NixOS · May 29, 2020 · May 29, 2020 · May 29, 2020 · Jul 7, 2020 · Jul 7, 2020
diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
@@ -1646,6 +1646,16 @@
     githubId = 411324;
     name = "Carles Pagès";
   };
+  cpu = {
+    email = "daniel@binaryparadox.net";
+    github = "cpu";
+    githubId = 292650;
+    name = "Daniel McCarney";
+    keys = [{
+      longkeyid = "rsa2048/0x08FB2BFC470E75B4";
+      fingerprint = "8026 D24A A966 BF9C D3CD  CB3C 08FB 2BFC 470E 75B4";
+    }];
+  };
   craigem = {
     email = "craige@mcwhirter.io";
     github = "craigem";

diff --git a/nixos/modules/services/x11/display-managers/lightdm-greeters/pantheon.nix b/nixos/modules/services/x11/display-managers/lightdm-greeters/pantheon.nix
@@ -43,7 +43,7 @@ in
     services.xserver.displayManager.lightdm.extraSeatDefaults = "greeter-show-manual-login=true";
 
     environment.etc."lightdm/io.elementary.greeter.conf".source = "${pkgs.pantheon.elementary-greeter}/etc/lightdm/io.elementary.greeter.conf";
-    environment.etc."wingpanel.d/io.elementary.greeter.whitelist".source = "${pkgs.pantheon.elementary-default-settings}/etc/wingpanel.d/io.elementary.greeter.whitelist";
+    environment.etc."wingpanel.d/io.elementary.greeter.allowed".source = "${pkgs.pantheon.elementary-default-settings}/etc/wingpanel.d/io.elementary.greeter.allowed";
 
   };
 }
diff --git a/pkgs/applications/misc/lutris/default.nix b/pkgs/applications/misc/lutris/default.nix
@@ -57,6 +57,7 @@ let
     fluidsynth
     xorgserver
     xorg.setxkbmap
+    xorg.xkbcomp
   ];
 
   gstDeps = with gst_all_1; [

diff --git a/pkgs/applications/version-management/git-and-tools/stgit/default.nix b/pkgs/applications/version-management/git-and-tools/stgit/default.nix
@@ -1,28 +1,26 @@
-{ stdenv, python3, python3Packages, fetchFromGitHub, git }:
+{ stdenv, python3Packages, fetchFromGitHub, git, installShellFiles }:
 
 python3Packages.buildPythonApplication rec {
   pname = "stgit";
-  version = "0.22";
+  version = "0.23";
 
   src = fetchFromGitHub {
     owner = "ctmarinas";
     repo = "stgit";
     rev = "v${version}";
-    sha256 = "0xpvs5fa50rrvl2c8naha1nblk5ip2mgg63a9srqqxfx6z8qmrfz";
+    sha256 = "1r9y8qnl6kdvq61788pnfhhgyv2xrnyrizbhy4qz4l1bpqkwfr2r";
   };
 
-  nativeBuildInputs = [ git ];
+  nativeBuildInputs = [ installShellFiles ];
 
-  makeFlags = [ "prefix=$$out" ];
+  checkInputs = [ git ];
 
   postInstall = ''
-    mkdir -p "$out/etc/bash_completion.d/"
-    ln -s ../../share/stgit/completion/stgit-completion.bash "$out/etc/bash_completion.d/"
+    installShellCompletion $out/share/stgit/completion/stg.fish
+    installShellCompletion --name stg $out/share/stgit/completion/stgit.bash
+    installShellCompletion --name _stg $out/share/stgit/completion/stgit.zsh
   '';
 
