NixOS · Jan 8, 2020 · May 20, 2020 · May 24, 2020 · May 24, 2020 · May 24, 2020
diff --git a/nixos/modules/services/x11/desktop-managers/enlightenment.nix b/nixos/modules/services/x11/desktop-managers/enlightenment.nix
@@ -32,15 +32,14 @@ in
 
   config = mkIf cfg.enable {
 
-    environment.systemPackages = [
-      e.efl e.enlightenment
-      e.terminology e.econnman
-      pkgs.xorg.xauth # used by kdesu
-      pkgs.gtk2 # To get GTK's themes.
-      pkgs.tango-icon-theme
-
-      pkgs.gnome-icon-theme
-      pkgs.xorg.xcursorthemes
+    environment.systemPackages = with pkgs; [
+      enlightenment.econnman
+      enlightenment.efl
+      enlightenment.enlightenment
+      enlightenment.ephoto
+      enlightenment.rage
+      enlightenment.terminology
+      xorg.xcursorthemes
     ];
 
     environment.pathsToLink = [
@@ -50,24 +49,26 @@ in
       "/share/locale"
     ];
 
-    services.xserver.desktopManager.session = [
-    { name = "Enlightenment";
-      start = ''
-        export XDG_MENU_PREFIX=e-
+    services.xserver.displayManager.sessionPackages = [ pkgs.enlightenment.enlightenment ];
 
+    services.xserver.displayManager.sessionCommands = ''
+      if test "$XDG_CURRENT_DESKTOP" = "Enlightenment"; then
         export GST_PLUGIN_PATH="${GST_PLUGIN_PATH}"
 
         # make available for D-BUS user services
         #export XDG_DATA_DIRS=$XDG_DATA_DIRS''${XDG_DATA_DIRS:+:}:${config.system.path}/share:${e.efl}/share
 
         # Update user dirs as described in http://freedesktop.org/wiki/Software/xdg-user-dirs/
         ${pkgs.xdg-user-dirs}/bin/xdg-user-dirs-update
-
-        exec ${e.enlightenment}/bin/enlightenment_start
-      '';
-    }];
-
-    security.wrappers = (import "${e.enlightenment}/e-wrappers.nix").security.wrappers;
+      fi
+    '';
+
+    # Wrappers for programs installed by enlightenment that should be setuid
+    security.wrappers = {
+      enlightenment_ckpasswd.source = "${pkgs.enlightenment.enlightenment}/lib/enlightenment/utils/enlightenment_ckpasswd";
+      enlightenment_sys.source = "${pkgs.enlightenment.enlightenment}/lib/enlightenment/utils/enlightenment_sys";
+      enlightenment_system.source = "${pkgs.enlightenment.enlightenment}/lib/enlightenment/utils/enlightenment_system";
+    };
 
     environment.etc."X11/xkb".source = xcfg.xkbDir;
 

diff --git a/nixos/modules/services/x11/desktop-managers/lumina.nix b/nixos/modules/services/x11/desktop-managers/lumina.nix
@@ -23,12 +23,9 @@ in
 
   config = mkIf cfg.enable {
 
-    services.xserver.desktopManager.session = singleton {
-      name = "lumina";
-      start = ''
-        exec ${pkgs.lumina.lumina}/bin/start-lumina-desktop
-      '';
-    };
+    services.xserver.displayManager.sessionPackages = [
+      pkgs.lumina.lumina
+    ];
 
     environment.systemPackages =
       pkgs.lumina.preRequisitePackages ++

diff --git a/nixos/tests/enlightenment.nix b/nixos/tests/enlightenment.nix
@@ -41,28 +41,24 @@ import ./make-test-python.nix ({ pkgs, ...} :
 
     with subtest("First time wizard"):
         machine.wait_for_text("Default")  # Language
-        machine.succeed("xdotool mousemove 512 185 click 1")  # Default Language
         machine.screenshot("wizard1")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
-
-        machine.wait_for_text("English")  # Keyboard (default)
         machine.screenshot("wizard2")
-        machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
-        machine.wait_for_text("Standard")  # Profile (default)
+        machine.wait_for_text("English")  # Keyboard (default)
         machine.screenshot("wizard3")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
-        machine.wait_for_text("Title")  # Sizing (default)
+        machine.wait_for_text("Standard")  # Profile (default)
         machine.screenshot("wizard4")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
-        machine.wait_for_text("clicked")  # Windows Phocus
-        machine.succeed("xdotool mousemove 512 370 click 1")  # Click
+        machine.wait_for_text("Title")  # Sizing (default)
         machine.screenshot("wizard5")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
-        machine.wait_for_text("bindings")  # Mouse Modifiers (default)
+        machine.wait_for_text("clicked")  # Windows Focus
+        machine.succeed("xdotool mousemove 512 370 click 1")  # Click
         machine.screenshot("wizard6")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
@@ -74,7 +70,7 @@ import ./make-test-python.nix ({ pkgs, ...} :
         machine.screenshot("wizard8")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 
-        machine.wait_for_text("Compositing")  # Compositing (default)
+        machine.wait_for_text("OpenGL")  # Compositing (default)
         machine.screenshot("wizard9")
         machine.succeed("xdotool mousemove 512 740 click 1")  # Next
 

