accounts_daemon --debug";
+    };
+  };
+
+  systemd.services.google-clock-skew-daemon = {
+    description = "Google Compute Engine Clock Skew Daemon";
+    after = [
+      "network.target"
+      "google-instance-setup.service"
+      "google-network-setup.service"
+    ];
+    requires = ["network.target"];
+    wantedBy = ["multi-user.target"];
+    serviceConfig = {
+      Type = "simple";
+      ExecStart = "${gce}/bin/google_clock_skew_daemon --debug";
+    };
+  };
+
+  systemd.services.google-instance-setup = {
+    description = "Google Compute Engine Instance Setup";
+    after = ["local-fs.target" "network-online.target" "network.target" "rsyslog.service"];
+    before = ["sshd.service"];
+    wants = ["local-fs.target" "network-online.target" "network.target"];
+    wantedBy = [ "sshd.service" "multi-user.target" ];
+    path = with pkgs; [ ethtool openssh ];
+    serviceConfig = {
+      ExecStart = "${gce}/bin/google_instance_setup --debug";
+      Type = "oneshot";
+    };
+  };
+
+  systemd.services.google-network-daemon = {
+    description = "Google Compute Engine Network Daemon";
+    after = ["local-fs.target" "network-online.target" "network.target" "rsyslog.service" "google-instance-setup.service"];
+    wants = ["local-fs.target" "network-online.target" "network.target"];
+    requires = ["network.target"];
+    partOf = ["network.target"];
+    wantedBy = [ "multi-user.target" ];
+    path = with pkgs; [ iproute ];
+    serviceConfig = {
+      ExecStart = "${gce}/bin/google_network_daemon --debug";
+    };
+  };
+
+  systemd.services.google-shutdown-scripts = {
+    description = "Google Compute Engine Shutdown Scripts";
+    after = [
+      "local-fs.target"
+      "network-online.target"
+      "network.target"
+      "rsyslog.service"
+      "systemd-resolved.service"
+      "google-instance-setup.service"
+      "google-network-daemon.service"
+    ];
+    wants = [ "local-fs.target" "network-online.target" "network.target"];
+    wantedBy = [ "multi-user.target" ];
+    serviceConfig = {
+      ExecStart = "${pkgs.coreutils}/bin/true";
+      ExecStop = "${gce}/bin/google_metadata_script_runner --debug --script-type shutdown";
+      Type = "oneshot";
+      RemainAfterExit = true;
+      TimeoutStopSec = "infinity";
+    };
+  };
+
+  systemd.services.google-startup-scripts = {
+    description = "Google Compute Engine Startup Scripts";
+    after = [
+      "local-fs.target"
+      "network-online.target"
+      "network.target"
+      "rsyslog.service"
+      "google-instance-setup.service"
+      "google-network-daemon.service"
+    ];
+    wants = ["local-fs.target" "network-online.target" "network.target"];
+    wantedBy = [ "multi-user.target" ];
+    serviceConfig = {
+      ExecStart = "${gce}/bin/google_metadata_script_runner --debug --script-type startup";
+      KillMode = "process";
+      Type = "oneshot";
+    };
+  };
+
+
+  # Settings taken from https://github.com/GoogleCloudPlatform/compute-image-packages/blob/master/google_config/sysctl/11-gce-network-security.conf
+  boot.kernel.sysctl = {
+    # Turn on SYN-flood protections.  Starting with 2.6.26, there is no loss
+    # of TCP functionality/features under normal conditions.  When flood
+    # protections kick in under high unanswered-SYN load, the system
+    # should remain more stable, with a trade off of some loss of TCP
+    # functionality/features (e.g. TCP Window scaling).
+    "net.ipv4.tcp_syncookies" = mkDefault "1";
+
+    # ignores source-routed packets
+    "net.ipv4.conf.all.accept_source_route" = mkDefault "0";
+
+    # ignores source-routed packets
+    "net.ipv4.conf.default.accept_source_route" = mkDefault "0";
+
+    # ignores ICMP redirects
+    "net.ipv4.conf.all.accept_redirects" = mkDefault "0";
+
+    # ignores ICMP redirects
+    "net.ipv4.conf.default.accept_redirects" = mkDefault "0";
+
+    # ignores ICMP redirects from non-GW hosts
+    "net.ipv4.conf.all.secure_redirects" = mkDefault "1";
+
+    # ignores ICMP redirects from non-GW hosts
+    "net.ipv4.conf.default.secure_redirects" = mkDefault "1";
+
+    # don't allow traffic between networks or act as a router
+    "net.ipv4.ip_forward" = mkDefault "0";
+
+    # don't allow traffic between networks or act as a router
+    "net.ipv4.conf.all.send_redirects" = mkDefault "0";
+
+    # don't allow traffic between networks or act as a router
+    "net.ipv4.conf.default.send_redirects" = mkDefault "0";
+
+    # reverse path filtering - IP spoofing protection
+    "net.ipv4.conf.all.rp_filter" = mkDefault "1";
+
+    # reverse path filtering - IP spoofing protection
+    "net.ipv4.conf.default.rp_filter" = mkDefault "1";
+
+    # ignores ICMP broadcasts to avoid participating in Smurf attacks
+    "net.ipv4.icmp_echo_ignore_broadcasts" = mkDefault "1";
+
+    # ignores bad ICMP errors
+    "net.ipv4.icmp_ignore_bogus_error_responses" = mkDefault "1";
+
+    # logs spoofed, source-routed, and redirect packets
+    "net.ipv4.conf.all.log_martians" = mkDefault "1";
+
+    # log spoofed, source-routed, and redirect packets
+    "net.ipv4.conf.default.log_martians" = mkDefault "1";
+
+    # implements RFC 1337 fix
+    "net.ipv4.tcp_rfc1337" = mkDefault "1";
+
+    # randomizes addresses of mmap base, heap, stack and VDSO page
+    "kernel.randomize_va_space" = mkDefault "2";
+
+    # Reboot the machine soon after a kernel panic.
+    "kernel.panic" = mkDefault "10";
+
+    ## Not part of the original config
+
+    # provides protection from ToCToU races
+    "fs.protected_hardlinks" = mkDefault "1";
+
+    # provides protection from ToCToU races
+    "fs.protected_symlinks" = mkDefault "1";
+
+    # makes locating kernel addresses more difficult
+    "kernel.kptr_restrict" = mkDefault "1";
+
+    # set ptrace protections
+    "kernel.yama.ptrace_scope" = mkOverride 500 "1";
+
+    # set perf only available to root
+    "kernel.perf_event_paranoid" = mkDefault "2";
+
+  };
+
 }

nixos/modules/virtualisation/google-compute-image.nix

@@ -2,333 +2,59 @@
 
 with lib;
 let
-  diskSize = 1536; # MB
+  cfg = config.virtualisation.googleComputeImage;
-  gce = pkgs.google-compute-engine;
+  defaultConfigFile = pkgs.writeText "configuration.nix" ''
+    { ... }:
+    {
+      imports = [
+        <nixpkgs/nixos/modules/virtualisation/google-compute-image.nix>
+      ];
+    }
+  '';
 in
 {
-  imports = [ ../profiles/headless.nix ../profiles/qemu-guest.nix ];
 
-  system.build.googleComputeImage = import ../../lib/make-disk-image.nix {
+  imports = [ ./google-compute-config.nix ];
-    name = "google-compute-image";
-    postVM = ''
-      PATH=$PATH:${pkgs.stdenv.lib.makeBinPath [ pkgs.gnutar pkgs.gzip ]}
-      pushd $out
-      mv $diskImage disk.raw
-      tar -Szcf nixos-image-${config.system.nixos.label}-${pkgs.stdenv.hostPlatform.system}.raw.tar.gz disk.raw
-      rm $out/disk.raw
-      popd
-    '';
-    configFile = <nixpkgs/nixos/modules/virtualisation/google-compute-config.nix>;
-    format = "raw";
-    inherit diskSize;
-    inherit config lib pkgs;
-  };
 
-  fileSystems."/" = {
+  options = {
-    device = "/dev/disk/by-label/nixos";
+    virtualisation.googleComputeImage.diskSize = mkOption {
-    autoResize = true;
+      type = with types; int;
-  };
+      default = 1536;
+      description = ''
+        Size of disk image. Unit is MB.
+      '';
+    };
 
-  boot.growPartition = true;
+    virtualisation.googleComputeImage.configFile = mkOption {
-  boot.kernelParams = [ "console=ttyS0" "panic=1" "boot.panic_on_fail" ];
+      type = with types; nullOr str;
-  boot.initrd.kernelModules = [ "virtio_scsi" ];
+      default = null;
-  boot.kernelModules = [ "virtio_pci" "virtio_net" ];
+      description = ''
-
+        A path to a configuration file which will be placed at `/etc/nixos/configuration.nix`
-  # Generate a GRUB menu.  Amazon's pv-grub uses this to boot our kernel/initrd.
+        and be used when switching to a new configuration.
-  boot.loader.grub.device = "/dev/sda";
+        If set to `null`, a default configuration is used, where the only import is
-  boot.loader.timeout = 0;
+        `<nixpkgs/nixos/modules/virtualisation/google-compute-image.nix>`.
-
+      '';
-  # Don't put old configurations in the GRUB menu.  The user has no
-  # way to select them anyway.
-  boot.loader.grub.configurationLimit = 0;
-
-  # Allow root logins only using the SSH key that the user specified
-  # at instance creation time.
-  services.openssh.enable = true;
-  services.openssh.permitRootLogin = "prohibit-password";
-  services.openssh.passwordAuthentication = mkDefault false;
-
-  # Use GCE udev rules for dynamic disk volumes
-  services.udev.packages = [ gce ];
-
-  # Force getting the hostname from Google Compute.
-  networking.hostName = mkDefault "";
-
-  # Always include cryptsetup so that NixOps can use it.
-  environment.systemPackages = [ pkgs.cryptsetup ];
-
-  # Make sure GCE image does not replace host key that NixOps sets
-  environment.etc."default/instance_configs.cfg".text = lib.mkDefault ''
-    [InstanceSetup]
-    set_host_keys = false
-  '';
-
-  # Rely on GCP's firewall instead
-  networking.firewall.enable = mkDefault false;
-
-  # Configure default metadata hostnames
-  networking.extraHosts = ''
-    169.254.169.254 metadata.google.internal metadata
-  '';
-
-  networking.timeServers = [ "metadata.google.internal" ];
-
-  networking.usePredictableInterfaceNames = false;
-
-  # GC has 1460 MTU
-  networking.interfaces.eth0.mtu = 1460;
-
-  # allow the google-accounts-daemon to manage users
-  users.mutableUsers = true;
-  # and allow users to sudo without password
-  security.sudo.enable = true;
-  security.sudo.extraConfig = ''
-  %google-sudoers ALL=(ALL:ALL) NOPASSWD:ALL
-  '';
-
-  # NOTE: google-accounts tries to write to /etc/sudoers.d but the folder doesn't exist
-  # FIXME: not such file or directory on dynamic SSH provisioning
-  systemd.services.google-accounts-daemon = {
-    description = "Google Compute Engine Accounts Daemon";
-    # This daemon creates dynamic users
-    enable = config.users.mutableUsers;
-    after = [
-      "network.target"
-      "google-instance-setup.service"
-      "google-network-setup.service"
-    ];
-    requires = ["network.target"];
-    wantedBy = ["multi-user.target"];
-    path = with pkgs; [ shadow ];
-    serviceConfig = {
-      Type = "simple";
-      ExecStart = "${gce}/bin/google_accounts_daemon --debug";
     };
   };
 