-  doCheck = false;
-  checkTarget = "test";
-
   meta = with stdenv.lib; {
     description = "A patch manager implemented on top of Git";
     homepage = "http://procode.org/stgit/";

diff --git a/pkgs/desktops/pantheon/apps/elementary-calendar/default.nix b/pkgs/desktops/pantheon/apps/elementary-calendar/default.nix
@@ -25,15 +25,15 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-calendar";
-  version = "5.0.5";
+  version = "5.0.6";
 
   repoName = "calendar";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = repoName;
     rev = version;
-    sha256 = "1dn2h7riajrn619z69626qnr8w6lp62dnm3d4pjkr0g5l4dp1cdb";
+    sha256 = "0lmadk4yzf1kiiqshwqcxzcyia1haq1avv6pyzvsaywxhqwdsini";
   };
 
   passthru = {

diff --git a/pkgs/desktops/pantheon/apps/elementary-dock/default.nix b/pkgs/desktops/pantheon/apps/elementary-dock/default.nix
@@ -27,7 +27,7 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-dock";
-  version = "unstable-2020-02-28";
+  version = "unstable-2020-06-11";
 
   outputs = [ "out" "dev" ];
 
@@ -36,8 +36,8 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "elementary";
     repo = repoName;
-    rev = "ac87d9063dc9c81d90f42f3002ad9c5b49460a82";
-    sha256 = "0lhjzd370fza488dav8n155ss486wqv6y7ldkahwg0c3zvlsvha7";
+    rev = "0a389ee58939d8c91c340df4e5340fc4b23d0b80";
+    sha256 = "01vinik73s0vmk56samgf49zr2bl4wjv44x15sz2cmh744llckja";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/desktops/pantheon/apps/elementary-videos/default.nix b/pkgs/desktops/pantheon/apps/elementary-videos/default.nix
@@ -19,15 +19,15 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-videos";
-  version = "2.7.1";
+  version = "2.7.2";
 
   repoName = "videos";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = repoName;
     rev = version;
-    sha256 = "00arim4i9bv9mbms1irkp44grkgrfnmqzraswyn1xiz9nvl1bsb9";
+    sha256 = "07dwhshdc78wia0fsbzz6iv651znzzasfil91w60v29kgc4s2b1i";
   };
 
   passthru = {

diff --git a/pkgs/desktops/pantheon/desktop/elementary-default-settings/default.nix b/pkgs/desktops/pantheon/desktop/elementary-default-settings/default.nix
@@ -83,8 +83,10 @@ stdenv.mkDerivation rec {
     cp -avr ${./launchers} $out/etc/skel/.config/plank/dock1/launchers
 
     # Whitelist wingpanel indicators to be used in the greeter
-    # TODO: is this needed or installed upstream?
-    install -D ${./io.elementary.greeter.whitelist} $out/etc/wingpanel.d/io.elementary.greeter.whitelist
+    # hhttps://github.com/elementary/greeter/blob/fc19752f147c62767cd2097c0c0c0fcce41e5873/debian/io.elementary.greeter.whitelist
+    # wingpanel 2.3.2 renamed this to .allowed to .forbidden
+    # https://github.com/elementary/wingpanel/pull/326
+    install -D ${./io.elementary.greeter.allowed} $out/etc/wingpanel.d/io.elementary.greeter.allowed
   '';
 
   postFixup = ''

diff --git a/...-settings/io.elementary.greeter.whitelist → ...lt-settings/io.elementary.greeter.allowed b/...-settings/io.elementary.greeter.whitelist → ...lt-settings/io.elementary.greeter.allowed
diff --git a/pkgs/desktops/pantheon/desktop/elementary-session-settings/default.nix b/pkgs/desktops/pantheon/desktop/elementary-session-settings/default.nix
@@ -1,7 +1,8 @@
 { stdenv
 , fetchFromGitHub
-, fetchpatch
 , substituteAll
+, desktop-file-utils
+, pkg-config
 , writeScript
 , pantheon
 , gnome-keyring
@@ -16,7 +17,6 @@
 , writeText
 , meson
 , ninja
-, pkg-config
 }:
 
 let
@@ -69,53 +69,43 @@ let
 in
 
 stdenv.mkDerivation rec {
-  pname = "elementary-session-settings";
-  version = "unstable-2019-11-12";
+  pname = "elementary-session-settings-unstable";
+  version = "2020-06-11";
 
   repoName = "session-settings";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = repoName;
-    rev = "f9d5afed16ce447cf6ae3c2d1c1db5eece84daca";
-    sha256 = "0n1m41aapr58rb1ffvfkjq6c6w3f0ynjzzhja50s4di98p4m7y0q";
+    rev = "130c9ae221913032ed18bcf6d21e3dcdba3c4209";
+    sha256 = "0bzg9vbq0ssnxgcb2vxpx6x9zv8ngkm9r3ki5q83m9al9919n0pr";
   };
 
