Merge master into staging

doc/package-notes.xml

@@ -705,4 +705,52 @@ overrides = super: self: rec {
 </programlisting>
   </para>
  </section>
+ <section xml:id="sec-citrix">
+  <title>Citrix Receiver</title>
+
+  <para>
+   The <link xlink:href="https://www.citrix.com/products/receiver/">Citrix Receiver</link> is a remote
+   desktop viewer which provides access to
+   <link xlink:href="https://www.citrix.com/products/xenapp-xendesktop/">XenDesktop</link> installations.
+  </para>
+
+  <section xml:id="sec-citrix-base">
+   <title>Basic usage</title>
+   <para>
+    The tarball archive needs to be downloaded manually as the licenses agreements of the vendor
+    need to be accepted first. This is available at the
+    <link xlink:href="https://www.citrix.com/downloads/citrix-receiver/">download page at citrix.com</link>.
+    Then run <literal>nix-prefetch-url file://$PWD/linuxx64-$version.tar.gz</literal>.
+    With the archive available in the store the package can be built and installed with Nix.
+   </para>
+
+   <para>
+    <emphasis>Note: it's recommended to install <literal>Citrix Receiver</literal> using
+    <literal>nix-env -i</literal> or globally to ensure that the <literal>.desktop</literal> files
+    are installed properly into <literal>$XDG_CONFIG_DIRS</literal>. Otherwise it won't
+    be possible to open <literal>.ica</literal> files
+    automatically from the browser to start a Citrix connection.</emphasis>
+   </para>
+  </section>
+  <section xml:id="sec-citrix-custom-certs">
+   <title>Custom certificates</title>
+   <para>
+    The <literal>Citrix Receiver</literal> in <literal>nixpkgs</literal> trusts several certificates
+    <link xlink:href="https://curl.haxx.se/docs/caextract.html">from the Mozilla database</link> by default.
+    However several companies using Citrix might require their own corporate certificate. On distros with imperative
+    packaging these certs can be stored easily in
+    <link xlink:href="https://developer-docs.citrix.com/projects/receiver-for-linux-command-reference/en/13.7/"><literal>$ICAROOT</literal></link>,
+    however this directory is a store path in <literal>nixpkgs</literal>. In order to work around this issue the package provides a simple
+    mechanism to add custom certificates without rebuilding the entire package using <literal>symlinkJoin</literal>:
+
+<programlisting>
+<![CDATA[with import <nixpkgs> { config.allowUnfree = true; };
+let extraCerts = [ ./custom-cert-1.pem ./custom-cert-2.pem /* ... */ ]; in
+citrix_receiver.override {
+  inherit extraCerts;
+}]]>
+</programlisting>
+   </para>
+  </section>
+ </section>
 </chapter>

doc/reviewing-contributions.xml

@@ -103,8 +103,9 @@
     <itemizedlist>
      <listitem>
       <para>
-       mention-bot usually notifies GitHub users based on the submitted changes,
+       <link xlink:href="https://help.github.com/articles/about-codeowners/">CODEOWNERS</link>
-       but it can happen that it misses some of the package maintainers.
+       will make GitHub notify users based on the submitted changes, but it can
+       happen that it misses some of the package maintainers.
       </para>
      </listitem>
     </itemizedlist>
@@ -376,8 +377,9 @@ $ nix-shell -p nox --run "nox-review -k pr PRNUMBER"
     <itemizedlist>
      <listitem>
       <para>
-       Mention-bot notify GitHub users based on the submitted changes, but it
+       <link xlink:href="https://help.github.com/articles/about-codeowners/">CODEOWNERS</link>
-       can happen that it miss some of the package maintainers.
+       will make GitHub notify users based on the submitted changes, but it can
+       happen that it misses some of the package maintainers.
       </para>
      </listitem>
     </itemizedlist>

maintainers/maintainer-list.nix

@@ -807,6 +807,11 @@
     github = "coroa";
     name = "Jonas Hörsch";
   };
+  costrouc = {
+    email = "chris.ostrouchov@gmail.com";
+    github = "costrouc";
+    name = "Chris Ostrouchov";
+  };
   couchemar = {
     email = "couchemar@yandex.ru";
     github = "couchemar";
@@ -1689,6 +1694,11 @@
     github = "imalsogreg";
     name = "Greg Hale";
   };
+  imuli = {
+    email = "i@imu.li";
+    github = "imuli";
+    name = "Imuli";
+  };
   infinisil = {
     email = "infinisil@icloud.com";
     github = "infinisil";
@@ -1837,6 +1847,11 @@
     github = "jluttine";
     name = "Jaakko Luttinen";
   };
+  jmettes = {
+    email = "jonathan@jmettes.com";
+    github = "jmettes";
+    name = "Jonathan Mettes";
+  };
   Jo = {
     email = "0x4A6F@shackspace.de";
     name = "Joachim Ernst";
@@ -2094,6 +2109,11 @@
     github = "kuznero";
     name = "Roman Kuznetsov";
   };
+  kylewlacy = {
+    email = "kylelacy+nix@pm.me";
+    github = "kylewlacy";
+    name = "Kyle Lacy";
+  };
   lasandell = {
     email = "lasandell@gmail.com";
     github = "lasandell";
@@ -2180,7 +2200,7 @@
     name = "Nathaniel Baxter";
   };
   lightdiscord = {
-    email = "arnaud@lightdiscord.me";
+    email = "root@arnaud.sh";
     github = "lightdiscord";
     name = "Arnaud Pascal";
   };

nixos/doc/manual/release-notes/rl-1809.xml

@@ -73,6 +73,20 @@ $ nix-instantiate -E '(import <nixpkgsunstable> {}).gitFull'
   </para>
 
   <itemizedlist>
+   <listitem>
+    <para>
+     The <varname>services.cassandra</varname> module has been reworked and
+     was rewritten from scratch. The service has succeeding tests for
+     the versions 2.1, 2.2, 3.0 and 3.11 of <link
+     xlink:href="https://cassandra.apache.org/">Apache Cassandra</link>.
+    </para>
+   </listitem>
+   <listitem>
+    <para>
+     There is a new <varname>services.foundationdb</varname> module for deploying
+     <link xlink:href="https://www.foundationdb.org">FoundationDB</link> clusters.
+    </para>
+   </listitem>
    <listitem>
     <para>
      When enabled the <literal>iproute2</literal> will copy the files expected
@@ -113,6 +127,12 @@ $ nix-instantiate -E '(import &lt;nixpkgsunstable&gt; {}).gitFull'
   </para>
 
   <itemizedlist>
+   <listitem>
+    <para>
+     The deprecated <varname>services.cassandra</varname> module has
+     seen a complete rewrite. (See above.)
+    </para>
+   </listitem>
    <listitem>
     <para>
      <literal>lib.strict</literal> is removed. Use
@@ -170,6 +190,16 @@ $ nix-instantiate -E '(import &lt;nixpkgsunstable&gt; {}).gitFull'
       which indicates that the nix output hash will be used as tag.
     </para>
    </listitem>
+   <listitem>
+    <para>
+      Options
+      <literal>boot.initrd.luks.devices.<replaceable>name</replaceable>.yubikey.ramfsMountPoint</literal>
+      <literal>boot.initrd.luks.devices.<replaceable>name</replaceable>.yubikey.storage.mountPoint</literal>
+      were removed. <literal>luksroot.nix</literal> module never supported more than one YubiKey at
+      a time anyway, hence those options never had any effect. You should be able to remove them
+      from your config without any issues.
+    </para>
+   </listitem>
   </itemizedlist>
  </section>
 

nixos/modules/installer/cd-dvd/installation-cd-base.nix

@@ -29,8 +29,5 @@ with lib;
   # Add Memtest86+ to the CD.
   boot.loader.grub.memtest86.enable = true;
 
-  # Allow the user to log in as root without a password.
-  users.users.root.initialHashedPassword = "";
-
   system.stateVersion = mkDefault "18.03";
 }

nixos/modules/installer/cd-dvd/sd-image-aarch64.nix

@@ -33,9 +33,6 @@ in
   # Also increase the amount of CMA to ensure the virtual console on the RPi3 works.
   boot.kernelParams = ["cma=32M" "console=ttyS0,115200n8" "console=ttyAMA0,115200n8" "console=tty0"];
 
-  # FIXME: this probably should be in installation-device.nix
-  users.users.root.initialHashedPassword = "";
-
   sdImage = {
     populateBootCommands = let
       configTxt = pkgs.writeText "config.txt" ''

nixos/modules/installer/cd-dvd/sd-image-armv7l-multiplatform.nix

@@ -34,9 +34,6 @@ in
   # - ttySAC2: for Exynos (ODROID-XU3)
   boot.kernelParams = ["console=ttyS0,115200n8" "console=ttymxc0,115200n8" "console=ttyAMA0,115200n8" "console=ttyO0,115200n8" "console=ttySAC2,115200n8" "console=tty0"];
 
-  # FIXME: this probably should be in installation-device.nix
-  users.users.root.initialHashedPassword = "";
-
   sdImage = {
     populateBootCommands = let
       configTxt = pkgs.writeText "config.txt" ''

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

@@ -27,9 +27,6 @@ in
   boot.consoleLogLevel = lib.mkDefault 7;
   boot.kernelPackages = pkgs.linuxPackages_rpi;
 
-  # FIXME: this probably should be in installation-device.nix
-  users.users.root.initialHashedPassword = "";
-
   sdImage = {
     populateBootCommands = let
       configTxt = pkgs.writeText "config.txt" ''

nixos/modules/installer/netboot/netboot-base.nix

@@ -14,7 +14,4 @@ with lib;
       ../../profiles/base.nix
       ../../profiles/installation-device.nix
     ];
-
-  # Allow the user to log in as root without a password.
-  users.users.root.initialHashedPassword = "";
 }

nixos/modules/installer/tools/nixos-generate-config.pl

@@ -536,6 +536,13 @@ if ($showHardwareConfig) {
   # Use the systemd-boot EFI boot loader.
   boot.loader.systemd-boot.enable = true;
   boot.loader.efi.canTouchEfiVariables = true;
+EOF
+        } elsif (-e "/boot/extlinux") {
+            $bootLoaderConfig = <<EOF;
+  # Use the extlinux boot loader. (NixOS wants to enable GRUB by default)
+  boot.loader.grub.enable = false;
+  # Enables the generation of /boot/extlinux/extlinux.conf
+  boot.loader.generic-extlinux-compatible.enable = true;
 EOF
         } elsif ($virt ne "systemd-nspawn") {
             $bootLoaderConfig = <<EOF;

nixos/modules/misc/ids.nix

@@ -324,6 +324,7 @@
       hadoop = 297;
       hydron = 298;
       cfssl = 299;
+      cassandra = 300;
 
       # When adding a uid, make sure it doesn't match an existing gid. And don't use uids above 399!
 
@@ -608,6 +609,7 @@
       hadoop = 297;
       hydron = 298;
       cfssl = 299;
+      cassandra = 300;
 
       # When adding a gid, make sure it doesn't match an existing
       # uid. Users and groups with the same name should have equal

nixos/modules/module-list.nix

@@ -201,6 +201,7 @@
   ./services/databases/4store-endpoint.nix
   ./services/databases/4store.nix
   ./services/databases/aerospike.nix
+  ./services/databases/cassandra.nix
   ./services/databases/clickhouse.nix
   ./services/databases/couchdb.nix
   ./services/databases/firebird.nix

nixos/modules/profiles/installation-device.nix

@@ -86,5 +86,9 @@ with lib;
     networking.firewall.logRefusedConnections = mkDefault false;
 
     environment.systemPackages = [ pkgs.vim ];
+
+
+    # Allow the user to log in as root without a password.
+    users.users.root.initialHashedPassword = "";
   };
 }

nixos/modules/rename.nix

@@ -9,7 +9,6 @@ with lib;
     (mkRenamedOptionModule [ "system" "nixos" "stateVersion" ] [ "system" "stateVersion" ])
     (mkRenamedOptionModule [ "system" "nixos" "defaultChannel" ] [ "system" "defaultChannel" ])
 
-    (mkRenamedOptionModule [ "dysnomia" ] [ "services" "dysnomia" ])
     (mkRenamedOptionModule [ "environment" "x11Packages" ] [ "environment" "systemPackages" ])
     (mkRenamedOptionModule [ "environment" "enableBashCompletion" ] [ "programs" "bash" "enableCompletion" ])
     (mkRenamedOptionModule [ "environment" "nix" ] [ "nix" "package" ])

nixos/modules/services/databases/cassandra.nix

@@ -4,444 +4,287 @@ with lib;
 
 let
   cfg = config.services.cassandra;
-  cassandraPackage = cfg.package.override {
+  defaultUser = "cassandra";
-    jre = cfg.jre;
+  cassandraConfig = flip recursiveUpdate cfg.extraConfig
-  };
+    ({ commitlog_sync = "batch";
-  cassandraUser = {
+       commitlog_sync_batch_window_in_ms = 2;
-    name = cfg.user;
+       partitioner = "org.apache.cassandra.dht.Murmur3Partitioner";
-    home = "/var/lib/cassandra";
+       endpoint_snitch = "SimpleSnitch";
-    description = "Cassandra role user";
+       seed_provider =
-  };
+         [{ class_name = "org.apache.cassandra.locator.SimpleSeedProvider";
+            parameters = [ { seeds = "127.0.0.1"; } ];
+         }];
+       data_file_directories = [ "${cfg.homeDir}/data" ];
+       commitlog_directory = "${cfg.homeDir}/commitlog";
+       saved_caches_directory = "${cfg.homeDir}/saved_caches";
+     } // (if builtins.compareVersions cfg.package.version "3" >= 0
+             then { hints_directory = "${cfg.homeDir}/hints"; }
+             else {})
+    );
+  cassandraConfigWithAddresses = cassandraConfig //
+    ( if isNull cfg.listenAddress
+        then { listen_interface = cfg.listenInterface; }
+        else { listen_address = cfg.listenAddress; }
+    ) // (
+      if isNull cfg.rpcAddress
+        then { rpc_interface = cfg.rpcInterface; }
+        else { rpc_address = cfg.rpcAddress; }
+    );
+  cassandraEtc = pkgs.stdenv.mkDerivation
+    { name = "cassandra-etc";
+      cassandraYaml = builtins.toJSON cassandraConfigWithAddresses;
+      cassandraEnvPkg = "${cfg.package}/conf/cassandra-env.sh";
+      buildCommand = ''
+        mkdir -p "$out"
 
-  cassandraRackDcProperties = ''
+        echo "$cassandraYaml" > "$out/cassandra.yaml"
-    dc=${cfg.dc}
+        ln -s "$cassandraEnvPkg" "$out/cassandra-env.sh"
-    rack=${cfg.rack}
       '';
-
-  cassandraConf = ''
-    cluster_name: ${cfg.clusterName}
-    num_tokens: 256
-    auto_bootstrap: ${boolToString cfg.autoBootstrap}
-    hinted_handoff_enabled: ${boolToString cfg.hintedHandOff}
-    hinted_handoff_throttle_in_kb: ${builtins.toString cfg.hintedHandOffThrottle}
-    max_hints_delivery_threads: 2
-    max_hint_window_in_ms: 10800000 # 3 hours
-    authenticator: ${cfg.authenticator}
-    authorizer: ${cfg.authorizer}
-    permissions_validity_in_ms: 2000
-    partitioner: org.apache.cassandra.dht.Murmur3Partitioner
-    data_file_directories:
-    ${builtins.concatStringsSep "\n" (map (v: "  - "+v) cfg.dataDirs)}
-    commitlog_directory: ${cfg.commitLogDirectory}
-    disk_failure_policy: stop
-    key_cache_size_in_mb:
-    key_cache_save_period: 14400
-    row_cache_size_in_mb: 0
-    row_cache_save_period: 0
-    saved_caches_directory: ${cfg.savedCachesDirectory}
-    commitlog_sync: ${cfg.commitLogSync}
-    commitlog_sync_period_in_ms: ${builtins.toString cfg.commitLogSyncPeriod}
-    commitlog_segment_size_in_mb: 32
-    seed_provider:
-      - class_name: org.apache.cassandra.locator.SimpleSeedProvider
-        parameters:
-          - seeds: "${builtins.concatStringsSep "," cfg.seeds}"
-    concurrent_reads: ${builtins.toString cfg.concurrentReads}
-    concurrent_writes: ${builtins.toString cfg.concurrentWrites}
-    memtable_flush_queue_size: 4
-    trickle_fsync: false
-    trickle_fsync_interval_in_kb: 10240
-    storage_port: 7000
-    ssl_storage_port: 7001
-    listen_address: ${cfg.listenAddress}
-    start_native_transport: true
-    native_transport_port: 9042
-    start_rpc: true
-    rpc_address: ${cfg.rpcAddress}
-    rpc_port: 9160
-    rpc_keepalive: true
-    rpc_server_type: sync
-    thrift_framed_transport_size_in_mb: 15
-    incremental_backups: ${boolToString cfg.incrementalBackups}
-    snapshot_before_compaction: false
-    auto_snapshot: true
-    column_index_size_in_kb: 64
-    in_memory_compaction_limit_in_mb: 64
-    multithreaded_compaction: false
-    compaction_throughput_mb_per_sec: 16
-    compaction_preheat_key_cache: true
-    read_request_timeout_in_ms: 10000
-    range_request_timeout_in_ms: 10000
-    write_request_timeout_in_ms: 10000
-    cas_contention_timeout_in_ms: 1000
-    truncate_request_timeout_in_ms: 60000
-    request_timeout_in_ms: 10000
-    cross_node_timeout: false
-    endpoint_snitch: ${cfg.snitch}
-    dynamic_snitch_update_interval_in_ms: 100
-    dynamic_snitch_reset_interval_in_ms: 600000
-    dynamic_snitch_badness_threshold: 0.1
-    request_scheduler: org.apache.cassandra.scheduler.NoScheduler
-    server_encryption_options:
-      internode_encryption: ${cfg.internodeEncryption}
-      keystore: ${cfg.keyStorePath}
-      keystore_password: ${cfg.keyStorePassword}
-      truststore: ${cfg.trustStorePath}
-      truststore_password: ${cfg.trustStorePassword}
-    client_encryption_options:
-      enabled: ${boolToString cfg.clientEncryption}
-      keystore: ${cfg.keyStorePath}
-      keystore_password: ${cfg.keyStorePassword}
-    internode_compression: all
-    inter_dc_tcp_nodelay: false
-    preheat_kernel_page_cache: false
-    streaming_socket_timeout_in_ms: ${toString cfg.streamingSocketTimoutInMS}
-  '';
-
-  cassandraLog = ''
-    log4j.rootLogger=${cfg.logLevel},stdout
-    log4j.appender.stdout=org.apache.log4j.ConsoleAppender
-    log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
-    log4j.appender.stdout.layout.ConversionPattern=%5p [%t] %d{HH:mm:ss,SSS} %m%n
-  '';
-
-  cassandraConfFile = pkgs.writeText "cassandra.yaml" cassandraConf;
-  cassandraLogFile = pkgs.writeText "log4j-server.properties" cassandraLog;
-  cassandraRackFile = pkgs.writeText "cassandra-rackdc.properties" cassandraRackDcProperties;
-
-  cassandraEnvironment = {
-    CASSANDRA_HOME = cassandraPackage;
-    JAVA_HOME = cfg.jre;
-    CASSANDRA_CONF = "/etc/cassandra";
     };
-
 in {
-
-  ###### interface
-
   options.services.cassandra = {
-    enable = mkOption {
+    enable = mkEnableOption ''
-      description = "Whether to enable cassandra.";
+      Apache Cassandra – Scalable and highly available database.
-      default = false;
+    '';
-      type = types.bool;
-    };
-    package = mkOption {
-      description = "Cassandra package to use.";
-      default = pkgs.cassandra;
-      defaultText = "pkgs.cassandra";
-      type = types.package;
-    };
-    jre = mkOption {
-      description = "JRE package to run cassandra service.";
-      default = pkgs.jre;
-      defaultText = "pkgs.jre";
-      type = types.package;
-    };
     user = mkOption {
-      description = "User that runs cassandra service.";
+      type = types.str;
-      default = "cassandra";
+      default = defaultUser;
-      type = types.string;
+      description = "Run Apache Cassandra under this user.";
     };
     group = mkOption {
-      description = "Group that runs cassandra service.";
-      default = "cassandra";
-      type = types.string;
-    };
-    envFile = mkOption {
-      description = "path to cassandra-env.sh";
-      default = "${cassandraPackage}/conf/cassandra-env.sh";
-      defaultText = "\${cassandraPackage}/conf/cassandra-env.sh";
-      type = types.path;
-    };
-    clusterName = mkOption {
-      description = "set cluster name";
-      default = "cassandra";
-      example = "prod-cluster0";
-      type = types.string;
-    };
-    commitLogDirectory = mkOption {
-      description = "directory for commit logs";
-      default = "/var/lib/cassandra/commit_log";
-      type = types.string;
-    };
-    savedCachesDirectory = mkOption {
-      description = "directory for saved caches";
-      default = "/var/lib/cassandra/saved_caches";
-      type = types.string;
-    };
-    hintedHandOff = mkOption {
-      description = "enable hinted handoff";
-      default = true;
-      type = types.bool;
-    };
-    hintedHandOffThrottle = mkOption {
-      description = "hinted hand off throttle rate in kb";
-      default = 1024;
-      type = types.int;
-    };
-    commitLogSync = mkOption {
-      description = "commitlog sync method";
-      default = "periodic";
       type = types.str;
-      example = "batch";
+      default = defaultUser;
+      description = "Run Apache Cassandra under this group.";
     };
-    commitLogSyncPeriod = mkOption {
+    homeDir = mkOption {
-      description = "commitlog sync period in ms ";
-      default = 10000;
-      type = types.int;
-    };
-    envScript = mkOption {
-      default = "${cassandraPackage}/conf/cassandra-env.sh";
-      defaultText = "\${cassandraPackage}/conf/cassandra-env.sh";
       type = types.path;
-      description = "Supply your own cassandra-env.sh rather than using the default";
+      default = "/var/lib/cassandra";
+      description = ''
+        Home directory for Apache Cassandra.
+      '';
     };
-    extraParams = mkOption {
+    package = mkOption {
-      description = "add additional lines to cassandra-env.sh";
+      type = types.package;
+      default = pkgs.cassandra;
+      defaultText = "pkgs.cassandra";
+      example = literalExample "pkgs.cassandra_3_11";
+      description = ''
+        The Apache Cassandra package to use.
+      '';
+    };
+    jvmOpts = mkOption {
+      type = types.listOf types.str;
       default = [];
-      example = [''JVM_OPTS="$JVM_OPTS -Dcassandra.available_processors=1"''];
+      description = ''
-      type = types.listOf types.str;
+        Populate the JVM_OPT environment variable.
-    };
+      '';
-    dataDirs = mkOption {
-      type = types.listOf types.path;
-      default = [ "/var/lib/cassandra/data" ];
-      description = "Data directories for cassandra";
-    };
-    logLevel = mkOption {
-      type = types.str;
-      default = "INFO";
-      description = "default logging level for log4j";
-    };
-    internodeEncryption = mkOption {
-      description = "enable internode encryption";
-      default = "none";
-      example = "all";
-      type = types.str;
-    };
-    clientEncryption = mkOption {
-      description = "enable client encryption";
-      default = false;
-      type = types.bool;
-    };
-    trustStorePath = mkOption {
-      description = "path to truststore";
-      default = ".conf/truststore";
-      type = types.str;
-    };
-    keyStorePath = mkOption {
-      description = "path to keystore";
-      default = ".conf/keystore";
-      type = types.str;
-    };
-    keyStorePassword = mkOption {
-      description = "password to keystore";
-      default = "cassandra";
-      type = types.str;
-    };
-    trustStorePassword = mkOption {
-      description = "password to truststore";
-      default = "cassandra";
-      type = types.str;
-    };
-    seeds = mkOption {
-      description = "password to truststore";
-      default = [ "127.0.0.1" ];
-      type = types.listOf types.str;
-    };
-    concurrentWrites = mkOption {
-      description = "number of concurrent writes allowed";
-      default = 32;
-      type = types.int;
-    };
-    concurrentReads = mkOption {
-      description = "number of concurrent reads allowed";
-      default = 32;
-      type = types.int;
     };
     listenAddress = mkOption {
-      description = "listen address";
+      type = types.nullOr types.str;
-      default = "localhost";
+      default = "127.0.0.1";
-      type = types.str;
+      example = literalExample "null";
+      description = ''
+        Address or interface to bind to and tell other Cassandra nodes
+        to connect to. You _must_ change this if you want multiple
+        nodes to be able to communicate!
+
+        Set listenAddress OR listenInterface, not both.
+
+        Leaving it blank leaves it up to
+        InetAddress.getLocalHost(). This will always do the Right
+        Thing _if_ the node is properly configured (hostname, name
+        resolution, etc), and the Right Thing is to use the address
+        associated with the hostname (it might not be).
+
+        Setting listen_address to 0.0.0.0 is always wrong.
+      '';
+    };
+    listenInterface = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      example = "eth1";
+      description = ''
+        Set listenAddress OR listenInterface, not both. Interfaces
+        must correspond to a single address, IP aliasing is not
+        supported.
+      '';
     };
     rpcAddress = mkOption {
-      description = "rpc listener address";
+      type = types.nullOr types.str;
-      default = "localhost";
+      default = "127.0.0.1";
-      type = types.str;
+      example = literalExample "null";
-    };
-    incrementalBackups = mkOption {
-      description = "enable incremental backups";
-      default = false;
-      type = types.bool;
-    };
-    snitch = mkOption {
-      description = "snitch to use for topology discovery";
-      default = "GossipingPropertyFileSnitch";
-      example = "Ec2Snitch";
-      type = types.str;
-    };
-    dc = mkOption {
-      description = "datacenter for use in topology configuration";
-      default = "DC1";
-      example = "DC1";
-      type = types.str;
-    };
-    rack = mkOption {
-      description = "rack for use in topology configuration";
-      default = "RAC1";
-      example = "RAC1";
-      type = types.str;
-    };
-    authorizer = mkOption {
-      description = "
-        Authorization backend, implementing IAuthorizer; used to limit access/provide permissions
-      ";
-      default = "AllowAllAuthorizer";
-      example = "CassandraAuthorizer";
-      type = types.str;
-    };
-    authenticator = mkOption {
-      description = "
-        Authentication backend, implementing IAuthenticator; used to identify users
-      ";
-      default = "AllowAllAuthenticator";
-      example = "PasswordAuthenticator";
-      type = types.str;
-    };
-    autoBootstrap = mkOption {
-      description = "It makes new (non-seed) nodes automatically migrate the right data to themselves.";
-      default = true;
-      type = types.bool;
-    };
-    streamingSocketTimoutInMS = mkOption {
-      description = "Enable or disable socket timeout for streaming operations";
-      default = 3600000; #CASSANDRA-8611
-      example = 120;
-      type = types.int;
-    };
-    repairStartAt = mkOption {
-      default = "Sun";
-      type = types.string;
       description = ''
-      Defines realtime (i.e. wallclock) timers with calendar event
+        The address or interface to bind the native transport server to.
-      expressions. For more details re: systemd OnCalendar at
+
-      https://www.freedesktop.org/software/systemd/man/systemd.time.html#Displaying%20Time%20Spans
+        Set rpcAddress OR rpcInterface, not both.
-      '';
+
-      example = ["weekly" "daily" "08:05:40" "mon,fri *-1/2-1,3 *:30:45"];
+        Leaving rpcAddress blank has the same effect as on
-    };
+        listenAddress (i.e. it will be based on the configured hostname
-    repairRandomizedDelayInSec = mkOption {
+        of the node).
-      default = 0;
+
-      type = types.int;
+        Note that unlike listenAddress, you can specify 0.0.0.0, but you
-      description = ''Delay the timer by a randomly selected, evenly distributed
+        must also set extraConfig.broadcast_rpc_address to a value other
-      amount of time between 0 and the specified time value. re: systemd timer
+        than 0.0.0.0.
-      RandomizedDelaySec for more details
+
+        For security reasons, you should not expose this port to the
+        internet. Firewall it if needed.
       '';
     };
-    repairPostStop = mkOption {
+    rpcInterface = mkOption {
+      type = types.nullOr types.str;
       default = null;
-      type = types.nullOr types.string;
+      example = "eth1";
       description = ''
-      Run a script when repair is over. One can use it to send statsd events, email, etc.
+        Set rpcAddress OR rpcInterface, not both. Interfaces must
+        correspond to a single address, IP aliasing is not supported.
       '';
     };
-    repairPostStart = mkOption {
-      default = null;
-      type = types.nullOr types.string;
-      description = ''
-      Run a script when repair starts. One can use it to send statsd events, email, etc.
-      It has same semantics as systemd ExecStopPost; So, if it fails, unit is consisdered
-      failed.
-      '';
-    };
-  };
 