diff --git a/pkgs/applications/editors/lite/default.nix b/pkgs/applications/editors/lite/default.nix
@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   pname = "lite";
-  version = "1.03";
+  version = "1.05";
 
   src = fetchFromGitHub {
     owner = "rxi";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1h8z4fav5ns9sm92axs3k9v6jgkqq0vg9mixza14949blr426mlj";
+    sha256 = "0xh29ddl5h92n1c4nlh4kx9mchwkzn4r3l16kklix3a1jm1c878a";
   };
 
   nativeBuildInputs = [ makeWrapper pkg-config ];

diff --git a/pkgs/applications/science/biology/bppsuite/default.nix b/pkgs/applications/science/biology/bppsuite/default.nix
@@ -0,0 +1,21 @@
+{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq, bpp-phyl, bpp-popgen }:
+
+stdenv.mkDerivation rec {
+  pname = "bppsuite";
+
+  inherit (bpp-core) version;
+
+  src = fetchFromGitHub {
+    owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ bpp-core bpp-seq bpp-phyl bpp-popgen ];
+
+  meta = bpp-core.meta // {
+    changelog = "https://github.com/BioPP/bppsuite/blob/master/ChangeLog";
+  };
+}
diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, lib, fetchurl, wrapQtAppsHook, qmake }:
+
+stdenv.mkDerivation rec {
+  pname = "xflr5";
+  version = "6.47";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/xflr5/${pname}_v${version}_src.tar.gz";
+    sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav";
+  };
+
+  enableParallelBuilding = true;
+
+  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+
+  meta = with stdenv.lib; {
+    description = "An analysis tool for airfoils, wings and planes";
+    homepage = https://sourceforge.net/projects/xflr5/;
+    license = licenses.gpl3;
+    maintainers = [ maintainers.esclear ];
+    platforms = platforms.linux;
+  };
+}
diff --git a/pkgs/applications/virtualization/conmon/default.nix b/pkgs/applications/virtualization/conmon/default.nix
@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "conmon";
-  version = "2.0.16";
+  version = "2.0.17";
 
   src = fetchFromGitHub {
     owner = "containers";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0z0hds95mjxm703ig2aisghvpd2l3wn6m72jnnlv8jnz2iq2nc4g";
+    sha256 = "01bicv0qr4aiahkw9cp6igk3jv1fqkbxmsp80nfvq6rxx873v0q7";
   };
 
   nativeBuildInputs = [ pkg-config ];

diff --git a/pkgs/desktops/deepin/deepin-icon-theme/default.nix b/pkgs/desktops/deepin/deepin-icon-theme/default.nix
@@ -3,19 +3,19 @@
 , gtk3
 , xcursorgen
 , papirus-icon-theme
-, deepin
 , hicolor-icon-theme
+, deepin
 }:
 
 stdenv.mkDerivation rec {
   pname = "deepin-icon-theme";
-  version = "15.12.71";
+  version = "2020.05.21";
 
   src = fetchFromGitHub {
     owner = "linuxdeepin";
     repo = pname;
     rev = version;
-    sha256 = "12rzzjp906np95ckbxrd4mb345lm198wz69kxy48f8q1zg78q8iw";
+    sha256 = "0b1s6kf0q804zbbghly981wzacy1spi8168shf3x8w95rqj6463p";
   };
 
   nativeBuildInputs = [
@@ -30,22 +30,29 @@ stdenv.mkDerivation rec {
 
   dontDropIconThemeCache = true;
 
+  buildTargets = "all hicolor-links";
+
   postPatch = ''
-    patchShebangs tools/hicolor.links
-    patchShebangs tools/display_unused_links.sh
-    patchShebangs cursors-src/cursors/bitmaps/make.sh
-    patchShebangs cursors-src/render-cursors.sh
+    # fix: hicolor links should follow the deepin -> bloom naming change
+    # https://github.com/linuxdeepin/deepin-icon-theme/pull/24
+    substituteInPlace tools/hicolor.links --replace deepin bloom
 
-    # keep icon-theme.cache
-    sed -i -e 's|\(-rm -f .*/icon-theme.cache\)|# \1|g' Makefile
+    substituteInPlace Sea/index.theme --replace Inherits=deepin Inherits=bloom
   '';
 