-  patches = [
-    # Map Pantheon required components by g-s-d versions
-    # https://github.com/elementary/session-settings/pull/23
-    (fetchpatch {
-      url = "https://github.com/elementary/session-settings/commit/39918f4ec64fa9ed5affa109d6a692b97ae4ff01.patch";
-      sha256 = "0v2kqcsibymnslnnw4v67yh098znsrhrcycgxkw8vymvwlinc502";
-    })
-  ];
-
   nativeBuildInputs = [
+    desktop-file-utils
     meson
     ninja
     pkg-config
   ];
 
   buildInputs = [
-    elementary-settings-daemon
+    pantheon.elementary-settings-daemon
+    gnome-keyring
+    onboard
+    orca
   ];
 
   mesonFlags = [
-    "-Ddefaults-list=false"
-    "-Dpatched-gsd-autostarts=false"
-    "-Dpatched-ubuntu-autostarts=false"
+    "-Dmimeapps-list=false"
     "-Dfallback-session=GNOME"
+    "-Ddetect-program-prefixes=true"
+    "--sysconfdir=${placeholder "out"}/etc"
   ];
 
   postInstall = ''
     mkdir -p $out/share/applications
     cp -av ${./pantheon-mimeapps.list} $out/share/applications/pantheon-mimeapps.list
 
-    mkdir -p $out/etc/xdg/autostart
-    for package in ${gnome-keyring} ${orca} ${onboard} ${at-spi2-core}; do
-      cp -av $package/etc/xdg/autostart/* $out/etc/xdg/autostart
-    done
-
     cp "${dockitemAutostart}" $out/etc/xdg/autostart/default-elementary-dockitems.desktop
 
     mkdir -p $out/libexec
@@ -127,21 +117,16 @@ stdenv.mkDerivation rec {
     substituteInPlace $out/share/xsessions/pantheon.desktop \
       --replace "gnome-session --session=pantheon" "$out/libexec/pantheon" \
       --replace "wingpanel" "${wingpanel}/bin/wingpanel"
-
-    for f in $out/etc/xdg/autostart/*; do mv "$f" "''${f%.desktop}-pantheon.desktop"; done
-
-    for autostart in $(grep -rl "OnlyShowIn=GNOME;" $out/etc/xdg/autostart)
-    do
-      echo "Patching OnlyShowIn to Pantheon in: $autostart"
-      sed -i "s,OnlyShowIn=GNOME;,OnlyShowIn=Pantheon;," $autostart
-    done
   '';
 
   passthru = {
     updateScript = pantheon.updateScript {
       attrPath = "pantheon.${pname}";
     };
-    providedSessions = [ "pantheon" ];
+
+    providedSessions = [
+      "pantheon"
+    ];
   };
 
   meta = with stdenv.lib; {

diff --git a/pkgs/desktops/pantheon/desktop/wingpanel-indicators/datetime/default.nix b/pkgs/desktops/pantheon/desktop/wingpanel-indicators/datetime/default.nix
@@ -19,13 +19,13 @@
 
 stdenv.mkDerivation rec {
   pname = "wingpanel-indicator-datetime";
-  version = "2.2.4";
+  version = "2.2.5";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = pname;
     rev = version;
-    sha256 = "0wrvya9438ncb2rvcz99aa497v95b4yhdw1479iacnb9f94jacns";
+    sha256 = "0z5a4jkmg8jw3yjdq89njhqcpms2rbq7rnsh83q9gh8v3qidk75d";
   };
 
   passthru = {

diff --git a/pkgs/desktops/pantheon/desktop/wingpanel/default.nix b/pkgs/desktops/pantheon/desktop/wingpanel/default.nix
@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation rec {
   pname = "wingpanel";
-  version = "2.3.1";
+  version = "2.3.2";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = pname;
     rev = version;
-    sha256 = "0yvn1crylrdc9gq6gc7v4ynb5ii4n0c3bnswfq72p8cs3vvvvv24";
+    sha256 = "0sz3m64s5clirmiamx67iq42spba7sggcb29sny44z9f939vly4r";
   };
 