-  ###### implementation
+    extraConfig = mkOption {
+      type = types.attrs;
+      default = {};
+      example =
+        { commitlog_sync_batch_window_in_ms = 3;
+        };
+      description = ''
+        Extra options to be merged into cassandra.yaml as nix attribute set.
+      '';
+    };
+    fullRepairInterval = mkOption {
+      type = types.nullOr types.str;
+      default = "3w";
+      example = literalExample "null";
+      description = ''
+          Set the interval how often full repairs are run, i.e.
+          `nodetool repair --full` is executed. See
+          https://cassandra.apache.org/doc/latest/operating/repair.html
+          for more information.
+
+          Set to `null` to disable full repairs.
+        '';
+    };
+    fullRepairOptions = mkOption {
+      type = types.listOf types.str;
+      default = [];
+      example = [ "--partitioner-range" ];
+      description = ''
+          Options passed through to the full repair command.
+        '';
+    };
+    incrementalRepairInterval = mkOption {
+      type = types.nullOr types.str;
+      default = "3d";
+      example = literalExample "null";
+      description = ''
+          Set the interval how often incremental repairs are run, i.e.
+          `nodetool repair` is executed. See
+          https://cassandra.apache.org/doc/latest/operating/repair.html
+          for more information.
+
+          Set to `null` to disable incremental repairs.
+        '';
+    };
+    incrementalRepairOptions = mkOption {
+      type = types.listOf types.string;
+      default = [];
+      example = [ "--partitioner-range" ];
+      description = ''
+          Options passed through to the incremental repair command.
+        '';
+    };
+  };
 
   config = mkIf cfg.enable {
+    assertions =
+      [ { assertion =
+            ((isNull cfg.listenAddress)
+             || (isNull cfg.listenInterface)
+            ) && !((isNull cfg.listenAddress)
+                   && (isNull cfg.listenInterface)
+                  );
+          message = "You have to set either listenAddress or listenInterface";
+        }
+        { assertion =
+            ((isNull cfg.rpcAddress)
+             || (isNull cfg.rpcInterface)
+            ) && !((isNull cfg.rpcAddress)
+                   && (isNull cfg.rpcInterface)
+                  );
+          message = "You have to set either rpcAddress or rpcInterface";
+        }
+      ];
+    users = mkIf (cfg.user == defaultUser) {
+      extraUsers."${defaultUser}" =
+        {  group = cfg.group;
+           home = cfg.homeDir;
+           createHome = true;
+           uid = config.ids.uids.cassandra;
+           description = "Cassandra service user";
+        };
+      extraGroups."${defaultUser}".gid = config.ids.gids.cassandra;
+    };
 
-    environment.etc."cassandra/cassandra-rackdc.properties" = {
+    systemd.services.cassandra =
-      source = cassandraRackFile;
+      { description = "Apache Cassandra service";
-    };
-    environment.etc."cassandra/cassandra.yaml" = {
-      source = cassandraConfFile;
-    };
-    environment.etc."cassandra/log4j-server.properties" = {
-      source = cassandraLogFile;
-    };
-    environment.etc."cassandra/cassandra-env.sh" = {
-      text = ''
-        ${builtins.readFile cfg.envFile}
-        ${concatStringsSep "\n" cfg.extraParams}
-      '';
-    };
-    systemd.services.cassandra = {
-      description = "Cassandra Daemon";
-      wantedBy = [ "multi-user.target" ];
         after = [ "network.target" ];
-      environment = cassandraEnvironment;
+        environment =
-      restartTriggers = [ cassandraConfFile cassandraLogFile cassandraRackFile ];
+          { CASSANDRA_CONF = "${cassandraEtc}";
-      serviceConfig = {
+            JVM_OPTS = builtins.concatStringsSep " " cfg.jvmOpts;
-
-        User = cfg.user;
-        PermissionsStartOnly = true;
-        LimitAS = "infinity";
-        LimitNOFILE = "100000";
-        LimitNPROC = "32768";
-        LimitMEMLOCK = "infinity";
-
           };
-      script = ''
+        wantedBy = [ "multi-user.target" ];
-         ${cassandraPackage}/bin/cassandra -f
+        serviceConfig =
-        '';
+          { User = cfg.user;
-      path = [
+            Group = cfg.group;
-        cfg.jre
+            ExecStart = "${cfg.package}/bin/cassandra -f";
-        cassandraPackage
+            SuccessExitStatus = 143;
-        pkgs.coreutils
-      ];
-      preStart = ''
-        mkdir -m 0700 -p /etc/cassandra/triggers
-        mkdir -m 0700 -p /var/lib/cassandra /var/log/cassandra
-        chown ${cfg.user} /var/lib/cassandra /var/log/cassandra /etc/cassandra/triggers
-      '';
-      postStart = ''
-        sleep 2
-        while ! nodetool status >/dev/null 2>&1; do
-          sleep 2
-        done
-        nodetool status
-      '';
-    };
-
-    environment.systemPackages = [ cassandraPackage ];
-
-    networking.firewall.allowedTCPPorts = [
-      7000
-      7001
-      9042
-      9160
-    ];
-
-    users.users.cassandra =
-      if config.ids.uids ? "cassandra"
-      then { uid = config.ids.uids.cassandra; } // cassandraUser
-      else cassandraUser ;
-
-    boot.kernel.sysctl."vm.swappiness" = pkgs.lib.mkOptionDefault 0;
-
-    systemd.timers."cassandra-repair" = {
-      timerConfig = {
-        OnCalendar = "${toString cfg.repairStartAt}";
-        RandomizedDelaySec = cfg.repairRandomizedDelayInSec;
           };
       };
 
-    systemd.services."cassandra-repair" = {
+    systemd.services.cassandra-full-repair =
-      description = "Cassandra repair daemon";
+      { description = "Perform a full repair on this Cassandra node";
-      environment = cassandraEnvironment;
+        after = [ "cassandra.service" ];
-      script = "${cassandraPackage}/bin/nodetool repair -pr";
+        requires = [ "cassandra.service" ];
-      postStop = mkIf (cfg.repairPostStop != null) cfg.repairPostStop;
+        serviceConfig =
-      postStart = mkIf (cfg.repairPostStart != null) cfg.repairPostStart;
+          { User = cfg.user;
-      serviceConfig = {
+            Group = cfg.group;
-        User = cfg.user;
+            ExecStart =
+              lib.concatStringsSep " "
+                ([ "${cfg.package}/bin/nodetool" "repair" "--full"
+                 ] ++ cfg.fullRepairOptions);
+          };
+      };
+    systemd.timers.cassandra-full-repair =
+      mkIf (!isNull cfg.fullRepairInterval) {
+        description = "Schedule full repairs on Cassandra";
+        wantedBy = [ "timers.target" ];
+        timerConfig =
+          { OnBootSec = cfg.fullRepairInterval;
+            OnUnitActiveSec = cfg.fullRepairInterval;
+            Persistent = true;
+          };
+      };
+
+    systemd.services.cassandra-incremental-repair =
+      { description = "Perform an incremental repair on this cassandra node.";
+        after = [ "cassandra.service" ];
+        requires = [ "cassandra.service" ];
+        serviceConfig =
+          { User = cfg.user;
+            Group = cfg.group;
+            ExecStart =
+              lib.concatStringsSep " "
+                ([ "${cfg.package}/bin/nodetool" "repair"
+                 ] ++ cfg.incrementalRepairOptions);
+          };
+      };
+    systemd.timers.cassandra-incremental-repair =
+      mkIf (!isNull cfg.incrementalRepairInterval) {
+        description = "Schedule incremental repairs on Cassandra";
+        wantedBy = [ "timers.target" ];
+        timerConfig =
+          { OnBootSec = cfg.incrementalRepairInterval;
+            OnUnitActiveSec = cfg.incrementalRepairInterval;
+            Persistent = true;
           };
       };
   };

nixos/modules/services/databases/foundationdb.xml

@@ -12,12 +12,10 @@
 
 <para><emphasis>Maintainer:</emphasis> Austin Seipp</para>
 
-<para><emphasis>Available version(s):</emphasis> 5.1.x</para>
+<para><emphasis>Available version(s):</emphasis> 5.1.x, 5.2.x, 6.0.x</para>
 
-<para>FoundationDB (or "FDB") is a distributed, open source, high performance,
+<para>FoundationDB (or "FDB") is an open source, distributed, transactional
-transactional key-value store. It can store petabytes of data and deliver
+key-value store.</para>
-exceptional performance while maintaining consistency and ACID semantics
-(serializable transactions) over a large cluster.</para>
 
 <section><title>Configuring and basic setup</title>
 
@@ -26,12 +24,12 @@ exceptional performance while maintaining consistency and ACID semantics
 
 <programlisting>
 services.foundationdb.enable = true;
-services.foundationdb.package = pkgs.foundationdb51; # FoundationDB 5.1.x
+services.foundationdb.package = pkgs.foundationdb52; # FoundationDB 5.2.x
 </programlisting>
 </para>
 
 <para>The <option>services.foundationdb.package</option> option is required,
-and must always be specified. Because FoundationDB network protocols and
+and must always be specified. Due to the fact FoundationDB network protocols and
 on-disk storage formats may change between (major) versions, and upgrades must
 be explicitly handled by the user, you must always manually specify this
 yourself so that the NixOS module will use the proper version. Note that minor,
@@ -70,6 +68,40 @@ fdb>
 </programlisting>
 </para>
 
+<para>You can also write programs using the available client libraries.
+For example, the following Python program can be run in order to grab the
+cluster status, as a quick example. (This example uses
+<command>nix-shell</command> shebang support to automatically supply the
+necessary Python modules).
+
+<programlisting>
+a@link> cat fdb-status.py
+#! /usr/bin/env nix-shell
+#! nix-shell -i python -p python pythonPackages.foundationdb52
+
+import fdb
+import json
+
+def main():
+    fdb.api_version(520)
+    db = fdb.open()
+
+    @fdb.transactional
+    def get_status(tr):
+        return str(tr['\xff\xff/status/json'])
+
+    obj = json.loads(get_status(db))
+    print('FoundationDB available: %s' % obj['client']['database_status']['available'])
+
+if __name__ == "__main__":
+    main()
+a@link> chmod +x fdb-status.py
+a@link> ./fdb-status.py
+FoundationDB available: True
+a@link>
+</programlisting>
+</para>
+
 <para>FoundationDB is run under the <command>foundationdb</command> user and
 group by default, but this may be changed in the NixOS configuration. The
 systemd unit <command>foundationdb.service</command> controls the
@@ -295,7 +327,6 @@ only undergone fairly basic testing of all the available functionality.</para>
       individual <command>fdbserver</command> processes. Currently, all server
       processes inherit all the global <command>fdbmonitor</command> settings.
       </para></listitem>
-  <listitem><para>Python bindings are not currently installed.</para></listitem>
   <listitem><para>Ruby bindings are not currently installed.</para></listitem>
   <listitem><para>Go bindings are not currently installed.</para></listitem>
 </itemizedlist>
@@ -306,8 +337,9 @@ only undergone fairly basic testing of all the available functionality.</para>
 
 <para>NixOS's FoundationDB module allows you to configure all of the most
 relevant configuration options for <command>fdbmonitor</command>, matching it
-quite closely. For a complete list of all options, check <command>man
+quite closely. A complete list of options for the FoundationDB module may be
-configuration.nix</command>.</para>
+found <link linkend="opt-services.foundationdb.enable">here</link>. You should
+also read the FoundationDB documentation as well.</para>
 
 </section>
 

nixos/modules/services/hardware/fwupd.nix

@@ -71,6 +71,13 @@ in {
           BlacklistPlugins=${lib.concatStringsSep ";" cfg.blacklistPlugins}
         '';
       };
+      "fwupd/uefi.conf" = {
+        source = pkgs.writeText "uefi.conf" ''
+          [uefi]
+          OverrideESPMountPoint=${config.boot.loader.efi.efiSysMountPoint}
+        '';
+      };
+
     } // originalEtc // extraTrustedKeys;
 
     services.dbus.packages = [ pkgs.fwupd ];

nixos/modules/services/misc/disnix.nix

@@ -47,7 +47,7 @@ in
   ###### implementation
 
   config = mkIf cfg.enable {
-    services.dysnomia.enable = true;
+    dysnomia.enable = true;
 
     environment.systemPackages = [ pkgs.disnix ] ++ optional cfg.useWebServiceInterface pkgs.DisnixWebService;
 

nixos/modules/services/misc/docker-registry.nix

@@ -5,6 +5,43 @@ with lib;
 let
   cfg = config.services.dockerRegistry;
 
+  blobCache = if cfg.enableRedisCache
+    then "redis"
+    else "inmemory";
+
+  registryConfig = {
+    version =  "0.1";
+    log.fields.service = "registry";
+    storage = {
+      cache.blobdescriptor = blobCache;
+      filesystem.rootdirectory = cfg.storagePath;
+      delete.enabled = cfg.enableDelete;
+    };
+    http = {
+      addr = ":${builtins.toString cfg.port}";
+      headers.X-Content-Type-Options = ["nosniff"];
+    };
+    health.storagedriver = {
+      enabled = true;
+      interval = "10s";
+      threshold = 3;
+    };
+  };
+
+  registryConfig.redis = mkIf cfg.enableRedisCache {
+    addr = "${cfg.redisUrl}";
+    password = "${cfg.redisPassword}";
+    db = 0;
+    dialtimeout = "10ms";
+    readtimeout = "10ms";
+    writetimeout = "10ms";
+    pool = {
+      maxidle = 16;
+      maxactive = 64;
+      idletimeout = "300s";
+    };
+  };
+
   configFile = pkgs.writeText "docker-registry-config.yml" (builtins.toJSON (recursiveUpdate registryConfig cfg.extraConfig));
 
 in {

nixos/modules/services/misc/dysnomia.nix

@@ -3,7 +3,7 @@
 with lib;
 
 let
-  cfg = config.services.dysnomia;
+  cfg = config.dysnomia;
 
   printProperties = properties:
     concatMapStrings (propertyName:
@@ -69,7 +69,7 @@ let
 in
 {
   options = {
-    services.dysnomia = {
+    dysnomia = {
 
       enable = mkOption {
         type = types.bool;
@@ -142,7 +142,7 @@ in
 
     environment.systemPackages = [ cfg.package ];
 
-    services.dysnomia.package = pkgs.dysnomia.override (origArgs: {
+    dysnomia.package = pkgs.dysnomia.override (origArgs: {
       enableApacheWebApplication = config.services.httpd.enable;
       enableAxis2WebService = config.services.tomcat.axis2.enable;
       enableEjabberdDump = config.services.ejabberd.enable;
@@ -153,7 +153,7 @@ in
       enableMongoDatabase = config.services.mongodb.enable;
     });
 
-    services.dysnomia.properties = {
+    dysnomia.properties = {
       hostname = config.networking.hostName;
       inherit (config.nixpkgs.localSystem) system;
 
@@ -171,7 +171,7 @@ in
       }}");
     };
 
-    services.dysnomia.containers = lib.recursiveUpdate ({
+    dysnomia.containers = lib.recursiveUpdate ({
       process = {};
       wrapper = {};
     }

nixos/modules/services/monitoring/graphite.nix

@@ -57,12 +57,6 @@ let
     --nodaemon --syslog --prefix=${name} --pidfile /run/${name}/${name}.pid ${name}
   '';
 
-  mkPidFileDir = name: ''
-    mkdir -p /run/${name}
-    chmod 0700 /run/${name}
-    chown -R graphite:graphite /run/${name}
-  '';
-
   carbonEnv = {
     PYTHONPATH = let
       cenv = pkgs.python.buildEnv.override {
@@ -412,18 +406,16 @@ in {
         after = [ "network.target" ];
         environment = carbonEnv;
         serviceConfig = {
+          RuntimeDirectory = name;
           ExecStart = "${pkgs.pythonPackages.twisted}/bin/twistd ${carbonOpts name}";
           User = "graphite";
           Group = "graphite";
           PermissionsStartOnly = true;
           PIDFile="/run/${name}/${name}.pid";
         };
-        preStart = mkPidFileDir name + ''
+        preStart = ''
-
+          install -dm0700 -o graphite -g graphite ${cfg.dataDir}
-          mkdir -p ${cfg.dataDir}/whisper
+          install -dm0700 -o graphite -g graphite ${cfg.dataDir}/whisper
-          chmod 0700 ${cfg.dataDir}/whisper
-          chown graphite:graphite ${cfg.dataDir}
-          chown graphite:graphite ${cfg.dataDir}/whisper
         '';
       };
     })
@@ -436,12 +428,12 @@ in {
         after = [ "network.target" ];
         environment = carbonEnv;
         serviceConfig = {
+          RuntimeDirectory = name;
           ExecStart = "${pkgs.pythonPackages.twisted}/bin/twistd ${carbonOpts name}";
           User = "graphite";
           Group = "graphite";
           PIDFile="/run/${name}/${name}.pid";
         };
-        preStart = mkPidFileDir name;
       };
     })
 
@@ -452,12 +444,12 @@ in {
         after = [ "network.target" ];
         environment = carbonEnv;
         serviceConfig = {
+          RuntimeDirectory = name;
           ExecStart = "${pkgs.pythonPackages.twisted}/bin/twistd ${carbonOpts name}";
           User = "graphite";
           Group = "graphite";
           PIDFile="/run/${name}/${name}.pid";
         };
-        preStart = mkPidFileDir name;
       };
     })
 

nixos/modules/services/monitoring/netdata.nix

@@ -14,6 +14,10 @@ let
     global = {
       "plugins directory" = "${wrappedPlugins}/libexec/netdata/plugins.d ${pkgs.netdata}/libexec/netdata/plugins.d";
     };
+    web = {
+      "web files owner" = "root";
+      "web files group" = "root";
+    };
   };
   mkConfig = generators.toINI {} (recursiveUpdate localConfig cfg.config);
   configFile = pkgs.writeText "netdata.conf" (if cfg.configText != null then cfg.configText else mkConfig);

nixos/modules/services/networking/zerotierone.nix

@@ -17,6 +17,15 @@ in
     '';
   };
 
+  options.services.zerotierone.port = mkOption {
+    default = 9993;
+    example = 9993;
+    type = types.int;
+    description = ''
+      Network port used by ZeroTier.
+    '';
+  };
+
   options.services.zerotierone.package = mkOption {
     default = pkgs.zerotierone;
     defaultText = "pkgs.zerotierone";
@@ -40,7 +49,7 @@ in
         touch "/var/lib/zerotier-one/networks.d/${netId}.conf"
       '') cfg.joinNetworks);
       serviceConfig = {
-        ExecStart = "${cfg.package}/bin/zerotier-one";
+        ExecStart = "${cfg.package}/bin/zerotier-one -p${toString cfg.port}";
         Restart = "always";
         KillMode = "process";
       };
@@ -49,8 +58,8 @@ in
     # ZeroTier does not issue DHCP leases, but some strangers might...
     networking.dhcpcd.denyInterfaces = [ "zt*" ];
 
-    # ZeroTier receives UDP transmissions on port 9993 by default
+    # ZeroTier receives UDP transmissions
-    networking.firewall.allowedUDPPorts = [ 9993 ];
+    networking.firewall.allowedUDPPorts = [ cfg.port ];
 
     environment.systemPackages = [ cfg.package ];
   };

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

@@ -104,8 +104,9 @@ in
     systemd.services.cloud-init =
       { description = "Initial cloud-init job (metadata service crawler)";
         wantedBy = [ "multi-user.target" ];
-        wants = [ "local-fs.target" "cloud-init-local.service" "sshd.service" "sshd-keygen.service" ];
+        wants = [ "local-fs.target" "network-online.target" "cloud-init-local.service"
-        after = [ "local-fs.target" "network.target" "cloud-init-local.service" ];
+                  "sshd.service" "sshd-keygen.service" ];
+        after = [ "local-fs.target" "network-online.target" "cloud-init-local.service" ];
         before = [ "sshd.service" "sshd-keygen.service" ];
         requires = [ "network.target "];
         path = path;
@@ -121,8 +122,8 @@ in
     systemd.services.cloud-config =
       { description = "Apply the settings specified in cloud-config";
         wantedBy = [ "multi-user.target" ];
-        wants = [ "network.target" ];
+        wants = [ "network-online.target" ];
-        after = [ "network.target" "syslog.target" "cloud-config.target" ];
+        after = [ "network-online.target" "syslog.target" "cloud-config.target" ];
 
         path = path;
         serviceConfig =
@@ -137,8 +138,8 @@ in
     systemd.services.cloud-final =
       { description = "Execute cloud user/final scripts";
         wantedBy = [ "multi-user.target" ];
-        wants = [ "network.target" ];
+        wants = [ "network-online.target" ];
-        after = [ "network.target" "syslog.target" "cloud-config.service" "rc-local.service" ];
+        after = [ "network-online.target" "syslog.target" "cloud-config.service" "rc-local.service" ];
         requires = [ "cloud-config.target" ];
         path = path;
         serviceConfig =

nixos/modules/services/x11/desktop-managers/plasma5.nix

@@ -224,7 +224,7 @@ in
       # Update the start menu for each user that has `isNormalUser` set.
       system.activationScripts.plasmaSetup = stringAfter [ "users" "groups" ]
         (concatStringsSep "\n"
-          (mapAttrsToList (name: value: "${pkgs.su}/bin/su ${name} -c kbuildsycoca5")
+          (mapAttrsToList (name: value: "${pkgs.su}/bin/su ${name} -c ${pkgs.libsForQt5.kservice}/bin/kbuildsycoca5")
             (filterAttrs (n: v: v.isNormalUser) config.users.users)));
     })
   ];

nixos/modules/services/x11/display-managers/lightdm-greeters/gtk.nix

@@ -23,7 +23,7 @@ let
       makeWrapper ${pkgs.lightdm_gtk_greeter}/sbin/lightdm-gtk-greeter \
         $out/greeter \
         --prefix PATH : "${pkgs.glibc.bin}/bin" \
-        --set GDK_PIXBUF_MODULE_FILE "${pkgs.gdk_pixbuf.out}/lib/gdk-pixbuf-2.0/2.10.0/loaders.cache" \
+        --set GDK_PIXBUF_MODULE_FILE "${pkgs.librsvg.out}/lib/gdk-pixbuf-2.0/2.10.0/loaders.cache" \
         --set GTK_PATH "${theme}:${pkgs.gtk3.out}" \
         --set GTK_EXE_PREFIX "${theme}" \
         --set GTK_DATA_PREFIX "${theme}" \

nixos/modules/system/boot/loader/systemd-boot/systemd-boot-builder.py

@@ -43,6 +43,7 @@ def write_loader_conf(profile, generation):
             f.write("default nixos-generation-%d\n" % (generation))
         if not @editor@:
             f.write("editor 0");
+        f.write("console-mode @consoleMode@\n");
     os.rename("@efiSysMountPoint@/loader/loader.conf.tmp", "@efiSysMountPoint@/loader/loader.conf")
 
 def profile_path(profile, generation, name):

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

@@ -22,6 +22,8 @@ let
 
     editor = if cfg.editor then "True" else "False";
 
+    inherit (cfg) consoleMode;
+
     inherit (efi) efiSysMountPoint canTouchEfiVariables;
   };
 in {
@@ -52,6 +54,38 @@ in {
         compatibility.
       '';
     };
+
+    consoleMode = mkOption {
+      default = "keep";
+
+      type = types.enum [ "0" "1" "2" "auto" "max" "keep" ];
+
+      description = ''
+        The resolution of the console. The following values are valid:
+        </para>
+        <para>
+        <itemizedlist>
+          <listitem><para>
+            <literal>"0"</literal>: Standard UEFI 80x25 mode
+          </para></listitem>
+          <listitem><para>
+            <literal>"1"</literal>: 80x50 mode, not supported by all devices
+          </para></listitem>
+          <listitem><para>
+            <literal>"2"</literal>: The first non-standard mode provided by the device firmware, if any
+          </para></listitem>
+          <listitem><para>
+            <literal>"auto"</literal>: Pick a suitable mode automatically using heuristics
+          </para></listitem>
+          <listitem><para>
+            <literal>"max"</literal>: Pick the highest-numbered available mode
+          </para></listitem>
+          <listitem><para>
+            <literal>"keep"</literal>: Keep the mode selected by firmware (the default)
+          </para></listitem>
+        </itemizedlist>
+      '';
+    };
   };
 
   config = mkIf cfg.enable {

nixos/modules/system/boot/luksroot.nix

@@ -5,61 +5,171 @@ with lib;
 let
   luks = config.boot.initrd.luks;
 
-  openCommand = name': { name, device, header, keyFile, keyFileSize, allowDiscards, yubikey, fallbackToPassword, ... }: assert name' == name; ''
+  commonFunctions = ''
+    die() {
+      echo "$@" >&2
+      exit 1
+    }
 
-    # Wait for a target (e.g. device, keyFile, header, ...) to appear.
     wait_target() {
         local name="$1"
         local target="$2"
+        local secs="''${3:-10}"
+        local desc="''${4:-$name $target to appear}"
 
         if [ ! -e $target ]; then
-            echo -n "Waiting 10 seconds for $name $target to appear"
+            echo -n "Waiting $secs seconds for $desc..."
             local success=false;
-            for try in $(seq 10); do
+            for try in $(seq $secs); do
                 echo -n "."
                 sleep 1
-                if [ -e $target ]; then success=true break; fi
+                if [ -e $target ]; then
+                    success=true
+                    break
+                fi
             done
-            if [ $success = true ]; then
+            if [ $success == true ]; then
                 echo " - success";
+                return 0
             else
                 echo " - failure";
+                return 1
             fi
         fi
+        return 0
     }
 
+    wait_yubikey() {
+      local secs="''${1:-10}"
+
+      ykinfo -v 1>/dev/null 2>&1
+      if [ $? != 0 ]; then
+          echo -n "Waiting $secs seconds for Yubikey to appear..."
+          local success=false
+          for try in $(seq $secs); do
+              echo -n .
+              sleep 1
+              ykinfo -v 1>/dev/null 2>&1
+              if [ $? == 0 ]; then
+                  success=true
+                  break
+              fi
+          done
+          if [ $success == true ]; then
+              echo " - success";
+              return 0
+          else
+              echo " - failure";
+              return 1
+          fi
+      fi
+      return 0
+    }
+  '';
+
+  preCommands = ''
+    # A place to store crypto things
+
+    # A ramfs is used here to ensure that the file used to update
+    # the key slot with cryptsetup will never get swapped out.
+    # Warning: Do NOT replace with tmpfs!
+    mkdir -p /crypt-ramfs
+    mount -t ramfs none /crypt-ramfs
+
+    # For Yubikey salt storage
+    mkdir -p /crypt-storage
+
+    # Disable all input echo for the whole stage. We could use read -s
+    # instead but that would ocasionally leak characters between read
+    # invocations.
+    stty -echo
+  '';
+
+  postCommands = ''
+    stty echo
+    umount /crypt-storage 2>/dev/null
+    umount /crypt-ramfs 2>/dev/null
+  '';
+
+  openCommand = name': { name, device, header, keyFile, keyFileSize, keyFileOffset, allowDiscards, yubikey, fallbackToPassword, ... }: assert name' == name;
+  let
+    csopen   = "cryptsetup luksOpen ${device} ${name} ${optionalString allowDiscards "--allow-discards"} ${optionalString (header != null) "--header=${header}"}";
+    cschange = "cryptsetup luksChangeKey ${device} ${optionalString (header != null) "--header=${header}"}";
+  in ''
     # Wait for luksRoot (and optionally keyFile and/or header) to appear, e.g.
     # if on a USB drive.
-    wait_target "device" ${device}
+    wait_target "device" ${device} || die "${device} is unavailable"
-
-    ${optionalString (keyFile != null) ''
-      wait_target "key file" ${keyFile}
-    ''}
 
     ${optionalString (header != null) ''
-      wait_target "header" ${header}
+      wait_target "header" ${header} || die "${header} is unavailable"
     ''}
 