-  systemd.services.google-clock-skew-daemon = {
+  #### implementation
-    description = "Google Compute Engine Clock Skew Daemon";
+  config = {
-    after = [
+
-      "network.target"
+    system.build.googleComputeImage = import ../../lib/make-disk-image.nix {
-      "google-instance-setup.service"
+      name = "google-compute-image";
-      "google-network-setup.service"
+      postVM = ''
-    ];
+        PATH=$PATH:${with pkgs; stdenv.lib.makeBinPath [ gnutar gzip ]}
-    requires = ["network.target"];
+        pushd $out
-    wantedBy = ["multi-user.target"];
+        mv $diskImage disk.raw
-    serviceConfig = {
+        tar -Szcf nixos-image-${config.system.nixos.label}-${pkgs.stdenv.hostPlatform.system}.raw.tar.gz disk.raw
-      Type = "simple";
+        rm $out/disk.raw
-      ExecStart = "${gce}/bin/google_clock_skew_daemon --debug";
+        popd
+      '';
+      format = "raw";
+      configFile = if isNull cfg.configFile then defaultConfigFile else cfg.configFile;
+      inherit (cfg) diskSize;
+      inherit config lib pkgs;
     };
-  };
-
-  systemd.services.google-instance-setup = {
-    description = "Google Compute Engine Instance Setup";
-    after = ["local-fs.target" "network-online.target" "network.target" "rsyslog.service"];
-    before = ["sshd.service"];
-    wants = ["local-fs.target" "network-online.target" "network.target"];
-    wantedBy = [ "sshd.service" "multi-user.target" ];
-    path = with pkgs; [ ethtool openssh ];
-    serviceConfig = {
-      ExecStart = "${gce}/bin/google_instance_setup --debug";
-      Type = "oneshot";
-    };
-  };
-
-  systemd.services.google-network-daemon = {
-    description = "Google Compute Engine Network Daemon";
-    after = ["local-fs.target" "network-online.target" "network.target" "rsyslog.service" "google-instance-setup.service"];
-    wants = ["local-fs.target" "network-online.target" "network.target"];
-    requires = ["network.target"];
-    partOf = ["network.target"];
-    wantedBy = [ "multi-user.target" ];
-    path = with pkgs; [ iproute ];
-    serviceConfig = {
-      ExecStart = "${gce}/bin/google_network_daemon --debug";
-    };
-  };
-
-  systemd.services.google-shutdown-scripts = {
-    description = "Google Compute Engine Shutdown Scripts";
-    after = [
-      "local-fs.target"
-      "network-online.target"
-      "network.target"
-      "rsyslog.service"
-      "systemd-resolved.service"
-      "google-instance-setup.service"
-      "google-network-daemon.service"
-    ];
-    wants = [ "local-fs.target" "network-online.target" "network.target"];
-    wantedBy = [ "multi-user.target" ];
-    serviceConfig = {
-      ExecStart = "${pkgs.coreutils}/bin/true";
-      ExecStop = "${gce}/bin/google_metadata_script_runner --debug --script-type shutdown";
-      Type = "oneshot";
-      RemainAfterExit = true;
-      TimeoutStopSec = 0;
-    };
-  };
-
-  systemd.services.google-startup-scripts = {
-    description = "Google Compute Engine Startup Scripts";
-    after = [
-      "local-fs.target"
-      "network-online.target"
-      "network.target"
-      "rsyslog.service"
-      "google-instance-setup.service"
-      "google-network-daemon.service"
-    ];
-    wants = ["local-fs.target" "network-online.target" "network.target"];
-    wantedBy = [ "multi-user.target" ];
-    serviceConfig = {
-      ExecStart = "${gce}/bin/google_metadata_script_runner --debug --script-type startup";
-      KillMode = "process";
-      Type = "oneshot";
-    };
-  };
-
-  # TODO: remove this
-  systemd.services.fetch-ssh-keys =
-    { description = "Fetch host keys and authorized_keys for root user";
-
-      wantedBy = [ "sshd.service" ];
-      before = [ "sshd.service" ];
-      after = [ "network-online.target" ];
-      wants = [ "network-online.target" ];
-
-      script = let wget = "${pkgs.wget}/bin/wget --retry-connrefused -t 15 --waitretry=10 --header='Metadata-Flavor: Google'";
-                   mktemp = "mktemp --tmpdir=/run"; in
-        ''
-          # When dealing with cryptographic keys, we want to keep things private.
-          umask 077
-          # Don't download the SSH key if it has already been downloaded
-          echo "Obtaining SSH keys..."
-          mkdir -m 0700 -p /root/.ssh
-          AUTH_KEYS=$(${mktemp})
-          ${wget} -O $AUTH_KEYS http://metadata.google.internal/computeMetadata/v1/instance/attributes/sshKeys
-          if [ -s $AUTH_KEYS ]; then
-
-            # Read in key one by one, split in case Google decided
-            # to append metadata (it does sometimes) and add to
-            # authorized_keys if not already present.
-            touch /root/.ssh/authorized_keys
-            NEW_KEYS=$(${mktemp})
-            # Yes this is a nix escape of two single quotes.
-            while IFS=''' read -r line || [[ -n "$line" ]]; do
-              keyLine=$(echo -n "$line" | cut -d ':' -f2)
-              IFS=' ' read -r -a array <<< "$keyLine"
-              if [ ''${#array[@]} -ge 3 ]; then
-                echo ''${array[@]:0:3} >> $NEW_KEYS
-                echo "Added ''${array[@]:2} to authorized_keys"
-              fi
-            done < $AUTH_KEYS
-            mv $NEW_KEYS /root/.ssh/authorized_keys
-            chmod 600 /root/.ssh/authorized_keys
-            rm -f $KEY_PUB
-          else
-            echo "Downloading http://metadata.google.internal/computeMetadata/v1/project/attributes/sshKeys failed."
-            false
-          fi
-          rm -f $AUTH_KEYS
-          SSH_HOST_KEYS_DIR=$(${mktemp} -d)
-          ${wget} -O $SSH_HOST_KEYS_DIR/ssh_host_ed25519_key http://metadata.google.internal/computeMetadata/v1/instance/attributes/ssh_host_ed25519_key
-          ${wget} -O $SSH_HOST_KEYS_DIR/ssh_host_ed25519_key.pub http://metadata.google.internal/computeMetadata/v1/instance/attributes/ssh_host_ed25519_key_pub
-          if [ -s $SSH_HOST_KEYS_DIR/ssh_host_ed25519_key -a -s $SSH_HOST_KEYS_DIR/ssh_host_ed25519_key.pub ]; then
-              mv -f $SSH_HOST_KEYS_DIR/ssh_host_ed25519_key* /etc/ssh/
-              chmod 600 /etc/ssh/ssh_host_ed25519_key
-              chmod 644 /etc/ssh/ssh_host_ed25519_key.pub
-          else
-              echo "Setup of ssh host keys from http://metadata.google.internal/computeMetadata/v1/instance/attributes/ failed."
-              false
-          fi
-          rm -rf $SSH_HOST_KEYS_DIR
-        '';
-      serviceConfig.Type = "oneshot";
-      serviceConfig.RemainAfterExit = true;
-      serviceConfig.StandardError = "journal+console";
-      serviceConfig.StandardOutput = "journal+console";
-    };
-
-  # Settings taken from https://github.com/GoogleCloudPlatform/compute-image-packages/blob/master/google_config/sysctl/11-gce-network-security.conf
-  boot.kernel.sysctl = {
-    # Turn on SYN-flood protections.  Starting with 2.6.26, there is no loss
-    # of TCP functionality/features under normal conditions.  When flood
-    # protections kick in under high unanswered-SYN load, the system
-    # should remain more stable, with a trade off of some loss of TCP
-    # functionality/features (e.g. TCP Window scaling).
-    "net.ipv4.tcp_syncookies" = mkDefault "1";
-
-    # ignores source-routed packets
-    "net.ipv4.conf.all.accept_source_route" = mkDefault "0";
-
-    # ignores source-routed packets
-    "net.ipv4.conf.default.accept_source_route" = mkDefault "0";
-
-    # ignores ICMP redirects
-    "net.ipv4.conf.all.accept_redirects" = mkDefault "0";
-
-    # ignores ICMP redirects
-    "net.ipv4.conf.default.accept_redirects" = mkDefault "0";
-
-    # ignores ICMP redirects from non-GW hosts
-    "net.ipv4.conf.all.secure_redirects" = mkDefault "1";
-
-    # ignores ICMP redirects from non-GW hosts
-    "net.ipv4.conf.default.secure_redirects" = mkDefault "1";
-
-    # don't allow traffic between networks or act as a router
-    "net.ipv4.ip_forward" = mkDefault "0";
-
-    # don't allow traffic between networks or act as a router
-    "net.ipv4.conf.all.send_redirects" = mkDefault "0";
-
-    # don't allow traffic between networks or act as a router
-    "net.ipv4.conf.default.send_redirects" = mkDefault "0";
-
-    # reverse path filtering - IP spoofing protection
-    "net.ipv4.conf.all.rp_filter" = mkDefault "1";
-
-    # reverse path filtering - IP spoofing protection
-    "net.ipv4.conf.default.rp_filter" = mkDefault "1";
-
-    # ignores ICMP broadcasts to avoid participating in Smurf attacks
-    "net.ipv4.icmp_echo_ignore_broadcasts" = mkDefault "1";
-
-    # ignores bad ICMP errors
-    "net.ipv4.icmp_ignore_bogus_error_responses" = mkDefault "1";
-
-    # logs spoofed, source-routed, and redirect packets
-    "net.ipv4.conf.all.log_martians" = mkDefault "1";
-
-    # log spoofed, source-routed, and redirect packets
-    "net.ipv4.conf.default.log_martians" = mkDefault "1";
-
-    # implements RFC 1337 fix
-    "net.ipv4.tcp_rfc1337" = mkDefault "1";
-
-    # randomizes addresses of mmap base, heap, stack and VDSO page
-    "kernel.randomize_va_space" = mkDefault "2";
-
-    # Reboot the machine soon after a kernel panic.
-    "kernel.panic" = mkDefault "10";
-
-    ## Not part of the original config
-
-    # provides protection from ToCToU races
-    "fs.protected_hardlinks" = mkDefault "1";
-
-    # provides protection from ToCToU races
-    "fs.protected_symlinks" = mkDefault "1";
-
-    # makes locating kernel addresses more difficult
-    "kernel.kptr_restrict" = mkDefault "1";
-
-    # set ptrace protections
-    "kernel.yama.ptrace_scope" = mkOverride 500 "1";
-
-    # set perf only available to root
-    "kernel.perf_event_paranoid" = mkDefault "2";
 
   };
 

nixos/tests/gitlab.nix

@@ -16,6 +16,7 @@ import ./make-test.nix ({ pkgs, lib, ...} : with lib; {
 
       services.nginx = {
         enable = true;
+        recommendedProxySettings = true;
         virtualHosts = {
           "localhost" = {
             locations."/".proxyPass = "http://unix:/run/gitlab/gitlab-workhorse.socket";
@@ -75,7 +76,8 @@ import ./make-test.nix ({ pkgs, lib, ...} : with lib; {
     $gitlab->waitForUnit("gitlab.service");
     $gitlab->waitForUnit("gitlab-sidekiq.service");
     $gitlab->waitForFile("/var/gitlab/state/tmp/sockets/gitlab.socket");
-    $gitlab->waitUntilSucceeds("curl -sSf http://localhost/users/sign_in");
+    $gitlab->waitUntilSucceeds("curl -sSf http://gitlab/users/sign_in");
+    $gitlab->succeed("curl -isSf http://gitlab  | grep -i location | grep -q http://gitlab/users/sign_in");
     $gitlab->succeed("${pkgs.sudo}/bin/sudo -u gitlab -H gitlab-rake gitlab:check 1>&2")
   '';
 })

nixos/tests/hardened.nix

@@ -10,6 +10,7 @@ import ./make-test.nix ({ pkgs, ...} : {
     { users.users.alice = { isNormalUser = true; extraGroups = [ "proc" ]; };
       users.users.sybil = { isNormalUser = true; group = "wheel"; };
       imports = [ ../modules/profiles/hardened.nix ];
+      nix.useSandbox = false;
       virtualisation.emptyDiskImages = [ 4096 ];
       boot.initrd.postDeviceCommands = ''
         ${pkgs.dosfstools}/bin/mkfs.vfat -n EFISYS /dev/vdb
@@ -63,5 +64,11 @@ import ./make-test.nix ({ pkgs, ...} : {
         $machine->succeed("mount /dev/disk/by-label/EFISYS /efi");
         $machine->succeed("mountpoint -q /efi"); # now mounted
       };
+
+      # Test Nix dæmon usage
+      subtest "nix-daemon", sub {
+        $machine->fail("su -l nobody -s /bin/sh -c 'nix ping-store'");
+        $machine->succeed("su -l alice -c 'nix ping-store'") =~ "OK";
+      };
     '';
 })

nixos/tests/mxisd.nix

@@ -0,0 +1,21 @@
+import ./make-test.nix ({ pkgs, ... } : {
+
+  name = "mxisd";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ mguentner ];
+  };
+
+  nodes = {
+    server_mxisd = args : {
+      services.mxisd.enable = true;
+      services.mxisd.matrix.domain = "example.org";
+    };
+  };
+
+  testScript = ''
+    startAll;
+    $server_mxisd->waitForUnit("mxisd.service");
+    $server_mxisd->waitForOpenPort(8090);
+    $server_mxisd->succeed("curl -Ssf \"http://127.0.0.1:8090/_matrix/identity/api/v1\"")
+  '';
+})

nixos/tests/rspamd.nix

@@ -235,6 +235,7 @@ in
       services.rspamd = {
         enable = true;
         postfix.enable = true;
+        workers.rspamd_proxy.type = "proxy";
       };
     };
     testScript = ''

pkgs/applications/audio/a2jmidid/default.nix

@@ -9,12 +9,12 @@ in stdenv.mkDerivation rec {
   version = "8";
 
   src = fetchurl {
-    url = "http://repo.or.cz/a2jmidid.git/snapshot/7383d268c4bfe85df9f10df6351677659211d1ca.tar.gz";
+    url = "https://repo.or.cz/a2jmidid.git/snapshot/7383d268c4bfe85df9f10df6351677659211d1ca.tar.gz";
     sha256 = "06dgf5655znbvrd7fhrv8msv6zw8vk0hjqglcqkh90960mnnmwz7";
   };
 
