Merge branch 'master' into staging-next

2019-12-30 05:22:23 +01:00 · 2019-12-30 05:22:23 +01:00 · 480fc1856a
commit 480fc1856a
parent fb66525297 e1ee43f514
97 changed files with 971 additions and 402 deletions
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@ -2123,6 +2123,12 @@
    githubId = 10492681;
    name = "Michael Hoang";
  };
+  eonpatapon = {
+    email = "eon@patapon.info";
+    github = "eonpatapon";
+    githubId = 418227;
+    name = "Jean-Philippe Braun";
+  };
  eperuffo = {
    email = "info@emanueleperuffo.com";
    github = "emanueleperuffo";
--- a/nixos/tests/hydra/default.nix
+++ b/nixos/tests/hydra/default.nix
@ -30,7 +30,7 @@ let
  callTest = f: f { inherit system pkgs; };

  hydraPkgs = {
-    inherit (pkgs) nixStable nixUnstable;
+    inherit (pkgs) nixStable nixUnstable nixFlakes;
  };

  tests = pkgs.lib.flip pkgs.lib.mapAttrs hydraPkgs (name: nix:
--- a/pkgs/applications/audio/cadence/default.nix
+++ b/pkgs/applications/audio/cadence/default.nix
@ -1,6 +1,7 @@
 { stdenv
 , mkDerivation
 , lib
+, fetchpatch
 , fetchzip
 , pkgconfig
 , qtbase
@ -17,6 +18,14 @@
    sha256 = "07z8grnnpkd0nf3y3r6qjlk1jlzrbhdrp9mnhrhhmws54p1bhl20";
  };

+  patches = [
+    # Fix installation without DESTDIR
+    (fetchpatch {
+      url = "https://github.com/falkTX/Cadence/commit/1fd3275e7daf4b75f59ef1f85a9e2e93bd5c0731.patch";
+      sha256 = "0q791jsh8vmjg678dzhbp1ykq8xrrlxl1mbgs3g8if1ccj210vd8";
+    })
+  ];
+
  nativeBuildInputs = [
    pkgconfig
  ];
@ -26,8 +35,8 @@
  ];

  makeFlags = [
-    "PREFIX=''"
-    "DESTDIR=${placeholder "out"}"
+    "PREFIX=${placeholder "out"}"
+    "SYSCONFDIR=${placeholder "out"}/etc"
  ];

  propagatedBuildInputs = with python3Packages; [
--- a/pkgs/applications/audio/projectm/default.nix
+++ b/pkgs/applications/audio/projectm/default.nix
@ -37,15 +37,15 @@ stdenv.mkDerivation {

  nativeBuildInputs = [ pkgconfig cmake ];

-  cmakeFlags = ''
-    -DprojectM_FONT_MENU=${ttf_bitstream_vera}/share/fonts/truetype/VeraMono.ttf
-    -DprojectM_FONT_TITLE=${ttf_bitstream_vera}/share/fonts/truetype/Vera.ttf
-    -DINCLUDE-PROJECTM-TEST=OFF
-    -DINCLUDE-PROJECTM-QT=${if withQt then "ON" else "OFF"}
-    -DINCLUDE-PROJECTM-LIBVISUAL=${if withLibvisual then "ON" else "OFF"}
-    -DINCLUDE-PROJECTM-JACK=${if withJack then "ON" else "OFF"}
-    -DINCLUDE-PROJECTM-PULSEAUDIO=${if withPulseAudio then "ON" else "OFF"}
-  '';
+  cmakeFlags = [
+    "-DprojectM_FONT_MENU=${ttf_bitstream_vera}/share/fonts/truetype/VeraMono.ttf"
+    "-DprojectM_FONT_TITLE=${ttf_bitstream_vera}/share/fonts/truetype/Vera.ttf"
+    "-DINCLUDE-PROJECTM-TEST=OFF"
+    "-DINCLUDE-PROJECTM-QT=${if withQt then "ON" else "OFF"}"
+    "-DINCLUDE-PROJECTM-LIBVISUAL=${if withLibvisual then "ON" else "OFF"}"
+    "-DINCLUDE-PROJECTM-JACK=${if withJack then "ON" else "OFF"}"
+    "-DINCLUDE-PROJECTM-PULSEAUDIO=${if withPulseAudio then "ON" else "OFF"}"
+  ];

  buildInputs = with stdenv.lib;
    [ glew ftgl ]
--- a/pkgs/applications/editors/emacs/default.nix
+++ b/pkgs/applications/editors/emacs/default.nix
@ -97,7 +97,7 @@ stdenv.mkDerivation rec {
    done
  '';

-  installTargets = "tags install";
+  installTargets = [ "tags" "install" ];

  postInstall = ''
    mkdir -p $out/share/emacs/site-lisp
--- a/pkgs/applications/graphics/pdfcpu/default.nix
+++ b/pkgs/applications/graphics/pdfcpu/default.nix
@ -2,13 +2,13 @@

 buildGoModule rec {
  pname = "pdfcpu";
-  version = "0.3";
+  version = "0.3.1";

  src = fetchFromGitHub {
    owner = "pdfcpu";
    repo = pname;
    rev = "v${version}";
-    sha256 = "03v4wc531dwmbjqgs3y3ncdn6g3xirv1w6h1mfgglb6sjll8jxp5";
+    sha256 = "13i9hz7gg82s17ky715a6czpisn4fpx2xjbmydq7j81b44x7m3vc";
  };

  modSha256 = "1nagb3k2ghfw27g4vcmn7v8s5flg387jpf1l18gw6c44a1xjcivs";
--- a/pkgs/applications/misc/osm2xmap/default.nix
+++ b/pkgs/applications/misc/osm2xmap/default.nix
@ -12,18 +12,15 @@ stdenv.mkDerivation rec {
  };

  makeFlags = [
-    "GIT_VERSION=$(version)"
+    "GIT_VERSION=${version}"
    "GIT_TIMESTAMP="
-    "SHAREDIR=$(out)/share/"
-    "INSTALL_BINDIR=$(out)/bin"
-    "INSTALL_MANDIR=$(out)/share/man/man1"
-    "INSTALL_SHAREDIR=$(out)/share/"
+    "SHAREDIR=${placeholder ''out''}/share/osm2xmap"
+    "INSTALL_BINDIR=${placeholder ''out''}/bin"
+    "INSTALL_MANDIR=${placeholder ''out''}/share/man/man1"
  ];

  NIX_CFLAGS_COMPILE = [ "-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" ];

-  installFlags = [ "DESTDIR=$(out)" ];
-
  buildInputs = [ libroxml proj libyamlcpp boost ];

  meta = with stdenv.lib; {
--- a/pkgs/applications/misc/waybar/default.nix
+++ b/pkgs/applications/misc/waybar/default.nix
@ -1,5 +1,5 @@
 { stdenv, fetchFromGitHub, meson, pkgconfig, ninja
-, wayland, wlroots, gtkmm3, libinput, libsigcxx, jsoncpp, fmt, scdoc, spdlog
+, wayland, wlroots, gtkmm3, libinput, libsigcxx, jsoncpp, fmt, scdoc, spdlog, gtk-layer-shell
 , traySupport  ? true,  libdbusmenu-gtk3
 , pulseSupport ? false, libpulseaudio
 , nlSupport    ? true,  libnl
@ -9,13 +9,13 @@
 }:
  stdenv.mkDerivation rec {
    pname = "waybar";
-    version = "0.8.0";
+    version = "0.9.0";

    src = fetchFromGitHub {
      owner = "Alexays";
      repo = "Waybar";
      rev = version;
-      sha256 = "0s8ck7qxka0l91ayma6amp9sc8cidi43byqgzcavi3a6id983r1z";
+      sha256 = "1w8a6jih872ry288k8ic6mjfi9ccf1jwc24wnh9p5c7w73247c2c";
    };

    nativeBuildInputs = [
@ -23,7 +23,7 @@
    ];

    buildInputs = with stdenv.lib;
-      [ wayland wlroots gtkmm3 libinput libsigcxx jsoncpp fmt spdlog ]
+      [ wayland wlroots gtkmm3 libinput libsigcxx jsoncpp fmt spdlog gtk-layer-shell ]
      ++ optional  traySupport  libdbusmenu-gtk3
      ++ optional  pulseSupport libpulseaudio
      ++ optional  nlSupport    libnl
@ -42,6 +42,7 @@
      }
    ) ++ [
      "-Dout=${placeholder "out"}"
+      "-Dsystemd=disabled"
    ];

    meta = with stdenv.lib; {
--- a/pkgs/applications/networking/mailreaders/lumail/default.nix
+++ b/pkgs/applications/networking/mailreaders/lumail/default.nix
@ -52,7 +52,7 @@ stdenv.mkDerivation {
    sed -e "s|^#\!\(.*/perl.*\)$|#\!\1$perlFlags|" -i perl.d/imap-proxy
  '';

-  buildFlags = if debugBuild then "lumail2-debug" else "";
+  buildFlags = stdenv.lib.optional debugBuild "lumail2-debug";

  installPhase = ''
    mkdir -p $out/bin || true
--- a/pkgs/applications/networking/p2p/eiskaltdcpp/default.nix
+++ b/pkgs/applications/networking/p2p/eiskaltdcpp/default.nix
@ -39,20 +39,20 @@ stdenv.mkDerivation rec {
    })
  ];

-  cmakeFlags = ''
-    -DUSE_ASPELL=ON
-    -DUSE_QT_QML=ON
-    -DFREE_SPACE_BAR_C=ON
-    -DUSE_MINIUPNP=ON
-    -DLOCAL_MINIUPNP=ON
-    -DDBUS_NOTIFY=ON
-    -DUSE_JS=ON
-    -DPERL_REGEX=ON
-    -DUSE_CLI_XMLRPC=ON
-    -DWITH_SOUNDS=ON
-    -DLUA_SCRIPT=ON
-    -DWITH_LUASCRIPTS=ON
-  '';
+  cmakeFlags = [
+    "-DUSE_ASPELL=ON"
+    "-DUSE_QT_QML=ON"
+    "-DFREE_SPACE_BAR_C=ON"
+    "-DUSE_MINIUPNP=ON"
+    "-DLOCAL_MINIUPNP=ON"
+    "-DDBUS_NOTIFY=ON"
+    "-DUSE_JS=ON"
+    "-DPERL_REGEX=ON"
+    "-DUSE_CLI_XMLRPC=ON"
+    "-DWITH_SOUNDS=ON"
+    "-DLUA_SCRIPT=ON"
+    "-DWITH_LUASCRIPTS=ON"
+  ];

  enableParallelBuilding = true;

--- a/pkgs/applications/networking/resilio-sync/default.nix
+++ b/pkgs/applications/networking/resilio-sync/default.nix
@ -9,13 +9,13 @@ let

 in stdenv.mkDerivation rec {
  pname = "resilio-sync";
-  version = "2.6.3";
+  version = "2.6.4";

  src = fetchurl {
    url = "https://download-cdn.resilio.com/${version}/linux-${arch}/resilio-sync_${arch}.tar.gz";
    sha256 = {
-      x86_64-linux = "114k7dsxn7lzv6mjq9alsqxypvkah4lmjn5w6brbvgd6m6pdwslz";
-      i686-linux   = "1dh0hxbd33bs51xib3qwxw58h9j30v0dc10b4x4rwkbgsj11nc83";
+      x86_64-linux = "1c1yksjag58p7yjm72iiz82p2r01lq7kxvq7z5phmq5z6gxdg4a8";
+      i686-linux   = "167baz9fzmzk50jffzvgmgyw1zw3955r3cb73z23qvw8zqzdqydc";
    }.${stdenv.hostPlatform.system};
  };

