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-rw-r--r--pkgs/top-level/aliases.nix3
-rw-r--r--pkgs/top-level/all-packages.nix176
-rw-r--r--pkgs/top-level/emacs-packages.nix5
-rw-r--r--pkgs/top-level/ocaml-packages.nix2
-rw-r--r--pkgs/top-level/perl-packages.nix36
-rw-r--r--pkgs/top-level/php-packages.nix6
-rw-r--r--pkgs/top-level/python-packages.nix77
7 files changed, 249 insertions, 56 deletions
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index fd873605056b..fe3f18519137 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -123,6 +123,7 @@ mapAliases ({
   go-pup = pup; # added 2017-12-19
   gobjectIntrospection = gobject-introspection; # added 2018-12-02
   goimports = gotools; # added 2018-09-16
+  google-gflags = gflags; # added 2019-07-25
   googleAuthenticator = google-authenticator; # added 2016-10-16
   grantlee5 = libsForQt5.grantlee;  # added 2015-12-19
   gsettings_desktop_schemas = gsettings-desktop-schemas; # added 2018-02-25
@@ -377,8 +378,6 @@ mapAliases ({
   xf86_video_nouveau = xorg.xf86videonouveau; # added 2015-09
   xlibs = xorg; # added 2015-09
   xpraGtk3 = xpra; # added 2018-09-13
-  yarn2nix = throw "Use upstream https://github.com/moretea/yarn2nix"; # added 2019-04-12
-  mkYarnPackage = yarn2nix; # added 2019-04-12
   youtubeDL = youtube-dl;  # added 2014-10-26
   zdfmediathk = mediathekview; # added 2019-01-19
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d893a5a52d46..89fc4364ffb4 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -553,6 +553,8 @@ in
 
   ansifilter = callPackage ../tools/text/ansifilter {};
 
+  antora = callPackage ../development/tools/documentation/antora {};
+
   apktool = callPackage ../development/tools/apktool {
     inherit (androidenv.androidPkgs_9_0) build-tools;
   };
@@ -661,6 +663,8 @@ in
 
   brakeman = callPackage ../development/tools/analysis/brakeman { };
 
+  brewtarget = libsForQt5.callPackage ../applications/misc/brewtarget { } ;
+
   ec2_api_tools = callPackage ../tools/virtualization/ec2-api-tools { };
 
   ec2_ami_tools = callPackage ../tools/virtualization/ec2-ami-tools { };
@@ -732,6 +736,8 @@ in
 
   container-linux-config-transpiler = callPackage ../development/tools/container-linux-config-transpiler { };
 
+  ccextractor = callPackage ../applications/video/ccextractor { };
+
   cconv = callPackage ../tools/text/cconv { };
 
   go-check = callPackage ../development/tools/check { };
@@ -780,6 +786,8 @@ in
 
   ezstream = callPackage ../tools/audio/ezstream { };
 
+  fxlinuxprintutil = callPackage ../tools/misc/fxlinuxprintutil { };
+
   genymotion = callPackage ../development/mobile/genymotion { };
 
   gamecube-tools = callPackage ../development/tools/gamecube-tools { };
@@ -852,6 +860,8 @@ in
     inherit (darwin.apple_sdk.frameworks) Carbon Cocoa;
   };
 
+  kjv = callPackage ../applications/misc/kjv { };
+
   luigi = callPackage ../applications/networking/cluster/luigi { };
 
   m-cli = callPackage ../os-specific/darwin/m-cli { };
@@ -1255,7 +1265,7 @@ in
   cdemu-client = callPackage ../misc/emulators/cdemu/client.nix { };
 
   ceres-solver = callPackage ../development/libraries/ceres-solver {
-    google-gflags = null; # only required for examples/tests
+    gflags = null; # only required for examples/tests
   };
 
   gcdemu = callPackage ../misc/emulators/cdemu/gui.nix { };
@@ -1304,6 +1314,8 @@ in
 
   clprover = callPackage ../applications/science/logic/clprover/clprover.nix { };
 
+  coloredlogs = with python3Packages; toPythonApplication coloredlogs;
+
   colord-kde = libsForQt5.callPackage ../tools/misc/colord-kde {};
 
   colpack = callPackage ../applications/science/math/colpack { };
@@ -1371,6 +1383,8 @@ in
 
   cucumber = callPackage ../development/tools/cucumber {};
 
+  dabtools = callPackage ../applications/radio/dabtools { };
+
   daemontools = callPackage ../tools/admin/daemontools { };
 
   dale = callPackage ../development/compilers/dale { };
@@ -1750,6 +1764,8 @@ in
 
   mpdris2 = callPackage ../tools/audio/mpdris2 { };
 