-  nativeBuildInputs = [ pkgconfig wafHook ];
+  nativeBuildInputs = [ pkgconfig makeWrapper wafHook ];
-  buildInputs = [ makeWrapper alsaLib dbus libjack2 python dbus-python ];
+  buildInputs = [ alsaLib dbus libjack2 python dbus-python ];
 
   postInstall = ''
     wrapProgram $out/bin/a2j_control --set PYTHONPATH $PYTHONPATH

pkgs/applications/audio/avldrums-lv2/default.nix

@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "avldrums.lv2";
-  version = "0.3.0";
+  version = "0.3.1";
 
   src = fetchFromGitHub {
     owner = "x42";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0w51gdshq2i5bix2x5l3g3gnycy84nlzf5sj0jkrw0zrnbk6ghwg";
+    sha256 = "0yhq3n5bahhqpj40mvlkxcjsdsw63jsbz20pl77bx2qj30w25i2j";
     fetchSubmodules = true;
   };
 

pkgs/applications/audio/cadence/default.nix

@@ -1,5 +1,5 @@
 { stdenv
-, fetchurl
+, fetchzip
 , pkgconfig
 , qtbase
 , makeWrapper
@@ -12,31 +12,13 @@
   version = "0.9.0";
   pname = "cadence";
 
-  src = fetchurl {
+  src = fetchzip {
     url = "https://github.com/falkTX/Cadence/archive/v${version}.tar.gz";
-    sha256 = "07z1mnb0bmldb3i31bgw816pnvlvr9gawr51rpx3mhixg5wpiqzb";
+    sha256 = "08vcggypkdfr70v49innahs5s11hi222dhhnm5wcqzdgksphqzwx";
   };
 
-  buildInputs = [
+  nativeBuildInputs = [ makeWrapper pkgconfig ];
-    makeWrapper
+  buildInputs = [ qtbase ];
-    pkgconfig
-    qtbase
-  ];
-
-  apps = [
-    "cadence"
-    "cadence-jacksettings"
-    "cadence-pulse2loopback"
-    "claudia"
-    "cadence-aloop-daemon"
-    "cadence-logs"
-    "cadence-render"
-    "catarina"
-    "claudia-launcher"
-    "cadence-pulse2jack"
-    "cadence-session-start"
-    "catia"
-  ];
 
   makeFlags = ''
     PREFIX=""
@@ -46,20 +28,54 @@
   propagatedBuildInputs = with python3Packages; [ pyqt5 ];
 
   postInstall = ''
-    # replace with our own wrappers.
+    # replace with our own wrappers. They need to be changed manually since it wouldn't work otherwise
-    for app in $apps; do
+    rm $out/bin/cadence
-      rm $out/bin/$app
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence \
-      makeWrapper ${python3Packages.python.interpreter} $out/bin/$app \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
-        --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/cadence.py"
-        --add-flags "-O $out/share/cadence/src/$app.py"
+    rm $out/bin/claudia
-    done
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/claudia \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/claudia.py"
+    rm $out/bin/catarina
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/catarina \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/catarina.py"
+    rm $out/bin/catia
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/catia \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/catia.py"
+    rm $out/bin/cadence-jacksettings
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence-jacksettings \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/jacksettings.py"
+    rm $out/bin/cadence-aloop-daemon
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence-aloop-daemon \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/cadence_aloop_daemon.py"
+    rm $out/bin/cadence-logs
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence-logs \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/logs.py"
+    rm $out/bin/cadence-render
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence-render \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/render.py"
+    rm $out/bin/claudia-launcher
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/claudia-launcher \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/claudia_launcher.py"
+    rm $out/bin/cadence-session-start
+    makeWrapper ${python3Packages.python.interpreter} $out/bin/cadence-session-start \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+      --add-flags "-O $out/share/cadence/src/cadence_session_start.py"
   '';
 
   meta = {
     homepage = https://github.com/falkTX/Cadence/;
     description = "Collection of tools useful for audio production";
-    license = stdenv.lib.licenses.mit;
+    license = stdenv.lib.licenses.gpl2Plus;
     maintainers = with stdenv.lib.maintainers; [ genesis ];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = [ "x86_64-linux" ];
   };
 }

pkgs/applications/audio/dragonfly-reverb/default.nix

@@ -6,8 +6,8 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "michaelwillis";
     repo = "dragonfly-reverb";
-    rev = "0.9.4";
+    rev = "1.0.0";
-    sha256 = "0lc45jybjwg4wrcz4s9lvzpvqawgj825rkqhz2xxvalfbvjazi53";
+    sha256 = "05m4hd8lg0a7iiia6cbiw5qmc4p8vbkxp2qh7ywaabawiwa9r24x";
     fetchSubmodules = true;
   };
 

pkgs/applications/audio/mopidy/iris.nix

@@ -2,11 +2,11 @@
 
 pythonPackages.buildPythonApplication rec {
   pname = "Mopidy-Iris";
-  version = "3.31.1";
+  version = "3.31.2";
 
   src = pythonPackages.fetchPypi {
     inherit pname version;
-    sha256 = "1djxkgjvfzijvlq3gill1p20l0q64dbv9wd55whbir1l7y8wdga5";
+    sha256 = "0639ib5nicrabckjd17wdmhl8n3822gc2p1bn0xv8mq70paspar6";
   };
 
   propagatedBuildInputs = [
@@ -17,7 +17,7 @@ pythonPackages.buildPythonApplication rec {
     pylast
     spotipy
     raven
-    tornado
+    tornado_4
   ]);
 
   postPatch = "sed -i /tornado/d setup.py";

pkgs/applications/audio/renoise/default.nix

@@ -1,4 +1,5 @@
-{ stdenv, fetchurl, libX11, libXext, libXcursor, libXrandr, libjack2, alsaLib, releasePath ? null }:
+{ stdenv, fetchurl, libX11, libXext, libXcursor, libXrandr, libjack2, alsaLib
+, mpg123, releasePath ? null }:
 
 with stdenv.lib;
 
@@ -35,7 +36,7 @@ stdenv.mkDerivation rec {
         releasePath
     else throw "Platform is not supported by Renoise";
 
-  buildInputs = [ libX11 libXext libXcursor libXrandr alsaLib libjack2 ];
+  buildInputs = [ alsaLib libjack2 libX11 libXcursor libXext libXrandr ];
 
   installPhase = ''
     cp -r Resources $out
@@ -54,13 +55,18 @@ stdenv.mkDerivation rec {
 
     mkdir $out/bin
     ln -s $out/renoise $out/bin/renoise
+  '';
 
-    patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) --set-rpath $out/lib $out/renoise
+  postFixup = ''
+    patchelf \
+      --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+      --set-rpath ${mpg123}/lib:$out/lib \
+      $out/renoise
   '';
 
   meta = {
     description = "Modern tracker-based DAW";
-    homepage = http://www.renoise.com/;
+    homepage = https://www.renoise.com/;
     license = licenses.unfree;
     maintainers = [];
     platforms = [ "i686-linux" "x86_64-linux" ];

pkgs/applications/audio/seq24/default.nix

@@ -5,7 +5,7 @@ stdenv.mkDerivation  rec {
   version = "0.9.3";
 
   src = fetchurl {
-    url = "http://launchpad.net/seq24/trunk/${version}/+download/${name}.tar.gz";
+    url = "https://launchpad.net/seq24/trunk/${version}/+download/${name}.tar.gz";
     sha256 = "1qpyb7355s21sgy6gibkybxpzx4ikha57a8w644lca6qy9mhcwi3";
   };
 

pkgs/applications/audio/synthv1/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "synthv1-${version}";
-  version = "0.9.2";
+  version = "0.9.3";
 
   src = fetchurl {
     url = "mirror://sourceforge/synthv1/${name}.tar.gz";
-    sha256 = "1r60l286n8y4a4rrlnbc3h7xk4s2pvqykvskls89prxg0lkpz7kl";
+    sha256 = "0f58k5n2k667q8wsigg7bzl3lfgaf6jdj98r2a5nvyb18v1wpy2c";
   };
 
   buildInputs = [ qt5.qtbase qt5.qttools libjack2 alsaLib liblo lv2 ];
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "An old-school 4-oscillator subtractive polyphonic synthesizer with stereo fx";
-    homepage = http://synthv1.sourceforge.net/;
+    homepage = https://synthv1.sourceforge.io/;
     license = licenses.gpl2Plus;
     platforms = platforms.linux;
     maintainers = [ maintainers.goibhniu ];

pkgs/applications/audio/transcribe/default.nix

@@ -1,33 +1,31 @@
-{ stdenv, fetchzip, lib, makeWrapper, alsaLib, atk, cairo, gdk_pixbuf
+{ stdenv, fetchzip, wrapGAppsHook, alsaLib, atk, cairo, gdk_pixbuf
-, glib, gst-ffmpeg, gst-plugins-bad, gst-plugins-base
+, glib, gst_all_1,  gtk3, libSM, libX11, libpng12, pango, zlib }:
-, gst-plugins-good, gst-plugins-ugly, gstreamer, gtk2, libSM, libX11
-, libpng12, pango, zlib }:
 
 stdenv.mkDerivation rec {
   name = "transcribe-${version}";
-  version = "8.40";
+  version = "8.72";
 
   src = if stdenv.hostPlatform.system == "i686-linux" then
     fetchzip {
-      url = "https://www.seventhstring.com/xscribe/downlinux32_old/xscsetup.tar.gz";
+      url = "https://www.seventhstring.com/xscribe/downlinux32/xscsetup.tar.gz";
-      sha256 = "1ngidmj9zz8bmv754s5xfsjv7v6xr03vck4kigzq4bpc9b1fdhjq";
+      sha256 = "1h5l7ry9c9awpxfnd29b0wm973ifrhj17xl5d2fdsclw2swsickb";
     }
   else if stdenv.hostPlatform.system == "x86_64-linux" then
     fetchzip {
-      url = "https://www.seventhstring.com/xscribe/downlinux64_old/xsc64setup.tar.gz";
+      url = "https://www.seventhstring.com/xscribe/downlinux64/xsc64setup.tar.gz";
-      sha256 = "0svzi8svj6zn06gj0hr8mpnhq4416dvb4g5al0gpb1g3paywdaf9";
+      sha256 = "1rpd3ppnx5i5yrnfbjrx7h7dk48kwl99i9lnpa75ap7nxvbiznm0";
     }
   else throw "Platform not supported";
 
-  nativeBuildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ wrapGAppsHook ];
 
-  buildInputs = [ gst-plugins-base gst-plugins-good
+  buildInputs = with gst_all_1; [ gst-plugins-base gst-plugins-good
-    gst-plugins-bad gst-plugins-ugly gst-ffmpeg ];
+    gst-plugins-bad gst-plugins-ugly ];
 
   dontPatchELF = true;
 
-  libPath = lib.makeLibraryPath [
+  libPath = with gst_all_1; stdenv.lib.makeLibraryPath [
-    stdenv.cc.cc glib gtk2 atk pango cairo gdk_pixbuf alsaLib
+    stdenv.cc.cc glib gtk3 atk pango cairo gdk_pixbuf alsaLib
     libX11 libSM libpng12 gstreamer gst-plugins-base zlib
   ];
 
@@ -42,13 +40,18 @@ stdenv.mkDerivation rec {
     patchelf \
       --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) \
       $out/libexec/transcribe
+  '';
 
-    wrapProgram $out/libexec/transcribe \
+  preFixup = ''
-      --prefix GST_PLUGIN_SYSTEM_PATH : "$GST_PLUGIN_SYSTEM_PATH" \
+    gappsWrapperArgs+=(
+      --prefix GST_PLUGIN_SYSTEM_PATH : "$GST_PLUGIN_SYSTEM_PATH_1_0"
       --prefix LD_LIBRARY_PATH : "${libPath}"
+    )
+  '';
 