--- a/pkgs/applications/science/biology/last/default.nix
+++ b/pkgs/applications/science/biology/last/default.nix
@ -0,0 +1,30 @@
+{ stdenv, fetchurl, unzip, zlib, python3, parallel }:
+
+stdenv.mkDerivation rec {
+  pname = "last";
+  version = "1042";
+
+  src = fetchurl {
+    url = "http://last.cbrc.jp/last-${version}.zip";
+    sha256 = "0mgbhd01m9riqza2gx56qk6x5682kg71zflhisr6d3q05wrv103f";
+  };
+
+  nativeBuildInputs = [ unzip ];
+  buildInputs = [ zlib python3 ];
+
+  makeFlags = [ "prefix=${placeholder "out"}" ];
+
+  postFixup = ''
+    for f in $out/bin/parallel-* ; do
+      sed -i 's|parallel |${parallel}/bin/parallel |' $f
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Genomic sequence aligner";
+    homepage = "http://last.cbrc.jp/";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
--- a/pkgs/applications/science/biology/minia/default.nix
+++ b/pkgs/applications/science/biology/minia/default.nix
@ -0,0 +1,33 @@
+{ stdenv, fetchFromGitHub, cmake, hdf5, boost }:
+
+stdenv.mkDerivation rec {
+  pname = "minia";
+  version = "3.2.1";
+
+  src = fetchFromGitHub {
+    owner = "GATB";
+    repo = "minia";
+    rev = "v${version}";
+    sha256 = "0bmfrywixaaql898l0ixsfkhxjf2hb08ssnqzlzacfizxdp46siq";
+    fetchSubmodules = true;
+  };
+
+  patches = [ ./no-bundle.patch ];
+
+  NIX_CFLAGS_COMPILE = [ "-Wformat" ];
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ hdf5 boost ];
+
+  prePatch = ''
+    rm -rf thirdparty/gatb-core/gatb-core/thirdparty/{hdf5,boost}
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Short read genome assembler";
+    homepage = "https://github.com/GATB/minia";
+    license = licenses.agpl3;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/science/biology/minia/no-bundle.patch
+++ b/pkgs/applications/science/biology/minia/no-bundle.patch
@ -0,0 +1,222 @@
+diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+index f48a70b..0e11ece 100644
+--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt
+@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty)
+ #  DEPENDENCIES 
+ ################################################################################
+ # we must be sure that hdf5 is built and installed before building gatb-core
+-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild)
+ 
+ ################################################################################
+ #  DOCUMENTATION GENERATION 
+@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt  DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE              DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md      DESTINATION . OPTIONAL)
+-    INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
+ ENDIF()
+ 
+ ################################################################################
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+index dfeee1c..d5553a2 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp
+@@ -35,7 +35,7 @@
+ #include <stdint.h>
+ #include <algorithm>
+ #include <iostream>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ #include <gatb/system/api/Exception.hpp>
+ #include <gatb/system/api/config.hpp>
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+index 60be5d5..25ae75e 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+@@ -33,7 +33,7 @@
+ /********************************************************************************/
+ 
+ #include <iostream>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+index 6a71bb0..b9205df 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+index c22b892..62e6586 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+index c06aaab..e0befba 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ extern const unsigned char revcomp_4NT[];
+ extern const unsigned char comp_NT    [];
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+index 9659874..0c79ff6 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+index 3cb84f8..cd5d382 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+@@ -31,7 +31,7 @@
+ /********************************************************************************/
+ 
+ #include <sys/types.h>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+index b8f6c79..a040832 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+@@ -28,7 +28,7 @@
+ 
+ #include <gatb/system/api/ISmartPointer.hpp>
+ #include <gatb/tools/storage/impl/Storage.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+index 2645abd..fad48c0 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+index a92b729..66d552f 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+index 29e0949..0565cc4 100644
+--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+@@ -33,7 +33,7 @@
+ #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
+ #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
+ #include <gatb/system/impl/System.hpp>
+-#include <hdf5/hdf5.h>
+#include <hdf5.h>
+ #include <sstream>
+ 
+ /********************************************************************************/
+diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+index 6e0b5c4..34aef28 100644
+--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt
+@@ -1,54 +1,3 @@
+-################################################################################
+-#  HDF5 GENERATION 
+-################################################################################
+-
+-#SET (HDF5_ENABLE_THREADSAFE       ON)
+-#SET (H5_HAVE_THREADSAFE 1)
+-
+-##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
+-SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
+-#SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
+-
+-SET (HDF5_EXTERNALLY_CONFIGURED     ON)
+-
+-#SET (HDF5_INSTALL_BIN_DIR           ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
+-#SET (HDF5_INSTALL_LIB_DIR           ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_BIN_DIR           bin)
+-SET (HDF5_INSTALL_LIB_DIR           lib)
+-
+-SET (HDF5_INSTALL_INCLUDE_DIR       ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
+-SET (HDF5_INSTALL_DATA_DIR          ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_CMAKE_DIR         ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-
+-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+-    SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
+-ENDIF()
+-
+-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
+-	OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
+-ENDIF()
+-
+-# We don't want warnings from HDF5 compilation
+-set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
+-add_definitions (${COMPILE_DEFINITIONS})
+-
+-# add HDF5 generation
+-ADD_SUBDIRECTORY (hdf5)
+-
+-# We add a custom target for copying header files.
+-add_custom_target (hdf5_postbuild ALL)
+-
+-# We build the output directory
+-add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
+-
+-# We define all the header files to be copied
+-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
+-
+-# We copy each header file
+-foreach (header ${headerfiles})
+-  add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR}  )
+-endforeach()
+-
+ # include other smaller libraries (json, Boophf)
+ 
+ add_custom_target (thirdparty_copy ALL)
--- a/pkgs/applications/science/biology/tebreak/default.nix
+++ b/pkgs/applications/science/biology/tebreak/default.nix
@ -0,0 +1,42 @@
+{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
+, samtools, findutils }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "tebreak";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "adamewing";
+    repo = "tebreak";
+    rev = version;
+    sha256 = "194av17wz66n4zxyi56mbkik31j2wmkly5i9qmxgaxymhavzi3kq";
+  };
+
+  nativeBuildInputs = [ findutils python3Packages.cython ];
+  propagatedBuildInputs = with python3Packages; [
+    pysam
+    scipy
+    bx-python
+    scikit-bio
+  ];
+
+  preConfigure = ''
+    # patch the paths to all required software
+    for f in $(find . -type f) ; do
+      sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f
+      sed -i "s|'minia'|'${minia}/bin/minia'|" $f
+      sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f
+      sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f
+      sed -i "s|'lastal'|'${last}/bin/lastal'|" $f
+      sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Find and characterise transposable element insertions";
+    homepage = "https://github.com/adamewing/tebreak";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
--- a/pkgs/applications/science/electronics/verilator/default.nix
+++ b/pkgs/applications/science/electronics/verilator/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  pname = "verilator";
-  version = "4.022";
+  version = "4.024";

  src = fetchurl {
    url    = "https://www.veripool.org/ftp/${pname}-${version}.tgz";
-    sha256 = "1sj0qzl387pl2ygii3ssx35c3m601nb07j16lqj5zcxzhcg62i9p";
+    sha256 = "0nmjazdv36ksjp8ys48c1grlzkd6yx3zhcd9y165d4sjm3m1pffs";
  };

  enableParallelBuilding = true;
--- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@ -1,4 +1,6 @@
-{ stdenv, fetchurl, cmake
+{ stdenv
+, fetchurl
+, cmake
 , singlePrec ? true
 , mpiEnabled ? false
 , fftw
@ -6,7 +8,6 @@
 , perl
 }:

-
 stdenv.mkDerivation {
  name = "gromacs-2019.4";

@ -19,18 +20,27 @@ stdenv.mkDerivation {
  buildInputs = [ fftw perl ]
  ++ (stdenv.lib.optionals mpiEnabled [ openmpi ]);

-  cmakeFlags = ''
-    ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"}
-    ${if mpiEnabled then "-DGMX_MPI:BOOL=TRUE
-                          -DGMX_CPU_ACCELERATION:STRING=SSE4.1
-                          -DGMX_OPENMP:BOOL=TRUE
-                          -DGMX_THREAD_MPI:BOOL=FALSE"
-                     else "-DGMX_MPI:BOOL=FALSE" }
-  '';
+  cmakeFlags = (
+    if singlePrec then [
+      "-DGMX_DOUBLE=OFF"
+    ] else [
+      "-DGMX_DOUBLE=ON"
+      "-DGMX_DEFAULT_SUFFIX=OFF"
+    ]
+  ) ++ (
+    if mpiEnabled then [
+      "-DGMX_MPI:BOOL=TRUE"
+      "-DGMX_CPU_ACCELERATION:STRING=SSE4.1"
+      "-DGMX_OPENMP:BOOL=TRUE"
+      "-DGMX_THREAD_MPI:BOOL=FALSE"
+    ] else [
+      "-DGMX_MPI:BOOL=FALSE"
+    ]
+  );

  meta = with stdenv.lib; {
-    homepage    = "http://www.gromacs.org";
-    license     = licenses.gpl2;
+    homepage = "http://www.gromacs.org";
+    license = licenses.gpl2;
    description = "Molecular dynamics software package";
    longDescription = ''
      GROMACS is a versatile package to perform molecular dynamics,
--- a/pkgs/applications/video/xawtv/default.nix
+++ b/pkgs/applications/video/xawtv/default.nix
@ -1,25 +1,54 @@
-{stdenv, fetchurl, ncurses, libjpeg, libX11, libXt, alsaLib, aalib, libXft, xorgproto, libv4l
-, libFS, libXaw, libXpm, libXext, libSM, libICE, perl, linux}:
+{ stdenv
+, fetchurl
+, ncurses
+, libjpeg
+, libX11
+, libXt
+, alsaLib
+, aalib
+, libXft
+, xorgproto
+, libv4l
+, libFS
+, libXaw
+, libXpm
+, libXext
+, libSM
+, libICE
+, perl
+}:

 stdenv.mkDerivation rec {
  name = "xawtv-3.106";
+
  src = fetchurl {
    url = "https://linuxtv.org/downloads/xawtv/${name}.tar.bz2";
    sha256 = "174wd36rk0k23mgx9nlnpc398yd1f0wiv060963axg6sz0v4rksp";
  };

-  preConfigure = ''
-    export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -I${linux}/lib/modules/${linux.modDirVersion}/build"
-  '';
+  buildInputs = [
+    ncurses
+    libjpeg
+    libX11
+    libXt
+    libXft
+    xorgproto
+    libFS
+    perl
+    alsaLib
+    aalib
+    libXaw
+    libXpm
+    libXext
+    libSM
+    libICE
+    libv4l
+  ];

-  configureFlags= [ "--prefix=" ];
-
-  NIX_LDFLAGS = "-lgcc_s";
-
-  makeFlags = "SUID_ROOT= DESTDIR=\$(out) PREFIX=";
-
-  buildInputs = [ncurses libjpeg libX11 libXt libXft xorgproto libFS perl alsaLib aalib
-                 libXaw libXpm libXext libSM libICE libv4l];
+  makeFlags = [
+    "SUID_ROOT=" # do not try to setuid
+    "resdir=${placeholder ''out''}/share/X11"
+  ];

  meta = {
    description = "TV application for Linux with apps and tools such as a teletext browser";
@ -28,5 +57,4 @@ stdenv.mkDerivation rec {
    maintainers = with stdenv.lib.maintainers; [ domenkozar ];
    platforms = stdenv.lib.platforms.linux;
  };
-  
 }
--- a/pkgs/applications/virtualization/bochs/bochs-2.6.10-glibc-2.26.patch
+++ b/pkgs/applications/virtualization/bochs/bochs-2.6.10-glibc-2.26.patch
@ -0,0 +1,13 @@
+diff -Naur bochs-2.6.10.orig/iodev/network/slirp/slirp.h bochs-2.6.10.mod/iodev/network/slirp/slirp.h
+--- bochs-2.6.10.orig/iodev/network/slirp/slirp.h	2019-11-02 16:30:39.843938000 -0300
+++ bochs-2.6.10.mod/iodev/network/slirp/slirp.h	2019-12-29 12:55:49.541630697 -0300
+@@ -44,8 +44,8 @@
+ #endif
+ 
+ #include <sys/types.h>
+-#if defined(__OpenBSD__) || defined(__linux__)
+ #include <stdint.h>
+#if defined(__OpenBSD__) || defined(__linux__)
+ #include <sys/wait.h>
+ #endif
+ #ifdef HAVE_SYS_BITYPES_H
--- a/pkgs/applications/virtualization/bochs/bochs-2.6.9-glibc-2.26.patch
+++ b/pkgs/applications/virtualization/bochs/bochs-2.6.9-glibc-2.26.patch
@ -1,14 +0,0 @@
-diff --git a/iodev/network/slirp/slirp.h b/iodev/network/slirp/slirp.h
-index 7c16aa3..202a1b7 100644
--- a/iodev/network/slirp/slirp.h
-+++ b/iodev/network/slirp/slirp.h
-@@ -33,8 +33,8 @@ typedef char *caddr_t;
- #endif
- 
- #include <sys/types.h>
-#if defined(__OpenBSD__)
- #include <stdint.h>
-+#if defined(__OpenBSD__)
- #include <sys/wait.h>
- #endif
- #ifdef HAVE_SYS_BITYPES_H
--- a/pkgs/applications/virtualization/bochs/default.nix
+++ b/pkgs/applications/virtualization/bochs/default.nix
@ -19,14 +19,14 @@ with stdenv.lib;
 stdenv.mkDerivation rec {

  pname = "bochs";
-  version = "2.6.9";
+  version = "2.6.10";

  src = fetchurl {
    url = "mirror://sourceforge/project/bochs/bochs/${version}/${pname}-${version}.tar.gz";
-    sha256 = "1379cq4cnfprhw8mgh60i0q9j8fz8d7n3d5fnn2g9fdiv5znfnzf";
+    sha256 = "1c3mw4b8wrjf8z44fvhycs95j1wd1c0b4khcv63giiia5j5q0gvj";
  };