+  mpd-mpris = callPackage ../tools/audio/mpd-mpris { };
+
   mq-cli = callPackage ../tools/system/mq-cli { };
 
   nfdump = callPackage ../tools/networking/nfdump { };
@@ -2143,11 +2159,15 @@ in
   };
 
   citrix_workspace_unwrapped = callPackage ../applications/networking/remote/citrix-workspace { };
+  citrix_workspace_unwrapped_19_6_0 = citrix_workspace_unwrapped.override { version = "19.6.0"; };
   citrix_workspace_unwrapped_19_3_0 = citrix_workspace_unwrapped.override { version = "19.3.0"; };
 
   citrix_workspace = callPackage ../applications/networking/remote/citrix-workspace/wrapper.nix {
     citrix_workspace = citrix_workspace_unwrapped;
   };
+  citrix_workspace_19_6_0 = callPackage ../applications/networking/remote/citrix-workspace/wrapper.nix {
+    citrix_workspace = citrix_workspace_unwrapped_19_6_0;
+  };
   citrix_workspace_19_3_0 = callPackage ../applications/networking/remote/citrix-workspace/wrapper.nix {
     citrix_workspace = citrix_workspace_unwrapped_19_3_0;
   };
@@ -2156,7 +2176,13 @@ in
 
   cmst = libsForQt5.callPackage ../tools/networking/cmst { };
 
-  codimd = callPackage ../servers/web-apps/codimd { };
+  codimd = callPackage ../servers/web-apps/codimd {
+    nodejs = nodejs-10_x;
+    yarn2nix = yarn2nix-moretea.override {
+      nodejs = nodejs-10_x;
+      yarn = yarn.override { nodejs = nodejs-10_x; };
+    };
+  };
 
   colord = callPackage ../tools/misc/colord { };
 
@@ -2685,6 +2711,8 @@ in
 
   sonota = callPackage ../tools/misc/sonota { };
 
+  sonobuoy = callPackage ../applications/networking/cluster/sonobuoy { };
+
   tealdeer = callPackage ../tools/misc/tealdeer { };
 
   teamocil = callPackage ../tools/misc/teamocil { };
@@ -2857,6 +2885,8 @@ in
 
   execline = skawarePackages.execline;
 
+  executor = with python3Packages; toPythonApplication executor;
+
   exif = callPackage ../tools/graphics/exif { };
 
   exiftags = callPackage ../tools/graphics/exiftags { };
@@ -3280,6 +3310,8 @@ in
 
   gitea = callPackage ../applications/version-management/gitea { };
 
+  gl2ps = callPackage ../development/libraries/gl2ps { };
+
   glusterfs = callPackage ../tools/filesystems/glusterfs { };
 
   glmark2 = callPackage ../tools/graphics/glmark2 { };
@@ -3666,6 +3698,8 @@ in
 
   heimdall-gui = heimdall.override { enableGUI = true; };
 
+  helio-workstation = callPackage ../applications/audio/helio-workstation { };
+
   hevea = callPackage ../tools/typesetting/hevea { };
 
   hexd = callPackage ../tools/misc/hexd { };
@@ -3723,6 +3757,8 @@ in
 
   hubicfuse = callPackage ../tools/filesystems/hubicfuse { };
 
+  humanfriendly = with python3Packages; toPythonApplication humanfriendly;
+
   hwinfo = callPackage ../tools/system/hwinfo { };
 
   hybridreverb2 = callPackage ../applications/audio/hybridreverb2 { };
@@ -3956,6 +3992,8 @@ in
 
   jpegrescan = callPackage ../applications/graphics/jpegrescan { };
 
+  jpylyzer = with pythonPackages; toPythonApplication jpylyzer;
+
   jq = callPackage ../development/tools/jq { };
 
   jo = callPackage ../development/tools/jo { };
@@ -3995,6 +4033,8 @@ in
   kakoune-unwrapped = callPackage ../applications/editors/kakoune { };
   kakoune = wrapKakoune kakoune-unwrapped { };
 
+  kak-lsp = callPackage ../tools/misc/kak-lsp { };
+
   kbdd = callPackage ../applications/window-managers/kbdd { };
 
   kdbplus = pkgsi686Linux.callPackage ../applications/misc/kdbplus { };
@@ -4040,6 +4080,8 @@ in
 
   klick = callPackage ../applications/audio/klick { };
 
+  klystrack = callPackage ../applications/audio/klystrack { };
+
   knockknock = callPackage ../tools/security/knockknock { };
 
   kore = callPackage ../development/web/kore { };
@@ -4306,8 +4348,6 @@ in
 
   nodePackages = nodePackages_10_x;
 
-  npm2nix = nodePackages.npm2nix;
-
   now-cli = callPackage ../development/web/now-cli {};
 
   file-rename = callPackage ../tools/filesystems/file-rename { };
@@ -4887,6 +4927,8 @@ in
 
   mpack = callPackage ../tools/networking/mpack { };
 
+  mtm = callPackage ../tools/misc/mtm { };
+
   pa_applet = callPackage ../tools/audio/pa-applet { };
 
   pandoc-imagine = python3Packages.callPackage ../tools/misc/pandoc-imagine { };
@@ -5100,6 +5142,8 @@ in
 
   oppai-ng = callPackage ../tools/misc/oppai-ng { };
 