+  postFixup = ''
     ln -s $out/libexec/transcribe $out/bin/
-    '';
+  '';
 
   meta = with stdenv.lib; {
     description = "Software to help transcribe recorded music";

pkgs/applications/audio/x42-plugins/default.nix

@@ -3,12 +3,12 @@
 , libGLU, lv2, gtk2, cairo, pango, fftwFloat, zita-convolver }:
 
 stdenv.mkDerivation rec {
-  version = "20180812";
+  version = "20181103";
   name = "x42-plugins-${version}";
 
   src = fetchurl {
     url = "https://gareus.org/misc/x42-plugins/${name}.tar.xz";
-    sha256 = "0gzwzxpa2k2w9c6j3pspwi9slfyd57wb192d6yqcg92pfmnxy9dz";
+    sha256 = "085d6qjj7nl22f0xamqdrnfxwi8zrfwgkwm1svm73bjkdv270438";
   };
 
   nativeBuildInputs = [ pkgconfig ];
@@ -34,6 +34,6 @@ stdenv.mkDerivation rec {
       homepage = https://github.com/x42/x42-plugins;
       maintainers = with maintainers; [ magnetophon ];
       license = licenses.gpl2;
-      platforms = platforms.linux;
+      platforms = [ "i686-linux" "x86_64-linux" ];
     };
 }

pkgs/applications/editors/android-studio/default.nix

@@ -13,14 +13,14 @@ let
     sha256Hash = "117skqjax1xz9plarhdnrw2rwprjpybdc7mx7wggxapyy920vv5r";
   };
   betaVersion = {
-    version = "3.3.0.16"; # "Android Studio 3.3 Beta 4"
+    version = "3.3.0.17"; # "Android Studio 3.3 RC 1"
-    build = "182.5114240";
+    build = "182.5138683";
-    sha256Hash = "12gzwnlvc1w5lywpdckdgwxy2yrhf0m0fvaljdsis2arw0x9qdh2";
+    sha256Hash = "0apc566l4gwkwvfgj50d4qxm2gw26rxdlyr8kj3kfcra9a33c2b7";
   };
   latestVersion = { # canary & dev
-    version = "3.4.0.3"; # "Android Studio 3.4 Canary 4"
+    version = "3.4.0.4"; # "Android Studio 3.4 Canary 5"
-    build = "183.5129585";
+    build = "183.5141831";
-    sha256Hash = "10y09sy0h4yp39dwpp8x7kjvw8r7hvk0qllbbaqj76j33xa85793";
+    sha256Hash = "0xfk5vyjk3pdb44jp43vb5394486z2qgzrdhjzbf1ncbhvaf0aji";
   };
 in rec {
   # Old alias

pkgs/applications/editors/eclipse/plugins.nix

@@ -555,12 +555,12 @@ rec {
 
   spotbugs = buildEclipseUpdateSite rec {
     name = "spotbugs-${version}";
-    version = "3.1.8";
+    version = "3.1.9";
 
     src = fetchzip {
       stripRoot = false;
       url = "https://github.com/spotbugs/spotbugs/releases/download/${version}/eclipsePlugin.zip";
-      sha256 = "0086shivxx745f69226f59xcv7l9xliwyr9kxm6zyn753c888js3";
+      sha256 = "0m68jbyaiz0rm4qq3nnwnvgndzv2c6ay6i29kh0p0vdbanggq3xz";
     };
 
     meta = with stdenv.lib; {

pkgs/applications/editors/jetbrains/default.nix

@@ -276,12 +276,12 @@ in
 
   goland = buildGoland rec {
     name = "goland-${version}";
-    version = "2018.2.4"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "Up and Coming Go IDE";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/go/${name}.tar.gz";
-      sha256 = "0aan23ggs314bvpsldsv9m4pdmnlgdcjac9x6hv1j145a1pp439i"; /* updated by script */
+      sha256 = "0hd44flxqnnxg390mkf4ppjs2nxv0nwdc7a2i65f69bp5h61x783"; /* updated by script */
     };
     wmClass = "jetbrains-goland";
     update-channel = "GoLand Release";
@@ -289,12 +289,12 @@ in
 
   idea-community = buildIdea rec {
     name = "idea-community-${version}";
-    version = "2018.2.6"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "Integrated Development Environment (IDE) by Jetbrains, community edition";
     license = stdenv.lib.licenses.asl20;
     src = fetchurl {
       url = "https://download.jetbrains.com/idea/ideaIC-${version}.tar.gz";
-      sha256 = "02hpbyivji9vnik7p04zrja1rhhl49r0365g0i6sa1rrwd1fhvwf"; /* updated by script */
+      sha256 = "01ccz5ksbv8xh8mnk3zxqpia8zgayy8bcgmbwqibrykz47y6r7yy"; /* updated by script */
     };
     wmClass = "jetbrains-idea-ce";
     update-channel = "IntelliJ IDEA Release";
@@ -302,12 +302,12 @@ in
 
   idea-ultimate = buildIdea rec {
     name = "idea-ultimate-${version}";
-    version = "2018.2.6"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "Integrated Development Environment (IDE) by Jetbrains, requires paid license";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/idea/ideaIU-${version}-no-jdk.tar.gz";
-      sha256 = "0x0ylcbj8spvzmwxrw3p4c64ad27iz58lwj4yb8a6vwh6p22gflk"; /* updated by script */
+      sha256 = "16z0pqmxjn5dl42rbz7mx8gi13xs3220pzkdsdkh1k1ny9caqzvj"; /* updated by script */
     };
     wmClass = "jetbrains-idea";
     update-channel = "IntelliJ IDEA Release";
@@ -328,12 +328,12 @@ in
 
   pycharm-community = buildPycharm rec {
     name = "pycharm-community-${version}";
-    version = "2018.2.5"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "PyCharm Community Edition";
     license = stdenv.lib.licenses.asl20;
     src = fetchurl {
       url = "https://download.jetbrains.com/python/${name}.tar.gz";
-      sha256 = "0zfnhrkv4y90a3myq13406vzivg234l69x0c5d7vyv6ys7dmq5fm"; /* updated by script */
+      sha256 = "0kgrh3w4lpk7qkp5gss24in1nqahdfllvf97qz6r77zn9n5k1wq7"; /* updated by script */
     };
     wmClass = "jetbrains-pycharm-ce";
     update-channel = "PyCharm Release";
@@ -341,12 +341,12 @@ in
 
   pycharm-professional = buildPycharm rec {
     name = "pycharm-professional-${version}";
-    version = "2018.2.5"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "PyCharm Professional Edition";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/python/${name}.tar.gz";
-      sha256 = "0yfq25kmzzd15x83zdbrq9j62c32maklzhsk1rzymabyb56blh5c"; /* updated by script */
+      sha256 = "0q4scwnqy0h725g9z5hd145c3n10iaj04z790s4lixg1c63h3y8q"; /* updated by script */
     };
     wmClass = "jetbrains-pycharm";
     update-channel = "PyCharm Release";
@@ -367,12 +367,12 @@ in
 
   ruby-mine = buildRubyMine rec {
     name = "ruby-mine-${version}";
-    version = "2018.2.4"; /* updated by script */
+    version = "2018.2.5"; /* updated by script */
     description = "The Most Intelligent Ruby and Rails IDE";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/ruby/RubyMine-${version}.tar.gz";
-      sha256 = "0dk3ch749ai5kyg9q8819ckrqw2jk4f656iqrkkpab9fjqfjylka"; /* updated by script */
+      sha256 = "0b01fnifk5iawyf2zi7r5ffz8dxlh18g2ilrkc5746vmnsp0jxq4"; /* updated by script */
     };
     wmClass = "jetbrains-rubymine";
     update-channel = "RubyMine 2018.2";
@@ -380,12 +380,12 @@ in
 
   webstorm = buildWebStorm rec {
     name = "webstorm-${version}";
-    version = "2018.2.6"; /* updated by script */
+    version = "2018.3"; /* updated by script */
     description = "Professional IDE for Web and JavaScript development";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/webstorm/WebStorm-${version}.tar.gz";
-      sha256 = "1snx59b6d0szd1a07agpqxlprhy2mc9jvbnxcck5hfwxl3ic7x5g"; /* updated by script */
+      sha256 = "0msvgdjbdipc4g8j705d1jya2mjmx4wwhb23nch3znh7grryr75s"; /* updated by script */
     };
     wmClass = "jetbrains-webstorm";
     update-channel = "WebStorm Release";

pkgs/applications/editors/monodevelop/default.nix

@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   };
 
   nunit2510 = fetchurl {
-    url = "http://launchpad.net/nunitv2/2.5/2.5.10/+download/NUnit-2.5.10.11092.zip";
+    url = "https://launchpad.net/nunitv2/2.5/2.5.10/+download/NUnit-2.5.10.11092.zip";
     sha256 = "0k5h5bz1p2v3d0w0hpkpbpvdkcszgp8sr9ik498r1bs72w5qlwnc";
   };
 

pkgs/applications/graphics/deskew/default.nix

@@ -0,0 +1,37 @@
+{ stdenv, fetchFromBitbucket, libtiff, fpc }:
+
+stdenv.mkDerivation rec {
+
+  name = "deskew-${version}";
+  version = "1.25";
+
+  src = fetchFromBitbucket {
+    owner = "galfar";
+    repo = "app-deskew";
+    rev = "v${version}";
+    sha256 = "0zjjj66qhgqkmfxl3q7p78dv4xl4ci918pgl4d5259pqdj1bfgc8";
+  };
+
+  nativeBuildInputs = [ fpc ];
+  buildInputs = [ libtiff ];
+
+  buildPhase = ''
+    rm -r Bin # Remove pre-compiled binary
+    mkdir Bin
+    chmod +x compile.sh
+    ./compile.sh
+  '';
+
+  installPhase = ''
+    install -Dt $out/bin Bin/*
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A command line tool for deskewing scanned text documents";
+    homepage = https://bitbucket.org/galfar/app-deskew/overview;
+    license = licenses.mit;
+    maintainers = with maintainers; [ryantm];
+    platforms = platforms.all;
+  };
+
+}

pkgs/applications/graphics/tesseract/4.x.nix

@@ -7,20 +7,20 @@
 
 stdenv.mkDerivation rec {
   name = "tesseract-${version}";
-  version = "4.00.00alpha-git-20170410";
+  version = "4.0.0";
 
   src = fetchFromGitHub {
     owner = "tesseract-ocr";
     repo = "tesseract";
-    rev = "36a995bdc92eb2dd8bc5a63205708944a3f990a1";
+    rev = version;
-    sha256 = "0xz3krvap8sdm27v1dyb34lcdmx11wzvxyszpppfsfmjgkvg19bq";
+    sha256 = "1b5fi2vibc4kk9b30kkk4ais4bw8fbbv24bzr5709194hb81cav8";
   };
 
   tessdata = fetchFromGitHub {
     owner = "tesseract-ocr";
     repo = "tessdata";
-    rev = "8bf2e7ad08db9ca174ae2b0b3a7498c9f1f71d40";
+    rev = version;
-    sha256 = "0idwkv4qsmmqhrxcgyhy32yldl3vk054m7dkv4fjswfnalgsx794";
+    sha256 = "1chw1ya5zf8aaj2ixr9x013x7vwwwjjmx6f2ag0d6i14lypygy28";
   };
 
   nativeBuildInputs = [ pkgconfig autoreconfHook autoconf-archive ];

pkgs/applications/kde/dolphin.nix

@@ -4,7 +4,8 @@
   baloo, baloo-widgets, kactivities, kbookmarks, kcmutils,
   kcompletion, kconfig, kcoreaddons, kdelibs4support, kdbusaddons,
   kfilemetadata, ki18n, kiconthemes, kinit, kio, knewstuff, knotifications,
-  kparts, ktexteditor, kwindowsystem, phonon, solid
+  kparts, ktexteditor, kwindowsystem, phonon, solid,
+  wayland, qtwayland
 }:
 
 mkDerivation {
@@ -19,6 +20,7 @@ mkDerivation {
     kcoreaddons kdelibs4support kdbusaddons kfilemetadata ki18n kiconthemes
     kinit kio knewstuff knotifications kparts ktexteditor kwindowsystem
     phonon solid
+    wayland qtwayland
   ];
   outputs = [ "out" "dev" ];
   # We need the RPATH for linking, because the `libkdeinit5_dolphin.so` links

pkgs/applications/misc/aminal/default.nix

@@ -0,0 +1,75 @@
+{ buildGoPackage
+, Carbon
+, Cocoa
+, Kernel
+, cf-private
+, fetchFromGitHub
+, lib
+, mesa_glu
+, stdenv
+, xorg
+}:
+
+buildGoPackage rec {
+  name = "aminal-${version}";
+  version = "0.7.4";
+
+  goPackagePath = "github.com/liamg/aminal";
+
+  buildInputs =
+    lib.optionals stdenv.isLinux [
+      mesa_glu
+      xorg.libX11
+      xorg.libXcursor
+      xorg.libXi
+      xorg.libXinerama
+      xorg.libXrandr
+      xorg.libXxf86vm
+    ] ++ lib.optionals stdenv.isDarwin [
+      Carbon
+      Cocoa
+      Kernel
+      cf-private  /* Needed for NSDefaultRunLoopMode */
+    ];
+
+  src = fetchFromGitHub {
+    owner = "liamg";
+    repo = "aminal";
+    rev = "v${version}";
+    sha256 = "0wnzxjlv98pi3gy4hp3d19pwpa4kf1h5rqy03s9bcqdbpb1v1b7v";
+  };
+
+  preBuild = ''
+    buildFlagsArray=("-ldflags=-X ${goPackagePath}/version.Version=${version}")
+  '';
+
+  meta = with lib; {
+    description = "Golang terminal emulator from scratch";
+    longDescription = ''
+      Aminal is a modern terminal emulator for Mac/Linux implemented in Golang
+      and utilising OpenGL.
+
+      The project is experimental at the moment, so you probably won't want to
+      rely on Aminal as your main terminal for a while.
+
+      Features:
+      - Unicode support
+      - OpenGL rendering
+      - Customisation options
+      - True colour support
+      - Support for common ANSI escape sequences a la xterm
+      - Scrollback buffer
+      - Clipboard access
+      - Clickable URLs
+      - Multi platform support (Windows coming soon...)
+      - Sixel support
+      - Hints/overlays
+      - Built-in patched fonts for powerline
+      - Retina display support
+    '';
+    homepage = https://github.com/liamg/aminal;
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ kalbasit ];
+    platforms = platforms.linux ++ platforms.darwin;
+  };
+}