-    open_normally() {
+    do_open_passphrase() {
-        echo luksOpen ${device} ${name} ${optionalString allowDiscards "--allow-discards"} \
+        local passphrase
-          ${optionalString (header != null) "--header=${header}"} \
+
-          > /.luksopen_args
+        while true; do
-        ${optionalString (keyFile != null) ''
+            echo -n "Passphrase for ${device}: "
-        ${optionalString fallbackToPassword "if [ -e ${keyFile} ]; then"}
+            passphrase=
-            echo " --key-file=${keyFile} ${optionalString (keyFileSize != null) "--keyfile-size=${toString keyFileSize}"}" \
+            while true; do
-              >> /.luksopen_args
+                if [ -e /crypt-ramfs/passphrase ]; then
-        ${optionalString fallbackToPassword ''
+                    echo "reused"
+                    passphrase=$(cat /crypt-ramfs/passphrase)
+                    break
                 else
-            echo "keyfile ${keyFile} not found -- fallback to interactive unlocking"
+                    # ask cryptsetup-askpass
+                    echo -n "${device}" > /crypt-ramfs/device
+
+                    # and try reading it from /dev/console with a timeout
+                    IFS= read -t 1 -r passphrase
+                    if [ -n "$passphrase" ]; then
+                       ${if luks.reusePassphrases then ''
+                         # remember it for the next device
+                         echo -n "$passphrase" > /crypt-ramfs/passphrase
+                       '' else ''
+                         # Don't save it to ramfs. We are very paranoid
+                       ''}
+                       echo
+                       break
                     fi
+                fi
+            done
+            echo -n "Verifiying passphrase for ${device}..."
+            echo -n "$passphrase" | ${csopen} --key-file=-
+            if [ $? == 0 ]; then
+                echo " - success"
+                ${if luks.reusePassphrases then ''
+                  # we don't rm here because we might reuse it for the next device
+                '' else ''
+                  rm -f /crypt-ramfs/passphrase
                 ''}
-        ''}
+                break
-        cryptsetup-askpass
+            else
-        rm /.luksopen_args
+                echo " - failure"
+                # ask for a different one
+                rm -f /crypt-ramfs/passphrase
+            fi
+        done
     }
 
-    ${optionalString (luks.yubikeySupport && (yubikey != null)) ''
+    # LUKS
+    open_normally() {
+        ${if (keyFile != null) then ''
+        if wait_target "key file" ${keyFile}; then
+            ${csopen} --key-file=${keyFile} \
+              ${optionalString (keyFileSize != null) "--keyfile-size=${toString keyFileSize}"} \
+              ${optionalString (keyFileOffset != null) "--keyfile-offset=${toString keyFileOffset}"}
+        else
+            ${if fallbackToPassword then "echo" else "die"} "${keyFile} is unavailable"
+            echo " - failing back to interactive password prompt"
+            do_open_passphrase
+        fi
+        '' else ''
+        do_open_passphrase
+        ''}
+    }
 
+    ${if luks.yubikeySupport && (yubikey != null) then ''
+    # Yubikey
     rbtohex() {
         ( od -An -vtx1 | tr -d ' \n' )
     }
@@ -68,8 +178,7 @@ let
         ( tr '[:lower:]' '[:upper:]' | sed -e 's/\([0-9A-F]\{2\}\)/\\\\\\x\1/gI' | xargs printf )
     }
 
-    open_yubikey() {
+    do_open_yubikey() {
-
         # Make all of these local to this function
         # to prevent their values being leaked
         local salt
@@ -85,19 +194,18 @@ let
         local new_response
         local new_k_luks
 
-        mkdir -p ${yubikey.storage.mountPoint}
+        mount -t ${yubikey.storage.fsType} ${yubikey.storage.device} /crypt-storage || \
-        mount -t ${yubikey.storage.fsType} ${toString yubikey.storage.device} ${yubikey.storage.mountPoint}
+          die "Failed to mount Yubikey salt storage device"
 
-        salt="$(cat ${yubikey.storage.mountPoint}${yubikey.storage.path} | sed -n 1p | tr -d '\n')"
+        salt="$(cat /crypt-storage${yubikey.storage.path} | sed -n 1p | tr -d '\n')"
-        iterations="$(cat ${yubikey.storage.mountPoint}${yubikey.storage.path} | sed -n 2p | tr -d '\n')"
+        iterations="$(cat /crypt-storage${yubikey.storage.path} | sed -n 2p | tr -d '\n')"
         challenge="$(echo -n $salt | openssl-wrap dgst -binary -sha512 | rbtohex)"
         response="$(ykchalresp -${toString yubikey.slot} -x $challenge 2>/dev/null)"
 
         for try in $(seq 3); do
-
             ${optionalString yubikey.twoFactor ''
             echo -n "Enter two-factor passphrase: "
-            read -s k_user
+            read -r k_user
             echo
             ''}
 
@@ -107,9 +215,9 @@ let
                 k_luks="$(echo | pbkdf2-sha512 ${toString yubikey.keyLength} $iterations $response | rbtohex)"
             fi
 
-            echo -n "$k_luks" | hextorb | cryptsetup luksOpen ${device} ${name} ${optionalString allowDiscards "--allow-discards"} --key-file=-
+            echo -n "$k_luks" | hextorb | ${csopen} --key-file=-
 
-            if [ $? == "0" ]; then
+            if [ $? == 0 ]; then
                 opened=true
                 break
             else
@@ -118,11 +226,7 @@ let
             fi
         done
 
-        if [ "$opened" == false ]; then
+        [ "$opened" == false ] && die "Maximum authentication errors reached"
-            umount ${yubikey.storage.mountPoint}
-            echo "Maximum authentication errors reached"
-            exit 1
-        fi
 
         echo -n "Gathering entropy for new salt (please enter random keys to generate entropy if this blocks for long)..."
         for i in $(seq ${toString yubikey.saltLength}); do
@@ -147,69 +251,52 @@ let
             new_k_luks="$(echo | pbkdf2-sha512 ${toString yubikey.keyLength} $new_iterations $new_response | rbtohex)"
         fi
 
-        mkdir -p ${yubikey.ramfsMountPoint}
+        echo -n "$new_k_luks" | hextorb > /crypt-ramfs/new_key
-        # A ramfs is used here to ensure that the file used to update
+        echo -n "$k_luks" | hextorb | ${cschange} --key-file=- /crypt-ramfs/new_key
-        # the key slot with cryptsetup will never get swapped out.
-        # Warning: Do NOT replace with tmpfs!
-        mount -t ramfs none ${yubikey.ramfsMountPoint}
 
-        echo -n "$new_k_luks" | hextorb > ${yubikey.ramfsMountPoint}/new_key
+        if [ $? == 0 ]; then
-        echo -n "$k_luks" | hextorb | cryptsetup luksChangeKey ${device} --key-file=- ${yubikey.ramfsMountPoint}/new_key
+            echo -ne "$new_salt\n$new_iterations" > /crypt-storage${yubikey.storage.path}
-
-        if [ $? == "0" ]; then
-            echo -ne "$new_salt\n$new_iterations" > ${yubikey.storage.mountPoint}${yubikey.storage.path}
         else
             echo "Warning: Could not update LUKS key, current challenge persists!"
         fi
 
-        rm -f ${yubikey.ramfsMountPoint}/new_key
+        rm -f /crypt-ramfs/new_key
-        umount ${yubikey.ramfsMountPoint}
+        umount /crypt-storage
-        rm -rf ${yubikey.ramfsMountPoint}
-
-        umount ${yubikey.storage.mountPoint}
     }
 
-    ${optionalString (yubikey.gracePeriod > 0) ''
+    open_yubikey() {
-    echo -n "Waiting ${toString yubikey.gracePeriod} seconds as grace..."
+        if wait_yubikey ${toString yubikey.gracePeriod}; then
-    for i in $(seq ${toString yubikey.gracePeriod}); do
+            do_open_yubikey
-        sleep 1
-        echo -n .
-    done
-    echo "ok"
-    ''}
-
-    yubikey_missing=true
-    ykinfo -v 1>/dev/null 2>&1
-    if [ $? != "0" ]; then
-        echo -n "waiting 10 seconds for yubikey to appear..."
-        for try in $(seq 10); do
-            sleep 1
-            ykinfo -v 1>/dev/null 2>&1
-            if [ $? == "0" ]; then
-                yubikey_missing=false
-                break
-            fi
-            echo -n .
-        done
-        echo "ok"
         else
-        yubikey_missing=false
+            echo "No yubikey found, falling back to non-yubikey open procedure"
-    fi
-
-    if [ "$yubikey_missing" == true ]; then
-        echo "no yubikey found, falling back to non-yubikey open procedure"
             open_normally
-    else
+        fi
+    }
+
     open_yubikey
-    fi
+    '' else ''
-    ''}
-
-    # open luksRoot and scan for logical volumes
-    ${optionalString ((!luks.yubikeySupport) || (yubikey == null)) ''
     open_normally
     ''}
   '';
 
+  askPass = pkgs.writeScriptBin "cryptsetup-askpass" ''
+    #!/bin/sh
+
+    ${commonFunctions}
+
+    while true; do
+        wait_target "luks" /crypt-ramfs/device 10 "LUKS to request a passphrase" || die "Passphrase is not requested now"
+        device=$(cat /crypt-ramfs/device)
+
+        echo -n "Passphrase for $device: "
+        IFS= read -rs passphrase
+        echo
+
+        rm /crypt-ramfs/device
+        echo -n "$passphrase" > /crypt-ramfs/passphrase
+    done
+  '';
+
   preLVM = filterAttrs (n: v: v.preLVM) luks.devices;
   postLVM = filterAttrs (n: v: !v.preLVM) luks.devices;
 
@@ -255,6 +342,22 @@ in
       '';
     };
 
+    boot.initrd.luks.reusePassphrases = mkOption {
+      type = types.bool;
+      default = true;
+      description = ''
+        When opening a new LUKS device try reusing last successful
+        passphrase.
+
+        Useful for mounting a number of devices that use the same
+        passphrase without retyping it several times.
+
+        Such setup can be useful if you use <command>cryptsetup
+        luksSuspend</command>. Different LUKS devices will still have
+        different master keys even when using the same passphrase.
+      '';
+    };
+
     boot.initrd.luks.devices = mkOption {
       default = { };
       example = { "luksroot".device = "/dev/disk/by-uuid/430e9eff-d852-4f68-aa3b-2fa3599ebe08"; };
@@ -316,6 +419,19 @@ in
             '';
           };
 
+          keyFileOffset = mkOption {
+            default = null;
+            example = 4096;
+            type = types.nullOr types.int;
+            description = ''
+              The offset of the key file. Use this in combination with
+              <literal>keyFileSize</literal> to use part of a file as key file
+              (often the case if a raw device or partition is used as a key file).
+              If not specified, the key begins at the first byte of
+              <literal>keyFile</literal>.
+            '';
+          };
+
           # FIXME: get rid of this option.
           preLVM = mkOption {
             default = true;
@@ -383,15 +499,9 @@ in
                 };
 
                 gracePeriod = mkOption {
-                  default = 2;
+                  default = 10;
                   type = types.int;
-                  description = "Time in seconds to wait before attempting to find the Yubikey.";
+                  description = "Time in seconds to wait for the Yubikey.";
-                };
-
-                ramfsMountPoint = mkOption {
-                  default = "/crypt-ramfs";
-                  type = types.str;
-                  description = "Path where the ramfs used to update the LUKS key will be mounted during early boot.";
                 };
 
                 /* TODO: Add to the documentation of the current module:
@@ -414,12 +524,6 @@ in
                     description = "The filesystem of the unencrypted device.";
                   };
 
-                  mountPoint = mkOption {
-                    default = "/crypt-storage";
-                    type = types.str;
-                    description = "Path where the unencrypted device will be mounted during early boot.";
-                  };
-
                   path = mkOption {
                     default = "/crypt-storage/default";
                     type = types.str;
@@ -432,8 +536,8 @@ in
               };
             });
           };
-
+        };
-        }; }));
+      }));
     };
 
     boot.initrd.luks.yubikeySupport = mkOption {
@@ -463,18 +567,8 @@ in
     # copy the cryptsetup binary and it's dependencies
     boot.initrd.extraUtilsCommands = ''
       copy_bin_and_libs ${pkgs.cryptsetup}/bin/cryptsetup
-
+      copy_bin_and_libs ${askPass}/bin/cryptsetup-askpass
-      cat > $out/bin/cryptsetup-askpass <<EOF
+      sed -i s,/bin/sh,$out/bin/sh, $out/bin/cryptsetup-askpass
-      #!$out/bin/sh -e
-      if [ -e /.luksopen_args ]; then
-        cryptsetup \$(cat /.luksopen_args)
-        killall -q cryptsetup
-      else
-        echo "Passphrase is not requested now"
-        exit 1
-      fi
-      EOF
-      chmod +x $out/bin/cryptsetup-askpass
 
       ${optionalString luks.yubikeySupport ''
         copy_bin_and_libs ${pkgs.yubikey-personalization}/bin/ykchalresp
@@ -506,8 +600,9 @@ in
       ''}
     '';
 
-    boot.initrd.preLVMCommands = concatStrings (mapAttrsToList openCommand preLVM);
+    boot.initrd.preFailCommands = postCommands;
-    boot.initrd.postDeviceCommands = concatStrings (mapAttrsToList openCommand postLVM);
+    boot.initrd.preLVMCommands = commonFunctions + preCommands + concatStrings (mapAttrsToList openCommand preLVM) + postCommands;
+    boot.initrd.postDeviceCommands = commonFunctions + preCommands + concatStrings (mapAttrsToList openCommand postLVM) + postCommands;
 
     environment.systemPackages = [ pkgs.cryptsetup ];
   };

nixos/modules/system/boot/stage-1.nix

@@ -248,6 +248,14 @@ let
 
     isExecutable = true;
 
+    postInstall = ''
+      echo checking syntax
+      # check both with bash
+      ${pkgs.bash}/bin/sh -n $target
+      # and with ash shell, just in case
+      ${extraUtils}/bin/ash -n $target
+    '';
+
     inherit udevRules extraUtils modulesClosure;
 
     inherit (config.boot) resumeDevice;

nixos/modules/system/boot/systemd.nix

@@ -190,9 +190,8 @@ let
     ];
 
   makeJobScript = name: text:
-    let mkScriptName =  s: (replaceChars [ "\\" ] [ "-" ] (shellEscape s) );
+    let mkScriptName =  s: "unit-script-" + (replaceChars [ "\\" "@" ] [ "-" "_" ] (shellEscape s) );
-        x = pkgs.writeTextFile { name = "unit-script"; executable = true; destination = "/bin/${mkScriptName name}"; inherit text; };
+    in  pkgs.writeTextFile { name = mkScriptName name; executable = true; inherit text; };
-    in "${x}/bin/${mkScriptName name}";
 
   unitConfig = { config, ... }: {
     config = {

nixos/modules/tasks/trackpoint.nix

@@ -55,6 +55,15 @@ with lib;
         '';
       };
 
+      device = mkOption {
+        default = "TPPS/2 IBM TrackPoint";
+        type = types.str;
+        description = ''
+          The device name of the trackpoint. You can check with xinput.
+          Some newer devices (example x1c6) use "TPPS/2 Elan TrackPoint".
+        '';
+      };
+
     };
 
   };
@@ -68,12 +77,12 @@ with lib;
     (mkIf cfg.enable {
       services.udev.extraRules =
       ''
-        ACTION=="add|change", SUBSYSTEM=="input", ATTR{name}=="TPPS/2 IBM TrackPoint", ATTR{device/speed}="${toString cfg.speed}", ATTR{device/sensitivity}="${toString cfg.sensitivity}"
+        ACTION=="add|change", SUBSYSTEM=="input", ATTR{name}=="${cfg.device}", ATTR{device/speed}="${toString cfg.speed}", ATTR{device/sensitivity}="${toString cfg.sensitivity}"
       '';
 
       system.activationScripts.trackpoint =
         ''
-          ${config.systemd.package}/bin/udevadm trigger --attr-match=name="TPPS/2 IBM TrackPoint"
+          ${config.systemd.package}/bin/udevadm trigger --attr-match=name="${cfg.device}"
         '';
     })
 
@@ -81,7 +90,7 @@ with lib;
       services.xserver.inputClassSections =
         [''
         Identifier "Trackpoint Wheel Emulation"
-          MatchProduct "${if cfg.fakeButtons then "PS/2 Generic Mouse" else "ETPS/2 Elantech TrackPoint|Elantech PS/2 TrackPoint|TPPS/2 IBM TrackPoint|DualPoint Stick|Synaptics Inc. Composite TouchPad / TrackPoint|ThinkPad USB Keyboard with TrackPoint|USB Trackpoint pointing device|Composite TouchPad / TrackPoint"}"
+          MatchProduct "${if cfg.fakeButtons then "PS/2 Generic Mouse" else "ETPS/2 Elantech TrackPoint|Elantech PS/2 TrackPoint|TPPS/2 IBM TrackPoint|DualPoint Stick|Synaptics Inc. Composite TouchPad / TrackPoint|ThinkPad USB Keyboard with TrackPoint|USB Trackpoint pointing device|Composite TouchPad / TrackPoint|${cfg.device}"}"
           MatchDevicePath "/dev/input/event*"
           Option "EmulateWheel" "true"
           Option "EmulateWheelButton" "2"

nixos/release.nix

@@ -277,6 +277,7 @@ in rec {
   tests.docker-tools = callTestOnMatchingSystems ["x86_64-linux"] tests/docker-tools.nix {};
   tests.docker-tools-overlay = callTestOnMatchingSystems ["x86_64-linux"] tests/docker-tools-overlay.nix {};
   tests.docker-edge = callTestOnMatchingSystems ["x86_64-linux"] tests/docker-edge.nix {};
+  tests.docker-registry = callTest tests/docker-registry.nix {};
   tests.dovecot = callTest tests/dovecot.nix {};
   tests.dnscrypt-proxy = callTestOnMatchingSystems ["x86_64-linux"] tests/dnscrypt-proxy.nix {};
   tests.ecryptfs = callTest tests/ecryptfs.nix {};

nixos/tests/acme.nix

@@ -12,7 +12,9 @@ let
         '';
       });
 
-      pythonPackages = (super.python.override {
+      # Override certifi so that it accepts fake certificate for Let's Encrypt
+      # Need to override the attribute used by simp_le, which is python3Packages
+      python3Packages = (super.python3.override {
         packageOverrides = lib.const (pysuper: {
           certifi = pysuper.certifi.overridePythonAttrs (attrs: {
             postPatch = (attrs.postPatch or "") + ''

nixos/tests/cassandra.nix

@@ -1,68 +1,71 @@
 import ./make-test.nix ({ pkgs, ...}:
 let
-  user = "cassandra";
+  # Change this to test a different version of Cassandra:
-  nodeCfg = nodes: selfIP: cassandraOpts:
+  testPackage = pkgs.cassandra;
-    {
+  cassandraCfg = 
-      services.cassandra = {
+    { enable = true;
-        enable = true;
+      listenAddress = null;
-        listenAddress = selfIP;
+      listenInterface = "eth1";
-        rpcAddress = "0.0.0.0";
+      rpcAddress = null;
-        seeds = [ "192.168.1.1" ];
+      rpcInterface = "eth1";
-        package = pkgs.cassandra_2_0;
+      extraConfig =
-        jre = pkgs.openjdk;
+        { start_native_transport = true;
-        clusterName = "ci ahoy";
+          seed_provider =
-        authenticator = "PasswordAuthenticator";
+            [{ class_name = "org.apache.cassandra.locator.SimpleSeedProvider";
-        authorizer = "CassandraAuthorizer";
+               parameters = [ { seeds = "cass0"; } ];
-        user = user;
+            }];
-      } // cassandraOpts;
+        };
-      nixpkgs.config.allowUnfree = true;
+      package = testPackage;
+    };
+  nodeCfg = extra: {pkgs, config, ...}:
+    { environment.systemPackages = [ testPackage ];
+      networking.firewall.enable = false;
+      services.cassandra = cassandraCfg // extra;
       virtualisation.memorySize = 1024;
     };
-
 in
 {
   name = "cassandra-ci";
 
   nodes = {
-    cass0 = { nodes, ... }: nodeCfg nodes "192.168.1.1" {};
+    cass0 = nodeCfg {};
-    cass1 = { nodes, ... }: nodeCfg nodes "192.168.1.2" {};
+    cass1 = nodeCfg {};
-    cass2 = { nodes, ... }: nodeCfg nodes "192.168.1.3" {
+    cass2 = nodeCfg { jvmOpts = [ "-Dcassandra.replace_address=cass1" ]; };
-      extraParams = [
-        ''JVM_OPTS="$JVM_OPTS -Dcassandra.replace_address=192.168.1.2"''
-      ];
-      listenAddress = "192.168.1.3";
-    };
   };
 
   testScript = ''
-    subtest "start seed", sub {
+    subtest "timers exist", sub {
+      $cass0->succeed("systemctl list-timers | grep cassandra-full-repair.timer");
+      $cass0->succeed("systemctl list-timers | grep cassandra-incremental-repair.timer");
+    };
+    subtest "can connect via cqlsh", sub {
       $cass0->waitForUnit("cassandra.service");
-      $cass0->waitForOpenPort(9160);
+      $cass0->waitUntilSucceeds("nc -z cass0 9042");
-      $cass0->execute("echo show version | cqlsh localhost -u cassandra -p cassandra");
+      $cass0->succeed("echo 'show version;' | cqlsh cass0");
-      sleep 2;
-      $cass0->succeed("echo show version | cqlsh localhost -u cassandra -p cassandra");
-      $cass1->start;
     };
-    subtest "cassandra user/group", sub {
+    subtest "nodetool is operational", sub {
-      $cass0->succeed("id \"${user}\" >/dev/null");
+      $cass0->waitForUnit("cassandra.service");
-      $cass1->succeed("id \"${user}\" >/dev/null");
+      $cass0->waitUntilSucceeds("nc -z localhost 7199");
+      $cass0->succeed("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass0'");
     };
-    subtest "bring up cassandra cluster", sub {
+    subtest "bring up cluster", sub {
       $cass1->waitForUnit("cassandra.service");
-      $cass0->waitUntilSucceeds("nodetool status | grep -c UN  | grep 2");
+      $cass1->waitUntilSucceeds("nodetool status | egrep -c '^UN' | grep 2");
+      $cass0->succeed("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass1'");
     };
     subtest "break and fix node", sub {
-      $cass0->block;
+      $cass1->block;
-      $cass0->waitUntilSucceeds("nodetool status | grep -c DN  | grep 1");
+      $cass0->waitUntilSucceeds("nodetool status --resolve-ip | egrep -c '^DN[[:space:]]+cass1'");
-      $cass0->unblock;
+      $cass0->succeed("nodetool status | egrep -c '^UN'  | grep 1");
-      $cass0->waitUntilSucceeds("nodetool status | grep -c UN  | grep 2");
+      $cass1->unblock;
+      $cass1->waitUntilSucceeds("nodetool status | egrep -c '^UN'  | grep 2");
+      $cass0->succeed("nodetool status | egrep -c '^UN'  | grep 2");
     };
     subtest "replace crashed node", sub {
       $cass1->crash;
-      $cass2->start;
       $cass2->waitForUnit("cassandra.service");
-      $cass0->waitUntilFails("nodetool status | grep UN  | grep 192.168.1.2");
+      $cass0->waitUntilFails("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass1'");
-      $cass0->waitUntilSucceeds("nodetool status | grep UN | grep 192.168.1.3");
+      $cass0->waitUntilSucceeds("nodetool status --resolve-ip | egrep '^UN[[:space:]]+cass2'");
     };
   '';
 })

nixos/tests/netdata.nix

@@ -19,6 +19,10 @@ import ./make-test.nix ({ pkgs, ...} : {
     startAll;
 
     $netdata->waitForUnit("netdata.service");
+
+    # check if the netdata main page loads.
+    $netdata->succeed("curl --fail http://localhost:19999/");
+
     # check if netdata can read disk ops for root owned processes.
     # if > 0, successful. verifies both netdata working and
     # apps.plugin has elevated capabilities.

pkgs/applications/altcoins/go-ethereum.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "go-ethereum-${version}";
-  version = "1.8.11";
+  version = "1.8.13";
   goPackagePath = "github.com/ethereum/go-ethereum";
 
   # Fix for usb-related segmentation faults on darwin
@@ -16,7 +16,7 @@ buildGoPackage rec {
     owner = "ethereum";
     repo = "go-ethereum";
     rev = "v${version}";
-    sha256 = "1b4za0hszb95jnj97g4xkrgcl0bydllznm0wj6rpi6cwmdr0h8na";
+    sha256 = "123jkyb293z7ww3sa9ji5rw7xd229isi03k4ayyh5p7rr0dg8al0";
   };
 
   meta = with stdenv.lib; {

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

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, cairo, fftw, gtkmm2, lv2, lvtk, pkgconfig, python }:
+{ stdenv, fetchFromGitHub, cairo, fftw, gtkmm2, lv2, lvtk, pkgconfig, python3 }:
 
 stdenv.mkDerivation  rec {
   name = "ams-lv2-${version}";
@@ -12,13 +12,13 @@ stdenv.mkDerivation  rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ cairo fftw gtkmm2 lv2 lvtk python ];
+  buildInputs = [ cairo fftw gtkmm2 lv2 lvtk ];
 
-  configurePhase = "python waf configure --prefix=$out";
+  configurePhase = "${python3.interpreter} waf configure --prefix=$out";
 
-  buildPhase = "python waf";
+  buildPhase = "${python3.interpreter} waf";
 
-  installPhase = "python waf install";
+  installPhase = "${python3.interpreter} waf install";
 
   meta = with stdenv.lib; {
     description = "An LV2 port of the internal modules found in Alsa Modular Synth";

pkgs/applications/audio/bitwig-studio/bitwig-studio2.nix

@@ -3,11 +3,11 @@
 
 bitwig-studio1.overrideAttrs (oldAttrs: rec {
   name = "bitwig-studio-${version}";
-  version = "2.3.2";
+  version = "2.3.5";
 
   src = fetchurl {
     url    = "https://downloads.bitwig.com/stable/${version}/bitwig-studio-${version}.deb";
-    sha256 = "10ji4jqnnlhv4bgvhqwysprax6jcjk4759jskr9imwj6qjnj3vzn";
+    sha256 = "1v62z08hqla8fz5m7hl9ynf2hpr0j0arm0nb5lpd99qrv36ibrsc";
   };
 
   buildInputs = bitwig-studio1.buildInputs ++ [ ffmpeg ];

pkgs/applications/audio/cadence/default.nix

@@ -0,0 +1,65 @@
+{ stdenv
+, fetchurl
+, pkgconfig
+, qtbase
+, makeWrapper
+, jack2Full
+, python3Packages
+, a2jmidid
+}:
+
+ stdenv.mkDerivation rec {
+  version = "0.9.0";
+  name = "cadence";
+
+  src = fetchurl {
+    url = "https://github.com/falkTX/Cadence/archive/v${version}.tar.gz";
+    sha256 = "07z1mnb0bmldb3i31bgw816pnvlvr9gawr51rpx3mhixg5wpiqzb";
+  };
+
+  buildInputs = [
+    makeWrapper
+    pkgconfig
+    qtbase
+  ];
+
+  apps = [
+    "cadence"
+    "cadence-jacksettings"
+    "cadence-pulse2loopback"
+    "claudia"
+    "cadence-aloop-daemon"
+    "cadence-logs"
+    "cadence-render"
+    "catarina"
+    "claudia-launcher"
+    "cadence-pulse2jack"
+    "cadence-session-start"
+    "catia"
+  ];
+
+  makeFlags = ''
+    PREFIX=""
+    DESTDIR=$(out)
+  '';
+
+  propagatedBuildInputs = with python3Packages; [ pyqt5 ];
+
+  postInstall = ''
+    # replace with our own wrappers.
+    for app in $apps; do
+      rm $out/bin/$app
+      makeWrapper ${python3Packages.python.interpreter} $out/bin/$app \
+        --set PYTHONPATH "$PYTHONPATH:$out/share/cadence" \
+        --add-flags "-O $out/share/cadence/src/$app.py"
+    done
+  '';
+
+  meta = {
+    homepage = https://github.com/falkTX/Cadence/;
+    description = "Collection of tools useful for audio production";
+    license = stdenv.lib.licenses.mit;
+    maintainers = with stdenv.lib.maintainers; [ genesis ];
+    platforms = stdenv.lib.platforms.linux;
+  };
+}

pkgs/applications/audio/cantata/default.nix

@@ -28,7 +28,7 @@ assert withOnlineServices -> withTaglib;
 assert withReplaygain -> withTaglib;
 
 let
-  version = "2.2.0";
+  version = "2.3.2";
   pname = "cantata";
   fstat = x: fn: "-DENABLE_" + fn + "=" + (if x then "ON" else "OFF");
   fstats = x: map (fstat x);
@@ -42,18 +42,9 @@ in stdenv.mkDerivation rec {
     owner  = "CDrummond";
     repo   = "cantata";
     rev    = "v${version}";
-    sha256 = "1b633chgfs8rya78bzzck5zijna15d1y4nmrz4dcjp862ks5y5q6";
+    sha256 = "11hjday5vj0wzkc8yb5wbs05jwa8mvgxswd5qvhpci0zkl975yzn";
   };
 