+  update-dotdee = with python3Packages; toPythonApplication update-dotdee;
+
   update-resolv-conf = callPackage ../tools/networking/openvpn/update-resolv-conf.nix { };
 
   opae = callPackage ../development/libraries/opae { };
@@ -5300,6 +5344,8 @@ in
   pinentry = callPackage ../tools/security/pinentry {
     libcap = if stdenv.isDarwin then null else libcap;
     gcr = null;
+    qt4 = null;
+    qt5 = null;
   };
 
   pinentry_ncurses = res.pinentry.override {
@@ -5315,11 +5361,13 @@ in
   };
 
   pinentry_qt4 = res.pinentry.override {
-    qt = qt4;
+    gtk2 = null;
+    inherit qt4;
   };
 
   pinentry_qt5 = res.pinentry.override {
-    qt = qt5.qtbase;
+    gtk2 = null;
+    inherit qt5;
   };
 
   pinentry_mac = callPackage ../tools/security/pinentry/mac.nix {
@@ -5863,6 +5911,8 @@ in
 
   seqdiag = with python3Packages; toPythonApplication seqdiag;
 
+  sequoia-tool = callPackage ../tools/security/sequoia-tool { inherit (llvmPackages) libclang; };
+
   sewer = callPackage ../tools/admin/sewer { };
 
   screenfetch = callPackage ../tools/misc/screenfetch { };
@@ -5993,6 +6043,8 @@ in
 
   sshguard = callPackage ../tools/security/sshguard {};
 
+  suricata = callPackage ../applications/networking/ids/suricata { };
+
   softhsm = callPackage ../tools/security/softhsm {
     inherit (darwin) libobjc;
     inherit (darwin.apple_sdk.frameworks) Security;
@@ -6250,6 +6302,8 @@ in
 
   theharvester = callPackage ../tools/security/theharvester { };
 
+  inherit (nodePackages) thelounge;
+
   thefuck = python3Packages.callPackage ../tools/misc/thefuck { };
 
   thin-provisioning-tools = callPackage ../tools/misc/thin-provisioning-tools {  };
@@ -6359,6 +6413,8 @@ in
 
   trace-cmd = callPackage ../os-specific/linux/trace-cmd { };
 
+  kernelshark = libsForQt5.callPackage ../os-specific/linux/trace-cmd/kernelshark.nix { };
+
   traceroute = callPackage ../tools/networking/traceroute { };
 
   tracebox = callPackage ../tools/networking/tracebox { };
@@ -6844,6 +6900,8 @@ in
 
   wml = callPackage ../development/web/wml { };
 
+  wmc-mpris = callPackage ../applications/misc/web-media-controller { };
+
   wol = callPackage ../tools/networking/wol { };
 
   wolf-shaper = callPackage ../applications/audio/wolf-shaper { };
@@ -6963,6 +7021,8 @@ in
 
   yarn = callPackage ../development/tools/yarn  { };
 
+  yarn2nix-moretea = callPackage ../development/tools/yarn2nix-moretea/yarn2nix { };
+
   yasr = callPackage ../applications/audio/yasr { };
 
   yank = callPackage ../tools/misc/yank { };
@@ -8111,12 +8171,19 @@ in
   };
   cargo-sweep = callPackage ../development/tools/rust/cargo-sweep { };
   cargo-xbuild = callPackage ../development/tools/rust/cargo-xbuild { };
+  cargo-generate = callPackage ../development/tools/rust/cargo-generate {
+    inherit (darwin.apple_sdk.frameworks) Security;
+  };
 
   pyo3-pack = callPackage ../development/tools/rust/pyo3-pack { };
   rainicorn = callPackage ../development/tools/rust/rainicorn { };
-  rls = callPackage ../development/tools/rust/rls { };
+  rls = callPackage ../development/tools/rust/rls {
+    inherit (darwin.apple_sdk.frameworks) CoreFoundation Security;
+  };
   rustfmt = callPackage ../development/tools/rust/rustfmt { };
-  rustracer = callPackage ../development/tools/rust/racer { };
+  rustracer = callPackage ../development/tools/rust/racer {
+    inherit (darwin.apple_sdk.frameworks) Security;
+  };
   rustracerd = callPackage ../development/tools/rust/racerd { };
   rust-bindgen = callPackage ../development/tools/rust/bindgen { };
   rust-cbindgen = callPackage ../development/tools/rust/cbindgen {
@@ -8211,6 +8278,8 @@ in
 
   urweb = callPackage ../development/compilers/urweb { };
 
+  vlang = callPackage ../development/compilers/vlang { };
+
   inherit (callPackage ../development/compilers/vala { })
     vala_0_36
     vala_0_38
@@ -8665,6 +8734,7 @@ in
   bundler = callPackage ../development/ruby-modules/bundler { };
   bundlerEnv = callPackage ../development/ruby-modules/bundler-env { };
   bundlerApp = callPackage ../development/ruby-modules/bundler-app { };
+  bundlerUpdateScript = callPackage ../development/ruby-modules/bundler-update-script { };
 
   bundler-audit = callPackage ../tools/security/bundler-audit { };
 
@@ -9668,6 +9738,8 @@ in
 
   redo = callPackage ../development/tools/build-managers/redo { };
 
+  redo-apenwarr = callPackage ../development/tools/build-managers/redo-apenwarr { };
+
   redo-sh = callPackage ../development/tools/build-managers/redo-sh { };
 
   reno = callPackage ../development/tools/reno { };
@@ -9794,6 +9866,8 @@ in
 
   teensy-loader-cli = callPackage ../development/tools/misc/teensy-loader-cli { };
 