-  buildTargets = "all hicolor-links";
-  installTargets = [ "install-icons" "install-cursors" ];
-  installFlags = [ "PREFIX=${placeholder "out"}" ];
+  installPhase = ''
+    runHook preInstall
+
+    mkdir -p $out/share/icons
+    cp -vai bloom* Sea $out/share/icons
+
+    for theme in $out/share/icons/*; do
+      gtk-update-icon-cache $theme
+    done
+
+    cp -vai usr/share/icons/hicolor $out/share/icons
 
-  postInstall = ''
-    cp -a ./Sea ./usr/share/icons/hicolor "$out"/share/icons/
+    runHook postInstall
   '';
 
   passthru.updateScript = deepin.updateScript { inherit pname version src; };

diff --git a/pkgs/desktops/deepin/disomaster/default.nix b/pkgs/desktops/deepin/disomaster/default.nix
@@ -10,13 +10,13 @@
 
 mkDerivation rec {
   pname = "disomaster";
-  version = "5.0.0";
+  version = "5.0.1";
 
   src = fetchFromGitHub {
     owner = "linuxdeepin";
     repo = pname;
     rev = version;
-    sha256 = "13144gq0mpbpclzxc79fb1kirh0vvi50jvjnbpla9s8lvh59xl62";
+    sha256 = "1kmhlnw37pdmlf7k9zry657xlhz40m9nzg361kiyisn186pfqpws";
   };
 
   nativeBuildInputs = [
@@ -32,11 +32,12 @@ mkDerivation rec {
 
   postPatch = ''
     searchHardCodedPaths  # debugging
-
-    sed -i '/^QMAKE_PKGCONFIG_DESTDIR/i QMAKE_PKGCONFIG_PREFIX = $$PREFIX' \
-       libdisomaster/libdisomaster.pro
   '';
 
+  qmakeFlags = [
+    "QMAKE_PKGCONFIG_PREFIX=${placeholder "out"}"
+  ];
+
   passthru.updateScript = deepin.updateScript { inherit pname version src; };
 
   meta = with stdenv.lib; {

diff --git a/pkgs/desktops/deepin/go-lib/default.nix b/pkgs/desktops/deepin/go-lib/default.nix
@@ -10,13 +10,13 @@
 
 stdenv.mkDerivation rec {
   pname = "go-lib";
-  version = "5.0.0";
+  version = "5.4.5";
 
   src = fetchFromGitHub {
     owner = "linuxdeepin";
     repo = pname;
     rev = version;
-    sha256 = "0j1ik5hfrysqgync8cyv815cwyjn67k8n69x6llxdp39jli1k8q0";
+    sha256 = "021sq7nzvfwsa5ccsb3vdjk53m7cf693xm4wkdkrkf8pja6vz94q";
   };
 
   buildInputs = [

diff --git a/pkgs/desktops/deepin/udisks2-qt5/default.nix b/pkgs/desktops/deepin/udisks2-qt5/default.nix
@@ -8,13 +8,13 @@
 
 mkDerivation rec {
   pname = "udisks2-qt5";
-  version = "5.0.0";
+  version = "5.0.3";
 
   src = fetchFromGitHub {
     owner = "linuxdeepin";
     repo = pname;
     rev = version;
-    sha256 = "0mqxm6ixzpbg0rr6ly2kvnkpag8gjza67ya7jv4i4rihbq1d0wzi";
+    sha256 = "0c87ks9glwhk4m2s7kf7mb43q011yi6l3qjq2ammmfqwl8xal69a";
   };
 
   nativeBuildInputs = [
@@ -27,11 +27,15 @@ mkDerivation rec {
   ];
 
   postPatch = ''
-    searchHardCodedPaths
+    searchHardCodedPaths # debugging
   '';
 
+  qmakeFlags = [
+    "QMAKE_PKGCONFIG_PREFIX=${placeholder "out"}"
+  ];
+
   postFixup = ''
-    searchHardCodedPaths $out
+    searchHardCodedPaths $out # debugging
   '';
 
   passthru.updateScript = deepin.updateScript { inherit pname version src; };