-  patches = [
-    # patch is needed for 2.2.0 with qt 5.10 (doesn't harm earlier versions)
-    (fetchpatch {
-      url    = "https://github.com/CDrummond/cantata/commit/4da7a9128f2c5eaf23ae2a5006d300dc4f21fc6a.patch";
-      sha256 = "1z21ax3542z7hm628xv110lmplaspb407jzgfk16xkphww5qyphj";
-      name   = "fix_qt_510.patch";
-    })
-
-  ];
   buildInputs = [ vlc qtbase qtmultimedia qtsvg ]
     ++ stdenv.lib.optionals withTaglib [ taglib taglib_extras ]
     ++ stdenv.lib.optionals withReplaygain [ ffmpeg speex mpg123 ]

pkgs/applications/audio/qjackctl/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchurl, pkgconfig, alsaLib, libjack2, dbus, qtbase, qttools, qtx11extras }:
 
 stdenv.mkDerivation rec {
-  version = "0.5.2";
+  version = "0.5.3";
   name = "qjackctl-${version}";
 
   # some dependencies such as killall have to be installed additionally
 
   src = fetchurl {
     url = "mirror://sourceforge/qjackctl/${name}.tar.gz";
-    sha256 = "0nqr5f82lry3i4if8wdmrqsw84m45ijyj4psll30plxx5732zzaz";
+    sha256 = "0x08af8m5l8qy9av3dlldsg58ny9nc69h1s4i6hqkvj24jwy6fw1";
   };
 
   buildInputs = [

pkgs/applications/audio/qsampler/default.nix

@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   name = "qsampler-${version}";
-  version = "0.5.1";
+  version = "0.5.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/qsampler/${name}.tar.gz";
-    sha256 = "18j4cwmn7waih9x5b66cba2aa85spqqp507bf19ahsb5gl358yhh";
+    sha256 = "0xb0j57k03pkdl7yl5mcv1i21ljnxcq6b9h3zp6mris916lj45zq";
   };
 
   nativeBuildInputs = [ autoconf automake libtool pkgconfig qttools ];

pkgs/applications/audio/qsynth/default.nix

@@ -2,15 +2,15 @@
 
 stdenv.mkDerivation  rec {
   name = "qsynth-${version}";
-  version = "0.5.1";
+  version = "0.5.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/qsynth/${name}.tar.gz";
-    sha256 = "0kpk1rnhbifbvm4xvw8i0d4ksk78pf505qvg08k89kqkg32494ap";
+    sha256 = "1rfkaxq1pyc4hv3l0i6wicianbcbm1wp53kh9i5d4jsljgisd1dv";
   };
 
   # cmake is looking for qsynth.desktop.in and fails if it doesn't find it
-  # seems like a bug and can presumable go in the next version after 0.5.1
+  # seems like a bug and can presumable go in the next version after 0.5.2
   postPatch = ''
     mv src/qsynth.desktop src/qsynth.desktop.in
   '';

pkgs/applications/audio/spotify/default.nix

@@ -1,13 +1,18 @@
-{ fetchurl, stdenv, dpkg, xorg, alsaLib, makeWrapper, openssl, freetype
+{ fetchurl, stdenv, squashfsTools, xorg, alsaLib, makeWrapper, openssl, freetype
 , glib, pango, cairo, atk, gdk_pixbuf, gtk2, cups, nspr, nss, libpng
 , libgcrypt, systemd, fontconfig, dbus, expat, ffmpeg_0_10, curl, zlib, gnome3 }:
 
 let
-  # Please update the stable branch!
+  # "rev" decides what is actually being downloaded
-  # Latest version number can be found at:
+  version = "1.0.80.474.gef6b503e-7";
-  # http://repository-origin.spotify.com/pool/non-free/s/spotify-client/
+  # To get the latest stable revision:
-  # Be careful not to pick the testing version.
+  # curl -H 'X-Ubuntu-Series: 16' 'https://api.snapcraft.io/api/v1/snaps/details/spotify?channel=stable' | jq '.download_url,.version,.last_updated'
-  version = "1.0.80.480.g51b03ac3-13";
+  # To get general information:
+  # curl -H 'Snap-Device-Series: 16' 'https://api.snapcraft.io/v2/snaps/info/spotify' | jq '.'
+  # More exapmles of api usage:
+  # https://github.com/canonical-websites/snapcraft.io/blob/master/webapp/publisher/snaps/views.py
+  rev = "16";
+
 
   deps = [
     alsaLib
@@ -49,12 +54,20 @@ in
 stdenv.mkDerivation {
   name = "spotify-${version}";
 
+  # fetch from snapcraft instead of the debian repository most repos fetch from.
+  # That is a bit more cumbersome. But the debian repository only keeps the last
+  # two versions, while snapcraft should provide versions indefinately:
+  # https://forum.snapcraft.io/t/how-can-a-developer-remove-her-his-app-from-snap-store/512
+
+  # This is the next-best thing, since we're not allowed to re-distribute
+  # spotify ourselves:
+  # https://community.spotify.com/t5/Desktop-Linux/Redistribute-Spotify-on-Linux-Distributions/td-p/1695334
   src = fetchurl {
-    url = "https://repository-origin.spotify.com/pool/non-free/s/spotify-client/spotify-client_${version}_amd64.deb";
+    url = "https://api.snapcraft.io/api/v1/snaps/download/pOBIoZ2LrCB3rDohMxoYGnbN14EHOgD7_${rev}.snap";
-    sha256 = "e32f4816ae79dbfa0c14086e76df3bc83d526402aac1dbba534127fc00fe50ea";
+    sha512 = "45b7ab574b30fb368e0b6f4dd60addbfd1ddc02173b4f98b31c524eed49073432352a361e75959ce8e2f752231e93c79ca1b538c4bd295c935d1e2e0585d147f";
   };
 
-  buildInputs = [ dpkg makeWrapper ];
+  buildInputs = [ squashfsTools makeWrapper ];
 
   doConfigure = false;
   doBuild = false;
@@ -63,7 +76,23 @@ stdenv.mkDerivation {
 
   unpackPhase = ''
     runHook preUnpack
-    dpkg-deb -x $src .
+    unsquashfs "$src" '/usr/share/spotify' '/usr/bin/spotify' '/meta/snap.yaml'
+    cd squashfs-root
+    if ! grep -q 'grade: stable' meta/snap.yaml; then
+      # Unfortunately this check is not reliable: At the moment (2018-07-26) the
+      # latest version in the "edge" channel is also marked as stable.
+      echo "The snap package is marked as unstable:"
+      grep 'grade: ' meta/snap.yaml
+      echo "You probably chose the wrong revision."
+      exit 1
+    fi
+    if ! grep -q '${version}' meta/snap.yaml; then
+      echo "Package version differs from version found in snap metadata:"
+      grep 'version: ' meta/snap.yaml
+      echo "While the nix package specifies: ${version}."
+      echo "You probably chose the wrong revision or forgot to update the nix version."
+      exit 1
+    fi
     runHook postUnpack
   '';
 
@@ -75,6 +104,8 @@ stdenv.mkDerivation {
       mkdir -p $libdir
       mv ./usr/* $out/
 
+      cp meta/snap.yaml $out
+
       # Work around Spotify referring to a specific minor version of
       # OpenSSL.
 

pkgs/applications/audio/spotify/update.sh

@@ -0,0 +1,49 @@
+channel="stable" # stable/candidate/edge
+nixpkgs="$(git rev-parse --show-toplevel)"
+spotify_nix="$nixpkgs/pkgs/applications/audio/spotify/default.nix"
+
+
+
+# create bash array from snap info
+snap_info=($(
+	curl -H 'X-Ubuntu-Series: 16' \
+		"https://api.snapcraft.io/api/v1/snaps/details/spotify?channel=$channel" \
+	| jq --raw-output \
+		'.revision,.download_sha512,.version,.last_updated'
+))
+
+revision="${snap_info[0]}"
+sha512="${snap_info[1]}"
+version="${snap_info[2]}"
+last_updated="${snap_info[3]}"
+
+# find the last commited version
+version_pre=$(
+	git  grep 'version\s*=' HEAD "$spotify_nix" \
+	| sed -Ene 's/.*"(.*)".*/\1/p'
+)
+
+if [[ "$version_pre" = "$version" ]]; then
+	echo "Spotify is already up ot date"
+	exit 0
+fi
+
+echo "Updating from ${version_pre} to ${version}, released on ${last_updated}"
+
+# search-andreplace revision, hash and version
+sed --regexp-extended \
+	-e 's/rev\s*=\s*"[0-9]+"\s*;/rev = "'"${revision}"'";/' \
+	-e 's/sha512\s*=\s*".{128}"\s*;/sha512 = "'"${sha512}"'";/' \
+	-e 's/version\s*=\s*".*"\s*;/version = "'"${version}"'";/' \
+	-i "$spotify_nix" 
+
+if ! nix-build -A spotify "$nixpkgs"; then
+	echo "The updated spotify failed to build."
+	exit 1
+fi
+
+git add "$spotify_nix"
+# show diff for review
+git diff HEAD
+# prepare commit message, but allow edit
+git commit --edit --message "spotify: $version_pre -> $version"

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

@@ -8,9 +8,9 @@ let
     inherit (gnome2) GConf gnome_vfs;
   };
   stableVersion = {
-    version = "3.1.3.0"; # "Android Studio 3.1.3"
+    version = "3.1.4.0"; # "Android Studio 3.1.4"
-    build = "173.4819257";
+    build = "173.4907809";
-    sha256Hash = "196yaswbxh2nd83gimjxr8ggr5xkdxq7n3xlh6ax73v59pj4hryq";
+    sha256Hash = "0xx6yprylmcb32ipmwdcfkgddlm1nrxi1w68miclvgrbk015brf2";
   };
   betaVersion = {
     version = "3.2.0.22"; # "Android Studio 3.2 Beta 5"
@@ -18,9 +18,9 @@ let
     sha256Hash = "016nyn1pqviy089hg0dq7m4cqb39fdxdcy4zknkaq7dmgv1dj6x9";
   };
   latestVersion = { # canary & dev
-    version = "3.3.0.3"; # "Android Studio 3.3 Canary 4"
+    version = "3.3.0.4"; # "Android Studio 3.3 Canary 5"
-    build = "182.4924367";
+    build = "182.4928781";
-    sha256Hash = "03fxjxlsbrpklsss1nvlkb41skr5ymmq9vdns8iikcm1ng925vfd";
+    sha256Hash = "110gh5ylgf1p8z0rdnvc6clkq3v721v6pjvll66a8v4zgz9ay8b4";
   };
 in rec {
   # Old alias

pkgs/applications/editors/atom/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, pkgs, fetchurl, makeWrapper, gvfs, atomEnv}:
+{ stdenv, pkgs, fetchurl, makeWrapper, wrapGAppsHook, gvfs, gtk3, atomEnv }:
 
 let
   common = pname: {version, sha256, beta ? null}:
@@ -14,7 +14,19 @@ let
       inherit sha256;
     };
 
-    nativeBuildInputs = [ makeWrapper ];
+    nativeBuildInputs = [
+      wrapGAppsHook  # Fix error: GLib-GIO-ERROR **: No GSettings schemas are installed on the system
+    ];
+
+    buildInputs = [
+      gtk3  # Fix error: GLib-GIO-ERROR **: Settings schema 'org.gtk.Settings.FileChooser' is not installed
+    ];
+
+    preFixup = ''
+      gappsWrapperArgs+=(
+        --prefix "PATH" : "${gvfs}/bin" \
+      )
+    '';
 
     buildCommand = ''
       mkdir -p $out/usr/
@@ -25,9 +37,6 @@ let
       rm -r $out/share/lintian
       rm -r $out/usr/
       sed -i "s/${pname})/.${pname}-wrapped)/" $out/bin/${pname}
-      # sed -i "s/'${pname}'/'.${pname}-wrapped'/" $out/bin/${pname}
-      wrapProgram $out/bin/${pname} \
-        --prefix "PATH" : "${gvfs}/bin"
 
       fixupPhase
 

pkgs/applications/editors/emacs-modes/melpa-packages.nix

@@ -52,19 +52,9 @@ self:
       # part of a larger package
       caml = dontConfigure super.caml;
 
-      # part of a larger package
-      # upstream issue: missing package version
-      cmake-mode = markBroken (dontConfigure super.cmake-mode);
-
       # Expects bash to be at /bin/bash
       company-rtags = markBroken super.company-rtags;
 
-      # upstream issue: missing file header
-      connection = markBroken super.connection;
-
-      # upstream issue: missing file header
-      dictionary = markBroken super.dictionary;
-
       easy-kill-extras = super.easy-kill-extras.override {
         inherit (self.melpaPackages) easy-kill;
       };
@@ -79,6 +69,17 @@ self:
         inherit (self.melpaPackages) ess ctable popup;
       };
 
+      evil-magit = super.evil-magit.overrideAttrs (attrs: {
+        # searches for Git at build time
+        nativeBuildInputs =
+          (attrs.nativeBuildInputs or []) ++ [ external.git ];
+      });
+
+      # missing dependencies
+      evil-search-highlight-persist = super.evil-search-highlight-persist.overrideAttrs (attrs: {
+        packageRequires = with self; [ evil highlight ];
+      });
+
       # missing OCaml
       flycheck-ocaml = markBroken super.flycheck-ocaml;
 
@@ -108,15 +109,17 @@ self:
       # upstream issue: missing file header
       initsplit = super.initsplit;
 
+      # tries to write a log file to $HOME
+      insert-shebang = super.insert-shebang.overrideAttrs (attrs: {
+        HOME = "/tmp";
+      });
+
       # Expects bash to be at /bin/bash
       ivy-rtags = markBroken super.ivy-rtags;
 
       # upstream issue: missing file header
       jsfmt = markBroken super.jsfmt;
 
-      # upstream issue: missing file header
-      link = markBroken super.link;
-
       # upstream issue: missing file header
       maxframe = markBroken super.maxframe;
 
@@ -131,6 +134,18 @@ self:
             (attrs.nativeBuildInputs or []) ++ [ external.git ];
         });
 
+      magit-annex = super.magit-annex.overrideAttrs (attrs: {
+        # searches for Git at build time
+        nativeBuildInputs =
+          (attrs.nativeBuildInputs or []) ++ [ external.git ];
+      });
+
+      magit-gitflow = super.magit-gitflow.overrideAttrs (attrs: {
+        # searches for Git at build time
+        nativeBuildInputs =
+          (attrs.nativeBuildInputs or []) ++ [ external.git ];
+      });
+
       # missing OCaml
       merlin = markBroken super.merlin;
 
@@ -154,8 +169,10 @@ self:
             (attrs.nativeBuildInputs or []) ++ [ external.git ];
          }));
 
-      # upstream issue: truncated file
+      # tries to write to $HOME
-      powershell = markBroken super.powershell;
+      php-auto-yasnippets = super.php-auto-yasnippets.overrideAttrs (attrs: {
+        HOME = "/tmp";
+      });
 
       # upstream issue: mismatched filename
       processing-snippets = markBroken super.processing-snippets;

pkgs/applications/editors/kakoune/default.nix

@@ -4,12 +4,12 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "kakoune-unstable-${version}";
-  version = "2018-05-21";
+  version = "2018-08-05";
   src = fetchFromGitHub {
     repo = "kakoune";
     owner = "mawww";
-    rev = "878d2a4bdb674a5e7703a66e530520f48efba641";
+    rev = "ae75032936ed9ffa2bf14589fef115d3d684a7c6";
-    sha256 = "0pwy6ilsb62s1792gjyvhvq8shj60l8lx26b58zvpfb54an4s6rk";
+    sha256 = "1qm6i8vzr4wjxxdvhr54pan0ysxq1sn880bz8p2w9y6qa91yd3m3";
   };
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ ncurses asciidoc docbook_xsl libxslt ];

pkgs/applications/editors/vim/configurable.nix

@@ -6,6 +6,7 @@ args@{ source ? "default", callPackage, fetchurl, stdenv, ncurses, pkgconfig, ge
 , libICE
 , vimPlugins
 , makeWrapper
+, wrapGAppsHook
 
 # apple frameworks
 , CoreServices, CoreData, Cocoa, Foundation, libobjc, cf-private
@@ -73,15 +74,6 @@ in stdenv.mkDerivation rec {
 
   src = builtins.getAttr source {
     "default" = common.src; # latest release
-
-    "vim-nox" =
-      {
-        # vim nox branch: client-server without X by uing sockets
-        # REGION AUTO UPDATE: { name="vim-nox"; type="hg"; url="https://code.google.com/r/yukihironakadaira-vim-cmdsrv-nox/"; branch="cmdsrv-nox"; }
-        src = (fetchurl { url = "http://mawercer.de/~nix/repos/vim-nox-hg-2082fc3.tar.bz2"; sha256 = "293164ca1df752b7f975fd3b44766f5a1db752de6c7385753f083499651bd13a"; });
-        name = "vim-nox-hg-2082fc3";
-        # END
-      }.src;
   };
 
   patches = [ ./cflags-prune.diff ] ++ stdenv.lib.optional ftNixSupport ./ft-nix-support.patch;
@@ -131,6 +123,7 @@ in stdenv.mkDerivation rec {
   ++ stdenv.lib.optional wrapPythonDrv makeWrapper
   ++ stdenv.lib.optional nlsSupport gettext
   ++ stdenv.lib.optional perlSupport perl
+  ++ stdenv.lib.optional (guiSupport == "gtk3") wrapGAppsHook
   ;
 
   buildInputs = [ ncurses libX11 libXext libSM libXpm libXt libXaw libXau

pkgs/applications/graphics/animbar/default.nix

@@ -0,0 +1,40 @@
+{ stdenv, lib, fetchurl, cmake, qt4, file, gcc }:
+
+stdenv.mkDerivation rec {
+  pname = "animbar";
+  version = "1.2";
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/${pname}/${name}.tar.bz2";
+    sha256 = "0836nwcpyfdrapyj3hbg3wh149ihc26pc78h01adpc7c0r7d9pr9";
+  };
+
+  nativeBuildInputs = [ cmake  ];
+
+  buildInputs = [ qt4 file ];
+
+  installPhase = ''
+    mkdir -p $out/bin $out/share/pixmaps
+    cp src/animbar $out/bin
+    cp ../icon/* $out/share/pixmaps
+  '';
+
+  meta = with lib; {
+    description = "Create your own animation on paper and transparancy";
+    longDescription = ''
+	Animbar lets you easily create your own animation on paper and
+	transparancy. From a set of input images two output images are
+	computed, that are printed one on paper and one on
+	transparency. By moving the transparency over the paper you
+	create a fascinating animation effect. This kind of animation
+	technique is hundreds of years old and known under several
+	names: picket fence animation, barrier grid animation, Moiré
+	animation, to name a few.
+    '';
+    homepage = http://animbar.mnim.org;
+    maintainers = with maintainers; [ leenaars ];
+    platforms = platforms.linux;
+    license = licenses.gpl3;
+  };
+}

pkgs/applications/graphics/processing3/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, fetchurl, xmlstarlet, makeWrapper, ant, jdk, rsync, javaPackages, libXxf86vm, gsettings-desktop-schemas }:
 
 stdenv.mkDerivation rec {
-  version = "3.3.7";
+  version = "3.4";
   name = "processing3-${version}";
 
   src = fetchFromGitHub {
     owner = "processing";
     repo = "processing";
-    rev = "processing-0264-3.3.7";
+    rev = "processing-0265-${version}";
-    sha256 = "0a20z19lmc4xarfnr7xshcmlv3xkc2dgjxknis0iv79gxnwlqhpq";
+    sha256 = "12wpxgn2wd5vbasx9584w5yb1s319smq1zh8m7dvp7gkqw9plwp4";
   };
 
   nativeBuildInputs = [ ant rsync makeWrapper ];
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     ${xmlstarlet}/bin/xmlstarlet ed --inplace -P -d '//get[@src="http://download.processing.org/reference.zip"]' build/build.xml
     install -D -m0444 ${fetchurl {
                           url    = http://download.processing.org/reference.zip;
-                          sha256 = "104zig026y8vbl4qksmscjq0bms8mi2jmri1ijdlbkxcqnv9bnlf";
+                          sha256 = "0dli1bdgw8hsx7g7b048ap81v2za9maa6pfcwdqm3qkfypr8q7pr";
                         }
                        } ./java/reference.zip
 

pkgs/applications/graphics/renderdoc/default.nix

@@ -12,14 +12,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "1.0";
+  version = "1.1";
   name = "renderdoc-${version}";
 
   src = fetchFromGitHub {
     owner = "baldurk";
     repo = "renderdoc";
     rev = "v${version}";
-    sha256 = "0l7pjxfrly4llryjnwk42dzx65n78wc98h56qm4yh04ja8fdbx2y";
+    sha256 = "0kb9m1dm0mnglqyh1srvl0f1bgjghxzbqarn0xfqw49wphqwhmcd";
   };
 
   buildInputs = [

pkgs/applications/misc/gutenberg/default.nix

@@ -1,19 +1,19 @@
-{ stdenv, fetchFromGitHub, rustPlatform, cmake, CoreServices, cf-private }:
+{ stdenv, fetchFromGitHub, rustPlatform, cmake, pkgconfig, openssl, CoreServices, cf-private }:
 
 rustPlatform.buildRustPackage rec {
   name = "gutenberg-${version}";
-  version = "0.3.4";
+  version = "0.4.0";
 
   src = fetchFromGitHub {
     owner = "Keats";
     repo = "gutenberg";
     rev = "v${version}";
-    sha256 = "1v26q1m3bx7mdmmwgd6p601ncf13rr4rrx9s06fiy8vnd0ar1vlf";
+    sha256 = "1i2jcyq6afswxyjifhl5irv84licsad7c83yiy17454mplvrmyg2";
   };
 
-  cargoSha256 = "0cdy0wvibkpnmlqwxvn02a2k2vqy6zdqzflj2dh6g1cjbz1j8qh5";
+  cargoSha256 = "0hzxwvb5m8mvpfxys4ikkaag6khflh5bfglmay11wf6ayighv834";
 
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake pkgconfig openssl ];
   buildInputs = stdenv.lib.optionals stdenv.isDarwin [ CoreServices cf-private ];
 
   postInstall = ''

pkgs/applications/misc/overmind/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "overmind-${version}";
-  version = "1.1.1";
+  version = "2.0.0.beta1";
   goPackagePath = "github.com/DarthSim/overmind";
 
   nativeBuildInputs = [ makeWrapper ];
@@ -15,7 +15,7 @@ buildGoPackage rec {
     owner = "DarthSim";
     repo = "overmind";
     rev = "v${version}";
-    sha256 = "0gdsbm54ln07jv1kgg53fiavx18xxw4f21lfcdl74ijk6bx4jbzv";
+    sha256 = "15fch3qszdm8bj1m9hxky9zgk6f5gpbswwfslg84qdjf4iwr5drq";
   };
 
   meta = with stdenv.lib; {

pkgs/applications/misc/ranger/default.nix

@@ -1,11 +1,11 @@
-{ stdenv, fetchFromGitHub, pythonPackages, file, less
+{ stdenv, fetchFromGitHub, python3Packages, file, less
 , imagePreviewSupport ? true, w3m ? null}:
 
 with stdenv.lib;
 
 assert imagePreviewSupport -> w3m != null;
 
-pythonPackages.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   name = "ranger-${version}";
   version = "1.9.1";
 
@@ -16,7 +16,7 @@ pythonPackages.buildPythonApplication rec {
     sha256= "1zhds37j1scxa9b183qbrjwxqldrdk581c5xiy81vg17sndb1kqj";
   };
 
-  checkInputs = with pythonPackages; [ pytest ];
+  checkInputs = with python3Packages; [ pytest ];
   propagatedBuildInputs = [ file ];
 
   checkPhase = ''

pkgs/applications/misc/rtl_433/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, autoreconfHook, pkgconfig, libusb1, rtl-sdr }:
 stdenv.mkDerivation rec {
 
-  version = "2018-02-23";
+  version = "18.05";
   name = "rtl_433-${version}";
 
   src = fetchFromGitHub {
     owner = "merbanan";
     repo = "rtl_433";
-    rev = "51d275c";
+    rev = "18.05";
-    sha256 = "1j443wmws5xgc18s47bvw3pqljk747izypz52rmlrvs16v96cg2g";
+    sha256 = "0vfhnjyrx6w1m8g1hww5vdz4zgdlhcaps9g0397mxlki4sm77wpc";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

pkgs/applications/misc/solaar/default.nix

@@ -1,11 +1,13 @@
-{fetchurl, stdenv, gtk3, python34Packages, gobjectIntrospection}:
+{fetchFromGitHub, stdenv, gtk3, python34Packages, gobjectIntrospection}:
 python34Packages.buildPythonApplication rec {
-  name = "solaar-${version}";
+  name = "solaar-unstable-${version}";
-  version = "0.9.2";
+  version = "2018-02-02";
   namePrefix = "";
-  src = fetchurl {
+  src = fetchFromGitHub {
-    sha256 = "0954grz2adggfzcj4df4mpr4d7qyl7w8rb4j2s0f9ymawl92i05j";
+    owner = "pwr";
-    url = "https://github.com/pwr/Solaar/archive/${version}.tar.gz";
+    repo = "Solaar";
+    rev = "59b7285fdfc875119f0c92cfd5f5909e8a8e578c";
+    sha256 = "0zy5vmjzdybnjf0mpp8rny11sc43gmm8172svsm9s51h7x0v83y3";
   };
 
   propagatedBuildInputs = [python34Packages.pygobject3 python34Packages.pyudev gobjectIntrospection gtk3];
@@ -35,6 +37,6 @@ python34Packages.buildPythonApplication rec {
     license = licenses.gpl2;
     homepage = https://pwr.github.io/Solaar/;
     platforms = platforms.linux;
-    maintainers = [maintainers.spinus];
+    maintainers = [maintainers.spinus maintainers.ysndr];
   };
 }

pkgs/applications/misc/toggldesktop/TogglDesktop.pro

@@ -0,0 +1,19 @@
+QT += core network widgets
+
+DEFINES += APP_ENVIRONMENT=\\\"production\\\"
+DEFINES += APP_VERSION=\\\"@version@\\\"
+
+TARGET = toggldesktop
+TEMPLATE = app
+
+SOURCES += *.cpp
+HEADERS += *.h
+FORMS += *.ui
+RESOURCES += *.qrc
+
+target.path = $$PREFIX
+
+INSTALLS += target
+
+CONFIG += link_pkgconfig
+PKGCONFIG += bugsnag-qt qxtglobalshortcut qt-oauth-lib toggl x11 xscrnsaver

pkgs/applications/misc/toggldesktop/default.nix

@@ -0,0 +1,148 @@
+{ stdenv, fetchzip, buildEnv, makeDesktopItem, runCommand, writeText, pkgconfig
+, cmake, qmake, cacert, jsoncpp, libX11, libXScrnSaver, lua, openssl, poco
+, qtbase, qtwebkit, qtx11extras, sqlite }:
+
+let
+  name = "toggldesktop-${version}";
+  version = "7.4.231";
+
+  src = fetchzip {
+    url = "https://github.com/toggl/toggldesktop/archive/v${version}.tar.gz";
+    sha256 = "01hqkx9dljnhwnyqi6mmzfp02hnbi2j50rsfiasniqrkbi99x9v1";
+  };
+
+  bugsnag-qt = stdenv.mkDerivation rec {
+    name = "bugsnag-qt-${version}";
+    version = "20180522.005732";
+
+    src = fetchzip {
+      url = "https://github.com/yegortimoshenko/bugsnag-qt/archive/${version}.tar.gz";
+      sha256 = "02s6mlggh0i4a856md46dipy6mh47isap82jlwmjr7hfsk2ykgnq";
+    };
+
+    nativeBuildInputs = [ qmake ];
+    buildInputs = [ qtbase ];
+  };
+
+  qxtglobalshortcut = stdenv.mkDerivation rec {
+    name = "qxtglobalshortcut-${version}";
+    version = "f584471dada2099ba06c574bdfdd8b078c2e3550";
+
+    src = fetchzip {
+      url = "https://github.com/hluk/qxtglobalshortcut/archive/${version}.tar.gz";
+      sha256 = "1iy17gypav10z8aa62s5jb6mq9y4kb9ms4l61ydmk3xwlap7igw1";
+    };
+
+    nativeBuildInputs = [ cmake ];
+    buildInputs = [ qtbase qtx11extras ];
+  };
+
+  qt-oauth-lib = stdenv.mkDerivation rec {
+    name = "qt-oauth-lib-${version}";
+    version = "20180521.233208";
+
+    src = fetchzip {
+      url = "https://github.com/yegortimoshenko/qt-oauth-lib/archive/${version}.tar.gz";
+      sha256 = "0f46d44slzvzaqx0lksvv14lsc1jp8vd2mragxd61r820hybf5z3";
+    };
+
+    nativeBuildInputs = [ qmake ];
+    buildInputs = [ qtbase qtwebkit ];
+  };
+
+  poco-pc = writeText "poco.pc" ''
+    Name: Poco
+    Description: ${poco.meta.description}
+    Version: ${poco.version}
+    Libs: -L${poco}/lib -lPocoDataSQLite -lPocoData -lPocoNet -lPocoNetSSL -lPocoCrypto -lPocoUtil -lPocoXML -lPocoFoundation
+    Cflags: -I${poco}/include/Poco
+  '';
+
+  poco-pc-wrapped = runCommand "poco-pc-wrapped" {} ''
+    mkdir -p $out/lib/pkgconfig && ln -s ${poco-pc} $_/poco.pc
+  '';
+
+  libtoggl = stdenv.mkDerivation {
+    name = "libtoggl-${version}";
+    inherit src version;
+
+    sourceRoot = "source/src";
+
+    nativeBuildInputs = [ qmake pkgconfig ];
+    buildInputs = [ jsoncpp lua openssl poco poco-pc-wrapped sqlite libX11 ];
+
+    postPatch = ''
+      cat ${./libtoggl.pro} > libtoggl.pro
+      rm get_focused_window_{mac,windows}.cc
+    '';
+  };
+
+  toggldesktop = stdenv.mkDerivation {
+    name = "${name}-unwrapped";
+    inherit src version;
+
+    sourceRoot = "source/src/ui/linux/TogglDesktop";
+
+    postPatch = ''
+      substituteAll ${./TogglDesktop.pro} TogglDesktop.pro
+      substituteInPlace toggl.cpp \
+        --replace ./../../../toggl_api.h toggl_api.h
+    '';
+
+    postInstall = ''
+      ln -s ${cacert}/etc/ssl/certs/ca-bundle.crt $out/cacert.pem
+    '';
+
+    nativeBuildInputs = [ qmake pkgconfig ];
+
+    buildInputs = [
+      bugsnag-qt
+      libtoggl
+      qxtglobalshortcut
+      qtbase
+      qtwebkit
+      qt-oauth-lib
+      qtx11extras
+      libX11
+      libXScrnSaver
+    ];
+  };
+
+  toggldesktop-icons = stdenv.mkDerivation {
+    name = "${name}-icons";
+    inherit (toggldesktop) src sourceRoot;
+
+    installPhase = ''
+      for f in icons/*; do
+        mkdir -p $out/share/icons/hicolor/$(basename $f)/apps
+        mv $f/toggldesktop.png $_
+      done
+    '';
+  };
+
+  toggldesktop-wrapped = runCommand "toggldesktop-wrapped" {} ''
+    mkdir -p $out/bin && ln -s ${toggldesktop}/toggldesktop $_
+  '';
+
+  desktopItem = makeDesktopItem rec {
+    categories = "Utility;";
+    desktopName = "Toggl";
+    genericName = desktopName;
+    name = "toggldesktop";
+    exec = "${toggldesktop-wrapped}/bin/toggldesktop";
+    icon = "toggldesktop";
+  };
+in
+
+buildEnv {
+  inherit name;
+  paths = [ desktopItem toggldesktop-icons toggldesktop-wrapped ];
+
+  meta = with stdenv.lib; {
+    description = "Client for Toggl time tracking service";
+    homepage = https://github.com/toggl/toggldesktop;
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ yegortimoshenko ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/misc/toggldesktop/libtoggl.pro