pkgs/applications/misc/autospotting/default.nix

@@ -0,0 +1,30 @@
+{ stdenv, buildGoPackage, fetchFromGitHub }:
+
+buildGoPackage rec {
+  name = "autospotting-${version}";
+  version = "unstable-2018-11-17";
+  goPackagePath = "github.com/AutoSpotting/AutoSpotting";
+
+  src = fetchFromGitHub {
+    owner = "AutoSpotting";
+    repo = "AutoSpotting";
+    rev = "122ab8f292a2f718dd85e79ec22acd455122907e";
+    sha256 = "0p48lgig9kblxvgq1kggczkn4qdbx6ciq9c8x0179i80vl4jf7v6";
+  };
+
+  goDeps = ./deps.nix;
+
+  # patching path where repository used to exist
+  postPatch = ''
+    sed -i "s+github.com/cristim/autospotting/core+github.com/AutoSpotting/AutoSpotting/core+" autospotting.go
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/AutoSpotting/AutoSpotting;
+    description = "Automatically convert your existing AutoScaling groups to up to 90% cheaper spot instances with minimal configuration changes";
+    license = licenses.free;
+    maintainers = [ maintainers.costrouc ];
+    platforms = platforms.linux;
+  };
+
+}

pkgs/applications/misc/autospotting/deps.nix

@@ -0,0 +1,75 @@
+# file generated from Gopkg.lock using dep2nix (https://github.com/nixcloud/dep2nix)
+[
+  {
+    goPackagePath  = "github.com/aws/aws-lambda-go";
+    fetch = {
+      type = "git";
+      url = "https://github.com/aws/aws-lambda-go";
+      rev =  "2d482ef09017ae953b1e8d5a6ddac5b696663a3c";
+      sha256 = "06v2yfvn4sn116lds0526a8mfrsng4vafrdjf1dhpalqarrbdvmz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/aws/aws-sdk-go";
+    fetch = {
+      type = "git";
+      url = "https://github.com/aws/aws-sdk-go";
+      rev =  "9333060a8d957db41bff1c80603a802aa674fad8";
+      sha256 = "0fnypw6zm6k70fzhm5a8g69ag64rxbrrpdk7l3rkfqd99slyg5kz";
+    };
+  }
+  {
+    goPackagePath  = "github.com/cristim/ec2-instances-info";
+    fetch = {
+      type = "git";
+      url = "https://github.com/cristim/ec2-instances-info";
+      rev =  "73c042a5558cd6d8b61fb82502d6f7aec334e9ed";
+      sha256 = "1xajrkxqqz5wlbi9w2wdhnk115rbmqxyga29f8v9psq8hzwgi0rg";
+    };
+  }
+  {
+    goPackagePath  = "github.com/davecgh/go-spew";
+    fetch = {
+      type = "git";
+      url = "https://github.com/davecgh/go-spew";
+      rev =  "d8f796af33cc11cb798c1aaeb27a4ebc5099927d";
+      sha256 = "19z27f306fpsrjdvkzd61w1bdazcdbczjyjck177g33iklinhpvx";
+    };
+  }
+  {
+    goPackagePath  = "github.com/go-ini/ini";
+    fetch = {
+      type = "git";
+      url = "https://github.com/go-ini/ini";
+      rev =  "5cf292cae48347c2490ac1a58fe36735fb78df7e";
+      sha256 = "0xbnw1nd22q6k863n5gs0nxld15w0p8qxbhfky85akcb5rk1vwi9";
+    };
+  }
+  {
+    goPackagePath  = "github.com/jmespath/go-jmespath";
+    fetch = {
+      type = "git";
+      url = "https://github.com/jmespath/go-jmespath";
+      rev =  "0b12d6b5";
+      sha256 = "1vv6hph8j6xgv7gwl9vvhlsaaqsm22sxxqmgmldi4v11783pc1ld";
+    };
+  }
+  {
+    goPackagePath  = "github.com/namsral/flag";
+    fetch = {
+      type = "git";
+      url = "https://github.com/namsral/flag";
+      rev =  "67f268f20922975c067ed799e4be6bacf152208c";
+      sha256 = "1lmxq3z276zrsggpfq9b7yklzzxdyib49zr8sznb1lcqlvxqsr47";
+    };
+  }
+  {
+    goPackagePath  = "github.com/pkg/errors";
+    fetch = {
+      type = "git";
+      url = "https://github.com/pkg/errors";
+      rev =  "645ef00459ed84a119197bfb8d8205042c6df63d";
+      sha256 = "001i6n71ghp2l6kdl3qq1v2vmghcz3kicv9a5wgcihrzigm75pp5";
+    };
+  }
+]

pkgs/applications/misc/llpp/default.nix

@@ -39,7 +39,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    homepage = http://repo.or.cz/w/llpp.git;
+    homepage = https://repo.or.cz/w/llpp.git;
     description = "A MuPDF based PDF pager written in OCaml";
     platforms = platforms.linux;
     maintainers = with maintainers; [ pSub ];

pkgs/applications/misc/mako/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "mako-${version}";
-  version = "1.1";
+  version = "1.2";
 
   src = fetchFromGitHub {
     owner = "emersion";
     repo = "mako";
     rev = "v${version}";
-    sha256 = "18krsyp9g6f689024dn1mq8dyj4yg8c3kcy5s88q1gm8py6c4493";
+    sha256 = "112b7s5bkvwlgsm2kng2vh8mn6wr3a6c7n1arl9adxlghdym449h";
   };
 
   nativeBuildInputs = [ meson ninja pkgconfig scdoc ];

pkgs/applications/misc/nnn/default.nix

@@ -4,13 +4,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "nnn-${version}";
-  version = "2.0";
+  version = "2.1";
 
   src = fetchFromGitHub {
     owner = "jarun";
     repo = "nnn";
     rev = "v${version}";
-    sha256 = "16c6fimr1ayb2x3mvli70x2va3nz106jdfyqn53bhss7zjqvszxl";
+    sha256 = "1vkrhsdwgacln335rjywdf7nj7fg1x55szmm8xrvwda8y2qjqhc4";
   };
 
   configFile = optionalString (conf!=null) (builtins.toFile "nnn.h" conf);

pkgs/applications/misc/pinfo/default.nix

@@ -5,7 +5,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     # homepage needed you to login to download the tarball
-    url = "http://src.fedoraproject.org/repo/pkgs/pinfo/pinfo-0.6.10.tar.bz2"
+    url = "https://src.fedoraproject.org/repo/pkgs/pinfo/pinfo-0.6.10.tar.bz2"
       + "/fe3d3da50371b1773dfe29bf870dbc5b/pinfo-0.6.10.tar.bz2";
     sha256 = "0p8wyrpz9npjcbx6c973jspm4c3xz4zxx939nngbq49xqah8088j";
   };

pkgs/applications/misc/sakura/default.nix

@@ -5,7 +5,7 @@ stdenv.mkDerivation rec {
   version = "3.6.0";
 
   src = fetchurl {
-    url = "http://launchpad.net/sakura/trunk/${version}/+download/${name}.tar.bz2";
+    url = "https://launchpad.net/sakura/trunk/${version}/+download/${name}.tar.bz2";
     sha256 = "1q463qm41ym7jb3kbzjz7b6x549vmgkb70arpkhsf86yxly1y5m1";
   };
 

pkgs/applications/misc/slic3r/prusa3d.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, makeWrapper, which, cmake, perl, perlPackages,
+{ stdenv, lib, fetchFromGitHub, makeWrapper, which, cmake, perl, perlPackages,
   boost, tbb, wxGTK30, pkgconfig, gtk3, fetchurl, gtk2, libGLU,
   glew, eigen, curl, gtest, nlopt, pcre, xorg }:
 let
@@ -98,6 +98,10 @@ stdenv.mkDerivation rec {
     # seems to be the easiest way.
     sed -i "s|\''${PERL_VENDORARCH}|$out/lib/slic3r-prusa3d|g" xs/CMakeLists.txt
     sed -i "s|\''${PERL_VENDORLIB}|$out/lib/slic3r-prusa3d|g" xs/CMakeLists.txt
+  '' + lib.optionalString (lib.versionOlder "2.5" nlopt.version) ''
+    # Since version 2.5.0 of nlopt we need to link to libnlopt, as libnlopt_cxx
+    # now seems to be integrated into the main lib.
+    sed -i 's|nlopt_cxx|nlopt|g' xs/src/libnest2d/cmake_modules/FindNLopt.cmake
   '';
 
   postInstall = ''
@@ -114,7 +118,7 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "prusa3d";
     repo = "Slic3r";
-    sha256 = "0068wwsjwmnxql7653vy3labcyslzf17kr8xdr4lg2jplm022hvy";
+    sha256 = "0crjrll8cjpkllval6abrqzvzp8g3rnb4vmwi5vivw0jvdv3w5y7";
     rev = "version_${version}";
   };
 

pkgs/applications/misc/tilda/default.nix

@@ -1,6 +1,6 @@
-{ stdenv, fetchurl, pkgconfig
+{ stdenv, fetchzip, pkgconfig
 , autoreconfHook, gettext, expat
-, confuse, vte, gtk
+, libconfuse, vte, gtk
 , makeWrapper }:
 
 stdenv.mkDerivation rec {
@@ -8,13 +8,13 @@ stdenv.mkDerivation rec {
   name = "tilda-${version}";
   version = "1.4.1";
 
-  src = fetchurl {
+  src = fetchzip {
     url = "https://github.com/lanoxx/tilda/archive/${name}.tar.gz";
-    sha256 = "0w2hry2bqcqrkik4l100b1a9jlsih6sq8zwhfpl8zzfq20i00lfs";
+    sha256 = "154rsldqjv2m1bddisb930qicb0y35kx7bxq392n2hn68jr2pxkj";
   };
 
-  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  nativeBuildInputs = [ autoreconfHook makeWrapper pkgconfig ];
-  buildInputs = [ gettext confuse vte gtk makeWrapper ];
+  buildInputs = [ gettext libconfuse vte gtk ];
 
   LD_LIBRARY_PATH = "${expat.out}/lib"; # ugly hack for xgettext to work during build
 

pkgs/applications/networking/browsers/brave/default.nix

@@ -75,10 +75,11 @@ let rpath = lib.makeLibraryPath [
 in stdenv.mkDerivation rec {
     pname = "brave";
     version = "0.56.12";
+    version = "0.56.15";
 
     src = fetchurl {
         url = "https://github.com/brave/brave-browser/releases/download/v${version}/brave-browser_${version}_amd64.deb";
-        sha256 = "1pvablwchpsm1fdhfp9kr2912yv4812r8prv5fn799qpflzxvyai";
+        sha256 = "1d18fgnxcgl95bhkgfqjyv4p81q6fciqibd3ss4vwh1ljjy1fv76";
     };
 
     dontConfigure = true;

pkgs/applications/networking/browsers/lynx/default.nix

@@ -8,14 +8,14 @@ assert sslSupport -> openssl != null;
 
 stdenv.mkDerivation rec {
   name = "lynx-${version}";
-  version = "2.8.9dev.17";
+  version = "2.8.9rel.1";
 
   src = fetchurl {
     urls = [
       "ftp://ftp.invisible-island.net/lynx/tarballs/lynx${version}.tar.bz2"
       "https://invisible-mirror.net/archives/lynx/tarballs/lynx${version}.tar.bz2"
     ];
-    sha256 = "1lvfsnrw5mmwrmn1m76q9mx287xwm3h5lg8sv7bcqilc0ywi2f54";
+    sha256 = "15cmyyma2kz1hfaa6mwjgli8zwdzq3jv0q2cl6nwzycjfwyijzrq";
   };
 
   enableParallelBuilding = true;

pkgs/applications/networking/browsers/vivaldi/default.nix

@@ -13,11 +13,11 @@
 stdenv.mkDerivation rec {
   name = "${product}-${version}";
   product = "vivaldi";
-  version = "2.1.1337.47-1";
+  version = "2.1.1337.51-1";
 
   src = fetchurl {
     url = "https://downloads.vivaldi.com/stable/${product}-stable_${version}_amd64.deb";
-    sha256 = "0i4dd5fgipplfq9jylm23jc9vn0qzf03ph1v85qh252hw5fgnyj2";
+    sha256 = "08x6abyz65vx4ycj8ys8sib9z1adb8ybmnrqjck69b30kbz78rj2";
   };
 
   unpackPhase = ''

pkgs/applications/networking/cluster/kubetail/default.nix

@@ -12,7 +12,10 @@ stdenv.mkDerivation rec {
   };
 
   installPhase = ''
-    install -Dm755 kubetail $out/bin/kubetail
+    install -Dm755 kubetail                 "$out/bin/kubetail"
+    install -Dm755 completion/kubetail.bash "$out/share/bash-completion/completions/kubetail"
+    install -Dm755 completion/kubetail.fish "$out/share/fish/vendor_completions.d/kubetail.fish"
+    install -Dm755 completion/kubetail.zsh  "$out/share/zsh/site-functions/_kubetail"
   '';
 
   meta = with lib; {

pkgs/applications/networking/cluster/stern/default.nix

@@ -1,4 +1,6 @@
-{ lib, buildGoPackage, fetchFromGitHub }:
+{ stdenv, lib, buildPackages, buildGoPackage, fetchFromGitHub }:
+
+let isCrossBuild = stdenv.hostPlatform != stdenv.buildPlatform; in
 
 buildGoPackage rec {
   name = "stern-${version}";
@@ -15,11 +17,20 @@ buildGoPackage rec {
 
   goDeps = ./deps.nix;
 