-  patches = [ ./bochs-2.6.9-glibc-2.26.patch ];
+  patches = [ ./bochs-2.6.10-glibc-2.26.patch ];

  buildInputs = with stdenv.lib;
  [ pkgconfig libtool gtk2 libGLU libGL readline libX11 libXpm docbook_xml_dtd_45 docbook_xsl ]
@ -120,7 +120,7 @@ stdenv.mkDerivation rec {
    '';
    homepage = http://bochs.sourceforge.net/;
    license = licenses.lgpl2Plus;
-    maintainers = [ maintainers.AndersonTorres ];
+    maintainers = with maintainers; [ AndersonTorres ];
    platforms = platforms.unix;
  };
 }
--- a/pkgs/applications/virtualization/runc/default.nix
+++ b/pkgs/applications/virtualization/runc/default.nix
@ -22,14 +22,14 @@ buildGoPackage rec {
  nativeBuildInputs = [ pkgconfig ];
  buildInputs = [ go-md2man libseccomp libapparmor apparmor-parser which ];

-  makeFlags = ''BUILDTAGS+=seccomp BUILDTAGS+=apparmor'';
+  makeFlags = [ "BUILDTAGS+=seccomp" "BUILDTAGS+=apparmor" ];

  buildPhase = ''
    cd go/src/${goPackagePath}
    patchShebangs .
    substituteInPlace libcontainer/apparmor/apparmor.go \
      --replace /sbin/apparmor_parser ${apparmor-parser}/bin/apparmor_parser
-    make ${makeFlags} runc
+    make ${toString makeFlags} runc
  '';

  installPhase = ''
--- a/pkgs/build-support/agda/default.nix
+++ b/pkgs/build-support/agda/default.nix
@ -47,9 +47,9 @@ let
    includeDirs = self.buildDependsAgdaShareAgda
                  ++ self.sourceDirectories ++ self.topSourceDirectories
                  ++ [ "." ];
-    buildFlags = concatStringsSep " " (map (x: "-i " + x) self.includeDirs);
+    buildFlags = stdenv.lib.concatMap (x: ["-i" x]) self.includeDirs;

-    agdaWithArgs = "${Agda}/bin/agda ${self.buildFlags}";
+    agdaWithArgs = "${Agda}/bin/agda ${toString self.buildFlags}";

    buildPhase = ''
      runHook preBuild
--- a/pkgs/data/misc/media-player-info/default.nix
+++ b/pkgs/data/misc/media-player-info/default.nix
@ -19,9 +19,7 @@ in
      patchShebangs ./tools
    '';

-    preConfigure = ''
-      configureFlags="$configureFlags --with-udevdir=$out/lib/udev"
-    '';
+    configureFlags = [ "--with-udevdir=${placeholder "out"}/lib/udev" ];

    meta = with stdenv.lib; {
      description = "A repository of data files describing media player capabilities";
--- a/pkgs/desktops/gnome-3/extensions/gsconnect/default.nix
+++ b/pkgs/desktops/gnome-3/extensions/gsconnect/default.nix
@ -4,13 +4,13 @@

 stdenv.mkDerivation rec {
  pname = "gnome-shell-gsconnect";
-  version = "27";
+  version = "30";

  src = fetchFromGitHub {
    owner = "andyholmes";
    repo = "gnome-shell-extension-gsconnect";
    rev = "v${version}";
-    sha256 = "0bpg7hl81wir3c15ri8kbvr6xhalpkfmcyazwmmwyj5lxpn40ykk";
+    sha256 = "17j96y72mj7vg2csn5c9rji7jy04x5qzl8knf5gky6wppxj9zjb4";
  };

  patches = [
--- a/pkgs/development/coq-modules/mathcomp/default.nix
+++ b/pkgs/development/coq-modules/mathcomp/default.nix
@ -92,7 +92,7 @@ let
           attrValues (mkMathcompGenFrom overrides (mathcomp-deps mathcomp-pkg) mathcomp-version);
        enableParallelBuilding = true;

-        buildFlags = optionalString withDoc "doc";
+        buildFlags = optional withDoc "doc";

        COQBIN = "${coq}/bin/";

--- a/pkgs/development/guile-modules/guile-sdl/default.nix
+++ b/pkgs/development/guile-modules/guile-sdl/default.nix
@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
      name = "sdl-env";
      paths = buildInputs;
    };
-  in "SDLMINUSI=-I${sdl}/include/SDL";
+  in [ "SDLMINUSI=-I${sdl}/include/SDL" ];

  meta = with stdenv.lib; {
    description = "Guile bindings for SDL";
--- a/pkgs/development/haskell-modules/non-hackage-packages.nix
+++ b/pkgs/development/haskell-modules/non-hackage-packages.nix
@ -8,7 +8,7 @@
 self: super: {

  multi-ghc-travis = throw ("haskellPackages.multi-ghc-travis has been renamed"
-    + "to haskell-ci, which is now on hackage");
+    + " to haskell-ci, which is now on hackage");

  # https://github.com/channable/vaultenv/issues/1
  vaultenv = self.callPackage ../tools/haskell/vaultenv { };
--- a/pkgs/development/interpreters/elixir/generic-builder.nix
+++ b/pkgs/development/interpreters/elixir/generic-builder.nix
@ -10,7 +10,7 @@
 } @ args:

 let
-  inherit (stdenv.lib) getVersion versionAtLeast;
+  inherit (stdenv.lib) getVersion versionAtLeast optional;

 in
  assert versionAtLeast (getVersion erlang) minimumOTPVersion;
@ -29,9 +29,7 @@ in

    inherit debugInfo;

-    buildFlags = if debugInfo
-      then "ERL_COMPILER_OPTIONS=debug_info"
-      else "";
+    buildFlags = optional debugInfo "ERL_COMPILER_OPTIONS=debug_info";

    preBuild = ''
      # The build process uses ./rebar. Link it to the nixpkgs rebar
--- a/pkgs/development/libraries/ffmpeg/3.4.nix
+++ b/pkgs/development/libraries/ffmpeg/3.4.nix
@ -6,7 +6,7 @@

 callPackage ./generic.nix (rec {
  version = branch;
-  branch = "3.4.6";
-  sha256 = "1s20wzgxxrm56gckyb8cf1lh36hdnkdxvmmnnvdxvia4zb3grf1b";
+  branch = "3.4.7";
+  sha256 = "0hj91gjps92f4w3yyqss89yrs6s75574hbj5gz9g5affd6294yhc";
  darwinFrameworks = [ Cocoa CoreMedia ];
 } // args)
--- a/pkgs/development/libraries/gdcm/default.nix
+++ b/pkgs/development/libraries/gdcm/default.nix
@ -16,11 +16,11 @@ stdenv.mkDerivation rec {
    cd ../build
  '';

-  cmakeFlags = ''
-    -DGDCM_BUILD_APPLICATIONS=ON
-    -DGDCM_BUILD_SHARED_LIBS=ON
-    -DGDCM_USE_VTK=ON
-  '';
+  cmakeFlags = [
+    "-DGDCM_BUILD_APPLICATIONS=ON"
+    "-DGDCM_BUILD_SHARED_LIBS=ON"
+    "-DGDCM_USE_VTK=ON"
+  ];

  enableParallelBuilding = true;
  buildInputs = [ cmake vtk ] ++ stdenv.lib.optional stdenv.isDarwin [ darwin.apple_sdk.frameworks.ApplicationServices darwin.apple_sdk.frameworks.Cocoa ];
--- a/pkgs/development/libraries/gegl/4.0.nix
+++ b/pkgs/development/libraries/gegl/4.0.nix
@ -57,6 +57,12 @@ stdenv.mkDerivation rec {
      url = "https://gitlab.gnome.org/GNOME/gegl/commit/2bc06bfedee4fb25f6a966c8235b75292e24e55f.patch";
      sha256 = "1psls61wsrdq5pzpvj22mrm46lpzrw3wkx6li7dv6fyb65wz2n4d";
    })
+
+    # Fix test timeout. Downstream debian patch.
+    (fetchpatch {
+      url = "https://salsa.debian.org/gnome-team/gegl/raw/9b7520b38d87cd8ad4b39bf0b8c62d011da25169/debian/patches/increase_test_timeout.patch";
+      sha256 = "1prc1h1aipjd9db0i1j7nzga4zvk3vl8qsjpz1jzv1wwvz02isly";
+    })
  ];

  nativeBuildInputs = [
--- a/pkgs/development/libraries/grpc/default.nix
+++ b/pkgs/development/libraries/grpc/default.nix
@ -1,20 +1,20 @@
 { stdenv, fetchFromGitHub, fetchpatch, cmake, zlib, c-ares, pkgconfig, openssl, protobuf, gflags }:

 stdenv.mkDerivation rec {
-  version = "1.25.0"; # N.B: if you change this, change pythonPackages.grpcio and pythonPackages.grpcio-tools to a matching version too
+  version = "1.26.0"; # N.B: if you change this, change pythonPackages.grpcio and pythonPackages.grpcio-tools to a matching version too
  pname = "grpc";
  src = fetchFromGitHub {
    owner = "grpc";
    repo = "grpc";
    rev = "v${version}";
-    sha256 = "02nbmbk1xpibjzvbhi8xpazmwry46ki24vks1sh2p0aqwy4hv6yb";
+    sha256 = "1fxydarl00vbhd9q153qn4ax1yc6xrd8wij6bfy9j8chipw1bgir";
    fetchSubmodules = true;
  };
  patches = [
    # Fix build on armv6l (https://github.com/grpc/grpc/pull/21341)
    (fetchpatch {
-      url = "https://github.com/grpc/grpc/commit/ffb8a278389c8e3403b23a9897b65a7390c34645.patch";
-      sha256 = "1lc12a3gccg9wxqhnwgldlj3zmlm6lxg8dssvvj1x7hf655kw3w3";
+      url = "https://github.com/grpc/grpc/commit/198d221e775cf73455eeb863672e7a6274d217f1.patch";
+      sha256 = "11k35w6ffvl192rgzzj2hzyzjhizdgk7i56zdkx6v60zxnyfn7yq";
    })
  ];

--- a/pkgs/development/libraries/gtk-layer-shell/default.nix
+++ b/pkgs/development/libraries/gtk-layer-shell/default.nix
@ -0,0 +1,40 @@
+{ stdenv
+, fetchFromGitHub
+, meson
+, ninja
+, pkgconfig
+, wayland
+, gtk3
+, gobject-introspection
+}:
+
+stdenv.mkDerivation rec {
+  pname = "gtk-layer-shell";
+  version = "0.1.0";
+
+  src = fetchFromGitHub {
+    owner = "wmww";
+    repo = "gtk-layer-shell";
+    rev = "v${version}";
+    sha256 = "1fwvlbwp5w1zly6mksvlzbx18ikq4bh7pdj9q0k94qlj6x2zdwg8";
+  };
+
+  nativeBuildInputs = [
+    meson ninja pkgconfig
+  ];
+
+  buildInputs = [
+    wayland gtk3 gobject-introspection
+  ];
+
+  mesonFlags = [
+    "-Dout=${placeholder "out"}"
+  ];
+
+  meta = with stdenv.lib; {
+    description = "A library to create panels and other desktop components for Wayland using the Layer Shell protocol";
+    license = licenses.mit;
+    maintainers = with maintainers; [ eonpatapon ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/development/libraries/libdbusmenu-qt/default.nix
+++ b/pkgs/development/libraries/libdbusmenu-qt/default.nix
@ -18,7 +18,7 @@ stdenv.mkDerivation {
  buildInputs = [ qt4 ];
  nativeBuildInputs = [ cmake ];