diff --git a/pkgs/desktops/enlightenment/0001-wrapped-setuid-executables.patch b/pkgs/desktops/enlightenment/0001-wrapped-setuid-executables.patch
@@ -0,0 +1,114 @@
+From a1e54ae0097a3b6a0dabf4639fe8bc594c4f602d Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Jos=C3=A9=20Romildo=20Malaquias?= <malaquias@gmail.com>
+Date: Thu, 14 May 2020 16:36:34 -0300
+Subject: [PATCH] wrapped setuid executables
+
+Installing programs with root ownership and setuid/setgid permissions
+in /nix/store is not allowed. They should be wrapped in the
+enlightenment service module, and the wrapped ones should be used
+instead.
+---
+ meson/meson_inst.sh           | 4 ++--
+ src/bin/e_auth.c              | 6 ++----
+ src/bin/e_fm/e_fm_main_eeze.c | 6 +++---
+ src/bin/e_start_main.c        | 2 +-
+ src/bin/e_system.c            | 2 +-
+ 5 files changed, 9 insertions(+), 11 deletions(-)
+
+diff --git a/meson/meson_inst.sh b/meson/meson_inst.sh
+index 321143e40..cd2399306 100755
+--- a/meson/meson_inst.sh
++++ b/meson/meson_inst.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+
+ for x in "$@" ; do
+-	chown root "$DESTDIR/$x"
+-	chmod a=rx,u+xs "$DESTDIR/$x"
++	echo TODO: chown root "$DESTDIR/$x"
++	echo TODO: chmod a=rx,u+xs "$DESTDIR/$x"
+ done
+diff --git a/src/bin/e_auth.c b/src/bin/e_auth.c
+index 8b0aa6641..63c68c4bc 100644
+--- a/src/bin/e_auth.c
++++ b/src/bin/e_auth.c
+@@ -12,8 +12,7 @@ e_auth_begin(char *passwd)
+    if (pwlen == 0) goto out;
+
+    snprintf(buf, sizeof(buf),
+-            "%s/enlightenment/utils/enlightenment_ckpasswd pw",
+-            e_prefix_lib_get());
++            "/run/wrappers/bin/enlightenment_ckpasswd pw");
+    exe = ecore_exe_pipe_run(buf, ECORE_EXE_PIPE_WRITE, NULL);
+    if (!exe) goto out;
+    if (ecore_exe_send(exe, passwd, pwlen) != EINA_TRUE) goto out;
+@@ -47,8 +46,7 @@ e_auth_polkit_begin(char *passwd, const char *cookie, unsigned int uid)
+    if (pwlen == 0) goto out;
+
+    snprintf(buf, sizeof(buf),
+-            "%s/enlightenment/utils/enlightenment_ckpasswd pk",
+-            e_prefix_lib_get());
++            "/run/wrappers/bin/enlightenment_ckpasswd pk");
+    exe = ecore_exe_pipe_run(buf, ECORE_EXE_PIPE_WRITE, NULL);
+    if (!exe) goto out;
+    snprintf(buf, sizeof(buf), "%s %u %s", cookie, uid, passwd);
+diff --git a/src/bin/e_fm/e_fm_main_eeze.c b/src/bin/e_fm/e_fm_main_eeze.c
+index 9b10b3117..0f0aa5b53 100644
+--- a/src/bin/e_fm/e_fm_main_eeze.c
++++ b/src/bin/e_fm/e_fm_main_eeze.c
+@@ -318,7 +318,7 @@ _e_fm_main_eeze_volume_eject(E_Volume *v)
+      {
+         char buf[PATH_MAX];
+
+-        snprintf(buf, sizeof(buf), "%s/enlightenment/utils/enlightenment_sys", eina_prefix_lib_get(pfx));
++        snprintf(buf, sizeof(buf), "/run/wrappers/bin/enlightenment_sys");
+         eeze_disk_mount_wrapper_set(v->disk, buf);
+      }
+    v->guard = ecore_timer_loop_add(E_FM_EJECT_TIMEOUT, (Ecore_Task_Cb)_e_fm_main_eeze_vol_eject_timeout, v);
+@@ -512,7 +512,7 @@ _e_fm_main_eeze_volume_unmount(E_Volume *v)
+      {
+         char buf[PATH_MAX];
+
+-        snprintf(buf, sizeof(buf), "%s/enlightenment/utils/enlightenment_sys", eina_prefix_lib_get(pfx));
++        snprintf(buf, sizeof(buf), "/run/wrappers/bin/enlightenment_sys");
+         eeze_disk_mount_wrapper_set(v->disk, buf);
+      }
+    v->guard = ecore_timer_loop_add(E_FM_UNMOUNT_TIMEOUT, (Ecore_Task_Cb)_e_fm_main_eeze_vol_unmount_timeout, v);
+@@ -548,7 +548,7 @@ _e_fm_main_eeze_volume_mount(E_Volume *v)
+      {
+         char buf2[PATH_MAX];
+
+-        snprintf(buf2, sizeof(buf2), "%s/enlightenment/utils/enlightenment_sys", eina_prefix_lib_get(pfx));
++        snprintf(buf2, sizeof(buf2), "/run/wrappers/bin/enlightenment_sys");
+         eeze_disk_mount_wrapper_set(v->disk, buf2);
+      }
+    v->guard = ecore_timer_loop_add(E_FM_MOUNT_TIMEOUT, (Ecore_Task_Cb)_e_fm_main_eeze_vol_mount_timeout, v);
+diff --git a/src/bin/e_start_main.c b/src/bin/e_start_main.c
+index 8534a7a8e..f0f0061a4 100644
+--- a/src/bin/e_start_main.c
++++ b/src/bin/e_start_main.c
+@@ -709,7 +709,7 @@ main(int argc, char **argv)
+             "E_ALERT_FONT_DIR=%s/data/fonts", eina_prefix_data_get(pfx));
+    putenv(buf2);
+    snprintf(buf3, sizeof(buf3),
+-            "E_ALERT_SYSTEM_BIN=%s/enlightenment/utils/enlightenment_system", eina_prefix_lib_get(pfx));
++            "E_ALERT_SYSTEM_BIN=/run/wrappers/bin/enlightenment_system");
+    putenv(buf3);
+
+    if ((valgrind_mode || valgrind_tool) &&
+diff --git a/src/bin/e_system.c b/src/bin/e_system.c
+index 1e7aabb64..5084933a1 100644
+--- a/src/bin/e_system.c
++++ b/src/bin/e_system.c
+@@ -132,7 +132,7 @@ _system_spawn(void)
+    else _respawn_count = 0;
+    if (_respawn_count > 5) return;
+    snprintf(buf, sizeof(buf),
+-            "%s/enlightenment/utils/enlightenment_system", e_prefix_lib_get());
++            "/run/wrappers/bin/enlightenment_system");
+    _system_exe = ecore_exe_pipe_run
+      (buf, ECORE_EXE_NOT_LEADER | ECORE_EXE_TERM_WITH_PARENT |
+       ECORE_EXE_PIPE_READ | ECORE_EXE_PIPE_WRITE, NULL);
+-- 
+2.26.2
+
diff --git a/pkgs/desktops/enlightenment/efl.nix b/pkgs/desktops/enlightenment/efl.nix
@@ -53,11 +53,11 @@
 