+  terraform-lsp = callPackage ../development/tools/misc/terraform-lsp { };
+
   texinfo413 = callPackage ../development/tools/misc/texinfo/4.13a.nix { };
   texinfo4 = texinfo413;
   texinfo5 = callPackage ../development/tools/misc/texinfo/5.2.nix { };
@@ -10738,8 +10812,7 @@ in
   goocanvas2 = callPackage ../development/libraries/goocanvas/2.x.nix { };
   goocanvasmm2 = callPackage ../development/libraries/goocanvasmm { };
 
-  google-gflags = callPackage ../development/libraries/google-gflags { };
-  gflags = google-gflags; # TODO: move to aliases.nix
+  gflags = callPackage ../development/libraries/gflags { };
 
   gperftools = callPackage ../development/libraries/gperftools { };
 
@@ -13121,6 +13194,8 @@ in
 
   rocksdb_lite = rocksdb.override { enableLite = true; };
 
+  rotate-backups = with python3Packages; toPythonApplication rotate-backups;
+
   rote = callPackage ../development/libraries/rote { };
 
   ronn = callPackage ../development/tools/ronn { };
@@ -14897,6 +14972,8 @@ in
 
   syncserver = callPackage ../servers/syncserver { };
 
+  thanos = callPackage ../servers/monitoring/thanos { };
+
   inherit (callPackages ../servers/http/tomcat { })
     tomcat7
     tomcat8
@@ -15784,6 +15861,7 @@ in
 
   aggregateModules = modules:
     callPackage ../os-specific/linux/kmod/aggregator.nix {
+      inherit (buildPackages) kmod;
       inherit modules;
     };
 
@@ -16391,7 +16469,8 @@ in
 
   fira-mono = callPackage ../data/fonts/fira-mono { };
 
-  font-awesome_5 = callPackage ../data/fonts/font-awesome-5 { };
+  font-awesome_4 = (callPackage ../data/fonts/font-awesome-5 { }).v4;
+  font-awesome_5 = (callPackage ../data/fonts/font-awesome-5 { }).v5;
   font-awesome = font-awesome_5;
 
   freefont_ttf = callPackage ../data/fonts/freefont-ttf { };
@@ -17010,6 +17089,7 @@ in
 
   bitcoin = altcoins.bitcoin;
   clightning = altcoins.clightning;
+  lnd = altcoins.lnd;
 
   bitcoin-xt = altcoins.bitcoin-xt;
   cryptop = altcoins.cryptop;
@@ -17077,7 +17157,7 @@ in
 
   baresip = callPackage ../applications/networking/instant-messengers/baresip { };
 
-  barrier = callPackage ../applications/misc/barrier {};
+  barrier = libsForQt5.callPackage ../applications/misc/barrier {};
 
   bashSnippets = callPackage ../applications/misc/bashSnippets { };
 
@@ -17135,7 +17215,10 @@ in
   bitwig-studio2 =  callPackage ../applications/audio/bitwig-studio/bitwig-studio2.nix {
     inherit (pkgs) bitwig-studio1;
   };
-  bitwig-studio = bitwig-studio2;
+  bitwig-studio3 =  callPackage ../applications/audio/bitwig-studio/bitwig-studio3.nix {
+    inherit (pkgs) bitwig-studio1;
+  };
+  bitwig-studio = bitwig-studio3;
 
   bgpdump = callPackage ../tools/networking/bgpdump { };
 
@@ -17387,6 +17470,8 @@ in
 
   cyclone = callPackage ../applications/audio/pd-plugins/cyclone  { };
 
+  dablin = callPackage ../applications/radio/dablin { };
+
   darcs = haskell.lib.overrideCabal (haskell.lib.justStaticExecutables haskellPackages.darcs) (drv: {
     configureFlags = (stdenv.lib.remove "-flibrary" drv.configureFlags or []) ++ ["-f-library"];
   });
@@ -17464,10 +17549,11 @@ in
   };
 
   inherit (callPackage ../applications/virtualization/docker {})
-    docker_18_09;
+    docker_18_09
+    docker_19_03;
 
-  docker = docker_18_09;
-  docker-edge = docker_18_09;
+  docker = docker_19_03;
+  docker-edge = docker_19_03;
 
   docker-proxy = callPackage ../applications/virtualization/docker/proxy.nix { };
 
@@ -17783,11 +17869,13 @@ in
     };
 
     external = {
-      inherit (haskellPackages) ghc-mod structured-haskell-mode Agda hindent;
+      inherit (haskellPackages)
+        ghc-mod structured-haskell-mode Agda hindent;
       inherit (pythonPackages) elpy;
       inherit
-        autoconf automake git libffi libpng pkgconfig poppler rtags w3m zlib
-        substituteAll rustPlatform cmake llvmPackages libtool zeromq;
+        autoconf automake editorconfig-core-c git libffi libpng pkgconfig
+        poppler rtags w3m zlib substituteAll rustPlatform cmake llvmPackages
+        libtool zeromq;
     };
   };
 