-  cmakeFlags = "-DWITH_DOC=OFF";
+  cmakeFlags = [ "-DWITH_DOC=OFF" ];

  meta = with stdenv.lib; {
    description = "Provides a Qt implementation of the DBusMenu spec";
--- a/pkgs/development/libraries/libdbusmenu-qt/qt-5.5.nix
+++ b/pkgs/development/libraries/libdbusmenu-qt/qt-5.5.nix
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
  buildInputs = [ qtbase ];
  nativeBuildInputs = [ cmake ];

-  cmakeFlags = "-DWITH_DOC=OFF";
+  cmakeFlags = [ "-DWITH_DOC=OFF" ];

  meta = with stdenv.lib; {
    homepage = https://launchpad.net/libdbusmenu-qt;
--- a/pkgs/development/libraries/libnabo/default.nix
+++ b/pkgs/development/libraries/libnabo/default.nix
@ -15,9 +15,9 @@ stdenv.mkDerivation rec {

  enableParallelBuilding = true;

-  cmakeFlags = "
-    -DEIGEN_INCLUDE_DIR=${eigen}/include/eigen3
-  ";
+  cmakeFlags = [
+    "-DEIGEN_INCLUDE_DIR=${eigen}/include/eigen3"
+  ];

  doCheck = true;
  checkTarget = "test";
--- a/pkgs/development/libraries/libpointmatcher/default.nix
+++ b/pkgs/development/libraries/libpointmatcher/default.nix
@ -16,9 +16,9 @@ stdenv.mkDerivation rec {

  enableParallelBuilding = true;

-  cmakeFlags = "
-    -DEIGEN_INCLUDE_DIR=${eigen}/include/eigen3
-  ";
+  cmakeFlags = [
+    "-DEIGEN_INCLUDE_DIR=${eigen}/include/eigen3"
+  ];

  doCheck = true;
  checkPhase = ''
--- a/pkgs/development/libraries/libtcod/default.nix
+++ b/pkgs/development/libraries/libtcod/default.nix
@ -19,7 +19,7 @@ stdenv.mkDerivation {
    echo 'INSTALL(DIRECTORY include DESTINATION .)' >> CMakeLists.txt
  '';

-  cmakeFlags="-DLIBTCOD_SAMPLES=OFF";
+  cmakeFlags = [ "-DLIBTCOD_SAMPLES=OFF" ];

  buildInputs = [ cmake SDL libGLU libGL upx zlib ];

--- a/pkgs/development/libraries/phonon/backends/gstreamer.nix
+++ b/pkgs/development/libraries/phonon/backends/gstreamer.nix
@ -52,10 +52,6 @@ stdenv.mkDerivation rec {
    qtx11extras
  ];

-  # cleanup: the build system creates (empty) $out/$out/share/icons (double prefix)
-  # if DESTDIR is unset
-  DESTDIR="/";
-
  nativeBuildInputs = [
    cmake
    pkgconfig
--- a/pkgs/development/libraries/tbb/default.nix
+++ b/pkgs/development/libraries/tbb/default.nix
@ -11,10 +11,8 @@ with stdenv.lib; stdenv.mkDerivation rec {
    sha256 = "1a39nflw7b2n51jfp3fdprnkpgzaspzww1dckfvaigflfli9s8rj";
  };

-  makeFlags = concatStringsSep " " (
-    optional (compiler != null) "compiler=${compiler}" ++
-    optional (stdver != null) "stdver=${stdver}"
-  );
+  makeFlags = optional (compiler != null) "compiler=${compiler}"
+    ++ optional (stdver != null) "stdver=${stdver}";

  patches = stdenv.lib.optional stdenv.hostPlatform.isMusl ./glibc-struct-mallinfo.patch;

--- a/pkgs/development/ocaml-modules/conduit/default.nix
+++ b/pkgs/development/ocaml-modules/conduit/default.nix
@ -1,26 +1,26 @@
 { stdenv, fetchFromGitHub, buildDunePackage
-, ppx_sexp_conv
-, astring, ipaddr, uri
+, ppx_sexp_conv, sexplib
+, astring, ipaddr, macaddr, uri,
 }:

 buildDunePackage rec {
  pname = "conduit";
-	version = "1.0.0";
+  version = "1.4.0";

-	src = fetchFromGitHub {
-		owner = "mirage";
-		repo = "ocaml-conduit";
-		rev = "v${version}";
-		sha256 = "1ryigzh7sfif1mly624fpm87aw5h60n5wzdlrvqsf71qcpxc6iiz";
-	};
+  src = fetchFromGitHub {
+    owner = "mirage";
+    repo = "ocaml-conduit";
+    rev = "v${version}";
+    sha256 = "1qzamqcmf9ywz04bkwrv17mz9j6zq2w9h1xmnjvp11pnwrs2xq8l";
+  };

-	buildInputs = [ ppx_sexp_conv ];
-	propagatedBuildInputs = [ astring ipaddr uri ];
+  buildInputs = [ ppx_sexp_conv ];
+  propagatedBuildInputs = [ astring ipaddr macaddr sexplib uri ];

-	meta = {
-		description = "Network connection library for TCP and SSL";
-		license = stdenv.lib.licenses.isc;
-		maintainers = [ stdenv.lib.maintainers.vbgl ];
-		inherit (src.meta) homepage;
-	};
+  meta = {
+    description = "Network connection library for TCP and SSL";
+    license = stdenv.lib.licenses.isc;
+    maintainers = with stdenv.lib.maintainers; [ alexfmpe vbgl ];
+    inherit (src.meta) homepage;
+  };
 }
--- a/pkgs/development/ocaml-modules/ipaddr/default.nix
+++ b/pkgs/development/ocaml-modules/ipaddr/default.nix
@ -1,20 +1,22 @@
-{ stdenv, fetchurl, buildDunePackage, sexplib, ppx_sexp_conv }:
+{ lib, buildDunePackage
+, macaddr, ounit
+}:

 buildDunePackage rec {
  pname = "ipaddr";
-  version = "2.8.0";

-  src = fetchurl {
-    url = "https://github.com/mirage/ocaml-${pname}/archive/${version}.tar.gz";
-    sha256 = "1amb1pbm9ybpxy6190qygpj6nmbzzs2r6vx4xh5r6v89szx9rfxw";
-  };
+  inherit (macaddr) version src;

-  propagatedBuildInputs = [ ppx_sexp_conv sexplib ];
+  buildInputs = [ ounit ];

-  meta = with stdenv.lib; {
+  propagatedBuildInputs = [ macaddr ];
+
+  doCheck = true;
+
+  meta = with lib; {
    homepage = https://github.com/mirage/ocaml-ipaddr;
    description = "A library for manipulation of IP (and MAC) address representations ";
    license = licenses.isc;
-    maintainers = [ maintainers.ericbmerritt ];
+    maintainers = with maintainers; [ alexfmpe ericbmerritt ];
  };
 }
--- a/pkgs/development/ocaml-modules/macaddr/default.nix
+++ b/pkgs/development/ocaml-modules/macaddr/default.nix
@ -0,0 +1,26 @@
+{ lib, fetchurl, buildDunePackage
+, ppx_sexp_conv
+}:
+
+buildDunePackage rec {
+  pname = "macaddr";
+  version = "3.1.0";
+
+  minimumOCamlVersion = "4.04";
+
+  src = fetchurl {
+    url = "https://github.com/mirage/ocaml-ipaddr/archive/v${version}.tar.gz";
+    sha256 = "1hi3v5dzg6h4qb268ch3h6v61gsc8bv21ajhb35z37v5nsdmyzbh";
+  };
+
+  propagatedBuildInputs = [ ppx_sexp_conv ];
+
+  doCheck = false; # ipaddr and macaddr tests are together, which requires mutual dependency
+
+  meta = with lib; {
+    homepage = https://github.com/mirage/ocaml-ipaddr;
+    description = "A library for manipulation of MAC address representations";
+    license = licenses.isc;
+    maintainers = [ maintainers.alexfmpe ];
+  };
+}
--- a/pkgs/development/python-modules/bx-python/default.nix
+++ b/pkgs/development/python-modules/bx-python/default.nix
@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, buildPythonPackage, isPy27, numpy, cython, zlib, six
+, python-lzo, nose }:
+
+buildPythonPackage rec {
+  pname = "bx-python";
+  version = "0.8.6";
+  disabled = isPy27;
+
+  src = fetchFromGitHub {
+    owner = "bxlab";
+    repo = "bx-python";
+    rev = "v${version}";
+    sha256 = "1i40vmn8n83vqcpqj843riv9vp16s753jc4wc90p0cmrnhmzcv13";
+  };
+
+  nativeBuildInputs = [ cython ];
+  buildInputs = [ zlib ];
+  propagatedBuildInputs = [ numpy six python-lzo ];
+  checkInputs = [ nose ];
+
+  postInstall = ''
+    cp -r scripts/* $out/bin
+
+    # This is a small hack; the test suit uses the scripts which need to
+    # be patched. Linking the patched scripts in $out back to the
+    # working directory allows the tests to run
+    rm -rf scripts
+    ln -s $out/bin scripts
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/bxlab/bx-python";
+    description =
+      "Tools for manipulating biological data, particularly multiple sequence alignments";
+    license = licenses.mit;
+    maintainers = [ maintainers.jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/development/python-modules/certipy/default.nix
+++ b/pkgs/development/python-modules/certipy/default.nix
@ -0,0 +1,27 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyopenssl
+}:
+
+buildPythonPackage rec {
+  pname = "certipy";
+  version = "0.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0n980gqpzh0fm58h3i4mi2i10wgj606lscm1r5sk60vbf6vh8mv9";
+  };
+
+  propagatedBuildInputs = [ pyopenssl ];
+  
+  doCheck = false; #no tests were included
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/LLNL/certipy;
+    description = "wrapper for pyOpenSSL";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ isgy ];
+  };
+
+}
--- a/pkgs/development/python-modules/dbf/default.nix
+++ b/pkgs/development/python-modules/dbf/default.nix
@ -9,7 +9,7 @@ buildPythonPackage rec {
      sha256 = "01d71vya2x87f3kl9x0s8xp0n7wixn6ksrd054y7idq3n1mjaxzh";
    };

-    propagatedBuildInputs = [ aenum ] ++ stdenv.lib.optional (pythonOlder "3.4") [ enum34 ];
+    propagatedBuildInputs = [ aenum ] ++ stdenv.lib.optional (pythonOlder "3.4") enum34;

    doCheck = !isPy3k;
    # tests are not yet ported.
--- a/pkgs/development/python-modules/grpcio-tools/default.nix
+++ b/pkgs/development/python-modules/grpcio-tools/default.nix
@ -2,11 +2,11 @@

 buildPythonPackage rec {
  pname = "grpcio-tools";
-  version = "1.25.0";
+  version = "1.26.0";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "988014c714ca654b3b7ca9f4dabfe487b00e023bfdd9eaf1bb0fed82bf8c4255";
+    sha256 = "5580b86cf49936c9c74f0def44d3582a7a1bb720eba8a14805c3a61efa790c70";
  };

  enableParallelBuilding = true;
--- a/pkgs/development/python-modules/hass-nabucasa/default.nix
+++ b/pkgs/development/python-modules/hass-nabucasa/default.nix
@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchFromGitHub, acme, aiohttp, snitun, attrs, pytest-aiohttp, warrant, pytest }:
+{ lib, buildPythonPackage, fetchFromGitHub, fetchpatch, acme, aiohttp, snitun, attrs, pytest-aiohttp, warrant, pytest }:

 buildPythonPackage rec {
  pname = "hass-nabucasa";
@ -11,6 +11,12 @@ buildPythonPackage rec {
    sha256 = "182nh5i3hlj0kqkbynk69md0ddq83w02l8lz4m03d8xbjixzi1k1";
  };

+  # upstreamed in https://github.com/NabuCasa/hass-nabucasa/pull/119
+  postPatch = ''
+    sed -i 's/"acme.*/"acme>=0.40.0,<2.0"/' setup.py
+    cat setup.py
+  '';
+
  propagatedBuildInputs = [ acme aiohttp snitun attrs warrant ];

  checkInputs = [ pytest pytest-aiohttp ];
--- a/pkgs/development/python-modules/hypothesis/default.nix
+++ b/pkgs/development/python-modules/hypothesis/default.nix
@ -22,7 +22,7 @@ buildPythonPackage rec {

  postUnpack = "sourceRoot=$sourceRoot/hypothesis-python";