 stdenv.mkDerivation rec {
   pname = "efl";
-  version = "1.24.1";
+  version = "1.24.2";
 
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/libs/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "1xsbz5kl74cgzyzwmjy3p50m0iigvi53lklkp92v49k4j99zpak7";
+    sha256 = "0w3srvigg4kfi7xq76c7y4hnq5yr2gxrrsvlyj1g2wc1igz1vyg1";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/desktops/enlightenment/enlightenment.nix b/pkgs/desktops/enlightenment/enlightenment.nix
@@ -1,19 +1,29 @@
-{ stdenv, fetchurl, meson, ninja, pkgconfig, gettext, alsaLib, bc,
-  bzip2, efl, gdbm, libXdmcp, libXrandr, libcap, libffi,
-  libpthreadstubs, libxcb, luajit, mesa, pam, pcre, xcbutilkeysyms,
-  xkeyboard_config,
+{ stdenv
+, fetchurl
+, meson
+, ninja
+, pkgconfig
+, gettext
+, alsaLib
+, acpid
+, bc
+, ddcutil
+, efl
+, pam
+, xkeyboard_config
+, udisks2
 
-  bluetoothSupport ? true, bluez5,
-  pulseSupport ? !stdenv.isDarwin, libpulseaudio,
+, bluetoothSupport ? true, bluez5
+, pulseSupport ? !stdenv.isDarwin, libpulseaudio
 }:
 
 stdenv.mkDerivation rec {
   pname = "enlightenment";
-  version = "0.23.1";
+  version = "0.24.0";
 
   src = fetchurl {
     url = "http://download.enlightenment.org/rel/apps/${pname}/${pname}-${version}.tar.xz";
-    sha256 = "0d1cyl07w9pvi2pf029kablazks2q9aislzl46b6fq5m1465jc75";
+    sha256 = "01053hxdmyjfb6gmz1pqmw0llrgc4356np515h5vsqcn59mhvfz7";
   };
 
   nativeBuildInputs = [
@@ -25,58 +35,35 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     alsaLib
-    bc  # for the Everything module calculator mode
-    bzip2
+    acpid # for systems with ACPI for lid events, AC/Battery plug in/out etc
+    bc # for the Everything module calculator mode
+    ddcutil # specifically libddcutil.so.2 for backlight control
     efl
-    gdbm
-    libXdmcp
-    libXrandr
-    libffi
-    libpthreadstubs
-    libxcb
-    luajit
-    mesa
     pam
-    pcre
-    xcbutilkeysyms
     xkeyboard_config
+    udisks2 # for removable storage mounting/unmounting
   ]
-  ++ stdenv.lib.optional stdenv.isLinux libcap
-  ++ stdenv.lib.optional bluetoothSupport bluez5
-  ++ stdenv.lib.optional pulseSupport libpulseaudio
+  ++ stdenv.lib.optional bluetoothSupport bluez5 # for bluetooth configuration and control
+  ++ stdenv.lib.optional pulseSupport libpulseaudio # for proper audio device control and redirection
   ;
 