@@ -18511,13 +18599,16 @@ in
 
   spectral = qt5.callPackage ../applications/networking/instant-messengers/spectral { };
 
+  spotifyd = callPackage ../applications/audio/spotifyd {
+    withALSA = stdenv.isLinux;
+    withPulseAudio = config.pulseaudio or true;
+    withPortAudio = stdenv.isDarwin;
+  };
+
   super-productivity = callPackage ../applications/networking/super-productivity { };
 
-  wlc = callPackage ../development/libraries/wlc { };
   wlroots = callPackage ../development/libraries/wlroots { };
 
-  orbment = callPackage ../applications/window-managers/orbment { };
-
   sway = callPackage ../applications/window-managers/sway { };
   swaybg = callPackage ../applications/window-managers/sway/bg.nix { };
   swayidle = callPackage ../applications/window-managers/sway/idle.nix { };
@@ -18527,11 +18618,6 @@ in
     pulseSupport = config.pulseaudio or false;
   };
 
-  velox = callPackage ../applications/window-managers/velox {
-    stConf = config.st.conf or null;
-    stPatches = config.st.patches or null;
-  };
-
   i3 = callPackage ../applications/window-managers/i3 {
     xcb-util-cursor = if stdenv.isDarwin then xcb-util-cursor-HEAD else xcb-util-cursor;
   };
@@ -18863,6 +18949,12 @@ in
 
   kubectl = callPackage ../applications/networking/cluster/kubectl { };
 
+  k9s = callPackage ../applications/networking/cluster/k9s { };
+
+  fluxctl = callPackage ../applications/networking/cluster/fluxctl { };
+
+  linkerd = callPackage ../applications/networking/cluster/linkerd { };
+
   kubernetes-helm = callPackage ../applications/networking/cluster/helm { };
 
   kubetail = callPackage ../applications/networking/cluster/kubetail { } ;
@@ -19407,10 +19499,10 @@ in
     githubSupport = true;
     mpdSupport = true;
     pulseSupport  = true;
-    iwSupport = true;
+    iwSupport = false;
     nlSupport = true;
     i3Support = true;
-    i3GapsSupport = true;
+    i3GapsSupport = false;
   };
 
   ptex = callPackage ../development/libraries/ptex {};
@@ -19604,7 +19696,7 @@ in
 
   openorienteering-mapper = libsForQt5.callPackage ../applications/gis/openorienteering-mapper { };
 
-  openscad = callPackage ../applications/graphics/openscad {};
+  openscad = libsForQt5.callPackage ../applications/graphics/openscad {};
 
   opentimestamps-client = python3Packages.callPackage ../tools/misc/opentimestamps-client {};
 
@@ -19842,7 +19934,7 @@ in
 
   properties-cpp = callPackage ../development/libraries/properties-cpp { };
 
-  protonmail-bridge = libsForQt511.callPackage ../applications/networking/protonmail-bridge { };
+  protonmail-bridge = libsForQt512.callPackage ../applications/networking/protonmail-bridge { };
 
   protonvpn-cli = callPackage ../applications/networking/protonvpn-cli { };
 
@@ -20488,7 +20580,7 @@ in
 
   tambura = callPackage ../applications/audio/tambura { };
 
-  teamspeak_client = libsForQt511.callPackage ../applications/networking/instant-messengers/teamspeak/client.nix { };
+  teamspeak_client = libsForQt512.callPackage ../applications/networking/instant-messengers/teamspeak/client.nix { };
   teamspeak_server = callPackage ../applications/networking/instant-messengers/teamspeak/server.nix { };
 
   taskell = callPackage ../applications/misc/taskell { };
@@ -20507,8 +20599,14 @@ in
 
   taskopen = callPackage ../applications/misc/taskopen { };
 
-  tdesktopPackages = dontRecurseIntoAttrs (callPackage ../applications/networking/instant-messengers/telegram/tdesktop { });
-  tdesktop = tdesktopPackages.stable;
+  # TODO (@primeos): Remove after the 19.09 branch-off:
+  tdesktopPackages = throw ''
+    The attributes "tdesktopPackages.*" where removed as the preview version
+    will not be maintained anymore (there are regular stable releases and we
+    depend on the patches from Arch Linux which only track the stable version
+    as well). Please switch to "tdesktop" (stable version).
+  '';
+  tdesktop = qt5.callPackage ../applications/networking/instant-messengers/telegram/tdesktop { };
 
   telegram-cli = callPackage ../applications/networking/instant-messengers/telegram/telegram-cli { };
 
@@ -20661,6 +20759,8 @@ in
 
   trayer = callPackage ../applications/window-managers/trayer { };
 
+  tree-from-tags = callPackage ../applications/audio/tree-from-tags { };
+
   tdrop = callPackage ../applications/misc/tdrop { };
 
   tree = callPackage ../tools/system/tree {};
@@ -21332,6 +21432,8 @@ in
     inherit (gnome2) scrollkeeper libglade;
   };
 
+  xygrib = libsForQt5.callPackage ../applications/misc/xygrib/default.nix {};
+
   xzgv = callPackage ../applications/graphics/xzgv { };
 
   yabar = callPackage ../applications/window-managers/yabar { };
@@ -22487,6 +22589,8 @@ in
 
   emboss = callPackage ../applications/science/biology/emboss { };
 