-  propagatedBuildInputs = [ attrs coverage ] ++ lib.optional (!isPy3k) [ enum34 ];
+  propagatedBuildInputs = [ attrs coverage ] ++ lib.optional (!isPy3k) enum34;

  checkInputs = [ pytest pytest_xdist flaky mock pexpect ];
  inherit doCheck;
--- a/pkgs/development/python-modules/ipykernel/default.nix
+++ b/pkgs/development/python-modules/ipykernel/default.nix
@ -1,4 +1,5 @@
 { lib
+, stdenv
 , buildPythonPackage
 , fetchPypi
 , fetchpatch
@ -7,7 +8,7 @@
 , traitlets
 , tornado
 , pythonOlder
-, pytest
+, pytestCheckHook
 , nose
 }:

@ -21,7 +22,6 @@ buildPythonPackage rec {
    sha256 = "04jx6ihj3zpj4c7acqa14gl37mpdnbgmfm4nvv97xkjc1cz920xm";
  };

-  checkInputs = [ pytest nose ];
  propagatedBuildInputs = [ ipython jupyter_client traitlets tornado ];

  # https://github.com/ipython/ipykernel/pull/377
@ -32,10 +32,17 @@ buildPythonPackage rec {
    })
  ];

-  # For failing tests, see https://github.com/ipython/ipykernel/issues/387
-  checkPhase = ''
-    HOME=$(mktemp -d) pytest ipykernel -k "not (test_sys_path or test_sys_path_profile_dir or test_complete)"
+  checkInputs = [ pytestCheckHook nose ];
+  dontUseSetuptoolsCheck = true;
+  preCheck = ''
+    export HOME=$(mktemp -d)
  '';
+  disabledTests = lib.optionals stdenv.isDarwin [
+    # see https://github.com/NixOS/nixpkgs/issues/76197
+    "test_subprocess_print"
+    "test_subprocess_error"
+    "test_ipython_start_kernel_no_userns"
+  ];

  # Some of the tests use localhost networking.
  __darwinAllowLocalNetworking = true;
--- a/pkgs/development/python-modules/jupyterhub/default.nix
+++ b/pkgs/development/python-modules/jupyterhub/default.nix
@ -16,6 +16,8 @@
 , notebook
 , pythonOlder
 , nodePackages
+, oauthlib
+, certipy
 }:

 let
@ -51,12 +53,12 @@ in

 buildPythonPackage rec {
  pname = "jupyterhub";
-  version = "0.9.4";
+  version = "1.0.0";
  disabled = pythonOlder "3.5";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "7848bbb299536641a59eb1977ec3c7c95d931bace4a2803d7e9b28b9256714da";
+    sha256 = "0zx6gw9yhgki05j21p6x1x2sf5a2mg2c2mx0ii8rl6q4b98ilm1k";
  };

  # Most of this only applies when building from source (e.g. js/css assets are
@ -107,7 +109,7 @@ buildPythonPackage rec {

  propagatedBuildInputs = [
    alembic ipython jinja2 pamela python-oauth2 requests sqlalchemy tornado
-    traitlets prometheus_client async_generator notebook
+    traitlets prometheus_client async_generator notebook certipy oauthlib
  ];

  # Disable tests because they take an excessive amount of time to complete.
--- a/pkgs/development/python-modules/mautrix-appservice/0001-Remove-coding-annotations.patch
+++ b/pkgs/development/python-modules/mautrix-appservice/0001-Remove-coding-annotations.patch
@ -1,53 +0,0 @@
-From 6750cda26821f703b120ba5c925cc696200570d3 Mon Sep 17 00:00:00 2001
-From: Maximilian Bosch <maximilian@mbosch.me>
-Date: Sat, 26 Oct 2019 10:31:02 +0200
-Subject: [PATCH] Remove coding annotations
-
-Those used to be needed for Python <=3.5. With `pluggy` 0.13.0 this breaks
-tests on newer python3 versions.
---
- mautrix_appservice/appservice.py  | 1 -
- mautrix_appservice/errors.py      | 1 -
- mautrix_appservice/intent_api.py  | 1 -
- mautrix_appservice/state_store.py | 1 -
- 4 files changed, 4 deletions(-)
-
-diff --git a/mautrix_appservice/appservice.py b/mautrix_appservice/appservice.py
-index 3a141b1..47e37fe 100644
--- a/mautrix_appservice/appservice.py
-+++ b/mautrix_appservice/appservice.py
-@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
- # Partly based on github.com/Cadair/python-appservice-framework (MIT license)
- from contextlib import contextmanager
- from typing import Optional, Callable, Awaitable, Union
-diff --git a/mautrix_appservice/errors.py b/mautrix_appservice/errors.py
-index 90d040f..702f541 100644
--- a/mautrix_appservice/errors.py
-+++ b/mautrix_appservice/errors.py
-@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
- from typing import Optional
- 
- 
-diff --git a/mautrix_appservice/intent_api.py b/mautrix_appservice/intent_api.py
-index 4021bf8..7236cbb 100644
--- a/mautrix_appservice/intent_api.py
-+++ b/mautrix_appservice/intent_api.py
-@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
- from urllib.parse import quote as urllib_quote
- from time import time
- from json.decoder import JSONDecodeError
-diff --git a/mautrix_appservice/state_store.py b/mautrix_appservice/state_store.py
-index 47bb970..6ebec2a 100644
--- a/mautrix_appservice/state_store.py
-+++ b/mautrix_appservice/state_store.py
-@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
- from typing import Optional
- from abc import ABC, abstractmethod
- import json
-- 
-2.23.0
-
--- a/pkgs/development/python-modules/mautrix-appservice/default.nix
+++ b/pkgs/development/python-modules/mautrix-appservice/default.nix
@ -1,32 +0,0 @@
-{ lib, buildPythonPackage, fetchPypi, aiohttp, future-fstrings, pythonOlder }:
-
-buildPythonPackage rec {
-  pname = "mautrix-appservice";
-  version = "0.3.11";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "60192920cff75afdd096eea3a43276e33ec15f4f00bd04d2d1dda616c84f22a5";
-  };
-
-  patches = lib.optional (!(pythonOlder "3.6")) [
-    ./0001-Remove-coding-annotations.patch
-  ];
-
-  propagatedBuildInputs = [
-    aiohttp
-    future-fstrings
-  ];
-
-  # No tests available
-  doCheck = false;
-
-  disabled = pythonOlder "3.5";
-
-  meta = with lib; {
-    homepage = https://github.com/tulir/mautrix-appservice-python;
-    description = "A Python 3 asyncio-based Matrix application service framework";
-    license = licenses.mit;
-    maintainers = with maintainers; [ nyanloutre ];
-  };
-}
--- a/pkgs/development/python-modules/mautrix/default.nix
+++ b/pkgs/development/python-modules/mautrix/default.nix
@ -0,0 +1,43 @@
+{ lib, buildPythonPackage, fetchPypi, aiohttp, future-fstrings, pythonOlder
+, sqlalchemy, ruamel_yaml, CommonMark, lxml, fetchpatch
+}:
+
+buildPythonPackage rec {
+  pname = "mautrix";
+  version = "0.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03m59d683nr547v5xr80wc3j07das2d2sc3i4bf03dpbkfg0h17w";
+  };
+
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/tulir/mautrix-python/commit/ac46f3bb1bea11d22d8a486cc4821604c844da5e.patch";
+      sha256 = "198g63s0iv8g1w22g4g5hb54y41ws82wraglibz33qhrwsfn8axn";
+    })
+  ];
+
+  propagatedBuildInputs = [
+    aiohttp
+    future-fstrings
+
+    # defined in optional-requirements.txt
+    sqlalchemy
+    ruamel_yaml
+    CommonMark
+    lxml
+  ];
+
+  disabled = pythonOlder "3.5";
+
+  # no tests available
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/tulir/mautrix-python;
+    description = "A Python 3 asyncio Matrix framework.";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ nyanloutre ma27 ];
+  };
+}
--- a/pkgs/development/python-modules/nipype/default.nix
+++ b/pkgs/development/python-modules/nipype/default.nix
@ -79,7 +79,7 @@ buildPythonPackage rec {
    simplejson
    traits
    xvfbwrapper
-  ] ++ stdenv.lib.optional (!isPy3k) [
+  ] ++ stdenv.lib.optionals (!isPy3k) [
    configparser
    futures
    pathlib2 # darwin doesn't receive this transitively, but it is in install_requires
--- a/pkgs/development/python-modules/pyside/shiboken.nix
+++ b/pkgs/development/python-modules/pyside/shiboken.nix
@ -27,7 +27,7 @@ buildPythonPackage rec {
  # gcc6 patch was also sent upstream: https://github.com/pyside/Shiboken/pull/86
  patches = [ ./gcc6.patch ] ++ (lib.optional (isPy35 || isPy36 || isPy37) ./shiboken_py35.patch);

-  cmakeFlags = if isPy3k then "-DUSE_PYTHON3=TRUE" else null;
+  cmakeFlags = lib.optional isPy3k "-DUSE_PYTHON3=TRUE";

  meta = {
    description = "Plugin (front-end) for pyside-generatorrunner, that generates bindings for C++ libraries using CPython source code";
--- a/pkgs/development/python-modules/pytest-benchmark/default.nix
+++ b/pkgs/development/python-modules/pytest-benchmark/default.nix
@ -19,7 +19,7 @@ buildPythonPackage rec {
    sha256 = "1hslzzinpwc1zqhbpllqh3sllmiyk69pcycl7ahr0rz3micgwczj";
  };

-  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optional (pythonOlder "3.4") [ pathlib statistics ];
+  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optionals (pythonOlder "3.4") [ pathlib statistics ];

  meta = {
    description = "Py.test fixture for benchmarking code";
--- a/pkgs/development/python-modules/python-lzf/default.nix
+++ b/pkgs/development/python-modules/python-lzf/default.nix
@ -0,0 +1,18 @@
+{ stdenv, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  version = "0.2.4";
+  pname = "python-lzf";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1l8m6vzwm1m8hn7ldw8j8r2b6r199k8z3q0wnhdyy4p68hahyhni";
+  };
+
+  meta = with stdenv.lib; {
+    description = "liblzf python bindings";
+    homepage = https://github.com/teepark/python-lzf;
+    license = licenses.mit;
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/development/python-modules/python-lzo/default.nix
+++ b/pkgs/development/python-modules/python-lzo/default.nix
@ -0,0 +1,22 @@
+{ lib, fetchPypi, buildPythonPackage, lzo, nose }:
+
+buildPythonPackage rec {
+  pname = "python-lzo";
+  version = "1.12";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0iakqgd51n1cd7r3lpdylm2rgbmd16y74cra9kcapwg84mlf9a4p";
+  };
+
+  buildInputs = [ lzo ];
+  propagatedBuildInputs = [ ];
+  checkInputs = [ nose ];
+
+  meta = with lib; {
+    homepage = "https://github.com/jd-boyd/python-lzo";
+    description = "Python bindings for the LZO data compression library";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.jbedo ];
+  };
+}
--- a/pkgs/development/python-modules/quandl/default.nix
+++ b/pkgs/development/python-modules/quandl/default.nix
@ -40,7 +40,7 @@ buildPythonPackage rec {
    python-dateutil
    six
    more-itertools
-  ] ++ lib.optional (!isPy3k) [
+  ] ++ lib.optionals (!isPy3k) [
    pyOpenSSL
    ndg-httpsclient
    pyasn1
--- a/pkgs/development/python-modules/tifffile/default.nix
+++ b/pkgs/development/python-modules/tifffile/default.nix
@ -23,7 +23,7 @@ buildPythonPackage rec {
  '';

  propagatedBuildInputs = [ numpy ]
-    ++ lib.optional isPy27 [ futures enum34 pathlib ];
+    ++ lib.optionals isPy27 [ futures enum34 pathlib ];

  meta = with lib; {
    description = "Read and write image data from and to TIFF files.";
--- a/pkgs/development/tools/analysis/cppcheck/default.nix
+++ b/pkgs/development/tools/analysis/cppcheck/default.nix
@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
  buildInputs = [ pcre ];
  nativeBuildInputs = [ libxslt docbook_xsl docbook_xml_dtd_45 ];