   patches = [
-    # Some programs installed by enlightenment (to set the cpu frequency,
-    # for instance) need root ownership and setuid/setgid permissions, which
-    # are not allowed for files in /nix/store. Instead of allowing the
-    # installer to try to do this, the file $out/e-wrappers.nix is created,
-    # containing the needed configuration for wrapping those programs. It
-    # can be used in the enlightenment module. The idea is:
-    #
-    #  1) rename the original binary adding the extension .orig
-    #  2) wrap the renamed binary at /run/wrappers/bin/
-    #  3) create a new symbolic link using the original binary name (in the
-    #     original directory where enlightenment wants it) pointing to the
-    #     wrapper
-
-    ./enlightenment.suid-exes.patch
+    # Executables cannot be made setuid in nix store. They should be
+    # wrapped in the enlightenment service module, and the wrapped
+    # executables should be used instead.
+    ./0001-wrapped-setuid-executables.patch
   ];
 
   postPatch = ''
-    # edge_cc is a binary provided by efl and cannot be found at the directory
-    # given by e_prefix_bin_get(), which is $out/bin
-
-    substituteInPlace src/bin/e_import_config_dialog.c \
-      --replace "e_prefix_bin_get()" "\"${efl}/bin\""
-
     substituteInPlace src/modules/everything/evry_plug_calc.c \
       --replace "ecore_exe_pipe_run(\"bc -l\"" "ecore_exe_pipe_run(\"${bc}/bin/bc -l\""
   '';
 
-  mesonFlags = [ "-Dsystemdunitdir=lib/systemd/user" ];
+  mesonFlags = [
+    "-D systemdunitdir=lib/systemd/user"
+  ];
 
-  enableParallelBuilding = true;
+  passthru.providedSessions = [ "enlightenment" ];
 
   meta = with stdenv.lib; {
     description = "The Compositing Window Manager and Desktop Shell";

diff --git a/pkgs/desktops/enlightenment/enlightenment.suid-exes.patch b/pkgs/desktops/enlightenment/enlightenment.suid-exes.patch
diff --git a/pkgs/desktops/lumina/lumina/default.nix b/pkgs/desktops/lumina/lumina/default.nix
@@ -1,18 +1,17 @@
-{ stdenv,
-  mkDerivation,
-  fetchFromGitHub,
-  desktop-file-utils,
-  fluxbox,
-  numlockx,
-  qmake,
-  qtbase,
-  qtmultimedia,
-  qtsvg,
-  qttools,
-  qtx11extras,
-  xorg,
-  xscreensaver,
-  wrapGAppsHook
+{ stdenv
+, mkDerivation
+, fetchFromGitHub
+, fluxbox
+, numlockx
+, qmake
+, qtbase
+, qtmultimedia
+, qtsvg
+, qttools
+, qtx11extras
+, xorg
+, xscreensaver
+, wrapGAppsHook
 }:
 
 mkDerivation rec {
@@ -33,19 +32,18 @@ mkDerivation rec {
   ];
 
   buildInputs = [
-    xorg.libxcb
-    xorg.libXcursor
-    xorg.libXdamage
-    xorg.xcbutilwm
-    xorg.xcbutilimage
+    fluxbox # window manager for Lumina DE
+    numlockx # required for changing state of numlock at login
     qtbase
-    qtsvg
     qtmultimedia
+    qtsvg
     qtx11extras
-    fluxbox
+    xorg.libXcursor
+    xorg.libXdamage
+    xorg.libxcb
+    xorg.xcbutilimage
+    xorg.xcbutilwm
     xscreensaver
-    desktop-file-utils
-    numlockx
   ];
 
   patches = [
@@ -67,6 +65,12 @@ mkDerivation rec {
     # Fix location of fluxbox styles
     substituteInPlace src-qt5/core-utils/lumina-config/pages/page_fluxbox_settings.cpp \
       --replace 'LOS::AppPrefix()+"share/fluxbox' "\"${fluxbox}/share/fluxbox"
+
+    # Fix desktop files
+    for i in $(grep -lir 'OnlyShowIn=Lumina' src-qt5); do
+      echo ===== $i
+      substituteInPlace $i --replace 'OnlyShowIn=Lumina' 'OnlyShowIn=X-Lumina'
+    done
   '';
 
   qmakeFlags = [
@@ -75,6 +79,8 @@ mkDerivation rec {
     "LRELEASE=${stdenv.lib.getDev qttools}/bin/lrelease"
   ];
 