@@ -0,0 +1,20 @@
+TARGET = toggl
+TEMPLATE = lib
+
+SOURCES += *.cc
+HEADERS += *.h
+
+headers.files = $$HEADERS
+headers.path = $$PREFIX/include
+target.path = $$PREFIX/lib
+
+INSTALLS += headers target
+
+CONFIG += create_prl create_pc link_pkgconfig
+PKGCONFIG += jsoncpp openssl lua poco sqlite3 x11
+
+QMAKE_PKGCONFIG_NAME = $$TARGET
+QMAKE_PKGCONFIG_PREFIX = $$PREFIX
+QMAKE_PKGCONFIG_LIBDIR = $$target.path
+QMAKE_PKGCONFIG_INCDIR = $$headers.path
+QMAKE_PKGCONFIG_DESTDIR = pkgconfig

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

@@ -1,31 +0,0 @@
-{ stdenv, fetchgit, pkgconfig, girara, gtk, webkitgtk, glib-networking, makeWrapper
-, gsettings-desktop-schemas }:
-
-stdenv.mkDerivation rec {
-  name = "jumanji-${version}";
-  version = "20150107";
-
-  src = fetchgit {
-    url = https://git.pwmt.org/pwmt/jumanji.git;
-    rev = "f8e04e5b5a9fec47d49ca63a096e5d35be281151";
-    sha256 = "1dsbyz489fx7dp07i29q1rjkl7nhrfscc8ks8an2rdyhx3457asg";
-  };
-
-  nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ girara gtk webkitgtk makeWrapper gsettings-desktop-schemas ];
-
-  makeFlags = [ "PREFIX=$(out)" ];
-
-  preFixup=''
-    wrapProgram "$out/bin/jumanji" \
-     --prefix GIO_EXTRA_MODULES : "${glib-networking.out}/lib/gio/modules" \
-     --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH"
-  '';
-
-  meta = with stdenv.lib; {
-    description = "Minimal web browser";
-    homepage = https://pwmt.org/projects/jumanji/;
-    platforms = platforms.all;
-    maintainers = [ maintainers.koral ];
-  };
-}

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

@@ -10,14 +10,14 @@
 
 stdenv.mkDerivation rec {
   name = "palemoon-${version}";
-  version = "27.9.2";
+  version = "27.9.4";
 
   src = fetchFromGitHub {
     name   = "palemoon-src";
     owner  = "MoonchildProductions";
     repo   = "Pale-Moon";
     rev    = version + "_Release";
-    sha256 = "0v6vgkxac2s1hw1namvrjysj2k1kbkabwdxrpq6kyd8svr7n974r";
+    sha256 = "0ir5gzhw98gfn15x58g1fwi11jd7gysvacqxg1v0jdjhgdl4m5sx";
   };
 
   desktopItem = makeDesktopItem {
@@ -79,6 +79,8 @@ stdenv.mkDerivation rec {
     chmod u+w .
   '';
 
+  hardeningDisable = [ "format" ];
+  
   buildPhase = ''
     cd $builddir
     $src/mach build

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

@@ -9,15 +9,17 @@
 with lib;
 
 let
-  version = "3.9.0";
+  version = "3.10.0";
   ver = stdenv.lib.elemAt (stdenv.lib.splitString "." version);
   versionMajor = ver 0;
   versionMinor = ver 1;
   versionPatch = ver 2;
-  gitCommit = "191fece";
+  gitCommit = "dd10d17";
   # version is in vendor/k8s.io/kubernetes/pkg/version/base.go
-  k8sversion = "v1.9.1";
+  k8sversion = "v1.10.0";
-  k8sgitcommit = "a0ce1bc657";
+  k8sgitcommit = "b81c8f8";
+  k8sgitMajor = "0";
+  k8sgitMinor = "1";
 in stdenv.mkDerivation rec {
   name = "openshift-origin-${version}";
   inherit version;
@@ -26,7 +28,7 @@ in stdenv.mkDerivation rec {
     owner = "openshift";
     repo = "origin";
     rev = "v${version}";
-    sha256 = "06k0zilfyvll7z34yirraslgpwgah9k6y5i6wgi7f00a79k76k78";
+    sha256 = "13aglz005jl48z17vnggkvr39l5h6jcqgkfyvkaz4c3jakms1hi9";
 };
 
   # go > 1.10
@@ -38,15 +40,15 @@ in stdenv.mkDerivation rec {
   patchPhase = ''
     patchShebangs ./hack
 
-    substituteInPlace pkg/oc/bootstrap/docker/host/host.go  \
+    substituteInPlace pkg/oc/clusterup/docker/host/host.go  \
       --replace 'nsenter --mount=/rootfs/proc/1/ns/mnt findmnt' \
       'nsenter --mount=/rootfs/proc/1/ns/mnt ${utillinux}/bin/findmnt'
 
-    substituteInPlace pkg/oc/bootstrap/docker/host/host.go  \
+    substituteInPlace pkg/oc/clusterup/docker/host/host.go  \
       --replace 'nsenter --mount=/rootfs/proc/1/ns/mnt mount' \
       'nsenter --mount=/rootfs/proc/1/ns/mnt ${utillinux}/bin/mount'
 
-    substituteInPlace pkg/oc/bootstrap/docker/host/host.go  \
+    substituteInPlace pkg/oc/clusterup/docker/host/host.go  \
       --replace 'nsenter --mount=/rootfs/proc/1/ns/mnt mkdir' \
       'nsenter --mount=/rootfs/proc/1/ns/mnt ${coreutils}/bin/mkdir'
   '';
@@ -61,6 +63,8 @@ in stdenv.mkDerivation rec {
     echo "OS_GIT_COMMIT=${gitCommit}" >> os-version-defs
     echo "KUBE_GIT_VERSION=${k8sversion}" >> os-version-defs
     echo "KUBE_GIT_COMMIT=${k8sgitcommit}" >> os-version-defs
+    echo "KUBE_GIT_MAJOR=${k8sgitMajor}" >> os-version-defs
+    echo "KUBE_GIT_MINOR=${k8sgitMinor}" >> os-version-defs
     export OS_VERSION_FILE="os-version-defs"
     export CC=clang
     make all WHAT='${concatStringsSep " " components}'

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

@@ -1,18 +1,18 @@
-{ stdenv, fetchFromGitHub, pythonPackages, openssl }:
+{ stdenv, fetchFromGitHub, python2Packages, openssl }:
 
-pythonPackages.buildPythonApplication rec {
+python2Packages.buildPythonApplication rec {
-  name = "pybitmessage-${version}";
+  pname = "pybitmessage";
 
-  version = "0.6.2";
+  version = "0.6.3.2";
 
   src = fetchFromGitHub {
     owner = "bitmessage";
     repo = "PyBitmessage";
-    rev = "v${version}";
+    rev = version;
-    sha256 = "04sgns9qczzw2152gqdr6bjyy4fmgs26cz8n3qck94l0j51rxhz8";
+    sha256 = "1lmhbpwsqh1v93krlqqhafw2pc3y0qp8zby186yllbph6s8kdp35";
   };
 
-  propagatedBuildInputs = with pythonPackages; [ msgpack-python pyqt4 numpy pyopencl ] ++ [ openssl ];
+  propagatedBuildInputs = with python2Packages; [ msgpack-python pyqt4 numpy pyopencl ] ++ [ openssl ];
 
   preConfigure = ''
     # Remove interaction and misleading output

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

@@ -3,9 +3,24 @@
 , dbus, libX11, xorg, libXi, libXcursor, libXdamage, libXrandr, libXcomposite
 , libXext, libXfixes, libXrender, libXtst, libXScrnSaver, nss, nspr, alsaLib
 , cups, expat, udev
+# Unfortunately this also overwrites the UI language (not just the spell
+# checking language!):
+, hunspellDicts, spellcheckerLanguage ? null # E.g. "de_DE"
+# For a full list of available languages:
+# $ cat pkgs/development/libraries/hunspell/dictionaries.nix | grep "dictFileName =" | awk '{ print $3 }'
 }:
 
 let
+  customLanguageWrapperArgs = (with lib;
+    let
+      # E.g. "de_DE" -> "de-de" (spellcheckerLanguage -> hunspellDict)
+      spellLangComponents = splitString "_" spellcheckerLanguage;
+      hunspellDict = elemAt spellLangComponents 0 + "-" + toLower (elemAt spellLangComponents 1);
+    in if spellcheckerLanguage != null
+      then ''
+        --set HUNSPELL_DICTIONARIES "${hunspellDicts.${hunspellDict}}/share/hunspell" \
+        --set LC_MESSAGES "${spellcheckerLanguage}"''
+      else "");
   rpath = lib.makeLibraryPath [
     alsaLib
     atk
@@ -40,11 +55,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "signal-desktop-${version}";
-  version = "1.15.0";
+  version = "1.15.3";
 
   src = fetchurl {
     url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "1q73jx92h8zwk1dn103ymskz35q6kfiqc44886jr0p7mlpndqsa4";
+    sha256 = "009bcy90dvwiizya387fqrh3a8l0czgs4wnddxndy9gd477sn704";
   };
 
   phases = [ "unpackPhase" "installPhase" ];
@@ -68,6 +83,7 @@ in stdenv.mkDerivation rec {
              --set-rpath ${rpath}:$out/libexec $out/libexec/signal-desktop
     wrapProgram $out/libexec/signal-desktop \
       --prefix XDG_DATA_DIRS : "${gtk3}/share/gsettings-schemas/${gtk3.name}/" \
+      ${customLanguageWrapperArgs} \
       "''${gappsWrapperArgs[@]}"
 
     # Symlink to bin

pkgs/applications/networking/instant-messengers/telegram/tdesktop/default.nix

@@ -14,7 +14,7 @@ in {
   stable = mkTelegram stableVersion;
   preview = mkTelegram (stableVersion // {
     stable = false;
-    version = "1.3.11";
+    version = "1.3.12";
-    sha256Hash = "057b7ccba7k2slzbp9xzcs3fni40x7gz3wy13xfgxywr12f04h1r";
+    sha256Hash = "00z4ljs4fvbk7sf8wv1v50kln26gv8q12x6q41ai9gfzkvq5f69a";
   });
 }

pkgs/applications/networking/ipfs/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "ipfs-${version}";
-  version = "0.4.15";
+  version = "0.4.17";
   rev = "v${version}";
 
   goPackagePath = "github.com/ipfs/go-ipfs";
@@ -10,7 +10,7 @@ buildGoPackage rec {
   extraSrcPaths = [
     (fetchgx {
       inherit name src;
-      sha256 = "0bysfh2hd040i8lnyzhy96frflls4kdnlw748cl51ngqg3rwbhgz";
+      sha256 = "0grdgnr67r3qh0ppc3flrhcw8zlvx10mxypd8q2mhkil9w4dpcna";
     })
   ];
 
@@ -18,7 +18,7 @@ buildGoPackage rec {
     owner = "ipfs";
     repo = "go-ipfs";
     inherit rev;
-    sha256 = "1ry4a4pq26dbwy2b9cwi3xjaiyq6sng9lxnb1n30zxhp4w7rla2h";
+    sha256 = "18skmchdqd54wfqhibscqvc360l5ig6vmxd73ivf3bcpj3zvgq7q";
   };
 
   meta = with stdenv.lib; {

pkgs/applications/networking/p2p/deluge/default.nix

@@ -18,7 +18,8 @@ pythonPackages.buildPythonPackage rec {
   ];
 
   propagatedBuildInputs = with pythonPackages; [
-    pyGtkGlade libtorrentRasterbar twisted Mako chardet pyxdg pyopenssl service-identity
+    pyGtkGlade twisted Mako chardet pyxdg pyopenssl service-identity
+    libtorrentRasterbar.dev libtorrentRasterbar.python
   ];
 
   nativeBuildInputs = [ intltool ];

pkgs/applications/networking/p2p/soulseekqt/default.nix

@@ -2,27 +2,35 @@
 , fetchurl
 , dbus
 , zlib, fontconfig
+, qtbase, qtmultimedia
+, libjson, libgpgerror
 , libX11, libxcb, libXau, libXdmcp, freetype, libbsd
+, pythonPackages, squashfsTools, makeDesktopItem
 }:
 
 with stdenv.lib;
 let
   libPath = makeLibraryPath
-    [ stdenv.cc.cc dbus libX11 zlib libX11 libxcb libXau libXdmcp freetype fontconfig libbsd ];
+    [ stdenv.cc.cc qtbase qtmultimedia dbus libX11 zlib libX11 libxcb libXau libXdmcp freetype fontconfig libbsd libjson libgpgerror];
 
-  version = "2016-1-17";
+  version = "2018-1-30";
 
   mainbin = "SoulseekQt-" + (version) +"-"+ (if stdenv.is64bit then "64bit" else "32bit");
   srcs = {
-    "i686-linux" = fetchurl {
+    "x86_64-linux" = fetchurl {
-      url = "https://www.dropbox.com/s/kebk1b5ib1m3xxw/${mainbin}.tgz";
+      url = "https://www.dropbox.com/s/0vi87eef3ooh7iy/${mainbin}.tgz";
-      sha256 = "0r9rhnfslkgbw3l7fnc0rcfqjh58amgh5p33kwam0qvn1h1frnir";
+      sha256 = "0d1cayxr1a4j19bc5a3qp9pg22ggzmd55b6f5av3lc6lvwqqg4w6";
+    };
   };
 
-    "x86_64-linux" = fetchurl {
+  desktopItem = makeDesktopItem {
-      url = "https://www.dropbox.com/s/7qh902qv2sxyp6p/${mainbin}.tgz";
+    name = "SoulseekQt";
-      sha256 = "05l3smpdvw8xdhv4v8a28j0yi1kvzhrha2ck23g4bl7x9wkay4cc";
+    exec = "soulseekqt";
-    };
+    icon = "$out/share/soulseekqt/";
+    comment = "Official Qt SoulSeek client"; 
+    desktopName = "SoulseekQt";
+    genericName = "SoulseekQt";
+    categories = "Network;";
   };
 
 in stdenv.mkDerivation rec {
@@ -31,12 +39,22 @@ in stdenv.mkDerivation rec {
   inherit version;
   src = srcs."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
 
-  sourceRoot = ".";
+  dontBuild = true;
-  buildPhase = ":";   # nothing to build
+
+  buildInputs = [ pythonPackages.binwalk squashfsTools ];
+
+  # avoid usage of appimagetool
+  unpackCmd = ''
+    export HOME=$(pwd) # workaround for binwalk
+    tar xvf $curSrc && binwalk --quiet \
+       ${mainbin}.AppImage -D 'squashfs:.squashfs:unsquashfs %e'
+    '';
 
   installPhase = ''
-    mkdir -p $out/bin
+    mkdir -p $out/{bin,share/soulseekqt}
-    cp ${mainbin} $out/bin/soulseekqt
+    cd squashfs-root/
+    cp -R soulseek.png translations $out/share/soulseekqt
+    cp SoulseekQt $out/bin/soulseekqt
   '';
 
   fixupPhase = ''
@@ -50,6 +68,6 @@ in stdenv.mkDerivation rec {
     homepage = http://www.soulseekqt.net;
     license = licenses.unfree;
     maintainers = [ maintainers.genesis ];
-    platforms = [ "i686-linux" "x86_64-linux" ];
+    platforms = [ "x86_64-linux" ];
   };
 }

pkgs/applications/networking/remote/citrix-receiver/default.nix

@@ -39,50 +39,6 @@ let
   });
 
   versionInfo = {
-    "13.4.0" = rec {
-      major     = "13";
-      minor     = "4";
-      patch     = "0";
-      x64hash   = "133brs0sq6d0mgr19rc6ig1n9ahm3ryi23v5nrgqfh0hgxqcrrjb";
-      x86hash   = "0r7jfl5yqv1s2npy8l9gsn0gbb82f6raa092ppkc8xy5pni5sh7l";
-      x64suffix = "10109380";
-      x86suffix = x64suffix;
-      homepage  = https://www.citrix.com/downloads/citrix-receiver/legacy-receiver-for-linux/receiver-for-linux-latest-13-4.html;
-    };
-
-    "13.5.0" = rec {
-      major     = "13";
-      minor     = "5";
-      patch     = "0";
-      x64hash   = "1r24mhkpcc0z95n597p07fz92pd1b8qqzp2z6w07rmb9wb8mpd4x";
-      x86hash   = "0pwxshlryzhkl86cj9ryybm54alhzjx0gpp67fnvdn5r64wy1nd1";
-      x64suffix = "10185126";
-      x86suffix = x64suffix;
-      homepage  = https://www.citrix.com/downloads/citrix-receiver/legacy-receiver-for-linux/receiver-for-linux-latest-13-5.html;
-    };
-
-    "13.6.0" = rec {
-      major     = "13";
-      minor     = "6";
-      patch     = "0";
-      x64hash   = "6e423be41d5bb8186bcca3fbb4ede54dc3f00b8d2aeb216ae4aabffef9310d34";
-      x86hash   = "0ba3eba208b37844904d540b3011075ed5cecf429a0ab6c6cd52f2d0fd841ad2";
-      x64suffix = "10243651";
-      x86suffix = x64suffix;
-      homepage  = https://www.citrix.com/downloads/citrix-receiver/legacy-receiver-for-linux/receiver-for-linux-136.html;
-    };
-
-    "13.7.0" = {
-      major     = "13";
-      minor     = "7";
-      patch     = "0";
-      x64hash   = "18fb374b9fb8e249b79178500dddca7a1f275411c6537e7695da5dcf19c5ba91";
-      x86hash   = "4c68723b0327cf6f12da824056fce2b7853c38e6163a48c9d222b93dd8da75b6";
-      x64suffix = "10276927";
-      x86suffix = "10276925";
-      homepage  = https://www.citrix.com/downloads/citrix-receiver/legacy-receiver-for-linux/receiver-for-linux-137.html;
-    };
-
     "13.8.0" = {
       major     = "13";
       minor     = "8";
@@ -156,7 +112,7 @@ let
         '';
       };
 
-      phases = [ "unpackPhase" "installPhase" ];
+      dontBuild = true;
 
       sourceRoot = ".";
 
@@ -203,6 +159,8 @@ let
       };
 
       installPhase = ''
+        runHook preInstall
+
         export ICAInstDir="$out/opt/citrix-icaclient"
 
         sed -i \
@@ -262,13 +220,15 @@ let
 
         # We introduce a dependency on the source file so that it need not be redownloaded everytime
         echo $src >> "$out/share/nix_dependencies.pin"
+
+        runHook postInstall
       '';
 
       meta = with stdenv.lib; {
         license     = stdenv.lib.licenses.unfree;
         inherit homepage;
         description = "Citrix Receiver";
-        maintainers = with maintainers; [ obadz a1russell ];
+        maintainers = with maintainers; [ obadz a1russell ma27 ];
         platforms   = platforms.linux;
       };
     };

pkgs/applications/networking/remote/citrix-receiver/wrapper.nix

@@ -0,0 +1,19 @@
+{ citrix_receiver, extraCerts ? [], symlinkJoin }:
+
+let
+
+  mkCertCopy = certPath:
+    "cp ${certPath} $out/opt/citrix-icaclient/keystore/cacerts/";
+
+in
+
+if builtins.length extraCerts == 0 then citrix_receiver else symlinkJoin {
+  name = "citrix-with-extra-certs-${citrix_receiver.version}";
+  paths = [ citrix_receiver ];
+
+  postBuild = ''
+    ${builtins.concatStringsSep "\n" (map mkCertCopy extraCerts)}
+
+    sed -i -E "s,-icaroot (.+citrix-icaclient),-icaroot $out/opt/citrix-icaclient," $out/bin/wfica
+  '';
+}

pkgs/applications/networking/remote/remmina/default.nix

@@ -10,7 +10,7 @@
 }:
 
 let
-  version = "1.2.30.1";
+  version = "1.2.31.2";
 
   desktopItem = makeDesktopItem {
     name = "remmina";
@@ -29,7 +29,7 @@ in stdenv.mkDerivation {
     owner  = "Remmina";
     repo   = "Remmina";
     rev    = "v${version}";
-    sha256 = "1jz20yv84a8m9gm9fsz0jii8ag90v1scmbkkx9gk38ax5il7ilvn";
+    sha256 = "09jdrs2hbr9wyd5yqw5bri41rnfnxxyh98mlv6ig2phlvs9cg73d";
   };
 
   nativeBuildInputs = [ pkgconfig ];

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

@@ -1,18 +1,26 @@
-{ stdenv, fetchFromGitHub, cmake, lua, pkgconfig, rsync,
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, lua, pkgconfig, rsync,
   asciidoc, libxml2, docbook_xml_dtd_45, docbook_xsl, libxslt }:
 
 stdenv.mkDerivation rec {
   name = "lsyncd-${version}";
-  version = "2.2.2";
+  version = "2.2.3";
 
   src = fetchFromGitHub {
     owner = "axkibe";
     repo = "lsyncd";
     rev = "release-${version}";
-    sha256 = "1q2ixp52r96ckghgmxdbms6xrq8dbziimp8gmgzqfq4lk1v1w80y";
+    sha256 = "1hbsih5hfq9lhgnxm0wb5mrj6xmlk2l0i9a79wzd5f6cnjil9l3x";
   };
 
-  patchPhase = ''
+  patches = [
+    (fetchpatch {
+      sha256 = "0b0h2qxh73l502p7phf6qgl8576nf6fvqqp2x5wy3nz7sc9qb1z8";
+      name = "fix-non-versioned-lua-not-search-in-cmake.patch";
+      url = "https://github.com/axkibe/lsyncd/pull/500/commits/0af99d8d5ba35118e8799684a2d4a8ea4b0c6957.patch";
+    })
+  ];
+
+  postPatch = ''
     substituteInPlace default-rsync.lua \
       --replace "/usr/bin/rsync" "${rsync}/bin/rsync"
   '';

pkgs/applications/office/tryton/default.nix

@@ -14,10 +14,10 @@ with stdenv.lib;
 
 python2Packages.buildPythonApplication rec {
   pname = "tryton";
-  version = "4.8.3";
+  version = "4.8.4";
   src = python2Packages.fetchPypi {
     inherit pname version;
-    sha256 = "1e2862bbe7c943afbbdf2232cdc55f75d2357640115c7f1483f0814b2c5a6882";
+    sha256 = "6cf3091424853e1270d61f3a9b15ad8e6b36a44c28becf216c324ca8dc1474b0";
   };
   nativeBuildInputs = [ pkgconfig gobjectIntrospection ];
   propagatedBuildInputs = with python2Packages; [

pkgs/applications/office/trytond/default.nix

@@ -5,10 +5,10 @@ with stdenv.lib;
 
 python2Packages.buildPythonApplication rec {
   pname = "trytond";
-  version = "4.8.2";
+  version = "4.8.3";
   src = python2Packages.fetchPypi {
     inherit pname version;
-    sha256 = "ec5c419418517bf9f7d2af08b2bfd3bcc7526f6d6f07d122abf1699c728ae2a9";
+    sha256 = "11d01dc984d9274229b5c80f883679d130a55e14e9124b051274fce9aea4ef77";
   };
 
   # Tells the tests which database to use

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

@@ -2,11 +2,11 @@
 
 with stdenv.lib;
 
+let version = "2.48"; in
 stdenv.mkDerivation {
   name = "gwyddion-${version}";
-  version = "2.48";
   src = fetchurl {
-    url = "http://sourceforge.net/projects/gwyddion/files/gwyddion/2.48/gwyddion-2.48.tar.xz";
+    url = "http://sourceforge.net/projects/gwyddion/files/gwyddion/${version}/gwyddion-${version}.tar.xz";
     sha256 = "119iw58ac2wn4cas6js8m7r1n4gmmkga6b1y711xzcyjp9hshgwx";
   };
   nativeBuildInputs = [ pkgconfig ];

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

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "symbiyosys-${version}";
-  version = "2018.05.03";
+  version = "2018.07.26";
 
   src = fetchFromGitHub {
     owner  = "yosyshq";
     repo   = "symbiyosys";
-    rev    = "35d956c7bb77c0602d198035b2d73a9c61cb4de4";
+    rev    = "2fef25f93dd1cb5137a08e71f507e3eee8100fb1";
-    sha256 = "02zg3nkwp3fdjwz1agvsn55k1xipwh2rradb0bgjrjpsmmw63gda";
+    sha256 = "103fga0n11h4n2q346xyz3k0615d9lgx2b8sqr1pwn2hx26kchav";
   };
 
   buildInputs = [ python3 yosys ];

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

@@ -13,10 +13,10 @@ assert useGoogleHashmap -> sparsehash != null;
 
 let
   inherit (stdenv.lib) optional;
+  version = "1.0";
 in
 stdenv.mkDerivation {
   name = "ripser-${version}";
-  version = "1.0";
 
   src = fetchFromGitHub {
     owner = "Ripser";

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

@@ -8,10 +8,6 @@ let
   # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
   python = nixpkgs.python2.override {
     packageOverrides = self: super: {
-      cypari2 = super.cypari2.override { inherit pari; };
-
-      cysignals = super.cysignals.override { inherit pari; };
-
       # 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
@@ -24,7 +20,7 @@ let
       pybrial = self.callPackage ./pybrial.nix {};
 
       sagelib = self.callPackage ./sagelib.nix {
-        inherit flint ecl pari eclib ntl arb;
+        inherit flint ecl arb;
         inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
         linbox = nixpkgs.linbox.override { withSage = true; };
       };
@@ -38,20 +34,20 @@ let
       };
 
       env-locations = self.callPackage ./env-locations.nix {
-        inherit pari_data ecl pari;
+        inherit pari_data ecl;
         inherit singular;
         three = nodePackages_8_x.three;
         mathjax = nodePackages_8_x.mathjax;
       };
 
       sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper openblas-cblas-pc ecl singular eclib pari palp flint pynac pythonEnv giac ntl;
+        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 pari eclib pythonEnv ntl;
+        inherit pythonEnv;
-        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular giac;
+        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_8_x.three;
       };
@@ -106,41 +102,18 @@ let
     });
   };
 