-  makeFlags = ''PREFIX=$(out) CFGDIR=$(out)/cfg HAVE_RULES=yes'';
+  makeFlags = [ "PREFIX=$(out)" "CFGDIR=$(out)/cfg" "HAVE_RULES=yes" ];

  outputs = [ "out" "man" ];

--- a/pkgs/development/tools/database/ephemeralpg/default.nix
+++ b/pkgs/development/tools/database/ephemeralpg/default.nix
@ -1,10 +1,10 @@
 { stdenv, fetchurl, postgresql, getopt, makeWrapper }:
 stdenv.mkDerivation rec {
  pname = "ephemeralpg";
-  version = "2.5";
+  version = "2.9";
  src = fetchurl {
    url = "http://ephemeralpg.org/code/${pname}-${version}.tar.gz";
-    sha256 = "004fcll7248h73adkqawn9bhkqj9wsxyi3w99x64f7s37r2518wk";
+    sha256 = "1ghp3kya4lxvfwz3c022cx9vqf55jbf9sjw60bxjcb5sszklyc89";
  };
  buildInputs = [ makeWrapper ];
  installPhase = ''
--- a/pkgs/development/tools/misc/hydra/default.nix
+++ b/pkgs/development/tools/misc/hydra/default.nix
@ -27,7 +27,7 @@ let
        CatalystPluginSessionStateCookie
        CatalystPluginSessionStoreFastMmap
        CatalystPluginStackTrace
-        CatalystRuntime
+        CatalystPluginUnicodeEncoding
        CatalystTraitForRequestProxyBase
        CatalystViewDownload
        CatalystViewJSON
@ -51,6 +51,7 @@ let
        LWP
        LWPProtocolHttps
        NetAmazonS3
+        NetPrometheus
        NetStatsd
        PadWalker
        Readonly
@ -58,6 +59,8 @@ let
        SetScalar
        Starman
        SysHostnameLong
+        TermSizeAny
+        TestMore
        TextDiff
        TextTable
        XMLSimple
@ -69,15 +72,15 @@ let
  };
 in stdenv.mkDerivation rec {
  pname = "hydra";
-  version = "2019-08-30";
+  version = "2019-11-13";

  inherit stdenv;

  src = fetchFromGitHub {
    owner = "NixOS";
    repo = pname;
-    rev = "242b8b7a314759ed33f69205d26a1b7c337511e0";
-    sha256 = "167ijcf9qdm10kjvqax3hcvs5mpa4mx2y2i9idwwc6xfvn8fhs84";
+    rev = "20dd0bbe6a90d9066e635ee82e98efec23b17e51";
+    sha256 = "06chiaa7p54zxngmy2q3ps7bbiqpdv9h2rfmprh83qz36xps9rs2";
  };

  buildInputs =
--- a/pkgs/development/tools/misc/universal-ctags/default.nix
+++ b/pkgs/development/tools/misc/universal-ctags/default.nix
@ -33,7 +33,7 @@ stdenv.mkDerivation {

  doCheck = true;

-  checkFlags = "units";
+  checkFlags = [ "units" ];

  meta = with stdenv.lib; {
    description = "A maintained ctags implementation";
--- a/pkgs/development/tools/rdbtools/default.nix
+++ b/pkgs/development/tools/rdbtools/default.nix
@ -0,0 +1,25 @@
+{ stdenv, python }:
+
+with python.pkgs;
+
+buildPythonApplication rec {
+  pname = "rdbtools";
+  version = "0.1.14";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03vdwwkqz8py6c3wfgx402rn8pjjfn44w3gbxzr60lbkx27m63yj";
+  };
+
+  propagatedBuildInputs = [ redis python-lzf ];
+
+  # No tests in published package
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Parse Redis dump.rdb files, Analyze Memory, and Export Data to JSON";
+    homepage = https://github.com/sripathikrishnan/redis-rdb-tools;
+    license = licenses.mit;
+    maintainers = with maintainers; [ offline ];
+  };
+}
--- a/pkgs/development/tools/unityhub/default.nix
+++ b/pkgs/development/tools/unityhub/default.nix
@ -1,12 +1,7 @@
 { stdenv, fetchurl, appimageTools, gsettings-desktop-schemas, gtk3 }:

-let
-  pname = "unityhub";
-  version = "2.2.2";
-in
-
 appimageTools.wrapType2 rec {
-  name = "${pname}-${version}";
+  name = "unityhub";

  extraPkgs = (pkgs: with pkgs; with xorg; [ gtk2 gdk_pixbuf glib libGL libGLU nss nspr
    alsaLib cups gnome2.GConf libcap fontconfig freetype pango
--- a/pkgs/games/frotz/default.nix
+++ b/pkgs/games/frotz/default.nix
@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
    sha256 = "0gjkk4gxzqmxfdirrz2lr0bms6l9fc31vkmlywigkbdlh8wxgypp";
  };

-  makeFlags = ''CC=cc PREFIX=$(out) CURSES=-lncurses'';
+  makeFlags = [ "CC=cc" "PREFIX=$(out)" "CURSES=-lncurses" ];

  buildInputs = [ ncurses ];

--- a/pkgs/games/xbomb/default.nix
+++ b/pkgs/games/xbomb/default.nix
@ -9,10 +9,9 @@ stdenv.mkDerivation rec {

  buildInputs = [ libX11 libXaw ];

-  preBuild = ''
-    substituteInPlace Makefile \
-      --replace /usr/local $out
-  '';
+  makeFlags = [
+    "INSTDIR=${placeholder ''out''}"
+  ];

  meta = with stdenv.lib; {
    homepage = http://www.gedanken.org.uk/software/xbomb/;
--- a/pkgs/os-specific/linux/apparmor/default.nix
+++ b/pkgs/os-specific/linux/apparmor/default.nix
@ -124,8 +124,8 @@ let
    prePatch = prePatchCommon;
    inherit patches;
    postPatch = "cd ./utils";
-    makeFlags = ''LANGS='';
-    installFlags = ''DESTDIR=$(out) BINDIR=$(out)/bin VIM_INSTALL_PATH=$(out)/share PYPREFIX='';
+    makeFlags = [ "LANGS=" ];
+    installFlags = [ "DESTDIR=$(out)" "BINDIR=$(out)/bin" "VIM_INSTALL_PATH=$(out)/share" "PYPREFIX=" ];

    postInstall = ''
      for prog in aa-audit aa-autodep aa-cleanprof aa-complain aa-disable aa-enforce aa-genprof aa-logprof aa-mergeprof aa-status aa-unconfined ; do
@ -162,8 +162,8 @@ let

    prePatch = prePatchCommon;
    postPatch = "cd ./binutils";
-    makeFlags = ''LANGS= USE_SYSTEM=1'';
-    installFlags = ''DESTDIR=$(out) BINDIR=$(out)/bin'';
+    makeFlags = [ "LANGS=" "USE_SYSTEM=1" ];
+    installFlags = [ "DESTDIR=$(out)" "BINDIR=$(out)/bin" ];

    inherit doCheck;

@ -187,8 +187,11 @@ let
    '';
    inherit patches;
    postPatch = "cd ./parser";
-    makeFlags = ''LANGS= USE_SYSTEM=1 INCLUDEDIR=${libapparmor}/include AR=${stdenv.cc.bintools.targetPrefix}ar'';
-    installFlags = ''DESTDIR=$(out) DISTRO=unknown'';
+    makeFlags = [
+      "LANGS=" "USE_SYSTEM=1" "INCLUDEDIR=${libapparmor}/include"
+      "AR=${stdenv.cc.bintools.targetPrefix}ar"
+    ];
+    installFlags = [ "DESTDIR=$(out)" "DISTRO=unknown" ];

    inherit doCheck;

@ -204,8 +207,8 @@ let
    buildInputs = [ libapparmor pam ];

    postPatch = "cd ./changehat/pam_apparmor";
-    makeFlags = ''USE_SYSTEM=1'';
-    installFlags = ''DESTDIR=$(out)'';
+    makeFlags = [ "USE_SYSTEM=1" ];
+    installFlags = [ "DESTDIR=$(out)" ];

    inherit doCheck;

@ -219,7 +222,7 @@ let
    nativeBuildInputs = [ which ];

    postPatch = "cd ./profiles";
-    installFlags = ''DESTDIR=$(out) EXTRAS_DEST=$(out)/share/apparmor/extra-profiles'';
+    installFlags = [ "DESTDIR=$(out)" "EXTRAS_DEST=$(out)/share/apparmor/extra-profiles" ];

    inherit doCheck;

--- a/pkgs/os-specific/linux/firmware/fwupd/default.nix
+++ b/pkgs/os-specific/linux/firmware/fwupd/default.nix
@ -211,6 +211,7 @@ stdenv.mkDerivation rec {
    "--localstatedir=/var"
    "--sysconfdir=/etc"
    "-Dsysconfdir_install=${placeholder "out"}/etc"
+    "--libexecdir=${placeholder "out"}/libexec"
  ] ++ stdenv.lib.optionals (!haveDell) [
    "-Dplugin_dell=false"
    "-Dplugin_synaptics=false"
@ -220,12 +221,6 @@ stdenv.mkDerivation rec {
    "-Dplugin_flashrom=true"
  ];

-  # TODO: We need to be able to override the directory flags from meson setup hook
-  # better – declaring them multiple times might become an error.
-  preConfigure = ''
-    mesonFlagsArray+=("--libexecdir=$out/libexec")
-  '';
-
  postInstall = ''
    moveToOutput share/installed-tests "$installedTests"
    wrapProgram $installedTests/share/installed-tests/fwupd/hardware.py \
--- a/pkgs/os-specific/linux/forktty/default.nix
+++ b/pkgs/os-specific/linux/forktty/default.nix
@ -25,7 +25,7 @@ stdenv.mkDerivation {
    mkdir -p "$out/bin"
    mkdir -p "$out/share/man/man8"
  '';
-  makeFlags='' prefix="''${out}" manprefix="''${out}/share/" '';
+  makeFlags = [ "prefix=$(out)" "manprefix=$(out)/share/" ];
  meta = {
    inherit (s) version;
    description = ''Tool to detach from controlling TTY and attach to another'';
--- a/pkgs/servers/dns/nsd/default.nix
+++ b/pkgs/servers/dns/nsd/default.nix
@ -16,11 +16,11 @@

 stdenv.mkDerivation rec {
  pname = "nsd";
-  version = "4.2.3";
+  version = "4.2.4";

  src = fetchurl {
    url = "https://www.nlnetlabs.nl/downloads/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "1664wpglrwqk627xma10f9qa652vzmf90gsjd8pribyj74xrczc1";
+    sha256 = "0z7j3vwqqj0hh8n5irb2yqwzl45k4sn2wczbq1b1lqv5cxv6vgcy";
  };

  prePatch = ''
--- a/pkgs/servers/mautrix-telegram/default.nix
+++ b/pkgs/servers/mautrix-telegram/default.nix
@ -4,23 +4,19 @@ with python3.pkgs;

 buildPythonPackage rec {
  pname = "mautrix-telegram";
-  version = "0.6.1";
+  version = "0.7.0";
  disabled = pythonOlder "3.6";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "1lsi6x5yr8f9yjxsh1rmcd6wnxr6s6rpr720lg7sq629m42d9p1d";
+    sha256 = "0xzivcn1s5j2nn9p7li9bzr0h225bnli4fr3yrh8v7npx2ymg1r3";
  };

  patches = [
+    # fix tests
    (fetchpatch {
-      url = https://github.com/tulir/mautrix-telegram/commit/be6d395ed66d86ec7f13a262f9ae37731987019c.patch;
-      sha256 = "1q69ip17r45yhyrxr0pj8bvqj2grw2l39wak8pi5pm7qrxra93j2";
-    })
-    # bump dependencies, remove on next bump
-    (fetchpatch {
-      url = "https://github.com/tulir/mautrix-telegram/commit/cdee0df5ab9e04d6831e34590959496061c6621c.patch";
-      sha256 = "0sbfaais0jgg305dcjg9hn8b975ymdivvhmlzsxm1nm2ksa4c0v1";
+      url = "https://github.com/tulir/mautrix-telegram/commit/fe52f0ad106122f08af72e356c4c62bb8875b453.patch";
+      sha256 = "0r7j7q78brqqx0rkchld328k00yq0ykdk7syvwpihqzj3gchacb7";
    })
  ];