+  passthru.providedSessions = [ "Lumina-DE" ];
+
   meta = with stdenv.lib; {
     description = "A lightweight, portable desktop environment";
     longDescription = ''

diff --git a/pkgs/development/compilers/ciao/default.nix b/pkgs/development/compilers/ciao/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "ciao";
+  version = "1.19.0";
+  src = fetchFromGitHub {
+    owner = "ciao-lang";
+    repo = "ciao";
+    rev = "v${version}";
+    sha256 = "03qzcb4ivgkiwdpw7a94dn74xqyxjwz5ilrr53rcblsh5ng299jp";
+  };
+
+  configurePhase = ''
+    ./ciao-boot.sh configure --instype=global --prefix=$prefix
+  '';
+
+  buildPhase = ''
+    ./ciao-boot.sh build
+  '';
+
+  installPhase = ''
+    ./ciao-boot.sh install
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://ciao-lang.org/";
+    description = "A general purpose, multi-paradigm programming language in the Prolog family";
+    license = licenses.lgpl21;
+    maintainers = with maintainers; [ suhr ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/development/libraries/science/biology/bpp-core/default.nix b/pkgs/development/libraries/science/biology/bpp-core/default.nix
@@ -0,0 +1,36 @@
+{ stdenv, fetchFromGitHub, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "bpp-core";
+  version = "2.4.1";
+
+  src = fetchFromGitHub { owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0ma2cl677l7s0n5sffh66cy9lxp5wycm50f121g8rx85p95vkgwv";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  preCheck = ''
+    export LD_LIBRARY_PATH=$(pwd)/src
+  '';
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/bpp-core/bpp-core-targets.cmake  \
+      --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX'
+  '';
+  # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES
+  # of form /nix/store/.../nix/store/.../include,
+  # probably due to relative vs absolute path issue
+
+  doCheck = !stdenv.isDarwin;
+
+  meta = with stdenv.lib; {
+    homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Main_Page";
+    changelog = "https://github.com/BioPP/bpp-core/blob/master/ChangeLog";
+    description = "C++ bioinformatics libraries and tools";
+    maintainers = with maintainers; [ bcdarwin ];
+    license = licenses.cecill20;
+  };
+}
diff --git a/pkgs/development/libraries/science/biology/bpp-phyl/default.nix b/pkgs/development/libraries/science/biology/bpp-phyl/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }:
+
+stdenv.mkDerivation rec {
+  pname = "bpp-phyl";
+
+  inherit (bpp-core) version;
+
+  src = fetchFromGitHub {
+    owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "192zks6wyk903n06c2lbsscdhkjnfwms8p7jblsmk3lvjhdipb20";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ bpp-core bpp-seq ];
+
+  preCheck = ''
+    export LD_LIBRARY_PATH=$(pwd)/src
+  '';
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake  \
+      --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX'
+  '';
+
+  doCheck = !stdenv.isDarwin;
+
+  meta = bpp-core.meta // {
+    changelog = "https://github.com/BioPP/bpp-phyl/blob/master/ChangeLog";
+  };
+}
diff --git a/pkgs/development/libraries/science/biology/bpp-popgen/default.nix b/pkgs/development/libraries/science/biology/bpp-popgen/default.nix
@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq }:
+
+stdenv.mkDerivation rec {
+  pname = "bpp-popgen";
+
+  inherit (bpp-core) version;
+
+  src = fetchFromGitHub {
+    owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0bz0fhrq3dri6a0hvfc3zlvrns8mrzzlnicw5pyfa812gc1qwfvh";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ bpp-core bpp-seq ];
+
+  preCheck = ''
+    export LD_LIBRARY_PATH=$(pwd)/src
+  '';
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake  \
+      --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX'
+  '';
+  # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES
+  # of form /nix/store/.../nix/store/.../include,
+  # probably due to relative vs absolute path issue
+
+  doCheck = !stdenv.isDarwin;
+
+  meta = bpp-core.meta // {
+    changelog = "https://github.com/BioPP/bpp-popgen/blob/master/ChangeLog";
+  };
+}
diff --git a/pkgs/development/libraries/science/biology/bpp-seq/default.nix b/pkgs/development/libraries/science/biology/bpp-seq/default.nix
@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake, bpp-core }:
+
+stdenv.mkDerivation rec {
+  pname = "bpp-seq";
+
+  inherit (bpp-core) version;
+
+  src = fetchFromGitHub {
+    owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1mc09g8jswzsa4wgrfv59jxn15ys3q8s0227p1j838wkphlwn2qk";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ bpp-core ];
+
+  preCheck = ''
+    export LD_LIBRARY_PATH=$(pwd)/src
+  '';
+
+  postFixup = ''
+    substituteInPlace $out/lib/cmake/${pname}/${pname}-targets.cmake  \
+      --replace 'set(_IMPORT_PREFIX' '#set(_IMPORT_PREFIX'
+  '';
+  # prevents cmake from exporting incorrect INTERFACE_INCLUDE_DIRECTORIES
+  # of form /nix/store/.../nix/store/.../include,
+  # probably due to relative vs absolute path issue
+
+  doCheck = !stdenv.isDarwin;
+
+  meta = bpp-core.meta // { 
+    changelog = "https://github.com/BioPP/bpp-seq/blob/master/ChangeLog";
+  };
+}
diff --git a/pkgs/development/python-modules/elementpath/default.nix b/pkgs/development/python-modules/elementpath/default.nix
@@ -1,15 +1,15 @@
 { lib, buildPythonPackage, fetchFromGitHub, isPy27 }:
 
 buildPythonPackage rec {
-  version = "1.4.4";
+  version = "1.4.5";
   pname = "elementpath";
   disabled = isPy27; # uses incompatible class syntax
 
   src = fetchFromGitHub {
     owner = "sissaschool";
     repo = "elementpath";
     rev = "v${version}";
-    sha256 = "1z7403ykfdb2zy6g4qcbjm87ibpi0k59dgmz1px7z7wy5p2vknxw";
+    sha256 = "1hqvi7ibhdz812dsjbyyz3rysc6242hi1k9187wwnjmilbbngi3c";
   };
 