+  est-sfs = callPackage ../applications/science/biology/est-sfs { };
+
   ezminc = callPackage ../applications/science/biology/EZminc { };
 
   exonerate = callPackage ../applications/science/biology/exonerate { };
@@ -22679,6 +22783,7 @@ in
   mathematica = callPackage ../applications/science/math/mathematica { };
   mathematica9 = callPackage ../applications/science/math/mathematica/9.nix { };
   mathematica10 = callPackage ../applications/science/math/mathematica/10.nix { };
+  mathematica11 = callPackage ../applications/science/math/mathematica/11.nix { };
 
   metis = callPackage ../development/libraries/science/math/metis {};
 
@@ -23907,6 +24012,8 @@ in
 
   brlaser = callPackage ../misc/cups/drivers/brlaser { };
 
+  fxlinuxprint = callPackage ../misc/cups/drivers/fxlinuxprint { };
+
   brscan4 = callPackage ../applications/graphics/sane/backends/brscan4 { };
 
   dsseries = callPackage ../applications/graphics/sane/backends/dsseries { };
@@ -24435,5 +24542,4 @@ in
   dapper = callPackage ../development/tools/dapper { };
 
   kube3d =  callPackage ../applications/networking/cluster/kube3d {};
-
 }
diff --git a/pkgs/top-level/emacs-packages.nix b/pkgs/top-level/emacs-packages.nix
index 29600670f61b..6696520c33eb 100644
--- a/pkgs/top-level/emacs-packages.nix
+++ b/pkgs/top-level/emacs-packages.nix
@@ -434,7 +434,10 @@ let
     };
     stripDebugList = [ "share" ];
     packageRequires = [ emacs ];
-    nativeBuildInputs = [ external.autoconf external.automake external.pkgconfig external.libtool external.zeromq ];
+    nativeBuildInputs = [
+      external.autoconf external.automake external.pkgconfig external.libtool
+      (external.zeromq.override { enableDrafts = true; })
+    ];
     preBuild = ''
       make
     '';
diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix
index 3b807c932f0a..949c5b6a3085 100644
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@@ -719,6 +719,8 @@ let
 
     stringext = callPackage ../development/ocaml-modules/stringext { };
 
+    toml = callPackage ../development/ocaml-modules/toml { };
+
     topkg = callPackage ../development/ocaml-modules/topkg { };
 
     tsdl = callPackage ../development/ocaml-modules/tsdl { };
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index f78cacd08bec..dd75f4e5b207 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -41,13 +41,29 @@ let
   };
 
   # Helper functions for packages that use Module::Build to build.
-  buildPerlModule = { buildInputs ? [], ... } @ args:
-    buildPerlPackage (args // {
-      buildInputs = buildInputs ++ [ ModuleBuild ];
-      preConfigure = "touch Makefile.PL";
-      buildPhase = "perl Build.PL --prefix=$out; ./Build build";
-      installPhase = "./Build install";
-      checkPhase = "./Build test";
+  buildPerlModule = args:
+    buildPerlPackage ({
+      buildPhase = ''
+        runHook preBuild
+        perl Build.PL --prefix=$out; ./Build build
+        runHook postBuild
+      '';
+      installPhase = ''
+        runHook preInstall
+        ./Build install
+        runHook postInstall
+      '';
+      checkPhase = ''
+        runHook preCheck
+        ./Build test
+        runHook postCheck
+      '';
+    } // args // {
+      preConfigure = ''
+        touch Makefile.PL
+        ${args.preConfigure or ""}
+      '';
+      buildInputs = (args.buildInputs or []) ++ [ ModuleBuild ];
     });
 
   /* Construct a perl search path (such as $PERL5LIB)
@@ -432,10 +448,6 @@ let
     buildInputs = [ pkgs.curl FileWhich IOAll ModuleBuildTiny PathClass TestException TestNoWarnings TestOutput TestSpec TestTempDirTiny ];
     propagatedBuildInputs = [ CPANPerlReleases CaptureTiny DevelPatchPerl locallib ];
 
-    preConfigure = ''
-      patchShebangs .
-    '';
-
     doCheck = false;
 
     meta = {
@@ -6119,7 +6131,7 @@ let
       sha256 = "c065fcd3e2f22ae769937bcc971b91f80294d5009fac140bfba83bf7d35305e3";
     };
     configurePhase = ''
-      preConfigure || true
+      runHook preConfigure
       perl Build.PL PREFIX="$out" prefix="$out"
     '';
     propagatedBuildInputs = [ IPCSystemSimple ];
diff --git a/pkgs/top-level/php-packages.nix b/pkgs/top-level/php-packages.nix
index 080754b4b1ff..3b7bb5692a22 100644
--- a/pkgs/top-level/php-packages.nix
+++ b/pkgs/top-level/php-packages.nix
@@ -189,11 +189,11 @@ let
     buildInputs = [ (if isPhp73 then pkgs.pcre2 else pkgs.pcre) ];
   };
 
-  mailparse = assert !isPhp73; buildPecl rec {
-    version = "3.0.2";
+  mailparse = buildPecl rec {
+    version = "3.0.3";
     pname = "mailparse";
 