-   meta = with lib; {
+  postInstall =
-      description      = "Multi pod and container log tailing for Kubernetes";
+    let stern = if isCrossBuild then buildPackages.stern else "$bin"; in
-      homepage         = "https://github.com/wercker/stern";
+    ''
-      license          = licenses.asl20;
+      mkdir -p $bin/share/bash-completion/completions
-      maintainers      = with maintainers; [ mbode ];
+      ${stern}/bin/stern --completion bash > $bin/share/bash-completion/completions/stern
-      platforms        = platforms.unix;
+      mkdir -p $bin/share/zsh/site-functions
-    };
+      ${stern}/bin/stern --completion zsh > $bin/share/zsh/site-functions/_stern
+    '';
+
+  meta = with lib; {
+    description      = "Multi pod and container log tailing for Kubernetes";
+    homepage         = "https://github.com/wercker/stern";
+    license          = licenses.asl20;
+    maintainers      = with maintainers; [ mbode ];
+    platforms        = platforms.unix;
+  };
 }

pkgs/applications/networking/cluster/terragrunt/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "terragrunt-${version}";
-  version = "0.17.2";
+  version = "0.17.3";
 
   goPackagePath = "github.com/gruntwork-io/terragrunt";
 
@@ -10,7 +10,7 @@ buildGoPackage rec {
     owner  = "gruntwork-io";
     repo   = "terragrunt";
     rev    = "v${version}";
-    sha256 = "069l9ynyl96rfs9zw6w6n1yzjjin27731nj1ajr9jsyc8rhd84wv";
+    sha256 = "1b0fwql9nr00qpvcbsbdymxf1wrgr590gkms7yz3yirb4xfl3gl3";
   };
 
   goDeps = ./deps.nix;

pkgs/applications/networking/instant-messengers/dino/default.nix

@@ -10,16 +10,17 @@
 , dbus
 , gpgme
 , pcre
+, qrencode
  }:
 
 stdenv.mkDerivation rec {
-  name = "dino-unstable-2018-09-21";
+  name = "dino-unstable-2018-11-27";
 
   src = fetchFromGitHub {
     owner = "dino";
     repo = "dino";
-    rev = "6b7ef800f54e781a618425236ba8d4ed2f2fef9c";
+    rev = "141db9e40a3a81cfa3ad3587dc47f69c541d0fde";
-    sha256 = "1si815b6y06lridj88hws0dgq54w9jfam9sqbrq3cfcvmhc38ysk";
+    sha256 = "006r1x7drlz39jjxlfdnxgrnambw9amhl9jcgf6p1dx71h1x8221";
     fetchSubmodules = true;
   };
 
@@ -32,6 +33,7 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
+    qrencode
     gobjectIntrospection
     glib-networking
     glib

pkgs/applications/networking/instant-messengers/signal-desktop/default.nix

@@ -56,11 +56,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "signal-desktop-${version}";
-  version = "1.18.0";
+  version = "1.18.1";
 
   src = fetchurl {
     url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "0l5q55k5dp7hbvw3dnjsz39blbsahx6nh9ln4c69752zg473yv4v";
+    sha256 = "1gak6nhv5gk37iv1bfmjx6wf0p1vcln5y29i6fkzmvcrp3j2cmfh";
   };
 
   phases = [ "unpackPhase" "installPhase" ];

pkgs/applications/networking/mailreaders/mutt/default.nix

@@ -35,8 +35,8 @@ stdenv.mkDerivation rec {
   };
 
   patches = optional smimeSupport (fetchpatch {
-    url    = "https://sources.debian.net/src/mutt/1.7.2-1/debian/patches/misc/smime.rc.patch";
+    url = "https://salsa.debian.org/mutt-team/mutt/raw/debian/1.10.1-2/debian/patches/misc/smime.rc.patch";
-    sha256 = "0mdqa9w1p6cmli6976v4wi0sw9r4p5prkj7lzfd1877wk11c9c73";
+    sha256 = "1rl27qqwl4nw321ll5jcvfmkmz4fkvcsh5vihjcrhzzyf6vz8wmj";
   });
 
   buildInputs =

pkgs/applications/networking/mailreaders/neomutt/default.nix

@@ -1,6 +1,7 @@
 { stdenv, fetchFromGitHub, gettext, makeWrapper, tcl, which, writeScript
 , ncurses, perl , cyrus_sasl, gss, gpgme, kerberos, libidn, libxml2, notmuch, openssl
-, lmdb, libxslt, docbook_xsl, docbook_xml_dtd_42, mime-types }:
+, lmdb, libxslt, docbook_xsl, docbook_xml_dtd_42, mailcap
+}:
 
 let
   muttWrapper = writeScript "mutt" ''
@@ -28,7 +29,7 @@ in stdenv.mkDerivation rec {
   buildInputs = [
     cyrus_sasl gss gpgme kerberos libidn ncurses
     notmuch openssl perl lmdb
-    mime-types
+    mailcap
   ];
 
   nativeBuildInputs = [
@@ -47,10 +48,11 @@ in stdenv.mkDerivation rec {
         --replace http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd ${docbook_xml_dtd_42}/xml/dtd/docbook/docbookx.dtd
     done
 
+
     # allow neomutt to map attachments to their proper mime.types if specified wrongly
     # and use a far more comprehensive list than the one shipped with neomutt
     substituteInPlace sendlib.c \
-      --replace /etc/mime.types ${mime-types}/etc/mime.types
+      --replace /etc/mime.types ${mailcap}/etc/mime.types
 
     # The string conversion tests all fail with the first version of neomutt
     # that has tests (20180223) as well as 20180716 so we disable them for now.

pkgs/applications/networking/mailreaders/realpine/default.nix

@@ -36,7 +36,7 @@ stdenv.mkDerivation {
     license = stdenv.lib.licenses.asl20;
     maintainers = [stdenv.lib.maintainers.raskin];
     platforms = stdenv.lib.platforms.linux;
-    homepage = http://re-alpine.sf.net/;
+    homepage = https://sourceforge.net/projects/re-alpine/;
-    downloadPage = "http://sourceforge.net/projects/re-alpine/files/";
+    downloadPage = "https://sourceforge.net/projects/re-alpine/files/";
   };
 }

pkgs/applications/networking/seafile-client/default.nix

@@ -5,14 +5,14 @@
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  version = "6.2.5";
+  version = "6.2.7";
   name = "seafile-client-${version}";
 
   src = fetchFromGitHub {
     owner = "haiwen";
     repo = "seafile-client";
     rev = "v${version}";
-    sha256 = "1g09gsaqr4swgwnjxz994xgjsv7mlfaypp6r37bbsiy89a7ppzfl";
+    sha256 = "16ikl6vkp9v16608bq2sfg48idn2p7ik3q8n6j866zxkmgdvkpsg";
   };
 
   nativeBuildInputs = [ pkgconfig cmake makeWrapper ];

pkgs/applications/networking/sync/rclone/default.nix

@@ -2,15 +2,16 @@
 
 buildGoPackage rec {
   name = "rclone-${version}";
-  version = "1.44";
+  version = "1.45";
 
   goPackagePath = "github.com/ncw/rclone";
+  subPackages = [ "." ];
 
   src = fetchFromGitHub {
     owner = "ncw";
     repo = "rclone";
     rev = "v${version}";
-    sha256 = "0kpx9r4kksscsvia7r79z9h8ghph25ay9dgpqrnp599fq1bqky61";
+    sha256 = "06xg0ibv9pnrnmabh1kblvxx1pk8h5rmkr9mjbymv497sx3zgz26";
   };
 
   outputs = [ "bin" "out" "man" ];

pkgs/applications/office/kmymoney/default.nix

@@ -61,11 +61,12 @@ stdenv.mkDerivation rec {
   '';
 
   doInstallCheck = stdenv.hostPlatform == stdenv.buildPlatform;
+  installCheckInputs = [ xvfb_run ];
   installCheckPhase = let
     pluginPath = "${qtbase.bin}/${qtbase.qtPluginPrefix}";
   in lib.optionalString doInstallCheck ''
     QT_PLUGIN_PATH=${lib.escapeShellArg pluginPath} \
-      ${xvfb_run}/bin/xvfb-run -s '-screen 0 1024x768x24' make test \
+      xvfb-run -s '-screen 0 1024x768x24' make test \
       ARGS="-E '(reports-chart-test)'" # Test fails, so exclude it for now.
   '';
 

pkgs/applications/office/marp/default.nix

@@ -1,24 +1,29 @@
-{ stdenv, fetchurl, atomEnv, libXScrnSaver }:
+{ stdenv, fetchurl, atomEnv, libXScrnSaver, gtk2 }:
 
 stdenv.mkDerivation rec {
   name = "marp-${version}";
-  version = "0.0.13";
+  version = "0.0.14";
 
   src = fetchurl {
     url = "https://github.com/yhatt/marp/releases/download/v${version}/${version}-Marp-linux-x64.tar.gz";
-    sha256 = "1120mbw4mf7v4qfmss3121gkgp5pn31alk9cssxbrmdcsdkaq5ld";
+    sha256 = "0nklzxwdx5llzfwz1hl2jpp2kwz78w4y63h5l00fh6fv6zisw6j4";
   };
-  sourceRoot = ".";
+
+  unpackPhase = ''
+    mkdir {locales,resources}
+    tar --delay-directory-restore -xf $src
+    chmod u+x {locales,resources}
+  '';
 
   installPhase = ''
-      mkdir -p $out/lib/marp $out/bin
+    mkdir -p $out/lib/marp $out/bin
-      cp -r ./* $out/lib/marp
+    cp -r ./* $out/lib/marp
-      ln -s $out/lib/marp/Marp $out/bin
+    ln -s $out/lib/marp/Marp $out/bin
   '';
 
   postFixup = ''
     patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
-      --set-rpath "${atomEnv.libPath}:${stdenv.lib.makeLibraryPath [ libXScrnSaver ]}:$out/lib/marp" \
+      --set-rpath "${atomEnv.libPath}:${stdenv.lib.makeLibraryPath [ libXScrnSaver gtk2 ]}:$out/lib/marp" \
       $out/bin/Marp
   '';
 

pkgs/applications/science/biology/picard-tools/default.nix

@@ -2,14 +2,15 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.18.14";
+  version = "2.18.17";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0xc5mqifav2j4zbln04q07wjlzpwp3w0y5iv5bkp4v5486cp2ha9";
+    sha256 = "0ks7ymrjfya5h77hp0bqyipzdri0kf97c8wks32nvwkj821687zm";
   };
 
-  buildInputs = [ jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
 
   phases = [ "installPhase" ];
 
@@ -21,7 +22,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.";
+    description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
     license = licenses.mit;
     homepage = https://broadinstitute.github.io/picard/;
     maintainers = with maintainers; [ jbedo ];

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

@@ -6,7 +6,7 @@ let version = "2.48"; in
 stdenv.mkDerivation {
   name = "gwyddion-${version}";
   src = fetchurl {
-    url = "http://sourceforge.net/projects/gwyddion/files/gwyddion/${version}/gwyddion-${version}.tar.xz";
+    url = "mirror://sourceforge/gwyddion/files/gwyddion/${version}/gwyddion-${version}.tar.xz";
     sha256 = "119iw58ac2wn4cas6js8m7r1n4gmmkga6b1y711xzcyjp9hshgwx";
   };
   nativeBuildInputs = [ pkgconfig ];

pkgs/applications/science/electronics/librepcb/default.nix

@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   name = "librepcb-${version}";
-  version = "20181031";
+  version = "0.1.0";
 
   src = fetchFromGitHub {
     owner = "LibrePCB";
     repo = "LibrePCB";
     fetchSubmodules = true;
-    rev = "3cf8dba9fa88e5b392d639c9fdbcf3a44664170a";
+    rev = "d7458d3b3e126499902e1a66a0ef889f516a7c97";
-    sha256 = "0kr4mii5w3kj3kqvhgq7zjxjrq44scx8ky0x77gyqmwvwfwk7nmx";
+    sha256 = "19wh0398fzzpd65nh4mmc4jllkrgcrwxvxdby0gb5wh1sqyaqac4";
   };
 
   enableParallelBuilding = true;

pkgs/applications/science/logic/z3/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "z3-${version}";
-  version = "4.8.1";
+  version = "4.8.3";
 
   src = fetchFromGitHub {
     owner  = "Z3Prover";
     repo   = "z3";
     rev    = name;
-    sha256 = "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f";
+    sha256 = "0p5gdmhd32x6zwmx7j5cgwh4jyfxa9yapym95nlmyfaqzak92qar";
   };
 
   buildInputs = [ python fixDarwinDylibNames ];

pkgs/applications/science/math/fricas/default.nix

@@ -8,7 +8,7 @@ stdenv.mkDerivation {
   inherit name;
 
   src = fetchurl {
-    url    = "http://sourceforge.net/projects/fricas/files/fricas/${version}/${name}-full.tar.bz2";
+    url    = "mirror://sourceforge/fricas/files/fricas/${version}/${name}-full.tar.bz2";
     sha256 = "156k9az1623y5808j845c56z2nvvdrm48dzg1v0ivpplyl7vp57x";
   };
 

pkgs/applications/science/math/sage/README.md

@@ -2,46 +2,7 @@
 
 Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex.
 