-  # https://trac.sagemath.org/ticket/25532
-  ntl = nixpkgs.ntl.overrideAttrs (oldAttrs: rec {
-    name = "ntl-10.5.0";
-    sourceRoot = "${name}/src";
-    src = fetchurl {
-      url = "http://www.shoup.net/ntl/${name}.tar.gz";
-      sha256 = "1lmldaldgfr2b2a6585m3np5ds8bq1bis2s1ajycjm49vp4kc2xr";
-    };
-  });
-
-  giac = nixpkgs.giac.override { inherit ntl; };
   arb = nixpkgs.arb.override { inherit flint; };
 
-  # update causes issues
+  singular = nixpkgs.singular.override { inherit flint; };
-  # https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso
-  # https://trac.sagemath.org/ticket/24735
-  singular = (nixpkgs.singular.override { inherit ntl flint; }).overrideAttrs (oldAttrs: {
-    name = "singular-4.1.0p3";
-    src = fetchurl {
-      url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz";
-      sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4";
-    };
-  });
 
   # *not* to confuse with the python package "pynac"
-  # https://trac.sagemath.org/ticket/24838 (depends on arb update)
   pynac = nixpkgs.pynac.override { inherit singular flint; };
 
-  eclib = nixpkgs.eclib.override { inherit pari ntl; };
-
   # 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; inherit ntl; };
+  flint = nixpkgs.flint.override { withBlas = false; };
 
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.
@@ -165,15 +138,6 @@ let
 
   # https://trac.sagemath.org/ticket/22191
   ecl = nixpkgs.ecl_16_1_2;
-
-  # sage currently uses an unreleased version of pari
-  pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec {
-    version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix`
-    src = fetchurl {
-      url = "mirror://sageupstream/pari/pari-${version}.tar.gz";
-      sha256 = "19gbsm8jqq3hraanbmsvzkbh88iwlqbckzbnga3y76r7k42akn7m";
-    };
-  });
 in
   python.pkgs.sage-wrapper // {
     doc = python.pkgs.sagedoc;

pkgs/applications/science/math/sage/patches/arb-2.13.0.patch

@@ -1,427 +0,0 @@
-commit c885927e25b29bd23869e02379c2918da430323e
-Author: Timo Kaufmann <timokau@zoho.com>
-Date:   Sat Jun 30 02:26:15 2018 +0200
-
-diff --git a/build/pkgs/arb/checksums.ini b/build/pkgs/arb/checksums.ini
-index 1924ee03c3..9323b97391 100644
---- a/build/pkgs/arb/checksums.ini
-+++ b/build/pkgs/arb/checksums.ini
-@@ -1,4 +1,4 @@
- tarball=arb-VERSION.tar.gz
--sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3
--md5=733285d9705d10b8024e551ffa81952f
--cksum=2391183744
-+sha1=44eda7bf8eaa666c45b1fc2c1b5bd08756d94b58
-+md5=fa24de9fffe4394fb6a7a6792e2ecc5f
-+cksum=3689220688
-diff --git a/build/pkgs/arb/package-version.txt b/build/pkgs/arb/package-version.txt
-index c8810e9bdb..fb2c0766b7 100644
---- a/build/pkgs/arb/package-version.txt
-+++ b/build/pkgs/arb/package-version.txt
-@@ -1 +1 @@
--2.12.0.p0
-+2.13.0
-diff --git a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch b/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch
-deleted file mode 100644
-index 3e5c0e708b..0000000000
---- a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch
-+++ /dev/null
-@@ -1,17 +0,0 @@
--In newer binutils, ld options -r and -pie conflict.
--Patch due to Jörg-Volker Peetz
--(source : https://groups.google.com/d/msg/sage-devel/TduebNoZuBE/sEULolL0BQAJ),
--packaged by Emmanuel Charpentier
--
--diff -ru arb-2.8.1-orig/Makefile.subdirs arb-2.8.1-new/Makefile.subdirs
----- arb-2.8.1-orig/Makefile.subdirs	2015-12-31 17:30:01.000000000 +0100
--+++ arb-2.8.1-new/Makefile.subdirs	2016-11-07 18:50:34.540051779 +0100
--@@ -52,7 +52,7 @@
-- 	$(QUIET_CC) $(CC) $(CFLAGS) $(INCS) -c $< -o $@ -MMD -MP -MF "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$@"
-- 
-- $(MOD_LOBJ): $(LOBJS)
---	$(QUIET_CC) $(CC) $(ABI_FLAG) -Wl,-r $^ -o $@ -nostdlib
--+	$(QUIET_CC) $(CC) $(ABI_FLAG) -r $^ -o $@ -nostdlib
-- 
-- -include $(LOBJS:.lo=.d)
-- 
-diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx
-index 70d51e655a..00e7caea2c 100644
---- a/src/sage/rings/complex_arb.pyx
-+++ b/src/sage/rings/complex_arb.pyx
-@@ -857,14 +857,14 @@ class ComplexBallField(UniqueRepresentation, Field):
-             [0.500000000000000 +/- 2.09e-16]
- 
-             sage: CBF.integral(lambda x, _: x.gamma(), 1 - CBF(i), 1 + CBF(i))
--            [+/- 3.95e-15] + [1.5723926694981 +/- 4.53e-14]*I
-+            [+/- 4...e-15] + [1.5723926694981 +/- 4...e-14]*I
- 
-             sage: C = ComplexBallField(100)
-             sage: C.integral(lambda x, _: x.cos() * x.sin(), 0, 1)
-             [0.35403670913678559674939205737 +/- 8.89e-30]
- 
-             sage: CBF.integral(lambda x, _: (x + x.exp()).sin(), 0, 8)
--            [0.34740017266 +/- 6.36e-12]
-+            [0.34740017266 +/- 6...e-12]
- 
-             sage: C = ComplexBallField(2000)
-             sage: C.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) # long time
-@@ -879,14 +879,14 @@ class ComplexBallField(UniqueRepresentation, Field):
-             ....:     else:
-             ....:         return z.sqrt()
-             sage: CBF.integral(my_sqrt, -1 + CBF(i), -1 - CBF(i))
--            [+/- 1.14e-14] + [-0.4752076627926 +/- 5.18e-14]*I
-+            [+/- 1.14e-14] + [-0.4752076627926 +/- 5...e-14]*I
- 
-         Note, though, that proper handling of the ``analytic`` flag is required
-         even when the path does not touch the branch cut::
- 
-             sage: correct = CBF.integral(my_sqrt, 1, 2); correct
-             [1.21895141649746 +/- 3.73e-15]
--            sage: RBF(integral(sqrt(x), x, 1, 2))
-+            sage: RBF(integral(sqrt(x), x, 1, 2))  # long time
-             [1.21895141649746 +/- 1.79e-15]
-             sage: wrong = CBF.integral(lambda z, _: z.sqrt(), 1, 2) # WRONG!
-             sage: correct - wrong
-@@ -915,9 +915,9 @@ class ComplexBallField(UniqueRepresentation, Field):
-         the integrand is unbounded::
- 
-             sage: CBF.integral(lambda x, _: 1/x, -1, 1)
--            [+/- inf] + [+/- inf]*I
-+            nan + nan*I
-             sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1)
--            [+/- inf] + [+/- inf]*I
-+            nan + nan*I
-             sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1, abs_tol=1e-10)
-             [2302.5850930 +/- 1.26e-8]
- 
-@@ -928,14 +928,15 @@ class ComplexBallField(UniqueRepresentation, Field):
-             sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=1e-450)
-             [2.304377150950e-439 +/- 9.74e-452]
-             sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=0)
--            [2.304377150949e-439 +/- 7.53e-452]
--            sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-4, abs_tol=0)
--            [2.30438e-439 +/- 3.90e-445]
-+            [2.304377150950e-439 +/- 7...e-452]
-+            sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-2, abs_tol=0)
-+            [2.30438e-439 +/- 5.94e-445]
- 
--            sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1)
--            [+/- 0.644]
--            sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1, use_heap=True)
--            [0.3785300 +/- 4.32e-8]
-+            sage: epsi = CBF(1e-10)
-+            sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1)
-+            [0.38 +/- 8.54e-3]
-+            sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1, use_heap=True)
-+            [0.37853002 +/- 8.73e-9]
- 
-         ALGORITHM:
- 
-@@ -951,12 +952,12 @@ class ComplexBallField(UniqueRepresentation, Field):
- 
-             sage: i = QuadraticField(-1).gen()
-             sage: CBF.integral(lambda x, _: (1 + i*x).gamma(), -1, 1)
--            [1.5723926694981 +/- 4.53e-14] + [+/- 3.95e-15]*I
-+            [1.5723926694981 +/- 4...e-14] + [+/- 4...e-15]*I
- 
--            sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-400)
--            [0.459... +/- ...e-4...]
-+            sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-300)
-+            [0.459... +/- ...e-3...]
-             sage: CBF.integral(lambda x, _: x.sin(), 0, 100, rel_tol=10)
--            [+/- 7.61]
-+            [0.138 +/- 5.53e-4]
- 
-             sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, abs_tol=1e-400)
-             [0.459697... +/- ...e-4...]
-@@ -2389,9 +2390,9 @@ cdef class ComplexBall(RingElement):
-             sage: ~CBF(i/3)
-             [-3.00000000000000 +/- 9.44e-16]*I
-             sage: ~CBF(0)
--            [+/- inf]
-+            nan
-             sage: ~CBF(RIF(10,11))
--            [0.1 +/- 9.53e-3]
-+            [0.1 +/- 9.10e-3]
-         """
-         cdef ComplexBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -2512,9 +2513,9 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(-2, 1)/CBF(1, 1/3)
-             [-1.500000000000000 +/- 8.83e-16] + [1.500000000000000 +/- 5.64e-16]*I
-             sage: CBF(2+I)/CBF(0)
--            [+/- inf] + [+/- inf]*I
-+            nan + nan*I
-             sage: CBF(1)/CBF(0)
--            [+/- inf]
-+            nan
-             sage: CBF(1)/CBF(RBF(0, 1.))
-             nan
-         """
-@@ -2543,9 +2544,9 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(0)^(1/3)
-             0
-             sage: CBF(0)^(-1)
--            [+/- inf]
-+            nan
-             sage: CBF(0)^(-2)
--            [+/- inf] + [+/- inf]*I
-+            nan + nan*I
- 
-         TESTS::
- 
-@@ -2656,12 +2657,12 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(1).rising_factorial(5)
-             120.0000000000000
-             sage: CBF(1/3, 1/2).rising_factorial(300)
--            [-3.87949484514e+612 +/- 5.23e+600] + [-3.52042209763e+612 +/- 5.55e+600]*I
-+            [-3.87949484514e+612 +/- 5...e+600] + [-3.52042209763e+612 +/- 5...e+600]*I
- 
-             sage: CBF(1).rising_factorial(-1)
-             nan
-             sage: CBF(1).rising_factorial(2**64)
--            [+/- 2.30e+347382171305201370464]
-+            [+/- 2.30e+347382171326740403407]
-             sage: ComplexBallField(128)(1).rising_factorial(2**64)
-             [2.343691126796861348e+347382171305201285713 +/- 4.71e+347382171305201285694]
-             sage: CBF(1/2).rising_factorial(CBF(2,3))
-@@ -2700,7 +2701,7 @@ cdef class ComplexBall(RingElement):
-             [1.000000000000000 +/- 2.83e-16] + [-0.441271200305303 +/- 2.82e-16]*I
- 
-             sage: CBF('inf').log()
--            nan + nan*I
-+            [+/- inf]
-             sage: CBF(2).log(0)
-             nan + nan*I
-         """
-@@ -2808,7 +2809,7 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(pi/2, 1/10).tan()
-             [+/- 2.87e-14] + [10.0333111322540 +/- 2.36e-14]*I
-             sage: CBF(pi/2).tan()
--            [+/- inf]
-+            nan
-         """
-         cdef ComplexBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -2825,7 +2826,7 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(pi, 1/10).cot()
-             [+/- 5.74e-14] + [-10.0333111322540 +/- 2.81e-14]*I
-             sage: CBF(pi).cot()
--            [+/- inf]
-+            nan
-         """
-         cdef ComplexBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -3211,9 +3212,9 @@ cdef class ComplexBall(RingElement):
-             1.000000000000000*I
- 
-             sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2])
--            [0.7871684267473 +/- 7.34e-14] + [0.2749254173721 +/- 9.23e-14]*I
-+            [0.7871684267473 +/- 7...e-14] + [0.2749254173721 +/- 9...e-14]*I
-             sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2],regularized=True)
--            [0.4441122268685 +/- 3.96e-14] + [0.1551100567338 +/- 5.75e-14]*I
-+            [0.4441122268685 +/- 3...e-14] + [0.1551100567338 +/- 5...e-14]*I
- 
-             sage: CBF(5).hypergeometric([2,3], [-5])
-             nan + nan*I
-@@ -4041,9 +4042,9 @@ cdef class ComplexBall(RingElement):
- 
-             sage: phi = CBF(1,1)
-             sage: (CBF.pi()/2).elliptic_e_inc(phi)
--            [1.283840957898 +/- 3.23e-13] + [-0.5317843366915 +/- 7.79e-14]*I
-+            [1.283840957898 +/- 3...e-13] + [-0.5317843366915 +/- 7...e-14]*I
-             sage: phi.elliptic_e()
--            [1.2838409578982 +/- 5.90e-14] + [-0.5317843366915 +/- 3.35e-14]*I
-+            [1.2838409578982 +/- 5...e-14] + [-0.5317843366915 +/- 3...e-14]*I
- 
-             sage: phi = CBF(2, 3/7)
-             sage: (CBF.pi()/2).elliptic_e_inc(phi)
-@@ -4312,8 +4313,7 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(10).laguerre_L(3, 2)
-             [-6.666666666667 +/- 4.15e-13]
-             sage: CBF(5,7).laguerre_L(CBF(2,3), CBF(1,-2))
--            [5515.315030271 +/- 4.37e-10] + [-12386.942845271 +/- 5.47e-10]*I
--
-+            [5515.315030271 +/- 4...e-10] + [-12386.942845271 +/- 5...e-10]*I
-         """
-         cdef ComplexBall my_n = self._parent.coerce(n)
-         cdef ComplexBall my_m = self._parent.coerce(m)
-@@ -4357,9 +4357,9 @@ cdef class ComplexBall(RingElement):
-         EXAMPLES::
- 
-             sage: CBF(1/2).legendre_P(5)
--            [0.08984375000000000 +/- 4.5...e-18]
-+            [0.0898437500000000 +/- 7...e-17]
-             sage: CBF(1,2).legendre_P(CBF(2,3), CBF(0,1))
--            [0.10996180744364 +/- 7.45e-15] + [0.14312767804055 +/- 8.38e-15]*I
-+            [0.10996180744364 +/- 7.12e-15] + [0.14312767804055 +/- 8.07e-15]*I
-             sage: CBF(-10).legendre_P(5, 325/100)
-             [-22104403.487377 +/- 6.81e-7] + [53364750.687392 +/- 7.25e-7]*I
-             sage: CBF(-10).legendre_P(5, 325/100, type=3)
-@@ -4393,9 +4393,9 @@ cdef class ComplexBall(RingElement):
-             sage: CBF(1/2).legendre_Q(5)
-             [0.55508089057168 +/- 2.79e-15]
-             sage: CBF(1,2).legendre_Q(CBF(2,3), CBF(0,1))
--            [0.167678710 +/- 4.60e-10] + [-0.161558598 +/- 7.47e-10]*I
-+            [0.167678710 +/- 3.91e-10] + [-0.161558598 +/- 6.77e-10]*I
-             sage: CBF(-10).legendre_Q(5, 325/100)
--            [-83825154.36008 +/- 4.94e-6] + [-34721515.80396 +/- 5.40e-6]*I
-+            [-83825154.36008 +/- 5.02e-6] + [-34721515.80396 +/- 5.42e-6]*I
-             sage: CBF(-10).legendre_Q(5, 325/100, type=3)
-             [-4.797306921692e-6 +/- 6.82e-19] + [-4.797306921692e-6 +/- 6.57e-19]*I
- 
-diff --git a/src/sage/rings/polynomial/polynomial_complex_arb.pyx b/src/sage/rings/polynomial/polynomial_complex_arb.pyx
-index c436d4705b..ef611a566b 100644
---- a/src/sage/rings/polynomial/polynomial_complex_arb.pyx
-+++ b/src/sage/rings/polynomial/polynomial_complex_arb.pyx
-@@ -543,7 +543,7 @@ cdef class Polynomial_complex_arb(Polynomial):
-             sage: (1 - x/3).inverse_series_trunc(3)
-             ([0.1111111111111111 +/- 5.99e-17])*x^2 + ([0.3333333333333333 +/- 7.04e-17])*x + 1.000000000000000
-             sage: x.inverse_series_trunc(1)
--            [+/- inf]
-+            nan
-             sage: Pol(0).inverse_series_trunc(2)
-             (nan + nan*I)*x + nan + nan*I
- 
-@@ -671,7 +671,7 @@ cdef class Polynomial_complex_arb(Polynomial):
-             sage: pol._sqrt_series(2)
-             ([+/- 7.51e-3] + [+/- 0.501]*I)*x + [+/- 5.01e-3] + [+/- 1.01]*I
-             sage: x._sqrt_series(2)
--            ([+/- inf] + [+/- inf]*I)*x
-+            (nan + nan*I)*x
-         """
-         cdef Polynomial_complex_arb res = self._new()
-         if n < 0:
-diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
-index c9f68e38d7..76e3037a9a 100644
---- a/src/sage/rings/real_arb.pyx
-+++ b/src/sage/rings/real_arb.pyx
-@@ -161,7 +161,7 @@ values and should be preferred::
- 
-     sage: RBF(NaN) < RBF(infinity)
-     False
--    sage: 1/RBF(0) <= RBF(infinity)
-+    sage: RBF(0).add_error(infinity) <= RBF(infinity)
-     True
- 
- TESTS::
-@@ -252,6 +252,8 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision):
-         (+infinity, +infinity)
-         sage: RBF(RIF(-infinity)).endpoints()
-         (-infinity, -infinity)
-+        sage: RBF(RIF(-infinity, infinity)).endpoints()
-+        (-infinity, +infinity)
-         sage: RIF(RBF(infinity)).endpoints()
-         (+infinity, +infinity)
-         sage: RIF(RBF(-infinity)).endpoints()
-@@ -266,10 +268,11 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision):
-     if _do_sig(precision): sig_on()
-     mpfi_get_left(left, source)
-     mpfi_get_right(right, source)
--    arb_set_interval_mpfr(target, left, right, precision)
--    # Work around weakness of arb_set_interval_mpfr(tgt, inf, inf)
--    if mpfr_equal_p(left, right):
--        mag_zero(arb_radref(target))
-+    if mpfr_inf_p(left) and mpfr_inf_p(right) and mpfr_sgn(left) < 0 < mpfr_sgn(right):
-+        # Work around a weakness of arb_set_interval_mpfr(tgt, -inf, inf)
-+        arb_zero_pm_inf(target)
-+    else:
-+        arb_set_interval_mpfr(target, left, right, precision)
-     if _do_sig(precision): sig_off()
- 
-     mpfr_clear(left)
-@@ -649,17 +652,15 @@ class RealBallField(UniqueRepresentation, Field):
-         EXAMPLES::
- 
-             sage: RBF.some_elements()
--            [1.000000000000000,
--            [0.3333333333333333 +/- 7.04e-17],
-+            [0, 1.000000000000000, [0.3333333333333333 +/- 7.04e-17],
-             [-4.733045976388941e+363922934236666733021124 +/- 3.46e+363922934236666733021108],
--            [+/- inf],
--            [+/- inf],
--            nan]
-+            [+/- inf], [+/- inf], [+/- inf], nan]
-         """
-         import sage.symbolic.constants
--        return [self(1), self(1)/3,
-+        inf = self(sage.rings.infinity.Infinity)
-+        return [self(0), self(1), self(1)/3,
-                 -self(2)**(Integer(2)**80),
--                self(sage.rings.infinity.Infinity), ~self(0),
-+                inf, -inf, self.zero().add_error(inf),
-                 self.element_class(self, sage.symbolic.constants.NotANumber())]
- 
-     def _sum_of_products(self, terms):
-@@ -881,7 +882,7 @@ class RealBallField(UniqueRepresentation, Field):
-             sage: RBF.gamma(5)
-             24.00000000000000
-             sage: RBF.gamma(10**20)
--            [+/- 5.92e+1956570551809674821757]
-+            [+/- 5.50e+1956570552410610660600]
-             sage: RBF.gamma(1/3)
-             [2.678938534707747 +/- 8.99e-16]
-             sage: RBF.gamma(-5)
-@@ -2247,7 +2248,7 @@ cdef class RealBall(RingElement):
-             sage: inf = RBF(+infinity)
-             sage: other_inf = RBF(+infinity, 42.r)
-             sage: neg_inf = RBF(-infinity)
--            sage: extended_line = 1/RBF(0)
-+            sage: extended_line = RBF(0).add_error(infinity)
-             sage: exact_nan = inf - inf
-             sage: exact_nan.mid(), exact_nan.rad()
-             (NaN, 0.00000000)
-@@ -2659,7 +2660,7 @@ cdef class RealBall(RingElement):
-             sage: ~RBF(5)
-             [0.2000000000000000 +/- 4.45e-17]
-             sage: ~RBF(0)
--            [+/- inf]
-+            nan
-             sage: RBF(RIF(-0.1,0.1))
-             [+/- 0.101]
- 
-@@ -2739,7 +2740,7 @@ cdef class RealBall(RingElement):
-             sage: RBF(pi)/RBF(e)
-             [1.155727349790922 +/- 8.43e-16]
-             sage: RBF(2)/RBF(0)
--            [+/- inf]
-+            nan
-         """
-         cdef RealBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -2765,7 +2766,7 @@ cdef class RealBall(RingElement):
-             sage: RBF(-1)^(1/3)
-             nan
-             sage: RBF(0)^(-1)
--            [+/- inf]
-+            nan
-             sage: RBF(-e)**RBF(pi)
-             nan
- 
-@@ -3129,7 +3130,7 @@ cdef class RealBall(RingElement):
-             sage: RBF(1).tan()
-             [1.557407724654902 +/- 3.26e-16]
-             sage: RBF(pi/2).tan()
--            [+/- inf]
-+            nan
-         """
-         cdef RealBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -3146,7 +3147,7 @@ cdef class RealBall(RingElement):
-             sage: RBF(1).cot()
-             [0.642092615934331 +/- 4.79e-16]
-             sage: RBF(pi).cot()
--            [+/- inf]
-+            nan
-         """
-         cdef RealBall res = self._new()
-         if _do_sig(prec(self)): sig_on()
-@@ -3257,7 +3258,7 @@ cdef class RealBall(RingElement):
-             sage: RBF(1).coth()
-             [1.313035285499331 +/- 4.97e-16]
-             sage: RBF(0).coth()
--            [+/- inf]
-+            nan
-         """
-         cdef RealBall res = self._new()
-         if _do_sig(prec(self)): sig_on()

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

@@ -0,0 +1,15 @@
+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/maxima-5.41.0-doctests.patch

@@ -1,48 +0,0 @@
-diff --git a/src/sage/interfaces/maxima_abstract.py b/src/sage/interfaces/maxima_abstract.py
-index 961c20aaac..3d601d8939 100644
---- a/src/sage/interfaces/maxima_abstract.py
-+++ b/src/sage/interfaces/maxima_abstract.py
-@@ -1743,7 +1743,7 @@ class MaximaAbstractElement(ExtraTabCompletion, InterfaceElement):
-             sage: y,d = var('y,d')
-             sage: f = function('f')
-             sage: latex(maxima(derivative(f(x*y), x)))
--            \left(\left.{{{\it \partial}}\over{{\it \partial}\,  {\it t_0}}}\,f\left({\it t_0}\right)  \right|_{{\it t_0}={\it x}\,  {\it y}}\right)\,{\it y}
-+            \left(\left.{{{\it \partial}}\over{{\it \partial}\,  {\it t}_{0}}}\,f\left({\it t}_{0}\right)  \right|_{{\it t}_{0}={\it x}\,  {\it y}}\right)\,{\it y}
-             sage: latex(maxima(derivative(f(x,y,d), d,x,x,y)))
-             {{{\it \partial}^4}\over{{\it \partial}\,{\it d}\,  {\it \partial}\,{\it x}^2\,{\it \partial}\,  {\it y}}}\,f\left({\it x} ,  {\it y} , {\it d}\right)
-             sage: latex(maxima(d/(d-2)))
-diff --git a/src/sage/manifolds/differentiable/metric.py b/src/sage/manifolds/differentiable/metric.py
-index 3cd6ad3235..1e18af1a6b 100644
---- a/src/sage/manifolds/differentiable/metric.py
-+++ b/src/sage/manifolds/differentiable/metric.py
-@@ -993,7 +993,7 @@ class PseudoRiemannianMetric(TensorField):
-              2-dimensional differentiable manifold S^2
-             sage: g.riemann()[:]
-             [[[[0, 0], [0, 0]], [[0, sin(th)^2], [-sin(th)^2, 0]]],
--             [[[0, (cos(th)^2 - 1)/sin(th)^2], [1, 0]], [[0, 0], [0, 0]]]]
-+             [[[0, -1], [1, 0]], [[0, 0], [0, 0]]]]
- 
-         In dimension 2, the Riemann tensor can be expressed entirely in terms of
-         the Ricci scalar `r`:
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index dfb8751467..27402e54ab 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -7154,7 +7154,7 @@ cdef class Expression(CommutativeRingElement):
-             sage: ex = lcm(sin(x)^2 - 1, sin(x)^2 + sin(x)); ex
-             (sin(x)^2 + sin(x))*(sin(x)^2 - 1)/(sin(x) + 1)
-             sage: ex.simplify_full()
--            -cos(x)^2*sin(x)
-+            sin(x)^3 - sin(x)
- 
-         TESTS:
- 
-@@ -10004,7 +10004,7 @@ cdef class Expression(CommutativeRingElement):
- 
-             sage: f=tan(3*x)
-             sage: f.simplify_trig()
--            (4*cos(x)^2 - 1)*sin(x)/(4*cos(x)^3 - 3*cos(x))
-+            -(4*cos(x)^2 - 1)*sin(x)/(4*cos(x)*sin(x)^2 - cos(x))
-             sage: f.simplify_trig(False)
-             sin(3*x)/cos(3*x)
- 

pkgs/applications/science/math/sage/patches/pari-no-threads.patch

@@ -0,0 +1,18 @@
+diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py
+index e451766474..77eda66097 100644
+--- a/src/sage/libs/pari/__init__.py
++++ b/src/sage/libs/pari/__init__.py
+@@ -205,6 +205,13 @@ def _get_pari_instance():
+     # messages in Sage.
+     P.default("debugmem", 0)
+ 
++    # Make sure pari doesn't use threads, regardless of how it was compiled.
++    # Threads cause some doctest failures (memory issues). Those could probably
++    # be solved without disabling threads. But that would require figuring out
++    # some sensible values for `threadsizemax`. See
++    # https://pari.math.u-bordeaux.fr/dochtml/html/GP_defaults.html
++    P.default("nbthreads", 1)
++
+     return P
+ 
+ pari = _get_pari_instance()

pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch

@@ -1,479 +0,0 @@
-diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py
-index 3a417d9d5c..fadaadbaf6 100644
---- a/src/sage/calculus/calculus.py
-+++ b/src/sage/calculus/calculus.py
-@@ -231,7 +231,7 @@ Another example::
-     sage: f(x=3)
-     arcsinh(1)
-     sage: f.derivative(x)
--    1/3/sqrt(1/9*x^2 + 1)
-+    1/sqrt(x^2 + 9)
- 
- We compute the length of the parabola from 0 to 2::
- 
-@@ -1509,8 +1509,8 @@ def laplace(ex, t, s, algorithm='maxima'):
-     Testing SymPy::
- 
-         sage: laplace(t^n, t, s, algorithm='sympy')
--        (s^(-n)*gamma(n + 1)/s, 0, -re(n) < 1)
--        
-+        (gamma(n + 1)/(s*s^n), 0, -re(n) < 1)
-+
-     Testing Maxima::
- 
-         sage: laplace(t^n, t, s, algorithm='maxima')
-diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py
-index 1fc2db5c94..f3e49b9cdb 100644
---- a/src/sage/functions/hypergeometric.py
-+++ b/src/sage/functions/hypergeometric.py
-@@ -34,7 +34,7 @@ Simplification (note that ``simplify_full`` does not yet call
-     sage: a.simplify_hypergeometric()
-     1/((-e^x + 1)^e^x)
-     sage: a.simplify_hypergeometric(algorithm='sage')
--    (-e^x + 1)^(-e^x)
-+    1/((-e^x + 1)^e^x)
- 
- Equality testing::
- 
-@@ -145,7 +145,7 @@ Series expansions of confluent hypergeometric functions::
- 
-     sage: hypergeometric_M(2, 2, x).series(x, 3)
-     1 + 1*x + 1/2*x^2 + Order(x^3)
--    sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n()
-+    sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() # known bug (see :trac:`25688`)
-     0.403652637676806
-     sage: hypergeometric_U(2, 2, 1).n()
-     0.403652637676806
-@@ -773,7 +773,7 @@ def closed_form(hyp):
-         sage: closed_form(hypergeometric([], [], z))
-         e^z
-         sage: closed_form(hypergeometric([a], [], z))
--        (-z + 1)^(-a)
-+        1/((-z + 1)^a)
-         sage: closed_form(hypergeometric([1, 1, 2], [1, 1], z))
-         (z - 1)^(-2)
-         sage: closed_form(hypergeometric([2, 3], [1], x))
-@@ -1121,7 +1121,7 @@ class Hypergeometric_U(BuiltinFunction):
-                 sage: var('a b z')
-                 (a, b, z)
-                 sage: hypergeometric_U(a, b, z).generalized()
--                z^(-a)*hypergeometric((a, a - b + 1), (), -1/z)
-+                hypergeometric((a, a - b + 1), (), -1/z)/z^a
-                 sage: hypergeometric_U(1, 3, 1/2).generalized()
-                 2*hypergeometric((1, -1), (), -2)
-                 sage: hypergeometric_U(3, I, 2).generalized()
-diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py
-index 75d1bf8060..61968582af 100644
---- a/src/sage/functions/log.py
-+++ b/src/sage/functions/log.py
-@@ -518,17 +518,17 @@ class Function_polylog(GinacFunction):
- 
-             sage: BF = RealBallField(100)
-             sage: polylog(2, BF(1/3))
--            [0.36621322997706348761674629766 +/- 4.51e-30]
-+            [0.36621322997706348761674629766... +/- ...]
-             sage: polylog(2, BF(4/3))
--            nan
-+            [2.27001825336107090380391448586 +/- 5.64e-30] + [-0.90377988538400159956755721265 +/- 8.39e-30]*I
-             sage: parent(_)
--            Real ball field with 100 bits of precision
-+            Complex ball field with 100 bits of precision
-             sage: polylog(2, CBF(1/3))
--            [0.366213229977063 +/- 5.85e-16]
-+            [0.366213229977063 +/- ...]
-             sage: parent(_)
-             Complex ball field with 53 bits of precision
-             sage: polylog(2, CBF(1))
--            [1.644934066848226 +/- 6.59e-16]
-+            [1.644934066848226 +/- ...]
-             sage: parent(_)
-             Complex ball field with 53 bits of precision
-         """
-diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py
-index e7e7a311cd..1f2926d6c9 100644
---- a/src/sage/functions/trig.py
-+++ b/src/sage/functions/trig.py
-@@ -529,13 +529,8 @@ class Function_arcsin(GinacFunction):
-             arcsin
-             sage: asin(complex(1,1))
-             (0.6662394324925152+1.0612750619050357j)
--
--        Check that :trac:`22823` is fixed::
--
--            sage: bool(asin(SR(2.1)) == NaN)
--            True
--            sage: asin(SR(2.1)).is_real()
--            False
-+            sage: asin(SR(2.1))
-+            1.57079632679490 - 1.37285914424258*I
-         """
-         GinacFunction.__init__(self, 'arcsin', latex_name=r"\arcsin",
-                 conversions=dict(maxima='asin', sympy='asin', fricas="asin", giac="asin"))
-@@ -595,13 +590,8 @@ class Function_arccos(GinacFunction):
-             arccos
-             sage: acos(complex(1,1))
-             (0.9045568943023814-1.0612750619050357j)
--
--        Check that :trac:`22823` is fixed::
--
--            sage: bool(acos(SR(2.1)) == NaN)
--            True
--            sage: acos(SR(2.1)).is_real()
--            False
-+            sage: acos(SR(2.1))
-+            1.37285914424258*I
-         """
-         GinacFunction.__init__(self, 'arccos', latex_name=r"\arccos",
-                 conversions=dict(maxima='acos', sympy='acos', fricas='acos', giac='acos'))
-@@ -807,7 +797,7 @@ class Function_arcsec(GinacFunction):
-             sage: arcsec(2).n(100)
-             1.0471975511965977461542144611
-             sage: arcsec(1/2).n(100)
--            NaN
-+            1.3169578969248167086250463473*I
-             sage: RDF(arcsec(2))  # abs tol 1e-15
-             1.0471975511965976
-             sage: arcsec(1 + I)
-@@ -958,7 +948,9 @@ class Function_arctan2(GinacFunction):
-             sage: atan2(0,0,hold=True)
-             arctan2(0, 0)
-             sage: atan2(0,0,hold=True).n()
--            NaN
-+            Traceback (most recent call last):
-+            ...
-+            RuntimeError: atan2(): division by zero
- 
-         Check if :trac:`10062` is fixed, this was caused by
-         ``(I*I).is_positive()`` returning ``True``::
-diff --git a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py
-index 3b5c8d1729..1c6b73a16c 100644
---- a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py
-+++ b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py
-@@ -1422,8 +1422,10 @@ class HyperbolicGeodesicUHP(HyperbolicGeodesic):
-         expressions do not generate runtime errors. ::
- 
-             sage: g=HyperbolicPlane().UHP().get_geodesic(-1+I,1+I)
--            sage: g.midpoint()
--            Point in UHP 1/2*(sqrt(2)*e^(1/2*arccosh(3)) - sqrt(2) + (I - 1)*e^(1/2*arccosh(3)) + I - 1)/((1/4*I - 1/4)*sqrt(2)*e^(1/2*arccosh(3)) - (1/4*I - 1/4)*sqrt(2) + 1/2*e^(1/2*arccosh(3)) + 1/2)
-+            sage: point = g.midpoint(); point
-+            Point in UHP -1/2*(sqrt(2)*...
-+            sage: QQbar(point.coordinates()).radical_expression()
-+            I*sqrt(2)
- 
-         Check that floating points remain floating points
-         in :meth:`midpoint` ::
-diff --git a/src/sage/interfaces/fricas.py b/src/sage/interfaces/fricas.py
-index 82aae78e37..8501ea2a18 100644
---- a/src/sage/interfaces/fricas.py
-+++ b/src/sage/interfaces/fricas.py
-@@ -1084,14 +1084,14 @@ class FriCASElement(ExpectElement):
-              0.451026811796262,
-              0.732815101786507,
-              0.837981225008390,
--             NaN,
--             NaN,
-+             1.57079632679490 - 0.467145308103262*I,
-+             0.467145308103262*I,
-              1.11976951499863,
-              0.451026811796262,
-              0.732815101786507,
-              0.837981225008390,
--             NaN,
--             NaN]
-+             1.57079632679490 - 0.467145308103262*I,
-+             0.467145308103262*I]
-             sage: l = [tanh, sinh, cosh, coth, sech, csch, asinh, acosh, atanh, acoth, asech, acsch, arcsinh, arccosh, arctanh, arccoth, arcsech, arccsch]
-             sage: [f(x)._fricas_().sage().subs(x=0.9) for f in l]               # optional - fricas
-             [0.716297870199024,
-diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx
-index 9e9d8f664b..e3406f007e 100644
---- a/src/sage/libs/pynac/pynac.pyx
-+++ b/src/sage/libs/pynac/pynac.pyx
-@@ -1824,7 +1824,7 @@ cdef py_atan2(x, y):
-         sage: atan2(CC(I), CC(I+1))
-         0.553574358897045 + 0.402359478108525*I
-         sage: atan2(CBF(I), CBF(I+1))
--        [0.55357435889705 +/- 5.58e-15] + [0.402359478108525 +/- 7.11e-16]*I
-+        [0.55357435889705 +/- ...] + [0.402359478108525 +/- ...]*I
- 
-     Check that :trac:`23776` is fixed and RDF input gives real output::
- 
-diff --git a/src/sage/matrix/matrix_symbolic_dense.pyx b/src/sage/matrix/matrix_symbolic_dense.pyx
-index 46a15e53eb..7a0beb437b 100644
---- a/src/sage/matrix/matrix_symbolic_dense.pyx
-+++ b/src/sage/matrix/matrix_symbolic_dense.pyx
-@@ -200,7 +200,7 @@ cdef class Matrix_symbolic_dense(Matrix_generic_dense):
-             sage: eval, [evec], mult = es[0]
-             sage: delta = eval*evec - evec*A
-             sage: abs(abs(delta)) < 1e-10
--            sqrt(9/25*((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + 9/25*((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10)
-+            3/5*sqrt(((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + ((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10)
-             sage: abs(abs(delta)).n() < 1e-10
-             True
- 
-diff --git a/src/sage/modules/matrix_morphism.py b/src/sage/modules/matrix_morphism.py
-index 17a1d6e290..03892ceec0 100644
---- a/src/sage/modules/matrix_morphism.py
-+++ b/src/sage/modules/matrix_morphism.py
-@@ -214,9 +214,9 @@ class MatrixMorphism_abstract(sage.categories.morphism.Morphism):
-             sage: f((1, 0))
-             Traceback (most recent call last):
-             ...
--            TypeError: Unable to coerce entries (=[1.00000000000000*I, 0.000000000000000]) to coefficients in Real Field with 53 bits of precision
-+            TypeError: Unable to coerce entries (=[1.00000000000000*I, 0]) to coefficients in Real Field with 53 bits of precision
-             sage: f((1, 0), coerce=False)
--            (1.00000000000000*I, 0.000000000000000)
-+            (1.00000000000000*I, 0)
- 
-         """
-         if self.domain().is_ambient():
-diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py
-index 77cdeb8c46..e501e74036 100644
---- a/src/sage/plot/plot.py
-+++ b/src/sage/plot/plot.py
-@@ -2061,7 +2061,7 @@ def _plot(funcs, xrange, parametric=False,
-     plot properly (:trac:`13246`)::
- 
-         sage: parametric_plot((x, arcsec(x)), (x, -2, 2))
--        Graphics object consisting of 1 graphics primitive
-+        Graphics object consisting of 2 graphics primitives
- 
-     """
-     from sage.plot.colors import Color
-diff --git a/src/sage/repl/display/formatter.py b/src/sage/repl/display/formatter.py
-index 8ce2e839d7..948207c95e 100644
---- a/src/sage/repl/display/formatter.py
-+++ b/src/sage/repl/display/formatter.py
-@@ -25,11 +25,11 @@ generally, all sage expression as an ASCII art object::
-     sage: shell = get_test_shell()
-     sage: shell.run_cell('%display ascii_art')
-     sage: shell.run_cell('integral(x^2/pi^x, x)')
--     / 2    2                      \  -x*log(pi)
--    -\x *log (pi) + 2*x*log(pi) + 2/*e
--    ---------------------------------------------
--                         3
--                      log (pi)
-+       -x / 2    2                      \ 
-+    -pi  *\x *log (pi) + 2*x*log(pi) + 2/ 
-+    --------------------------------------
-+                     3                   
-+                   log (pi)               
-     sage: shell.run_cell("i = var('i')")
-     sage: shell.run_cell('sum(i*x^i, i, 0, 10)')
-         10      9      8      7      6      5      4      3      2
-diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py
-index d8ebbf4f76..8c60f65e99 100644
---- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py
-+++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py
-@@ -151,8 +151,8 @@ A multiple point example (Example 6.5 of [RaWi2012]_)::
-      [(x + 2*y - 1, 1), (2*x + y - 1, 1)])
-     sage: F1 = decomp[1]
-     sage: F1.asymptotics(p, alpha, 2)
--    (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*((1/3)^(-a)*(1/3)^(-b))^r,
--     (1/3)^(-a)*(1/3)^(-b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9)
-+    (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*(1/((1/3)^a*(1/3)^b))^r,
-+     1/((1/3)^a*(1/3)^b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9)
-     sage: alpha = [4, 3]
-     sage: decomp =  F.asymptotic_decomposition(alpha)
-     sage: F1 = decomp[1]
-@@ -2159,7 +2159,7 @@ class FractionWithFactoredDenominator(RingElement):
-             sage: p = {x: 1/3, y: 1/3}
-             sage: alpha = (var('a'), var('b'))
-             sage: F.asymptotics_multiple(p, alpha, 2, var('r')) # long time
--            (3*((1/3)^(-a)*(1/3)^(-b))^r*e^(2/3), (1/3)^(-a)*(1/3)^(-b), 3*e^(2/3))
-+            (3*(1/((1/3)^a*(1/3)^b))^r*e^(2/3), 1/((1/3)^a*(1/3)^b), 3*e^(2/3))
-         """
-         from itertools import product
-         from sage.calculus.functions import jacobian
-diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py
-index 16a268a02c..5fd244e93b 100644
---- a/src/sage/stats/basic_stats.py
-+++ b/src/sage/stats/basic_stats.py
-@@ -183,7 +183,7 @@ def std(v, bias=False):
-         sage: std([])
-         NaN
-         sage: std([I, sqrt(2), 3/5])
--        sqrt(1/450*(10*sqrt(2) - 5*I - 3)^2 + 1/450*(5*sqrt(2) - 10*I + 3)^2 + 1/450*(5*sqrt(2) + 5*I - 6)^2)
-+        1/15*sqrt(1/2)*sqrt((10*sqrt(2) - 5*I - 3)^2 + (5*sqrt(2) - 10*I + 3)^2 + (5*sqrt(2) + 5*I - 6)^2)
-         sage: std([RIF(1.0103, 1.0103), RIF(2)])
-         0.6998235813403261?
-         sage: import numpy
-diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx
-index ab4c05de3a..60f0dc549a 100644
---- a/src/sage/symbolic/expression.pyx
-+++ b/src/sage/symbolic/expression.pyx
-@@ -622,7 +622,7 @@ cdef class Expression(CommutativeRingElement):
-             sage: x^(-5)
-             x^(-5)
-             sage: x^(-y)
--            x^(-y)
-+            1/(x^y)
-             sage: 2*x^(-1)
-             2/x
-             sage: i*x
-@@ -3621,14 +3621,14 @@ cdef class Expression(CommutativeRingElement):
-             sage: repl_dict = {b_0: b_0, b_3: b_1, b_2: b_3, b_1: b_2}
-             sage: P = precomp.substitute(repl_dict)
-             sage: P.expand()
--            -2^(-b_0)*2^(-b_2)*2^b_3 - 2^b_0*2^(-b_2)*2^b_3 -
--            2^(-b_0)*2^b_2*2^b_3 + 2^b_0*2^b_2*2^b_3 - 2*2^(-b_0)*2^(-b_2)
--            - 2*2^b_0*2^(-b_2) - 2*2^(-b_0)*2^b_2 + 2*2^b_0*2^b_2 +
--            2^(-b_0)*2^b_3 + 2^b_0*2^b_3 + 2^(-b_2)*2^b_3 + 2^b_2*2^b_3 +
--            2*2^(-b_0) + 2*2^b_0 + 2*2^(-b_2) + 2*2^b_2 - 9*2^b_3 -
--            2^(-b_0)*2^(-b_2)/2^b_3 - 2^b_0*2^(-b_2)/2^b_3 -
--            2^(-b_0)*2^b_2/2^b_3 + 2^b_0*2^b_2/2^b_3 + 2^(-b_0)/2^b_3 +
--            2^b_0/2^b_3 + 2^(-b_2)/2^b_3 + 2^b_2/2^b_3 - 9/2^b_3 - 18
-+            2^b_0*2^b_2*2^b_3 + 2*2^b_0*2^b_2 + 2^b_0*2^b_3 + 2^b_2*2^b_3 +
-+            2*2^b_0 + 2*2^b_2 - 9*2^b_3 + 2^b_0*2^b_2/2^b_3 -
-+            2^b_0*2^b_3/2^b_2 - 2^b_2*2^b_3/2^b_0 - 2*2^b_0/2^b_2 -
-+            2*2^b_2/2^b_0 + 2^b_0/2^b_3 + 2^b_2/2^b_3 + 2^b_3/2^b_0 +
-+            2^b_3/2^b_2 + 2/2^b_0 + 2/2^b_2 - 2^b_0/(2^b_2*2^b_3) -
-+            2^b_2/(2^b_0*2^b_3) - 9/2^b_3 - 2^b_3/(2^b_0*2^b_2) -
-+            2/(2^b_0*2^b_2) + 1/(2^b_0*2^b_3) + 1/(2^b_2*2^b_3) -
-+            1/(2^b_0*2^b_2*2^b_3) - 18
- 
-             sage: _0,b_1,b_2=var('b_0,b_1,b_2')
-             sage: f = 1/27*b_2^2/(2^b_2)^2 + 1/27*b_1^2/(2^b_1)^2 + \
-@@ -3809,7 +3809,7 @@ cdef class Expression(CommutativeRingElement):
- 
-             sage: x = SR.symbol('x', domain='real')
-             sage: (x^3)^(1/3)
--            (x^3)^(1/3)
-+            x
-             sage: (x^4)^(1/4)
-             abs(x)
-             sage: (x^8)^(1/4)
-@@ -3872,7 +3872,7 @@ cdef class Expression(CommutativeRingElement):
-             sage: 2^(x/log(2))
-             e^x
-             sage: 2^(-x^2/2/log(2))
--            e^(-1/2*x^2)
-+            1/e^(1/2*x^2)
-             sage: x^(x/log(x))
-             x^(x/log(x))
-             sage: assume(x > 0)
-@@ -4816,18 +4816,24 @@ cdef class Expression(CommutativeRingElement):
-             sage: ((x+y)^(x+y)).match(w0^w0)
-             {$0: x + y}
-             sage: t = ((a+b)*(a+c)).match((a+w0)*(a+w1))
--            sage: t[w0], t[w1]
--            (c, b)
-+            sage: set([t[w0], t[w1]]) == set([b, c])
-+            True
-             sage: ((a+b)*(a+c)).match((w0+b)*(w0+c))
-             {$0: a}
-             sage: t = ((a+b)*(a+c)).match((w0+w1)*(w0+w2))
--            sage: t[w0], t[w1], t[w2]
--            (a, c, b)
--            sage: print(((a+b)*(a+c)).match((w0+w1)*(w1+w2)))
--            None
-+            sage: t[w0]
-+            a
-+            sage: set([t[w1], t[w2]]) == set([b, c])
-+            True
-+            sage: t = ((a+b)*(a+c)).match((w0+w1)*(w1+w2))
-+            sage: t[w1]
-+            a
-+            sage: set([t[w0], t[w2]]) == set([b, c])
-+            True
-             sage: t = (a*(x+y)+a*z+b).match(a*w0+w1)
--            sage: t[w0], t[w1]
--            (x + y, a*z + b)
-+            sage: s = set([t[w0], t[w1]])
-+            sage: s == set([x+y, a*z+b]) or s == set([z, a*(x+y)+b])
-+            True
-             sage: print((a+b+c+d+f+g).match(c))
-             None
-             sage: (a+b+c+d+f+g).has(c)
-@@ -4836,7 +4842,7 @@ cdef class Expression(CommutativeRingElement):
-             {$0: a + b + d + f + g}
-             sage: (a+b+c+d+f+g).match(c+g+w0)
-             {$0: a + b + d + f}
--            sage: (a+b).match(a+b+w0)
-+            sage: (a+b).match(a+b+w0) # known bug
-             {$0: 0}
-             sage: print((a*b^2).match(a^w0*b^w1))
-             None
-@@ -5009,7 +5015,7 @@ cdef class Expression(CommutativeRingElement):
-             a^3 + b^3 + (x + y)^3
- 
-             sage: t.subs(w0 == w0^2)
--            (x^2 + y^2)^18 + a^16 + b^16
-+            a^8 + b^8 + (x^2 + y^2)^6
- 
-             sage: t.subs(a == b, b == c)
-             (x + y)^3 + b^2 + c^2
-@@ -8392,9 +8398,13 @@ cdef class Expression(CommutativeRingElement):
-             sage: SR(I).arctan2(1)
-             arctan2(I, 1)
-             sage: SR(CDF(0,1)).arctan2(1)
--            NaN + +infinity*I
--            sage: SR(1).arctan2(CDF(0,1))   # known bug
--            0.7853981633974484 - 19.012501686914433*I
-+            Traceback (most recent call last):
-+            ...
-+            ValueError: power::eval(): division by zero
-+            sage: SR(1).arctan2(CDF(0,1))
-+            Traceback (most recent call last):
-+            ...
-+            ValueError: power::eval(): division by zero
- 
-             sage: arctan2(0,oo)
-             0
-@@ -8656,7 +8666,7 @@ cdef class Expression(CommutativeRingElement):
-             1/2*I*pi
-             sage: SR(1/2).arccosh()
-             arccosh(1/2)
--            sage: SR(CDF(1/2)).arccosh()  # rel tol 1e-15
-+            sage: SR(CDF(1/2)).arccosh() #  rel tol 1e-15
-             1.0471975511965976*I
-             sage: maxima('acosh(0.5)')
-             1.04719755119659...*%i
-@@ -11687,7 +11697,7 @@ cdef class Expression(CommutativeRingElement):
-             sage: a.solve(t)
-             []
-             sage: b = a.canonicalize_radical(); b
--            -23040.0*(-2.0*e^(1800*t) + 25.0*e^(900*t) - 32.0)*e^(-2400*t)
-+            (46080.0*e^(1800*t) - 576000.0*e^(900*t) + 737280.0)*e^(-2400*t)
-             sage: b.solve(t)
-             []
-             sage: b.solve(t, to_poly_solve=True)
-@@ -12163,14 +12173,14 @@ cdef class Expression(CommutativeRingElement):
- 
-             sage: (n,k,j)=var('n,k,j')
-             sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n)
--            -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-+            -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-             sage: assume(j>-1)
-             sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n)
-             1
-             sage: forget()
-             sage: assume(n>=j)
-             sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n)
--            -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-+            -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-             sage: forget()
-             sage: assume(j==-1)
-             sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n)
-@@ -12178,7 +12188,7 @@ cdef class Expression(CommutativeRingElement):
-             sage: forget()
-             sage: assume(j<-1)
-             sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n)
--            -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-+            -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n)
-             sage: forget()
- 
-         Check that :trac:`16176` is fixed::
-diff --git a/src/sage/symbolic/relation.py b/src/sage/symbolic/relation.py
-index da6f0eef42..4bd65ef572 100644
---- a/src/sage/symbolic/relation.py
-+++ b/src/sage/symbolic/relation.py
-@@ -895,7 +895,7 @@ def solve(f, *args, **kwds):
-         sage: (r[0][x], r[0][y])
-         (2*lambert_w(1/2), 1)
-         sage: solve(-2*x**3 + 4*x**2 - 2*x + 6 > 0, x, algorithm='sympy')
--        [x < (1/6*sqrt(77) + 79/54)^(1/3) + 1/9/(1/6*sqrt(77) + 79/54)^(1/3) + 2/3]
-+        [x < 1/3*(1/2)^(1/3)*(9*sqrt(77) + 79)^(1/3) + 2/3*(1/2)^(2/3)/(9*sqrt(77) + 79)^(1/3) + 2/3]
-         sage: solve(sqrt(2*x^2 - 7) - (3 - x),x,algorithm='sympy')
-         [x == -8, x == 2]
-         sage: solve(sqrt(2*x + 9) - sqrt(x + 1) - sqrt(x + 4),x,algorithm='sympy')

pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch

@@ -1,40 +0,0 @@
-diff --git a/src/sage/tests/py3_syntax.py b/src/sage/tests/py3_syntax.py
-index e564860b48..86ab3725f9 100644
---- a/src/sage/tests/py3_syntax.py
-+++ b/src/sage/tests/py3_syntax.py
-@@ -179,15 +179,30 @@ class Python3SyntaxTest(SortedDirectoryWalkerABC):
-             sage: py3_syntax = Python3SyntaxTest()
-             sage: py3_syntax.test(src.name)
-             Invalid Python 3 syntax found:
--              File "...py", line 1
--                print "invalid print statement"
--                                              ^
--            SyntaxError: Missing parentheses in call to 'print'
-+            Missing parentheses in call to 'print'...
-             sage: os.unlink(src.name)
-         """
-+
-+        # compile all given files in memory, printing all errors
-+        # inspired by the py_compile module (but without writing to file)
-+        script = """
-+import sys
-+import importlib.machinery
-+rv = 0
-+for file in sys.argv[1:]:
-+    loader = importlib.machinery.SourceFileLoader('<sage_test>', file)
-+    source_bytes = loader.get_data(file)
-+    try:
-+        code = loader.source_to_code(source_bytes, file)
-+    except Exception as err:
-+        print(err)
-+        rv = 1
-+sys.exit(rv)
-+"""
-         cmd = [
-             'python3',
--            '-m', 'py_compile'
-+            '-c',
-+            script,
-         ] + list(filenames)
-         process = subprocess.Popen(
-             cmd,

pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch

@@ -1,31 +0,0 @@
-From 7419e0246230594ebfd5e7a2fe6b80d67abfc98a Mon Sep 17 00:00:00 2001
-From: Jeroen Demeyer <jdemeyer@cage.ugent.be>
-Date: Tue, 20 Mar 2018 10:40:41 +0100
-Subject: Fix sphinxify doctests
-
----
- sagenb/misc/sphinxify.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/sagenb/misc/sphinxify.py b/sagenb/misc/sphinxify.py
-index 4f76d41..15623d9 100644
---- a/sagenb/misc/sphinxify.py
-+++ b/sagenb/misc/sphinxify.py
-@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'):
- 
-         sage: from sage.misc.sphinxify import sphinxify
-         sage: sphinxify('A test')
--        '...<div class="docstring">\n    \n  <p>A test</p>\n\n\n</div>'
-+        '<div class="docstring">\n    \n  <p>A test</p>\n\n\n</div>'
-         sage: sphinxify('**Testing**\n`monospace`')
--        '...<div class="docstring"...<strong>Testing</strong>\n<span class="math"...</p>\n\n\n</div>'
-+        '<div class="docstring"...<strong>Testing</strong>\n<span class="math notranslate"...</p>\n\n\n</div>'
-         sage: sphinxify('`x=y`')
--        '...<div class="docstring">\n    \n  <p><span class="math">x=y</span></p>\n\n\n</div>'
-+        '<div class="docstring">\n    \n  <p><span class="math notranslate">x=y</span></p>\n\n\n</div>'
-         sage: sphinxify('`x=y`', format='text')
-         'x=y\n'
-         sage: sphinxify(':math:`x=y`', format='text')
--- 
-cgit v1.0-1-gd88e
-

pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch

@@ -0,0 +1,274 @@
+diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py
+index 9d65c9fa6c..a028bbe719 100644
+--- a/src/sage/interfaces/singular.py
++++ b/src/sage/interfaces/singular.py
+@@ -654,7 +654,7 @@ class Singular(ExtraTabCompletion, Expect):
+ 
+         s = Expect.eval(self, x, **kwds)
+ 
+-        if s.find("error") != -1 or s.find("Segment fault") != -1:
++        if s.find("error occurred") != -1 or s.find("Segment fault") != -1:
+             raise SingularError('Singular error:\n%s'%s)
+ 
+         if get_verbose() > 0:
+@@ -1079,7 +1079,7 @@ class Singular(ExtraTabCompletion, Expect):
+             sage: S = singular.ring('real', '(a,b)', 'lp')
+             sage: singular.current_ring()
+             polynomial ring, over a field, global ordering
+-            //   coefficients: float
++            //   coefficients: Float()
+             //   number of vars : 2
+             //        block   1 : ordering lp
+             //                  : names    a b
+@@ -1157,7 +1157,7 @@ class Singular(ExtraTabCompletion, Expect):
+              sage: singular._tab_completion()
+              ['exteriorPower',
+               ...
+-              'flintZ']
++              'crossprod']
+          """
+         p = re.compile("// *([a-z0-9A-Z_]*).*") #compiles regular expression
+         proclist = self.eval("listvar(proc)").splitlines()
+@@ -1183,7 +1183,7 @@ class Singular(ExtraTabCompletion, Expect):
+         EXAMPLES::
+ 
+             sage: singular.version()
+-            "Singular ... version 4.1.0 ...
++            "Singular ... version 4...
+         """
+         return singular_version()
+ 
+@@ -1562,7 +1562,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
+         elif charstr[0] in ['0', 'QQ']:
+             from sage.all import QQ
+             br = QQ
+-        elif charstr[0]=='real':
++        elif charstr[0].startswith('Float'):
+             from sage.all import RealField, ceil, log
+             prec = singular.eval('ringlist(basering)[1][2][1]')
+             br = RealField(ceil((ZZ(prec)+1)/log(2,10)))
+@@ -1750,7 +1750,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
+ 
+         # Singular 4 puts parentheses around floats and sign outside them
+         charstr = self.parent().eval('charstr(basering)').split(',',1)
+-        if charstr[0] in ['real', 'complex']:
++        if charstr[0]=='complex' or charstr[0].startswith('Float'):
+               for i in range(coeff_start, 2 * coeff_start):
+                   singular_poly_list[i] = singular_poly_list[i].replace('(','').replace(')','')
+ 
+@@ -1992,7 +1992,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
+             sage: S = singular.ring('real', '(a,b)', 'lp')
+             sage: singular.current_ring()
+             polynomial ring, over a field, global ordering
+-            //   coefficients: float
++            //   coefficients: Float()
+             //   number of vars : 2
+             //        block   1 : ordering lp
+             //                  : names    a b
+@@ -2072,7 +2072,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
+             sage: R._tab_completion()
+             ['exteriorPower',
+              ...
+-             'flintZ']
++             'crossprod']
+         """
+         return self.parent()._tab_completion()
+ 
+@@ -2358,7 +2358,7 @@ def singular_version():
+     EXAMPLES::
+ 
+         sage: singular.version()
+-        "Singular ... version 4.1.0 ...
++        "Singular ... version 4...
+     """
+     return singular.eval('system("--version");')
+ 
+diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd
+index 4b658c4807..d863740419 100644
+--- a/src/sage/libs/singular/decl.pxd
++++ b/src/sage/libs/singular/decl.pxd
+@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h":
+ 
+     int n_NumberOfParameters(const n_Procs_s* r)
+ 
+-    ctypedef struct poly "polyrec":
++    ctypedef struct poly "spolyrec":
+         poly *next
+         number *coef
+         unsigned long exp[1]
+@@ -630,9 +630,13 @@ cdef extern from "singular/Singular/libsingular.h":
+     # return p*q, destroys p and q
+     poly *p_Mult_q(poly *p, poly *q, ring *r)
+ 
++    # polynomial division, ignoring the rest
++    # via singclap_pdivide resp. idLift, destroys p,q
++    poly *p_Divide(poly *p, poly *q, ring *r)
++
+     # divide monomial p by monomial q, p,q const
+ 
+-    poly *pDivide(poly *p,poly *q)
++    poly *pMDivide(poly *p,poly *q)
+ 
+     # return the i-th power of p; p destroyed, requires global ring
+ 
+diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+index 2a8d9ae021..aeff53af6c 100644
+--- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
++++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
+@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport (
+     n_IsUnit, n_Invers,
+     p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q,
+     p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup,
+-    omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
+-    pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
++    omFree, pMDivide, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
++    pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
+     p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete,
+     p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize,
+     idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD,
+@@ -1693,8 +1693,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base):
+         if not g._poly:
+             raise ZeroDivisionError
+ 
+-        if r!=currRing: rChangeCurrRing(r)  # pDivide
+-        res = pDivide(f._poly, g._poly)
++        if r!=currRing: rChangeCurrRing(r)  # pMDivide
++        res = pMDivide(f._poly, g._poly)
+         if coeff:
+             if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
+                 n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
+@@ -1853,8 +1853,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base):
+                    and (<MPolynomial_libsingular>g) \
+                    and g.parent() is self \
+                    and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r):
+-                if r!=currRing: rChangeCurrRing(r)  # pDivide
+-                flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly)
++                if r!=currRing: rChangeCurrRing(r)  # pMDivide
++                flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly)
+                 #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r)
+                 p_SetCoeff(flt, n_Init(1, r), r)
+                 return new_MP(self,flt), g
+@@ -4023,16 +4023,6 @@ cdef class MPolynomial_libsingular(MPolynomial):
+             Traceback (most recent call last):
+             ...
+             NotImplementedError: Division of multivariate polynomials over non fields by non-monomials not implemented.
+-
+-        TESTS::
+-
+-            sage: P.<x,y> = ZZ[]
+-            sage: p = 3*(-x^8*y^2 - x*y^9 + 6*x^8*y + 17*x^2*y^6 - x^3*y^2)
+-            sage: q = 7*(x^2 + x*y + y^2 + 1)
+-            sage: p*q//q == p
+-            True
+-            sage: p*q//p == q
+-            True
+         """
+         cdef MPolynomialRing_libsingular parent = self._parent
+         cdef ring *r = self._parent_ring
+@@ -4052,13 +4042,18 @@ cdef class MPolynomial_libsingular(MPolynomial):
+         _right = <MPolynomial_libsingular>right
+ 
+         if r.cf.type != n_unknown:
++            if r.cf.type == n_Z:
++                P = parent.change_ring(RationalField())
++                f = P(self)//P(right)
++                CM = list(f)
++                return parent(sum([c.floor()*m for c,m in CM]))
+             if _right.is_monomial():
+                 p = _self._poly
+                 quo = p_ISet(0,r)
+-                if r != currRing: rChangeCurrRing(r)   # pDivide
++                if r != currRing: rChangeCurrRing(r)   # pMDivide
+                 while p:
+                     if p_DivisibleBy(_right._poly, p, r):
+-                        temp = pDivide(p, _right._poly)
++                        temp = pMDivide(p, _right._poly)
+                         p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r)
+                         quo = p_Add_q(quo, temp, r)
+                     p = pNext(p)
+@@ -4794,6 +4789,8 @@ cdef class MPolynomial_libsingular(MPolynomial):
+             sage: p = -x*y + x*z + 54*x - 2
+             sage: (5*p^2).lcm(3*p) == 15*p^2
+             True
++            sage: lcm(2*x,2*x*y)
++            2*x*y
+         """
+         cdef ring *_ring = self._parent_ring
+         cdef poly *ret
+@@ -4821,9 +4818,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
+         if _ring!=currRing: rChangeCurrRing(_ring)  # singclap_gcd
+         gcd = singclap_gcd(p_Copy(self._poly, _ring), p_Copy(_g._poly, _ring), _ring )
+         prod = pp_Mult_qq(self._poly, _g._poly, _ring)
+-        ret = singclap_pdivide(prod , gcd , _ring)
+-        p_Delete(&prod, _ring)
+-        p_Delete(&gcd, _ring)
++        ret = p_Divide(prod, gcd, _ring)
+         if count >= 20:
+             sig_off()
+         return new_MP(self._parent, ret)
+@@ -4866,7 +4861,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
+             sage: f.quo_rem(y)
+             (2*x^2, x + 1)
+             sage: f.quo_rem(3*x)
+-            (2*x*y + 1, -4*x^2*y - 2*x + 1)
++            (0, 2*x^2*y + x + 1)
+ 
+         TESTS::
+ 
+@@ -4888,7 +4883,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
+         if right.is_zero():
+             raise ZeroDivisionError
+ 
+-        if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base):
++        if not self._parent._base.is_field():
+             py_quo = self//right
+             py_rem = self - right*py_quo
+             return py_quo, py_rem
+diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx
+index d5439f7f08..ad20ebcca0 100644
+--- a/src/sage/rings/polynomial/plural.pyx
++++ b/src/sage/rings/polynomial/plural.pyx
+@@ -998,7 +998,7 @@ cdef class NCPolynomialRing_plural(Ring):
+         if not g._poly:
+             raise ZeroDivisionError
+ 
+-        res = pDivide(f._poly,g._poly)
++        res = pMDivide(f._poly,g._poly)
+         if coeff:
+             if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
+                 n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
+@@ -1193,7 +1193,7 @@ cdef class NCPolynomialRing_plural(Ring):
+             if isinstance(g, NCPolynomial_plural) \
+                    and (<NCPolynomial_plural>g) \
+                    and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r):
+-                flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly)
++                flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly)
+                 #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r)
+                 p_SetCoeff(flt, n_Init(1, r), r)
+                 return new_NCP(self,flt), g
+diff --git a/src/sage/rings/polynomial/polynomial_singular_interface.py b/src/sage/rings/polynomial/polynomial_singular_interface.py
+index 9331169f8b..f753610fd3 100644
+--- a/src/sage/rings/polynomial/polynomial_singular_interface.py
++++ b/src/sage/rings/polynomial/polynomial_singular_interface.py
+@@ -81,8 +81,8 @@ class PolynomialRing_singular_repr:
+             sage: R.<x,y> = PolynomialRing(CC)
+             sage: singular(R)
+             polynomial ring, over a field, global ordering
+-            //   coefficients: float[I](complex:15 digits, additional 0 digits)/(I^2+1)
+-            //   number of vars : 2
++            // coefficients: real[I](complex:15 digits, additional 0 digits)/(I^2+1)
++            // number of vars : 2
+             //        block   1 : ordering dp
+             //                  : names    x y
+             //        block   2 : ordering C
+@@ -90,8 +90,8 @@ class PolynomialRing_singular_repr:
+             sage: R.<x,y> = PolynomialRing(RealField(100))
+             sage: singular(R)
+             polynomial ring, over a field, global ordering
+-            //   coefficients: float
+-            //   number of vars : 2
++            // coefficients: Float()
++            // number of vars : 2
+             //        block   1 : ordering dp
+             //                  : names    x y
+             //        block   2 : ordering C

pkgs/applications/science/math/sage/patches/sphinx-1.7.patch

@@ -1,62 +0,0 @@
-diff --git a/src/bin/sage b/src/bin/sage
-index 397f30cbed..3fc473c343 100755
---- a/src/bin/sage
-+++ b/src/bin/sage
-@@ -980,8 +980,11 @@ if [ "$1" = '-rsyncdist' -o "$1" = "--rsyncdist" ]; then
- fi
- 
- if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
-+    # Redirect stdin from /dev/null. This helps with running TeX which
-+    # tends to ask interactive questions if something goes wrong. These
-+    # cause the build to hang. If stdin is /dev/null, TeX just aborts.
-     shift
--    exec sage-python23 -m "sage_setup.docbuild" "$@"
-+    exec sage-python23 -m sage_setup.docbuild "$@" </dev/null
- fi
- 
- if [ "$1" = '-gdb' -o "$1" = "--gdb" ]; then
-diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
-index 25f94f7b7d..3f07474d9b 100644
---- a/src/doc/common/conf.py
-+++ b/src/doc/common/conf.py
-@@ -627,7 +627,7 @@ def call_intersphinx(app, env, node, contnode):
-         sage: for line in open(thematic_index).readlines():
-         ....:     if "padics" in line:
-         ....:         sys.stdout.write(line)
--        <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics ...)"><span>Introduction to the -adics</span></a></li>
-+        <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics v...)"><span>Introduction to the -adics</span></a></li>
-     """
-     debug_inf(app, "???? Trying intersphinx for %s"%node['reftarget'])
-     builder = app.builder
-diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py
-index 4f76d4113a..8f426b5989 100644
---- a/src/sage/misc/sphinxify.py
-+++ b/src/sage/misc/sphinxify.py
-@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'):
- 
-         sage: from sage.misc.sphinxify import sphinxify
-         sage: sphinxify('A test')
--        '...<div class="docstring">\n    \n  <p>A test</p>\n\n\n</div>'
-+        '<div class="docstring">\n    \n  <p>A test</p>\n\n\n</div>'
-         sage: sphinxify('**Testing**\n`monospace`')
--        '...<div class="docstring"...<strong>Testing</strong>\n<span class="math"...</p>\n\n\n</div>'
-+        '<div class="docstring"...<strong>Testing</strong>\n<span class="math...</p>\n\n\n</div>'
-         sage: sphinxify('`x=y`')
--        '...<div class="docstring">\n    \n  <p><span class="math">x=y</span></p>\n\n\n</div>'
-+        '<div class="docstring">\n    \n  <p><span class="math notranslate nohighlight">x=y</span></p>\n\n\n</div>'
-         sage: sphinxify('`x=y`', format='text')
-         'x=y\n'
-         sage: sphinxify(':math:`x=y`', format='text')
-diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py
-index fda76a4174..d3413239dd 100644
---- a/src/sage_setup/docbuild/sphinxbuild.py
-+++ b/src/sage_setup/docbuild/sphinxbuild.py
-@@ -207,7 +207,7 @@ def runsphinx():
-     try:
-         sys.stdout = SageSphinxLogger(sys.stdout, os.path.basename(output_dir))
-         sys.stderr = SageSphinxLogger(sys.stderr, os.path.basename(output_dir))
--        sphinx.cmdline.main(sys.argv)
-+        sphinx.cmdline.main(sys.argv[1:])
-     finally:
-         sys.stdout = saved_stdout
-         sys.stderr = saved_stderr

pkgs/applications/science/math/sage/patches/spkg-scripts.patch

@@ -0,0 +1,46 @@
+commit f02714d4aea80e17cb8df62bab75d7c1a1b61a8e
+Author: Timo Kaufmann <timokau@zoho.com>
+Date:   Mon Jul 9 18:26:18 2018 +0200
+
+    Don't attempt to create dirs when showing pkg info
+    
+    The script dir cannot be assumed to be writeable after installation.
+
+diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
+index f3e02aeae5..190d558ad1 100755
+--- a/build/bin/sage-spkg
++++ b/build/bin/sage-spkg
+@@ -167,14 +167,6 @@ if [ -z "$SAGE_BUILD_DIR" ]; then
+     export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build"
+ fi
+ 
+-for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do
+-    mkdir -p "$dir"
+-    if [ $? -ne 0 ]; then
+-        error_msg "Error creating directory $dir"
+-        exit 1
+-    fi
+-done
+-
+ 
+ # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid
+ # trouble with setuptools / easy_install (cf. #10192, #10176):
+@@ -563,11 +555,13 @@ fi
+ # Setup directories
+ ##################################################################
+ 
+-mkdir -p "$SAGE_BUILD_DIR"
+-if [ $? -ne 0 ]; then
+-    error_msg "Error creating directory $SAGE_BUILD_DIR"
+-    exit 1
+-fi
++for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS" "$SAGE_BUILD_DIR"; do
++    mkdir -p "$dir"
++    if [ $? -ne 0 ]; then
++        error_msg "Error creating directory $dir"
++        exit 1
++    fi
++done
+ 
+ # Trac #5852: check write permissions
+ if [ ! -w "$SAGE_BUILD_DIR" ]; then

pkgs/applications/science/math/sage/patches/zn_poly_version.patch

@@ -1,13 +0,0 @@
-diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
-index 7ff4f21675..1d72168833 100644
---- a/src/sage/misc/package.py
-+++ b/src/sage/misc/package.py
-@@ -350,7 +350,7 @@ def package_versions(package_type, local=False):
-         sage: 'gap' in std
-         True
-         sage: std['zn_poly']
--        ('0.9.p11', '0.9.p11')
-+        ('0.9', '0.9.p11')
-     """
-     return {pkg['name']: (pkg['installed_version'], pkg['remote_version']) for pkg in list_packages(package_type, local=local).values()}
- 

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

@@ -3,17 +3,20 @@
 , fetchpatch
 }:
 stdenv.mkDerivation rec {
-  version = "8.2";
+  version = "8.3";
   name = "sage-src-${version}";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "0d7vc16s7dj23an2cb8v5bhbnc6nsw20qhnnxr0xh8qg629027b8";
+    sha256 = "0mbm99m5xry21xpi4q3q96gx392liwbifywf5awvl0j85a7rkfyx";
   };
 
   nixPatches = [
+    # https://trac.sagemath.org/ticket/25809
+    ./patches/spkg-scripts.patch
+
     # https://trac.sagemath.org/ticket/25309
     (fetchpatch {
       name = "spkg-paths.patch";
@@ -26,14 +29,7 @@ stdenv.mkDerivation rec {
       sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i";
     })
 
-    # https://trac.sagemath.org/ticket/25328
-    # https://trac.sagemath.org/ticket/25546
     # https://trac.sagemath.org/ticket/25722
-    (fetchpatch {
-      name = "install-jupyter-kernel-in-correct-prefix.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=72167b98e3f64326df6b2c78785df25539472fcc";
-      sha256 = "0pscnjhm7r2yr2rxnv4kkkq626vwaja720lixa3m3w9rwlxll5a7";
-    })
     ./patches/test-in-tmpdir.patch
 
     # https://trac.sagemath.org/ticket/25358
@@ -43,27 +39,13 @@ stdenv.mkDerivation rec {
       sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7";
     })
 
-    # https://trac.sagemath.org/ticket/25357 rebased on 8.2
+    # Unfortunately inclusion in upstream sage was rejected. Instead the bug was
-    ./patches/python3-syntax-without-write.patch
+    # fixed in python, but of course not backported to 2.7. So we'll probably
-
+    # have to keep this around until 2.7 is deprecated.
-    # https://trac.sagemath.org/ticket/25314
-    (fetchpatch {
-      name = "make-qepcad-test-optional.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=fe294c58bd035ef427e268901d54a6faa0058138";
-      sha256 = "003d5baf5c0n5rfg010ijwkwz8kg0s414cxwczs2vhdayxdixbix";
-    })
-
     # https://trac.sagemath.org/ticket/25316
+    # https://github.com/python/cpython/pull/7476
     ./patches/python-5755-hotpatch.patch
 
-    # https://trac.sagemath.org/ticket/25354
-    # https://trac.sagemath.org/ticket/25531
-    (fetchpatch {
-      name = "cysignals-include.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=28778bd25a37c80884d2b24e0683fb2989300cef";
-      sha256 = "0fiiiw91pgs8avm9ggj8hb64bhqzl6jcw094d94nhirmh8w2jmc5";
-    })
-
     # https://trac.sagemath.org/ticket/25315
     (fetchpatch {
       name = "find-libraries-in-dyld-library-path.patch";
@@ -71,16 +53,13 @@ stdenv.mkDerivation rec {
       sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc";
     })
 
-    # Pari upstream has since accepted a patch, so this patch won't be necessary once sage updates pari.
-    # https://trac.sagemath.org/ticket/25312
-    ./patches/pari-stackwarn.patch
-
-    # https://trac.sagemath.org/ticket/25311
-    ./patches/zn_poly_version.patch
-
     # https://trac.sagemath.org/ticket/25345
     # (upstream patch doesn't apply on 8.2 source)
     ./patches/dochtml-optional.patch
+
+    # work with pari with threads enabled at compile time (disable them at runtime)
+    # https://trac.sagemath.org/ticket/26002
+    ./patches/pari-no-threads.patch
   ];
 
   packageUpgradePatches = [
@@ -106,87 +85,62 @@ stdenv.mkDerivation rec {
     # the last version.
     ./patches/eclib-regulator-precision.patch
 
-    # sphinx 1.6 -> 1.7 upgrade
-    # https://trac.sagemath.org/ticket/24935
-    ./patches/sphinx-1.7.patch
-
-    # Adapt hashes to new boost version
-    # https://trac.sagemath.org/ticket/22243
-    # (this ticket doesn't only upgrade boost but also avoids this problem in the future)
-    (fetchpatch {
-      name = "boost-upgrade.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=a24a9c6b30b93957333a3116196214a931325b69";
-      sha256 = "0z3870g2ms2a81vnw08dc2i4k7jr62w8fggvcdwaavgd1wvdxwfl";
-    })
-
-    # gfan 0.6.2
-    # https://trac.sagemath.org/ticket/23353
-    (fetchpatch {
-      name = "gfan-update.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?h=420215fc469cde733ec7a339e59b78ad6eec804c&id=112498a293ea2bf563e41aed35f1aa608f01b349";
-      sha256 = "0ga3hkx8cr23dpc919lgvpi5lmy0d728jkq9z6kf0fl9s8g31mxb";
-    })
-
     # 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
     (fetchpatch {
       url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch";
       sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp";
       stripLen = 1;
     })
 
-    # https://trac.sagemath.org/ticket/25329
-    (fetchpatch {
-      name = "dont-check-exact-glpk-version.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=89d068d8d77316bfffa6bf8e9ebf70b3b3b88e5c";
-      sha256 = "00knwxs6fmymfgfl0q5kcavmxm9sf90a4r76y35n5s55gj8pl918";
-    })
-
-    # https://trac.sagemath.org/ticket/25355
-    (fetchpatch {
-      name = "maxima-5.41.0.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=87328023c4739abdf24108038201e3fa9bdfc739";
-      sha256 = "0hxi7qr5mfx1bc32r8j7iba4gzd7c6v63asylyf5cbyp86azpb7i";
-    })
-
-    # Update cddlib from 0.94g to 0.94h.
-    # https://trac.sagemath.org/ticket/25341 (doesn't apply to 8.2 sources)
-    (fetchpatch {
-      url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/u2-version-cddlib-094h.patch";
-      sha256 = "0fmw7pzbaxs2dshky6iw9pr8i23p9ih2y2lw661qypdrxh5xw03k";
-      stripLen = 1;
-    })
-    (fetchpatch {
-      name = "revert-cddlib-doctest-changes.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=269c1e1551285566b8ba7a2b890989e5590e9f11";
-      sha256 = "12bcjhq7hm2pmmj2bgjvcffjyls2x7q61ivlnaj5v5bsvhc183iy";
-      revert = true;
-    })
-
-
     # Only formatting changes.
     # https://trac.sagemath.org/ticket/25260
     ./patches/numpy-1.14.3.patch
 
-    # https://trac.sagemath.org/ticket/24374
-    (fetchpatch {
-      name = "networkx-2.1.patch";
-      url = "https://salsa.debian.org/science-team/sagemath/raw/487df9ae48ca1d93d9b1cb3af8745d31e30fb741/debian/patches/u0-version-networkx-2.1.patch";
-      sha256 = "1xxxawygbgxgvlv7b4w8hhzgdnva4rhmgdxaiaa3pwdwln0yc750";
-      stripLen = 1;
-    })
-
-    # https://trac.sagemath.org/ticket/24927 rebased
-    ./patches/arb-2.13.0.patch
-
-    # https://trac.sagemath.org/ticket/24838 rebased
-    ./patches/pynac-0.7.22.patch
-
     # https://trac.sagemath.org/ticket/25862
     ./patches/eclib-20180710.patch
+
+    # https://trac.sagemath.org/ticket/24735
+    ./patches/singular-4.1.1p2.patch
+
+    # https://trac.sagemath.org/ticket/25567 and dependency #25635
+    (fetchpatch {
+      name = "pari-upgrade-dependency.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?id=6995e7cae1b3476ad0145f8dfc897cf91f0c3c4d";
+      sha256 = "1dvhabl1c9pwd9xkjvbjjg15mvb14b24p1f3cby1mlqk34d4lrs6";
+    })
+    (fetchpatch {
+      name = "pari-2.11.0.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?id=7af4748cab37d651eaa88be501db88f4a5ffc584";
+      sha256 = "13f740ly3c19gcmhjngiycvmc3mcfj61y00i6jv0wmfgpm2z3ank";
+    })
+
+    # ntl upgrade
+    (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";
+      sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
+    })
+
+    # cddlib 0.94i -> 0.94j
+    (fetchpatch {
+      name = "cddlib-0.94j.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888";
+      sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb";
+    })
+
+    # arb 2.13.0 -> 2.14.0
+    (fetchpatch {
+      name = "arb-2.14.0.patch";
+      url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta0&id=8bef4fd2876a61969b516fe4eb3b8ad7cc076c5e";
+      sha256 = "00p3hfsfn3w2vxgd9fjd23mz7xfxjfravf8ysjxkyd657jbkpjmk";
+    })
   ];
 
-  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/scilab-bin/default.nix

@@ -3,7 +3,7 @@
 let
   name = "scilab-bin-${ver}";
 
-  ver = "5.5.2";
+  ver = "6.0.1";
 
   majorVer = builtins.elemAt (lib.splitString "." ver) 0;
 
@@ -24,9 +24,9 @@ stdenv.mkDerivation rec {
     url = "https://www.scilab.org/download/${ver}/scilab-${ver}.bin.linux-${architecture}.tar.gz";
     sha256 =
       if stdenv.system == "i686-linux" then
-        "6143a95ded40411a35630a89b365875a6526cd4db1e2865ac5612929a7db937a"
+        "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib"
       else if stdenv.system == "x86_64-linux" then
-        "c0dd7a5f06ec7a1df7a6b1b8b14407ff7f45e56821dff9b3c46bd09d4df8d350"
+        "1scswlznc14vyzg0gqa1q9gcpwx05kz1sbn563463mzkdp7nd35d"
       else
         badArch;
   };

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

@@ -1,5 +1,6 @@
 { stdenv, fetchurl, gmp, bison, perl, ncurses, readline, coreutils, pkgconfig
 , lib
+, fetchpatch
 , autoreconfHook
 , file
 , flint
@@ -36,6 +37,18 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
+  patches = [
+    # NTL error handler was introduced in the library part, preventing users of
+    # the library from implementing their own error handling
+    # https://www.singular.uni-kl.de/forum/viewtopic.php?t=2769
+    (fetchpatch {
+      name = "move_error_handler_out_of_libsingular.patch";
+      # rebased version of https://github.com/Singular/Sources/commit/502cf86d0bb2a96715be6764774b64a69c1ca34c.patch
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/singular/patches/singular-ntl-error-handler.patch?h=50b9ae2fd233c30860e1cbb3e63a26f2cc10560a";
+      sha256 = "0vgh4m9zn1kjl0br68n04j4nmn5i1igfn28cph0chnwf7dvr9194";
+    })
+  ];
+
   # For reference (last checked on commit 75f460d):
   # https://github.com/Singular/Sources/blob/spielwiese/doc/Building-Singular-from-source.md
   # https://github.com/Singular/Sources/blob/spielwiese/doc/external-packages-dynamic-modules.md

pkgs/applications/version-management/git-and-tools/cgit/default.nix

@@ -6,19 +6,19 @@
 
 stdenv.mkDerivation rec {
   name = "cgit-${version}";
-  version = "1.1";
+  version = "1.2.1";
 
   src = fetchurl {
     url = "https://git.zx2c4.com/cgit/snapshot/${name}.tar.xz";
-    sha256 = "142qcgs8dwnzhymn0a7xx47p9fc2z5wrb86ah4a9iz0mpqlsz288";
+    sha256 = "1gw2j5xc5qdx2hwiwkr8h6kgya7v9d9ff9j32ga1dys0cca7qm1w";
   };
 
   # cgit is tightly coupled with git and needs a git source tree to build.
   # IMPORTANT: Remember to check which git version cgit needs on every version
   # bump (look for "GIT_VER" in the top-level Makefile).
   gitSrc = fetchurl {
-    url    = "mirror://kernel/software/scm/git/git-2.10.2.tar.xz";
+    url    = "mirror://kernel/software/scm/git/git-2.18.0.tar.xz";
-    sha256 = "0wc64dzcxrzgi6kwcljz6y3cwm3ajdgf6aws7g58azbhvl1jk04l";
+    sha256 = "14hfwfkrci829a9316hnvkglnqqw1p03cw9k56p4fcb078wbwh4b";
   };
 
   nativeBuildInputs = [ pkgconfig ] ++ [ python wrapPython ];

pkgs/applications/version-management/subversion/default.nix

@@ -93,11 +93,12 @@ let
 
     doCheck = false; # fails 10 out of ~2300 tests
 
-    meta = {
+    meta = with stdenv.lib; {
       description = "A version control system intended to be a compelling replacement for CVS in the open source community";
+      license = licenses.asl20;
       homepage = http://subversion.apache.org/;
-      maintainers = with stdenv.lib.maintainers; [ eelco lovek323 ];
+      maintainers = with maintainers; [ eelco lovek323 ];
-      platforms = stdenv.lib.platforms.linux ++ stdenv.lib.platforms.darwin;
+      platforms = platforms.linux ++ platforms.darwin;
     };
 
   } // stdenv.lib.optionalAttrs stdenv.isDarwin {

pkgs/applications/video/mpc-qt/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "mpc-qt-${version}";
-  version = "18.03";
+  version = "18.08";
 
   src = fetchFromGitHub {
     owner = "cmdrkotori";
     repo = "mpc-qt";
     rev = "v${version}";
-    sha256 = "0mhzdgjgv08cvnscbfndpr0s8ndbcf91b61zfqspa1qv4wlqd716";
+    sha256 = "1rxlkg3vsrapazdlb1i6c5a1vvf2114bsqwzcm3n2wc5c93yqsna";
   };
 
   nativeBuildInputs = [ pkgconfig qmake qttools ];