-    sha256 = "0fw447ralqihsjnn0fm2hkaj8343cvb90v0d1wfclgz49256y6nq";
+    sha256 = "00nk14jbdbln93mx3ag691avc11ff94hkadrcv5pn51c6ihsxbmz";
   };
 
   memcached = buildPecl rec {
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 2cc3e62d2dac..be6a291b7c70 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -502,6 +502,8 @@ in {
 
   diff_cover = callPackage ../development/python-modules/diff_cover { };
 
+  diofant = callPackage ../development/python-modules/diofant { };
+
   docrep = callPackage ../development/python-modules/docrep { };
 
   dominate = callPackage ../development/python-modules/dominate { };
@@ -682,10 +684,12 @@ in {
 
   maxminddb = callPackage ../development/python-modules/maxminddb { };
 
-  monty = callPackage ../development/python-modules/monty { };
-
   mininet-python = (toPythonModule (pkgs.mininet.override{ inherit python; })).py;
 
+  mkl-service = callPackage ../development/python-modules/mkl-service { };
+
+  monty = callPackage ../development/python-modules/monty { };
+
   mpi4py = callPackage ../development/python-modules/mpi4py {
     mpi = pkgs.openmpi;
   };
@@ -1075,6 +1079,8 @@ in {
 
   rlp = callPackage ../development/python-modules/rlp { };
 
+  rq = callPackage ../development/python-modules/rq { };
+
   rx = callPackage ../development/python-modules/rx { };
 
   sabyenc = callPackage ../development/python-modules/sabyenc { };
@@ -1097,6 +1103,8 @@ in {
 
   simpleeval = callPackage ../development/python-modules/simpleeval { };
 
+  simple-salesforce = callPackage ../development/python-modules/simple-salesforce { };
+
   singledispatch = callPackage ../development/python-modules/singledispatch { };
 
   sip = callPackage ../development/python-modules/sip { };
@@ -1121,6 +1129,8 @@ in {
 
   spglib = callPackage ../development/python-modules/spglib { };
 
+  sshpubkeys = callPackage ../development/python-modules/sshpubkeys { };
+
   sslib = callPackage ../development/python-modules/sslib { };
 
   statistics = callPackage ../development/python-modules/statistics { };
@@ -1469,6 +1479,8 @@ in {
 
   capstone = callPackage ../development/python-modules/capstone { };
 
+  capturer = callPackage ../development/python-modules/capturer { };
+
   cement = callPackage ../development/python-modules/cement {};
 
   cgen = callPackage ../development/python-modules/cgen { };
@@ -1493,6 +1505,8 @@ in {
 
   colorcet = callPackage ../development/python-modules/colorcet { };
 
+  coloredlogs = callPackage ../development/python-modules/coloredlogs { };
+
   colorclass = callPackage ../development/python-modules/colorclass {};
 
   colorlog = callPackage ../development/python-modules/colorlog { };
@@ -2182,6 +2196,8 @@ in {
 
   execnet = callPackage ../development/python-modules/execnet { };
 
+  executor = callPackage ../development/python-modules/executor { };
+
   ezdxf = callPackage ../development/python-modules/ezdxf {};
 
   facebook-sdk = callPackage ../development/python-modules/facebook-sdk { };
@@ -2337,7 +2353,11 @@ in {
 
   image-match = callPackage ../development/python-modules/image-match { };
 
-  imbalanced-learn = callPackage ../development/python-modules/imbalanced-learn { };
+  imbalanced-learn =
+    if isPy27 then
+      callPackage ../development/python-modules/imbalanced-learn/0.4.nix { }
+    else
+      callPackage ../development/python-modules/imbalanced-learn { };
 
   immutables = callPackage ../development/python-modules/immutables {};
 
@@ -2369,6 +2389,8 @@ in {
 
   JPype1 = callPackage ../development/python-modules/JPype1 {};
 
+  jpylyzer = callPackage ../development/python-modules/jpylyzer {};
+
   josepy = callPackage ../development/python-modules/josepy {};
 
   jsbeautifier = callPackage ../development/python-modules/jsbeautifier {};
@@ -2454,6 +2476,8 @@ in {
 
   natsort = callPackage ../development/python-modules/natsort { };
 
+  naturalsort = callPackage ../development/python-modules/naturalsort { };
+
   ncclient = callPackage ../development/python-modules/ncclient {};
 
   logfury = callPackage ../development/python-modules/logfury { };
@@ -2671,6 +2695,8 @@ in {
 
   roman = callPackage ../development/python-modules/roman { };
 
+  rotate-backups = callPackage ../tools/backup/rotate-backups { };
+
   librosa = callPackage ../development/python-modules/librosa { };
 
   samplerate = callPackage ../development/python-modules/samplerate { };
@@ -3816,6 +3842,8 @@ in {
 
   numba = callPackage ../development/python-modules/numba { };
 
+  numcodecs = callPackage ../development/python-modules/numcodecs { };
+
   numexpr = callPackage ../development/python-modules/numexpr { };
 