@ -33,7 +29,7 @@ buildPythonPackage rec {
  propagatedBuildInputs = [
    Mako
    aiohttp
-    mautrix-appservice
+    mautrix
    sqlalchemy
    CommonMark
    ruamel_yaml
@ -69,6 +65,7 @@ buildPythonPackage rec {
    homepage = https://github.com/tulir/mautrix-telegram;
    description = "A Matrix-Telegram hybrid puppeting/relaybot bridge";
    license = licenses.agpl3Plus;
+    platforms = platforms.linux;
    maintainers = with maintainers; [ nyanloutre ma27 ];
  };
 }
--- a/pkgs/servers/metabase/default.nix
+++ b/pkgs/servers/metabase/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  pname = "metabase";
-  version = "0.33.6";
+  version = "0.33.7.1";

  src = fetchurl {
    url = "http://downloads.metabase.com/v${version}/metabase.jar";
-    sha256 = "1q5d323fzfvlc12v1g0mahlcz2sjii3k7cc6qg8q4q8yl0vg5c9k";
+    sha256 = "1rx9v0vcrpsjsclap4x9ic9jwhyd24v1n1v8si18blzn3iyr8c36";
  };

  nativeBuildInputs = [ makeWrapper ];
--- a/pkgs/servers/monitoring/plugins/default.nix
+++ b/pkgs/servers/monitoring/plugins/default.nix
@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, fetchpatch, autoreconfHook
+{ stdenv, fetchFromGitHub, fetchpatch, autoreconfHook, runCommand
 , coreutils, gnugrep, gnused, lm_sensors, net-snmp, openssh, openssl, perl
 , dnsutils, libdbi, libmysqlclient, zlib, openldap, procps
 , runtimeShell }:
@ -44,6 +44,11 @@ in stdenv.mkDerivation {
    configureFlagsArray=(
      --with-ping-command='/run/wrappers/bin/ping -4 -n -U -w %d -c %d %s'
      --with-ping6-command='/run/wrappers/bin/ping -6 -n -U -w %d -c %d %s'
+      --with-sudo-command='/run/wrappers/bin/sudo'
+      --with-mailq-command='${runCommand "mailq-wrapper" {preferLocalBuild=true;} ''
+        mkdir -p $out/bin
+        ln -s /run/wrappers/bin/sendmail $out/bin/mailq
+        ''}/bin/mailq'
    )
  '';

--- a/pkgs/tools/admin/certbot/0001-Don-t-use-distutils.StrictVersion-that-cannot-handle.patch
+++ b/pkgs/tools/admin/certbot/0001-Don-t-use-distutils.StrictVersion-that-cannot-handle.patch
@ -1,6 +1,6 @@
-From 411b8a413baf39e9b967949b17a992e81a11abfe Mon Sep 17 00:00:00 2001
+From 0de195de31dc311976af52a7c2b547bc23af2691 Mon Sep 17 00:00:00 2001
 From: Frederik Rietdijk <fridh@fridh.nl>
-Date: Tue, 29 Oct 2019 14:08:07 +0100
+Date: Sat, 14 Dec 2019 19:27:14 +0100
 Subject: [PATCH] Don't use distutils.StrictVersion that cannot handle certain
 versions