   # avoid circular dependency with xmlschema which directly depends on this

diff --git a/pkgs/development/python-modules/jellyfish/default.nix b/pkgs/development/python-modules/jellyfish/default.nix
@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "jellyfish";
-  version = "0.7.2";
+  version = "0.8.2";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "11jja4wlzcr2pwvp3blj1jg6570zr0mpcm3nzhkbkdrbgq6wa2fb";
+    sha256 = "02q3d9b933hf8lyvg7w7lgmhij8bjs748vjmsfxhabai04a796d4";
   };
 
   checkInputs = [ pytest unicodecsv ];

diff --git a/pkgs/development/python-modules/pysmb/default.nix b/pkgs/development/python-modules/pysmb/default.nix
@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "pysmb";
-  version = "1.1.28";
+  version = "1.2.1";
 
   src = fetchPypi {
     inherit pname version;
     format = "setuptools";
     extension = "zip";
-    sha256 = "0x44yq440c1j3xnl7qigz2fpfzhx68n9mbj7ps7rd0kj0plcmr2q";
+    sha256 = "1gkh28m74rf0ic51cxahiyw4sfz3sp3dz0iggsksi917ryyinwmb";
   };
 
   propagatedBuildInputs = [

diff --git a/pkgs/tools/networking/ssldump/default.nix b/pkgs/tools/networking/ssldump/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation {
   pname = "ssldump";
-  version = "0.9b3";
+  version = "1.1";
 
   src = fetchFromGitHub {
     owner = "adulau";
     repo = "ssldump";
-    rev = "4529d03a50d39d3697c3e39a3d6f6c9b29448aa0";
-    sha256 = "0wwsamzxabfxcil5y2g4v2261vdspxlp12wz4xhji8607jbyjwr1";
+    rev = "7491b9851505acff95b2c68097e9b9f630d418dc";
+    sha256 = "1j3rln86khdnc98v50hclvqaq83a24c1rfzbcbajkbfpr4yxpnpd";
   };
 
   buildInputs = [ libpcap openssl ];

diff --git a/pkgs/tools/text/snippetpixie/default.nix b/pkgs/tools/text/snippetpixie/default.nix
@@ -24,13 +24,13 @@
 
 stdenv.mkDerivation rec {
   pname = "snippetpixie";
-  version = "1.3.1";
+  version = "1.3.2";
 
   src = fetchFromGitHub {
     owner = "bytepixie";
     repo = pname;
     rev = version;
-    sha256 = "0cnx7snw3h7p77fhihvqxb6bgg4s2ffvjr8nbymb4bnqlg2a7v97";
+    sha256 = "0jhc47g5x34c36y4d32lcn32bpw4axxf1sydawgy4886hmkvb6kf";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
@@ -8082,6 +8082,8 @@ in
 
   bluespec = callPackage ../development/compilers/bluespec { };
 
+  ciao = callPackage ../development/compilers/ciao { };
+
   colm = callPackage ../development/compilers/colm { };
 
   colmap = libsForQt5.callPackage ../applications/science/misc/colmap { };
@@ -24493,6 +24495,16 @@ in
     inherit (darwin.apple_sdk.frameworks) ApplicationServices;
   };
 
+  bpp-core = callPackage ../development/libraries/science/biology/bpp-core { };
+
+  bpp-phyl = callPackage ../development/libraries/science/biology/bpp-phyl { };
+
+  bpp-popgen = callPackage ../development/libraries/science/biology/bpp-popgen { };
+
+  bpp-seq = callPackage ../development/libraries/science/biology/bpp-seq { };
+
+  bppsuite = callPackage ../applications/science/biology/bppsuite { };
+
   cd-hit = callPackage ../applications/science/biology/cd-hit { };
 
   cmtk = callPackage ../applications/science/biology/cmtk { };
@@ -24842,6 +24854,8 @@ in
 
   xfitter = callPackage ../applications/science/physics/xfitter {};
 
+  xflr5 = libsForQt5.callPackage ../applications/science/physics/xflr5 { };
+
   ### SCIENCE/PROGRAMMING
 
   dafny = dotnetPackages.Dafny;