   Nuitka = callPackage ../development/python-modules/nuitka { };
@@ -3899,6 +3927,8 @@ in {
 
   zake = callPackage ../development/python-modules/zake { };
 
+  zarr = callPackage ../development/python-modules/zarr { };
+
   kazoo = callPackage ../development/python-modules/kazoo { };
 
   FormEncode = callPackage ../development/python-modules/FormEncode { };
@@ -3985,6 +4015,8 @@ in {
 
   fixtures = callPackage ../development/python-modules/fixtures { };
 
+  fipy = callPackage ../development/python-modules/fipy { };
+
   pelican = callPackage ../development/python-modules/pelican {
     inherit (pkgs) glibcLocales git;
   };
@@ -4097,6 +4129,8 @@ in {
 
   prettytable = callPackage ../development/python-modules/prettytable { };
 
+  property-manager = callPackage ../development/python-modules/property-manager { };
+
   prompt_toolkit = let
     filename = if isPy3k then ../development/python-modules/prompt_toolkit else ../development/python-modules/prompt_toolkit/1.nix;
   in callPackage filename { };
@@ -4248,6 +4282,8 @@ in {
 
   pyspread = callPackage ../development/python-modules/pyspread { };
 
+  pysparse = callPackage ../development/python-modules/pysparse { };
+
   pyupdate = callPackage ../development/python-modules/pyupdate {};
 
   pyx = callPackage ../development/python-modules/pyx { };
@@ -4424,10 +4460,27 @@ in {
 
   pyxattr = callPackage ../development/python-modules/pyxattr { };
 
+  pyamg = callPackage ../development/python-modules/pyamg { };
+
   pyaml = callPackage ../development/python-modules/pyaml { };
 
   pyyaml = callPackage ../development/python-modules/pyyaml { };
 
+  pyyaml_3 = (callPackage ../development/python-modules/pyyaml { }).overridePythonAttrs (oldAttrs: rec {
+    version = "3.13";
+    src = oldAttrs.src.override {
+      inherit version;
+      sha256 = "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf";
+    };
+    # https://github.com/yaml/pyyaml/issues/298#issuecomment-511990948
+    patches = singleton (pkgs.fetchpatch {
+      url = "https://github.com/yaml/pyyaml/commit/c5b135fe39d41cffbdc006f28ccb2032df6005e0.patch";
+      sha256 = "0x1v45rkmj194c41d1nqi3ihj9z4rsy8zvpfcd8p960g1fia7fhn";
+    });
+    # https://github.com/yaml/pyyaml/issues/298#issuecomment-511990948
+    doCheck = false;
+  });
+
   rabbitpy = callPackage ../development/python-modules/rabbitpy { };
 
   rasterio = callPackage ../development/python-modules/rasterio {
@@ -4639,6 +4692,8 @@ in {
 
   scikit-tda = callPackage ../development/python-modules/scikit-tda { };
 
+  scikit-fmm = callPackage ../development/python-modules/scikit-fmm { };
+
   scp = callPackage ../development/python-modules/scp {};
 
   seaborn = callPackage ../development/python-modules/seaborn { };
@@ -4651,6 +4706,8 @@ in {
 
   setuptools_scm = callPackage ../development/python-modules/setuptools_scm { };
 
+  setuptools-scm-git-archive = callPackage ../development/python-modules/setuptools-scm-git-archive { };
+
   serverlessrepo = callPackage ../development/python-modules/serverlessrepo { };
 
   shippai = callPackage ../development/python-modules/shippai {};
@@ -4819,6 +4876,8 @@ in {
 
   update-copyright = callPackage ../development/python-modules/update-copyright {};
 
+  update-dotdee = callPackage ../development/python-modules/update-dotdee { };
+
   uritemplate = callPackage ../development/python-modules/uritemplate { };
 
   uproot = callPackage ../development/python-modules/uproot {};
@@ -4831,6 +4890,8 @@ in {
 
   user-agents = callPackage ../development/python-modules/user-agents { };
 
+  verboselogs = callPackage ../development/python-modules/verboselogs { };
+
   vega_datasets = callPackage ../development/python-modules/vega_datasets { };
 
   virtkey = callPackage ../development/python-modules/virtkey {
@@ -5118,6 +5179,8 @@ in {
 
   swagger-spec-validator = callPackage ../development/python-modules/swagger-spec-validator { };
 
+  openapi-spec-validator = callPackage ../development/python-modules/openapi-spec-validator { };
+
   freezegun = callPackage ../development/python-modules/freezegun { };
 
   taskw = callPackage ../development/python-modules/taskw { };
@@ -5991,6 +6054,14 @@ in {
   aioesphomeapi = callPackage ../development/python-modules/aioesphomeapi { };
 
   mwparserfromhell = callPackage ../development/python-modules/mwparserfromhell { };
+
+  starlette = callPackage ../development/python-modules/starlette { };
+
+  uvicorn = callPackage ../development/python-modules/uvicorn { };
+
+  pydantic = callPackage ../development/python-modules/pydantic { };
+
+  fastapi = callPackage ../development/python-modules/fastapi { };
 });
 
 in fix' (extends overrides packages)
generated by cgit-pink 1.4.1 (git 2.36.1) at 2024-07-30 13:07:02 +0000