@ -18,13 +18,13 @@ line 137, in parse
 ValueError: invalid version number '41.4.0.post20191022'
 ```
 ---
- setup.py | 15 +--------------
+ certbot/setup.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

-diff --git a/setup.py b/setup.py
-index 1f4838c90..831528d77 100644
--- a/setup.py
-+++ b/setup.py
+diff --git a/certbot/setup.py b/certbot/setup.py
+index c1bf914..7456bf2 100644
+--- a/certbot/setup.py
+++ b/certbot/setup.py
@@ -3,7 +3,6 @@ import os
 import re
 import sys
@ -40,7 +40,7 @@ index 1f4838c90..831528d77 100644
 -# However environment markers are supported only with setuptools >= 36.2.
 -# So this dependency is not added for old Linux distributions with old setuptools,
 -# in order to allow these systems to build certbot from sources.
- pywin32_req = 'pywin32>=224'
+ pywin32_req = 'pywin32>=227'  # do not forget to edit pywin32 dependency accordingly in windows-installer/construct.py
 -if StrictVersion(setuptools_version) >= StrictVersion('36.2'):
 -    install_requires.append(pywin32_req + " ; sys_platform == 'win32'")
 -elif 'bdist_wheel' in sys.argv[1:]:
@ -56,5 +56,5 @@ index 1f4838c90..831528d77 100644
 dev_extras = [
     'astroid==1.6.5',
 -- 
-2.23.0
+2.24.1

--- a/pkgs/tools/admin/certbot/0001-pebble_artifacts-hardcode-pebble-location.patch
+++ b/pkgs/tools/admin/certbot/0001-pebble_artifacts-hardcode-pebble-location.patch
@ -1,24 +0,0 @@
-From 8ddf2697508eca514a0dde4646ad14ac3ba34b2a Mon Sep 17 00:00:00 2001
-From: Florian Klink <flokli@flokli.de>
-Date: Fri, 18 Oct 2019 16:06:50 +0200
-Subject: [PATCH] pebble_artifacts: hardcode pebble location
-
---
- certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py b/certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py
-index 2b1557928..d2603c51a 100644
--- a/certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py
-+++ b/certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py
-@@ -22,6 +22,7 @@ def fetch(workspace):
- 
- 
- def _fetch_asset(asset, suffix):
-+    return "@pebble@"
-     asset_path = os.path.join(ASSETS_PATH, '{0}_{1}_{2}'.format(asset, PEBBLE_VERSION, suffix))
-     if not os.path.exists(asset_path):
-         asset_url = ('https://github.com/letsencrypt/pebble/releases/download/{0}/{1}_{2}'
-- 
-2.23.0
-
--- a/pkgs/tools/admin/certbot/default.nix
+++ b/pkgs/tools/admin/certbot/default.nix
@ -1,19 +1,18 @@
-{ stdenv, python37Packages, fetchFromGitHub, fetchurl, dialog, autoPatchelfHook, nginx, pebble }:
+{ stdenv, python37Packages, fetchFromGitHub, fetchurl, dialog, autoPatchelfHook }:


 python37Packages.buildPythonApplication rec {
  pname = "certbot";
-  version = "0.39.0";
+  version = "1.0.0";

  src = fetchFromGitHub {
    owner = pname;
    repo = pname;
    rev = "v${version}";
-    sha256 = "1s32xg2ljz7ci78wc8rqkjvgrz7vprb7fkznrlf9a4blm55pp54c";
+    sha256 = "180x7gcpfbrzw8k654s7b5nxdy2yg61lq513dykyn3wz4gssw465";
  };

  patches = [
-    ./0001-pebble_artifacts-hardcode-pebble-location.patch
    ./0001-Don-t-use-distutils.StrictVersion-that-cannot-handle.patch
  ];

@ -43,9 +42,8 @@ python37Packages.buildPythonApplication rec {
  ];

  postPatch = ''
-    substituteInPlace certbot/notify.py --replace "/usr/sbin/sendmail" "/run/wrappers/bin/sendmail"
-    substituteInPlace certbot/util.py --replace "sw_vers" "/usr/bin/sw_vers"
-    substituteInPlace certbot-ci/certbot_integration_tests/utils/pebble_artifacts.py --replace "@pebble@" "${pebble}/bin/pebble"
+    cd certbot
+    substituteInPlace certbot/_internal/notify.py --replace "/usr/sbin/sendmail" "/run/wrappers/bin/sendmail"
  '';

  postInstall = ''
@ -55,15 +53,7 @@ python37Packages.buildPythonApplication rec {
    done
  '';

-  # tests currently time out, because they're trying to do network access
-  # Upstream issue: https://github.com/certbot/certbot/issues/7450
-  doCheck = false;
-
-  checkPhase = ''
-    PATH="$out/bin:${nginx}/bin:$PATH" pytest certbot-ci/certbot_integration_tests
-  '';
-
-  dontUseSetuptoolsCheck = true;
+  doCheck = true;

  meta = with stdenv.lib; {
    homepage = src.meta.homepage;
--- a/pkgs/tools/admin/simp_le/default.nix
+++ b/pkgs/tools/admin/simp_le/default.nix
@ -2,11 +2,11 @@

 python3Packages.buildPythonApplication rec {
  pname = "simp_le-client";
-  version = "0.16.0";
+  version = "0.17.0";

  src = python3Packages.fetchPypi {
    inherit pname version;
-    sha256 = "17azqlb1xsnh9p0m75apb19j7pramgj00cf5k6fwzz2zqz0x0hpp";
+    sha256 = "0m1jynar4calaffp2zdxr5yy9vnhw2qf2hsfxwzfwf8fqb5h7bjb";
  };

  postPatch = ''
--- a/pkgs/tools/filesystems/fatresize/default.nix
+++ b/pkgs/tools/filesystems/fatresize/default.nix
@ -25,9 +25,7 @@ stdenv.mkDerivation rec {

  # Filesystem resize functions were reintroduced in parted 3.1 due to no other available free alternatives
  # but in a sepparate library -> libparted-fs-resize --- that's why the added LDFLAG
-  makeFlags = ''
-    LDFLAGS=-lparted-fs-resize
-  '';
+  makeFlags = [ "LDFLAGS=-lparted-fs-resize" ];

  propagatedBuildInputs = [ parted utillinux ];

--- a/pkgs/tools/inputmethods/fcitx/unwrapped.nix
+++ b/pkgs/tools/inputmethods/fcitx/unwrapped.nix
@ -75,20 +75,20 @@ stdenv.mkDerivation rec {
    libxkbcommon libxml2 dbus cairo gtk2 gtk3 pango qt4 libuuid
  ];

-  cmakeFlags = ''
-    -DENABLE_QT_IM_MODULE=ON
-    -DENABLE_GTK2_IM_MODULE=ON
-    -DENABLE_GTK3_IM_MODULE=ON
-    -DENABLE_GIR=OFF
-    -DENABLE_OPENCC=OFF
-    -DENABLE_PRESAGE=OFF
-    -DENABLE_XDGAUTOSTART=OFF
-    -DENABLE_PINYIN=${if withPinyin then "ON" else "OFF"}
-    -DENABLE_TABLE=ON
-    -DENABLE_SPELL=ON
-    -DENABLE_QT_GUI=ON
-    -DXKB_RULES_XML_FILE='${xkeyboard_config}/share/X11/xkb/rules/evdev.xml'
-    '';
+  cmakeFlags = [
+    "-DENABLE_QT_IM_MODULE=ON"
+    "-DENABLE_GTK2_IM_MODULE=ON"
+    "-DENABLE_GTK3_IM_MODULE=ON"
+    "-DENABLE_GIR=OFF"
+    "-DENABLE_OPENCC=OFF"
+    "-DENABLE_PRESAGE=OFF"
+    "-DENABLE_XDGAUTOSTART=OFF"
+    "-DENABLE_PINYIN=${if withPinyin then "ON" else "OFF"}"
+    "-DENABLE_TABLE=ON"
+    "-DENABLE_SPELL=ON"
+    "-DENABLE_QT_GUI=ON"
+    "-DXKB_RULES_XML_FILE='${xkeyboard_config}/share/X11/xkb/rules/evdev.xml'"
+  ];

  meta = with stdenv.lib; {
    homepage    = https://github.com/fcitx/fcitx;
--- a/pkgs/tools/misc/cpulimit/default.nix
+++ b/pkgs/tools/misc/cpulimit/default.nix
@ -9,12 +9,13 @@ stdenv.mkDerivation rec {
    sha256 = "0xf0r6zxaqan1drz61nqf95p2pkiiihpvrjhrr9dx9j3vswyx31g";
  };

-  buildFlags = with stdenv;
+  buildFlags = with stdenv; [ (
    if isDarwin then "osx"
    else if isFreeBSD then "freebsd"
-    else "cpulimit";
+    else "cpulimit"
+  ) ];

-  installFlags = "PREFIX=$(out)";
+  installFlags = [ "PREFIX=$(out)" ];

  meta = with stdenv.lib; {
    homepage = http://limitcpu.sourceforge.net/;
--- a/pkgs/tools/misc/ent/default.nix
+++ b/pkgs/tools/misc/ent/default.nix
@ -14,7 +14,7 @@ stdenv.mkDerivation {

  buildInputs = [ unzip ];

-  buildFlags = if stdenv.cc.isClang then [ "CC=clang" ] else null;
+  buildFlags = stdenv.lib.optional stdenv.cc.isClang "CC=clang";

  installPhase = ''
    mkdir -p $out/bin
--- a/pkgs/tools/misc/starship/default.nix
+++ b/pkgs/tools/misc/starship/default.nix
@ -3,13 +3,13 @@

 rustPlatform.buildRustPackage rec {
  pname = "starship";
-  version = "0.32.1";
+  version = "0.32.2";

  src = fetchFromGitHub {
    owner = "starship";
    repo = pname;
    rev = "v${version}";
-    sha256 = "047nvi231hzwjfci13x8lhszmaccb94mn5lvnyq24zb0im8br6d3";
+    sha256 = "1yn2xr7142xnrsglrabxzgv16hp16i5d2dybazpzxflfnn52c0am";
  };

  buildInputs = stdenv.lib.optionals stdenv.isDarwin [ libiconv Security ];
@ -19,7 +19,7 @@ rustPlatform.buildRustPackage rec {
      --replace "/bin/echo" "echo"
  '';

-  cargoSha256 = "0r1kbv6f5v95wnshxj1wkqvp1adyrivzlr606c6blhl9z9j7m3d7";
+  cargoSha256 = "0i3jrk7qyyzhk4855z0vsdf64n14xqqg9by0dr62jz83hdx89x1w";
  checkPhase = "cargo test -- --skip directory::home_directory --skip directory::directory_in_root";

  meta = with stdenv.lib; {
--- a/pkgs/tools/misc/trash-cli/default.nix
+++ b/pkgs/tools/misc/trash-cli/default.nix
@ -26,6 +26,12 @@ python3Packages.buildPythonApplication rec {
      url = "https://github.com/andreafrancia/trash-cli/commit/a21b80d1e69783bb09376c3f60dd2f2a10578805.patch";
      sha256 = "0w49rjh433sjfc2cl5a9wlbr6kcn9f1qg905qsyv7ay3ar75wvyp";
    })
+
+    # Fix listing trashed files over mount points, see https://github.com/andreafrancia/trash-cli/issues/95
+    (fetchpatch {
+      url = "https://github.com/andreafrancia/trash-cli/commit/436dfddb4c2932ba3ff696e4732750b7bdc58461.patch";
+      sha256 = "02pkcz7nj67jbnqpw1943nrv95m8xyjvab4j62fa64r73fagm8m4";
+    })
  ];

  checkInputs = with python3Packages; [
--- a/pkgs/tools/misc/uutils-coreutils/default.nix
+++ b/pkgs/tools/misc/uutils-coreutils/default.nix
@ -1,4 +1,6 @@
-{ stdenv, fetchFromGitHub, rustPlatform, cargo, cmake, sphinx, lib, prefix ? "uutils-" }:
+{ stdenv, fetchFromGitHub, rustPlatform, cargo, cmake, sphinx, lib, prefix ? "uutils-"
+, Security
+}:

 rustPlatform.buildRustPackage {
  name = "uutils-coreutils-2019-05-03";
@ -19,13 +21,13 @@ rustPlatform.buildRustPackage {
    ++ lib.optional (prefix != null) [ "PROG_PREFIX=${prefix}" ];

  nativeBuildInputs = [ cmake ];
-  buildInputs = [ cargo sphinx ];
+  buildInputs = [ cargo sphinx ] ++ lib.optional stdenv.isDarwin Security;

  # empty {build,install}Phase to use defaults of `stdenv.mkDerivation` rather than rust defaults
  buildPhase = "";
  installPhase = "";

-  meta = with stdenv.lib; {
+  meta = with lib; {
    description = "Cross-platform Rust rewrite of the GNU coreutils";
    longDescription = ''
      uutils is an attempt at writing universal (as in cross-platform)
--- a/pkgs/tools/networking/clash/default.nix
+++ b/pkgs/tools/networking/clash/default.nix
@ -0,0 +1,23 @@
+{ stdenv, fetchFromGitHub, buildGoModule }:
+
+buildGoModule rec {
+  pname = "clash";
+  version = "0.16.0";
+
+  src = fetchFromGitHub {
+    owner = "Dreamacro";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1k6afpazggpd7cabbw6ldv77bjj43083d5diy2w0iq5nw69gmwd3";
+  };
+
+  modSha256 = "1fx53df67mq7p3ampr96x8hd99v2991alb16v8iq36f032raa32f";
+
+  meta = with stdenv.lib; {
+    description = "A rule-based tunnel in Go";
+    homepage = "https://github.com/Dreamacro/clash";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ contrun ];
+    platforms = platforms.all;
+  };
+}
--- a/pkgs/tools/networking/miniupnpc/default.nix
+++ b/pkgs/tools/networking/miniupnpc/default.nix
@ -11,14 +11,13 @@ let
        inherit sha256;
      };

-      nativeBuildInputs = [] ++
-        stdenv.lib.optionals stdenv.isDarwin [ which cctools ];
+      nativeBuildInputs = stdenv.lib.optionals stdenv.isDarwin [ which cctools ];

      patches = stdenv.lib.optional stdenv.isFreeBSD ./freebsd.patch;

      doCheck = !stdenv.isFreeBSD;

-      makeFlags = "PREFIX=$(out) INSTALLPREFIX=$(out)";
+      makeFlags = [ "PREFIX=$(out)" "INSTALLPREFIX=$(out)" ];

      meta = with stdenv.lib; {
        homepage = http://miniupnp.free.fr/;
--- a/pkgs/tools/networking/uwimap/default.nix
+++ b/pkgs/tools/networking/uwimap/default.nix
@ -8,12 +8,12 @@ stdenv.mkDerivation ({
    sha256 = "0a2a00hbakh0640r2wdpnwr8789z59wnk7rfsihh3j0vbhmmmqak";
  };

-  makeFlags = if stdenv.isDarwin
+  makeFlags = [ (if stdenv.isDarwin
    then "osx"
-    else "lnp" # Linux with PAM modules;
+    else "lnp") ]  # Linux with PAM modules;
    # -fPIC is required to compile php with imap on x86_64 systems
-    + stdenv.lib.optionalString stdenv.isx86_64 " EXTRACFLAGS=-fPIC"
-    + stdenv.lib.optionalString (stdenv.buildPlatform != stdenv.hostPlatform) " CC=${stdenv.hostPlatform.config}-gcc RANLIB=${stdenv.hostPlatform.config}-ranlib";
+    ++ stdenv.lib.optional stdenv.isx86_64 "EXTRACFLAGS=-fPIC"
+    ++ stdenv.lib.optionals (stdenv.buildPlatform != stdenv.hostPlatform) [ "CC=${stdenv.hostPlatform.config}-gcc" "RANLIB=${stdenv.hostPlatform.config}-ranlib" ];

  hardeningDisable = [ "format" ];

--- a/pkgs/tools/package-management/librepo/default.nix
+++ b/pkgs/tools/package-management/librepo/default.nix
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {

  nativeBuildInputs = [ cmake pkgconfig ];

-  cmakeFlags="-DPYTHON_DESIRED=${stdenv.lib.substring 0 1 python.pythonVersion}";
+  cmakeFlags = ["-DPYTHON_DESIRED=${stdenv.lib.substring 0 1 python.pythonVersion}" ];

  buildInputs = [ python libxml2 glib openssl curl check gpgme ];

--- a/pkgs/tools/system/ipmitool/default.nix
+++ b/pkgs/tools/system/ipmitool/default.nix
@ -25,7 +25,7 @@ stdenv.mkDerivation {
      ${if static then "LDFLAGS=-static --enable-static --disable-shared" else "--enable-shared"}
    )
  '';
-  makeFlags = if static then "AM_LDFLAGS=-all-static" else "";
+  makeFlags = stdenv.lib.optional static "AM_LDFLAGS=-all-static";
  dontDisableStatic = static;

  meta = with lib; {
--- a/pkgs/tools/text/smu/default.nix
+++ b/pkgs/tools/text/smu/default.nix
@ -14,7 +14,9 @@ stdenv.mkDerivation rec {
  # _FORTIFY_SOURCE requires compiling with optimization (-O)
  NIX_CFLAGS_COMPILE = "-O";

-  makeFlags = [ "DESTDIR=$(out)" "PREFIX=" ];
+  makeFlags = [
+    "PREFIX=${placeholder "out"}"
+  ];

  meta = with lib; {
    description = "simple markup - markdown like syntax";
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -1396,6 +1396,8 @@ in

  clac = callPackage ../tools/misc/clac {};

+  clash = callPackage ../tools/networking/clash { };
+
  clasp = callPackage ../tools/misc/clasp { };

  cli53 = callPackage ../tools/admin/cli53 { };
@ -2957,6 +2959,7 @@ in

  uutils-coreutils = callPackage ../tools/misc/uutils-coreutils {
    inherit (pythonPackages) sphinx;
+    inherit (darwin.apple_sdk.frameworks) Security;
  };

  volctl = callPackage ../tools/audio/volctl { };
@ -5978,6 +5981,8 @@ in

  rc = callPackage ../shells/rc { };

+  rdbtools = callPackage ../development/tools/rdbtools { python = python3; };
+
  rdma-core = callPackage ../os-specific/linux/rdma-core { };

  react-native-debugger = callPackage ../development/tools/react-native-debugger { };
@ -11778,6 +11783,8 @@ in

  gtkspellmm = callPackage ../development/libraries/gtkspellmm { };

+  gtk-layer-shell = callPackage ../development/libraries/gtk-layer-shell { };
+
  gts = callPackage ../development/libraries/gts { };

  gumbo = callPackage ../development/libraries/gumbo { };
@ -23676,10 +23683,16 @@ in

  kssd = callPackage ../applications/science/biology/kssd { };

+  last = callPackage ../applications/science/biology/last { };
+
  macse = callPackage ../applications/science/biology/macse { };

  migrate = callPackage ../applications/science/biology/migrate { };

+  minia = callPackage ../applications/science/biology/minia {
+    boost = boost159;
+  };
+
  mirtk = callPackage ../development/libraries/science/biology/mirtk { };

  muscle = callPackage ../applications/science/biology/muscle { };
@ -23766,6 +23779,8 @@ in

  svaba = callPackage ../applications/science/biology/svaba { };

+  tebreak = callPackage ../applications/science/biology/tebreak { };
+
  trimal = callPackage ../applications/science/biology/trimal { };

  truvari = callPackage ../applications/science/biology/truvari { };
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@ -506,6 +506,8 @@ let
      lwt = ocaml_lwt;
    };

+    macaddr = callPackage ../development/ocaml-modules/macaddr { };
+
    macaque = callPackage ../development/ocaml-modules/macaque { };

    magic-mime = callPackage ../development/ocaml-modules/magic-mime { };
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@ -1702,6 +1702,10 @@ in {

  bumps = callPackage ../development/python-modules/bumps {};

+  bx-python = callPackage ../development/python-modules/bx-python {
+    inherit (pkgs) zlib;
+  };
+
  cached-property = callPackage ../development/python-modules/cached-property { };

  caffe = toPythonModule (pkgs.caffe.override {
@ -1940,6 +1944,8 @@ in {

  certifi = callPackage ../development/python-modules/certifi { };

+  certipy = callPackage ../development/python-modules/certipy {};
+ 
  characteristic = callPackage ../development/python-modules/characteristic { };

  chart-studio = callPackage ../development/python-modules/chart-studio { };
@ -2914,6 +2920,8 @@ in {
    inherit (pkgs) meson pkgconfig;
  };

+  python-lzf = callPackage ../development/python-modules/python-lzf { };
+
  pyramid = callPackage ../development/python-modules/pyramid { };

  pyramid_beaker = callPackage ../development/python-modules/pyramid_beaker { };
@ -2940,6 +2948,10 @@ in {

  python-ctags3 = callPackage ../development/python-modules/python-ctags3 { };

+  python-lzo = callPackage ../development/python-modules/python-lzo {
+    inherit (pkgs) lzo;
+  };
+
  junos-eznc = callPackage ../development/python-modules/junos-eznc {};

  raven = callPackage ../development/python-modules/raven { };
@ -3970,7 +3982,8 @@ in {

  matrix-nio = callPackage ../development/python-modules/matrix-nio { };

-  mautrix-appservice = callPackage ../development/python-modules/mautrix-appservice { };
+  mautrix = callPackage ../development/python-modules/mautrix { };
+  mautrix-appservice = self.mautrix; # alias 2019-12-28

  maya = callPackage ../development/python-modules/maya { };