-Don't feel discouraged to fix, simplify or improve things though. Here's a quick overview over the functions of the individual files:
+Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package.
-
-- `sage-src.nix`  
-  Downloads the source code and applies patches. This makes sure that all the other files work with the same sage source. If you want to apply a patch to sage or update sage to a new version, this is the place to do it.
-
-- `env-locations.nix`  
-  Creates a bash file that sets a bunch of environment variables telling sage where to find various packages and files. The definitions of those environment variables can be found in the sage source in the `src/env.py` file. This bash file needs to be sourced before sage is started (done in `sage-env.nix` and `sagedoc.nix`).
-
-- `sage-env.nix`  
-  Sets all environment variables sage needs to run. This includes the package locations defined in `env-locations.nix` as well as the location of sage itself and its various subdirectories.
-
-- `sagelib.nix`  
-  Defines the main sage package (without setting the necessary environments or running any tests).
-
-- `sage-with-env.nix`  
-  Wraps sage in the necessary environment.
-
-- `sage.nix`  
-  Runs sages doctests.
-
-- `sage-wrapper.nix`  
-  Optionally tells sage where do find the docs.
-
-- `sagedoc.nix`  
-  Builds and tests the sage html documentation. Can be used for offline documentation viewing as well as the sage `browse_sage_doc` and `search_doc` functions.
-
-- `sagenb.nix`  
-  The (semi deprecated) sage notebook.
-
-- `default.nix`  
-  Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package).
-
-- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix`
-  These are python packages that were rejected from the main nixpkgs tree because they appear unmaintained. They are needed for the (semi-deprecated) sage notebook. Since that notebook is still needed to run the sage doctests, these packages are included but not exposed to the rest of nixpkgs.
-
-- `pybrial.nix`  
-  pybrial is a dependency of sage. However, pybrial itself also has sage as a dependency. Because of that circular dependency, pybrial is hidden from the rest of nixpkgs (just as the flask packages and python-openid.
-
-- `openblas-pc.nix`  
-  This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`.
 
 ## The sage build is broken
 

pkgs/applications/science/math/sage/default.nix

@@ -1,68 +1,101 @@
-{ nixpkgs
+{ pkgs
 , withDoc ? false
 }:
 
+# Here sage and its dependencies are put together. Some dependencies may be pinned
+# as a last resort. Patching sage for compatibility with newer dependency versions
+# is always preferred, see `sage-src.nix` for that.
+
 let
-  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
+  inherit (pkgs) fetchurl symlinkJoin callPackage nodePackages;
 
   # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
-  python = nixpkgs.python2.override {
+  python = pkgs.python2.override {
     packageOverrides = self: super: {
       # python packages that appear unmaintained and were not accepted into the nixpkgs
       # tree because of that. These packages are only dependencies of the more-or-less
       # deprecated sagenb. However sagenb is still a default dependency and the doctests
       # depend on it.
       # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
+      # The dependency on the sage notebook (and therefore these packages) will be
+      # removed in the future:
+      # https://trac.sagemath.org/ticket/25837
       flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
       flask-openid = self.callPackage ./flask-openid.nix {};
       python-openid = self.callPackage ./python-openid.nix {};
-
-      pybrial = self.callPackage ./pybrial.nix {};
-
-      sagelib = self.callPackage ./sagelib.nix {
-        inherit flint ecl arb;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
-        linbox = nixpkgs.linbox.override { withSage = true; };
-      };
-
       sagenb = self.callPackage ./sagenb.nix {
         mathjax = nodePackages.mathjax;
       };
 
-      sagedoc = self.callPackage ./sagedoc.nix {
+      # Package with a cyclic dependency with sage
-        inherit sage-src;
+      pybrial = self.callPackage ./pybrial.nix {};
-      };
 
-      env-locations = self.callPackage ./env-locations.nix {
+      # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
-        inherit pari_data ecl;
+      sagelib = self.callPackage ./sagelib.nix {
-        inherit singular;
+        inherit flint ecl arb;
-        three = nodePackages.three;
+        inherit sage-src pynac singular;
-        mathjax = nodePackages.mathjax;
+        linbox = pkgs.linbox.override { withSage = true; };
-      };
-
-      sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper openblas-cblas-pc 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;
-        pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
-        three = nodePackages.three;
-      };
-
-      sage = self.callPackage ./sage.nix { };
-
-      sage-wrapper = self.callPackage ./sage-wrapper.nix {
-        inherit sage-src withDoc;
       };
     };
   };
 
-  openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
+  jupyter-kernel-definition = {
-  openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
+    displayName = "SageMath ${sage-src.version}";
-  openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
+    argv = [
+      "${sage-with-env}/bin/sage" # FIXME which sage
+      "--python"
+      "-m"
+      "sage.repl.ipython_kernel"
+      "-f"
+      "{connection_file}"
+    ];
+    language = "sagemath";
+    # just one 16x16 logo is available
+    logo32 = "${sage-src}/doc/common/themes/sage/static/sageicon.png";
+    logo64 = "${sage-src}/doc/common/themes/sage/static/sageicon.png";
+  };
+
+  # A bash script setting various environment variables to tell sage where
+  # the files its looking fore are located. Also see `sage-env`.
+  env-locations = callPackage ./env-locations.nix {
+    inherit pari_data ecl;
+    inherit singular;
+    cysignals = python.pkgs.cysignals;
+    three = nodePackages.three;
+    mathjax = nodePackages.mathjax;
+  };
+
+  # The shell file that gets sourced on every sage start. Will also source
+  # the env-locations file.
+  sage-env = callPackage ./sage-env.nix {
+    sagelib = python.pkgs.sagelib;
+    inherit env-locations;
+    inherit python rWrapper ecl singular palp flint pynac pythonEnv;
+    pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
+  };
+
+  # The documentation for sage, building it takes a lot of ram.
+  sagedoc = callPackage ./sagedoc.nix {
+    inherit sage-with-env;
+    inherit python;
+  };
+
+  # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run.
+  sage-with-env = callPackage ./sage-with-env.nix {
+    inherit pythonEnv;
+    inherit sage-env;
+    inherit pynac singular;
+    pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
+    three = nodePackages.three;
+  };
+
+  # Doesn't actually build anything, just runs sages testsuite. This is a
+  # separate derivation to make it possible to re-run the tests without
+  # rebuilding sagelib (which takes ~30 minutes).
+  # Running the tests should take something in the order of 1h.
+  sage-tests = callPackage ./sage-tests.nix {
+    inherit sage-with-env;
+  };
 
   sage-src = callPackage ./sage-src.nix {};
 
@@ -77,6 +110,7 @@ let
     sympy
     fpylll
     matplotlib
+    tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`)
     scipy
     ipywidgets
     rpy2
@@ -91,10 +125,11 @@ let
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
 
   # needs to be rWrapper, standard "R" doesn't include default packages
-  rWrapper = nixpkgs.rWrapper.override {
+  rWrapper = pkgs.rWrapper.override {
     # https://trac.sagemath.org/ticket/25674
-    R = nixpkgs.R.overrideAttrs (attrs: rec {
+    R = pkgs.R.overrideAttrs (attrs: rec {
       name = "R-3.4.4";
+      doCheck = false;
       src = fetchurl {
         url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
         sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk";
@@ -102,44 +137,45 @@ let
     });
   };
 
-  arb = nixpkgs.arb.override { inherit flint; };
+  arb = pkgs.arb.override { inherit flint; };
 
-  singular = nixpkgs.singular.override { inherit flint; };
+  singular = pkgs.singular.override { inherit flint; };
 
   # *not* to confuse with the python package "pynac"
-  pynac = nixpkgs.pynac.override { inherit singular flint; };
+  pynac = pkgs.pynac.override { inherit singular flint; };
 
   # With openblas (64 bit), the tests fail the same way as when sage is build with
   # openblas instead of openblasCompat. Apparently other packages somehow use flints
   # blas when it is available. Alternative would be to override flint to use
   # openblasCompat.
-  flint = nixpkgs.flint.override { withBlas = false; };
+  flint = pkgs.flint.override { withBlas = false; };
 
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.
   palp = symlinkJoin {
-    name = "palp-${nixpkgs.palp.version}";
+    name = "palp-${pkgs.palp.version}";
     paths = [
-      (nixpkgs.palp.override { dimensions = 4; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 4; doSymlink = false; })
-      (nixpkgs.palp.override { dimensions = 5; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 5; doSymlink = false; })
-      (nixpkgs.palp.override { dimensions = 6; doSymlink = true; })
+      (pkgs.palp.override { dimensions = 6; doSymlink = true; })
-      (nixpkgs.palp.override { dimensions = 11; doSymlink = false; })
+      (pkgs.palp.override { dimensions = 11; doSymlink = false; })
     ];
   };
 
   # Sage expects those in the same directory.
   pari_data = symlinkJoin {
     name = "pari_data";
-    paths = with nixpkgs; [
+    paths = with pkgs; [
       pari-galdata
       pari-seadata-small
     ];
   };
 
   # https://trac.sagemath.org/ticket/22191
-  ecl = nixpkgs.ecl_16_1_2;
+  ecl = pkgs.ecl_16_1_2;
 in
-  python.pkgs.sage-wrapper // {
+# A wrapper around sage that makes sure sage finds its docs (if they were build).
-    doc = python.pkgs.sagedoc;
+callPackage ./sage.nix {
-    lib = python.pkgs.sagelib;
+  inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition;
-  }
+  inherit withDoc;
+}

pkgs/applications/science/math/sage/env-locations.nix

@@ -16,6 +16,8 @@
 , cysignals
 }:
 
+# A bash script setting various environment variables to tell sage where
+# the files its looking fore are located. Also see `sage-env`.
 writeTextFile rec {
   name = "sage-env-locations";
   destination = "/${name}";

pkgs/applications/science/math/sage/openblas-pc.nix

@@ -1,17 +0,0 @@
-{ openblasCompat
-, writeTextFile
-, name
-}:
-
-writeTextFile {
-  name = "openblas-${name}-pc-${openblasCompat.version}";
-  destination = "/lib/pkgconfig/${name}.pc";
-  text = ''
-    Name: ${name}
-    Version: ${openblasCompat.version}
-
-    Description: ${name} for SageMath, provided by the OpenBLAS package.
-    Cflags: -I${openblasCompat}/include
-    Libs: -L${openblasCompat}/lib -lopenblas
-  '';
-}

pkgs/applications/science/math/sage/patches/eclib-20180710.patch

@@ -1,16 +0,0 @@
-diff --git a/src/sage/interfaces/mwrank.py b/src/sage/interfaces/mwrank.py
-index 4417b59276..ae57ca2991 100644
---- a/src/sage/interfaces/mwrank.py
-+++ b/src/sage/interfaces/mwrank.py
-@@ -54,8 +54,9 @@ def Mwrank(options="", server=None, server_tmpdir=None):
-         sage: M = Mwrank('-v 0 -l')
-         sage: print(M('0 0 1 -1 0'))
-         Curve [0,0,1,-1,0] :    Rank = 1
--        Generator 1 is [0:-1:1]; height 0.0511114082399688
--        Regulator = 0.0511114082399688
-+        Generator 1 is [0:-1:1]; height 0.051111408239969
-+        Regulator = 0.051111408239969
-+
-     """
-     global instances
-     try:

pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch

@@ -1,98 +0,0 @@
-diff --git a/src/sage/libs/eclib/interface.py b/src/sage/libs/eclib/interface.py
-index f77000c478..9d17d412ae 100644
---- a/src/sage/libs/eclib/interface.py
-+++ b/src/sage/libs/eclib/interface.py
-@@ -1014,7 +1014,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 2 will not be done;
-             ...
-             Gained index 2
--            New regulator =  93.857300720636393209
-+            New regulator =  93.85730...
-             (False, 2, '[ ]')
-             sage: EQ.points()
-             [[-2, 3, 1], [2707496766203306, 864581029138191, 2969715140223272], [-13422227300, -49322830557, 12167000000]]
-@@ -1025,7 +1025,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 3 will not be done;
-             ...
-             Gained index 3
--            New regulator =  10.4285889689595992455
-+            New regulator =  10.42858...
-             (False, 3, '[ ]')
-             sage: EQ.points()
-             [[-2, 3, 1], [-14, 25, 8], [-13422227300, -49322830557, 12167000000]]
-@@ -1036,7 +1036,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 5 will not be done;
-             ...
-             Gained index 5
--            New regulator =  0.417143558758383969818
-+            New regulator =  0.41714...
-             (False, 5, '[ ]')
-             sage: EQ.points()
-             [[-2, 3, 1], [-14, 25, 8], [1, -1, 1]]
-@@ -1221,7 +1221,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 2 will not be done;
-             ...
-             Gained index 2
--            New regulator =  93.857300720636393209
-+            New regulator =  93.85730...
-             (False, 2, '[ ]')
-             sage: EQ
-             Subgroup of Mordell-Weil group: [[-2:3:1], [2707496766203306:864581029138191:2969715140223272], [-13422227300:-49322830557:12167000000]]
-@@ -1235,7 +1235,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 3 will not be done;
-             ...
-             Gained index 3
--            New regulator =  10.4285889689595992455
-+            New regulator =  10.42858...
-             (False, 3, '[ ]')
-             sage: EQ
-             Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [-13422227300:-49322830557:12167000000]]
-@@ -1249,7 +1249,7 @@ class mwrank_MordellWeil(SageObject):
-             WARNING: saturation at primes p > 5 will not be done;
-             ...
-             Gained index 5
--            New regulator =  0.417143558758383969818
-+            New regulator =  0.41714...
-             (False, 5, '[ ]')
-             sage: EQ
-             Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [1:-1:1]]
-diff --git a/src/sage/libs/eclib/mwrank.pyx b/src/sage/libs/eclib/mwrank.pyx
-index a4f89e1ca5..f8a22d2f55 100644
---- a/src/sage/libs/eclib/mwrank.pyx
-+++ b/src/sage/libs/eclib/mwrank.pyx
-@@ -1234,9 +1234,9 @@ cdef class _two_descent:
-             sage: D2.saturate()
-             Searching for points (bound = 8)...done:
-               found points which generate a subgroup of rank 3
--              and regulator 0.417143558758383969817119544618093396749810106098479
-+              and regulator 0.41714...
-             Processing points found during 2-descent...done:
--              now regulator = 0.417143558758383969817119544618093396749810106098479
-+              now regulator = 0.41714...
-             No saturation being done
-             sage: D2.getbasis()
-             '[[1:-1:1], [-2:3:1], [-14:25:8]]'
-@@ -1281,9 +1281,9 @@ cdef class _two_descent:
-             sage: D2.saturate()
-             Searching for points (bound = 8)...done:
-               found points which generate a subgroup of rank 3
--              and regulator 0.417143558758383969817119544618093396749810106098479
-+              and regulator 0.41714...
-             Processing points found during 2-descent...done:
--              now regulator = 0.417143558758383969817119544618093396749810106098479
-+              now regulator = 0.41714...
-             No saturation being done
-             sage: D2.getbasis()
-             '[[1:-1:1], [-2:3:1], [-14:25:8]]'
-@@ -1329,9 +1329,9 @@ cdef class _two_descent:
-             sage: D2.saturate()
-             Searching for points (bound = 8)...done:
-               found points which generate a subgroup of rank 3
--              and regulator 0.417143558758383969817119544618093396749810106098479
-+              and regulator 0.41714...
-             Processing points found during 2-descent...done:
--              now regulator = 0.417143558758383969817119544618093396749810106098479
-+              now regulator = 0.41714...
-             No saturation being done
-             sage: D2.getbasis()
-             '[[1:-1:1], [-2:3:1], [-14:25:8]]'

pkgs/applications/science/math/sage/patches/known-padics-bug.patch

@@ -1,15 +0,0 @@
-diff --git a/build/pkgs/openblas/package-version.txt b/build/pkgs/openblas/package-version.txt
-index 3bc45c25d4..7c7c224887 100644
---- a/src/sage/schemes/elliptic_curves/padics.py
-+++ b/src/sage/schemes/elliptic_curves/padics.py
-@@ -292,8 +292,8 @@ def padic_regulator(self, p, prec=20, height=None, check_hypotheses=True):
- 
-         sage: max_prec = 30    # make sure we get past p^2    # long time
-         sage: full = E.padic_regulator(5, max_prec)           # long time
--        sage: for prec in range(1, max_prec):                 # long time
--        ....:     assert E.padic_regulator(5, prec) == full   # long time
-+        sage: for prec in range(1, max_prec):                 # known bug (#25969) # long time
-+        ....:     assert E.padic_regulator(5, prec) == full   # known bug (#25969) # long time
- 
-     A case where the generator belongs to the formal group already
-     (:trac:`3632`)::

pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch

@@ -1,12 +0,0 @@
-diff --git a/src/sage/all.py b/src/sage/all.py
-index 14cec431f1..25a35a0522 100644
---- a/src/sage/all.py
-+++ b/src/sage/all.py
-@@ -310,6 +310,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
- # Ignore all deprecations from IPython etc.
- warnings.filterwarnings('ignore',
-     module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
-+warnings.filterwarnings('ignore', "The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.") # matplotlib normed deprecation
- # However, be sure to keep OUR deprecation warnings
- warnings.filterwarnings('default',
-     '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.')

pkgs/applications/science/math/sage/sage-env.nix

@@ -2,7 +2,6 @@
 , lib
 , writeTextFile
 , python
-, sage-src
 , sagelib
 , env-locations
 , gfortran
@@ -37,7 +36,7 @@
 , lcalc
 , rubiks
 , flintqs
-, openblas-cblas-pc
+, openblasCompat
 , flint
 , gmp
 , mpfr
@@ -47,6 +46,10 @@
 , ntl
 }:
 
+# This generates a `sage-env` shell file that will be sourced by sage on startup.
+# It sets up various environment variables, telling sage where to find its
+# dependencies.
+
 let
   runtimepath = (lib.makeBinPath ([
     "@sage-local@"
@@ -96,26 +99,27 @@ writeTextFile rec {
   destination = "/${name}";
   text = ''
     export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
-        # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
+        # This is only needed in the src/sage/misc/cython.py test and I'm not
-        # for it outside of the tests. However since singular and openblas are runtime dependencies anyways
+        # sure if there's really a usecase for it outside of the tests. However
-        # and openblas-cblas-pc is tiny, it doesn't really hurt to include.
+        # since singular and openblas are runtime dependencies anyways, it doesn't
+        # really hurt to include.
         singular
-        openblas-cblas-pc
+        openblasCompat
       ])
     }'
-    export SAGE_ROOT='${sage-src}'
+    export SAGE_ROOT='${sagelib.src}'
     export SAGE_LOCAL='@sage-local@'
     export SAGE_SHARE='${sagelib}/share'
     orig_path="$PATH"
     export PATH='${runtimepath}'
 
     # set dependent vars, like JUPYTER_CONFIG_DIR
-    source "${sage-src}/src/bin/sage-env"
+    source "${sagelib.src}/src/bin/sage-env"
     export PATH="${runtimepath}:$orig_path" # sage-env messes with PATH
 
     export SAGE_LOGS="$TMPDIR/sage-logs"
     export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}"
-    export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sage-src}/src/doc}"
+    export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sagelib.src}/src/doc}"
 
     # set locations of dependencies
     . ${env-locations}/sage-env-locations
@@ -154,9 +158,11 @@ writeTextFile rec {
 
     export SAGE_LIB='${sagelib}/${python.sitePackages}'
 
-    export SAGE_EXTCODE='${sage-src}/src/ext'
+    export SAGE_EXTCODE='${sagelib.src}/src/ext'
 
-    # for find_library
+  # for find_library
     export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH"
   '';
+} // {
+  lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support
 }

pkgs/applications/science/math/sage/sage-src.nix

@@ -2,6 +2,12 @@
 , fetchFromGitHub
 , fetchpatch
 }:
+
+# This file is responsible for fetching the sage source and adding necessary patches.
+# It does not actually build anything, it just copies the patched sources to $out.
+# This is done because multiple derivations rely on these sources and they should
+# all get the same sources with the same patches applied.
+
 stdenv.mkDerivation rec {
   version = "8.4";
   name = "sage-src-${version}";
@@ -13,6 +19,8 @@ stdenv.mkDerivation rec {
     sha256 = "0gips1hagiz9m7s21bg5as8hrrm2x5k47h1bsq0pc46iplfwmv2d";
   };
 
+  # Patches needed because of particularities of nix or the way this is packaged.
+  # The goal is to upstream all of them and get rid of this list.
   nixPatches = [
     # https://trac.sagemath.org/ticket/25358
     (fetchpatch {
@@ -31,6 +39,7 @@ stdenv.mkDerivation rec {
     # Revert the commit that made the sphinx build fork even in the single thread
     # case. For some yet unknown reason, that breaks the docbuild on nix and archlinux.
     # See https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ.
+    # https://trac.sagemath.org/ticket/26608
     ./patches/revert-sphinx-always-fork.patch
 
     # Make sure py2/py3 tests are only run when their expected context (all "sage"
@@ -39,10 +48,16 @@ stdenv.mkDerivation rec {
     ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
   ];
 
+  # Patches needed because of package updates. We could just pin the versions of
+  # dependencies, but that would lead to rebuilds, confusion and the burdons of
+  # maintaining multiple versions of dependencies. Instead we try to make sage
+  # compatible with never dependency versions when possible. All these changes
+  # should come from or be proposed to upstream. This list will probably never
+  # be empty since dependencies update all the time.
   packageUpgradePatches = let
-    # fetch a diff between base and rev on sage's git server
+    # Fetch a diff between `base` and `rev` on sage's git server.
-    # used to fetch trac tickets by setting the base to the release and the
+    # Used to fetch trac tickets by setting the `base` to the last release and the
-    # revision to the last commit that should be included
+    # `rev` to the last commit of the ticket.
     fetchSageDiff = { base, rev, ...}@args: (
       fetchpatch ({
         url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
@@ -54,7 +69,7 @@ stdenv.mkDerivation rec {
   in [
     # New glpk version has new warnings, filter those out until upstream sage has found a solution
     # https://trac.sagemath.org/ticket/24824
-    ./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply
+    ./patches/pari-stackwarn.patch # not actually necessary since the pari upgrade, but necessary for the glpk patch to apply
     (fetchpatch {
       url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
       sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
@@ -64,8 +79,8 @@ stdenv.mkDerivation rec {
     # https://trac.sagemath.org/ticket/25260
     ./patches/numpy-1.15.1.patch
 
-    # ntl upgrade
+    # needed for ntl update
-    # https://trac.sagemath.org/ticket/25532#comment:29
+    # https://trac.sagemath.org/ticket/25532
     (fetchpatch {
       name = "lcalc-c++11.patch";
       url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
@@ -100,9 +115,7 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  patches = nixPatches ++ packageUpgradePatches ++ [
+  patches = nixPatches ++ packageUpgradePatches;
-    ./patches/known-padics-bug.patch
-  ];
 
   postPatch = ''
     # make sure shebangs etc are fixed, but sage-python23 still works

pkgs/applications/science/math/sage/sage-tests.nix

@@ -0,0 +1,51 @@
+{ stdenv
+, lib
+, sage-with-env
+, makeWrapper
+, files ? null # "null" means run all tests
+, longTests ? true # run tests marked as "long time"
+}:
+
+# for a quick test of some source files:
+# nix-build -E 'with (import ./. {}); sage.tests.override { files = [ "src/sage/misc/cython.py" ];}'
+
+let
+  src = sage-with-env.env.lib.src;
+  runAllTests = files == null;
+  testArgs = if runAllTests then "--all" else testFileList;
+  patienceSpecifier = if longTests then "--long" else "";
+  relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute
+  testFileList = lib.concatStringsSep " " (map relpathToArg files);
+in
+stdenv.mkDerivation rec {
+  version = src.version;
+  name = "sage-tests-${version}";
+  inherit src;
+
+  buildInputs = [
+    makeWrapper
+    sage-with-env
+  ];
+
+  unpackPhase = "#do nothing";
+  configurePhase = "#do nothing";
+  buildPhase = "#do nothing";
+
+  installPhase = ''
+    # This output is not actually needed for anything, the package just
+    # exists to decouple the sage build from its t ests.
+
+    mkdir -p "$out/bin"
+    # Like a symlink, but make sure that $0 points to the original.
+    makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage"
+  '';
+
+  doInstallCheck = true;
+  installCheckPhase = ''
+    export HOME="$TMPDIR/sage-home"
+    mkdir -p "$HOME"
+
+    # "--long" tests are in the order of 1h, without "--long" its 1/2h
+    "sage" -t --timeout=0 --nthreads "$NIX_BUILD_CORES" --optional=sage ${patienceSpecifier} ${testArgs}
+  '';
+}