   passthru = {

diff --git a/pkgs/desktops/pantheon/granite/default.nix b/pkgs/desktops/pantheon/granite/default.nix
@@ -17,15 +17,15 @@
 
 stdenv.mkDerivation rec {
   pname = "granite";
-  version = "5.4.0";
+  version = "5.5.0";
 
   outputs = [ "out" "dev" ];
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = pname;
     rev = version;
-    sha256 = "0acicv3f9gksb352v88lwap8ailjsxdrfknl2xql7blasbjzl2q0";
+    sha256 = "13qfhq8xndikk6kmybibs6a4ddyp6mhvbsp2yy4qr7aiiyxf7mna";
   };
 
   passthru = {

diff --git a/pkgs/desktops/pantheon/services/pantheon-agent-polkit/default.nix b/pkgs/desktops/pantheon/services/pantheon-agent-polkit/default.nix
@@ -14,13 +14,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pantheon-agent-polkit";
-  version = "1.0.2";
+  version = "1.0.3";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = pname;
     rev = version;
-    sha256 = "1gkispg1wr3fmwhbaaw722hc7cfqvj18gwb1nvv7rz3ghk9ih4jy";
+    sha256 = "1kd6spwfwy5r2mrf7xh5l2wrazqia8vr4j3g27s97vn7fcg4pgb0";
   };
 
   passthru = {

diff --git a/pkgs/development/libraries/libvirt/default.nix b/pkgs/development/libraries/libvirt/default.nix
@@ -17,19 +17,19 @@ let
   buildFromTarball = stdenv.isDarwin;
 in stdenv.mkDerivation rec {
   pname = "libvirt";
-  version = "6.2.0";
+  version = "6.3.0";
 
   src =
     if buildFromTarball then
       fetchurl {
         url = "http://libvirt.org/sources/${pname}-${version}.tar.xz";
-        sha256 = "1c8grqf751blsgs15wx2p05wvankdrady6290vwc85v94cgqij5f";
+        sha256 = "1xcng497hs1gary3pz3fp590a4r1kqs4d0d8k5p370j0scw981kl";
       }
     else
       fetchgit {
         url = "git://libvirt.org/libvirt.git";
         rev = "v${version}";
-        sha256 = "1wyihi8bhwsck9b7f3b8yhlz145sjdyyj3ykjiszrqnp0y99xxy2";
+        sha256 = "129b3p72jlb40dsidak3nvpssv75xx2v99y63gzp5k074fp8y8x4";
         fetchSubmodules = true;
       };
 

diff --git a/pkgs/development/python-modules/cnvkit/default.nix b/pkgs/development/python-modules/cnvkit/default.nix
@@ -6,6 +6,7 @@
 , biopython
 , numpy
 , scipy
+, scikitlearn
 , pandas
 , matplotlib
 , reportlab
@@ -29,6 +30,7 @@ buildPythonPackage rec {
     biopython
     numpy
     scipy
+    scikitlearn
     pandas
     matplotlib
     reportlab
@@ -44,6 +46,8 @@ buildPythonPackage rec {
       --replace "pandas >= 0.20.1, < 0.25.0" "pandas"
   '';
 
+  pythonImportsCheck = [ "cnvlib" ];
+
   meta = with lib; {
     homepage = "https://cnvkit.readthedocs.io";
     description = "A Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data";

diff --git a/pkgs/development/python-modules/libvirt/default.nix b/pkgs/development/python-modules/libvirt/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "libvirt";
-  version = "6.2.0";
+  version = "6.3.0";
 
   src = assert version == libvirt.version; fetchgit {
     url = "git://libvirt.org/libvirt-python.git";
     rev = "v${version}";
-    sha256 = "0a8crk29rmnw1kcgi72crb7syacdk03lkl05yand5cxs0l65jwdl";
+    sha256 = "088cksq59jxkkzbvmwl8jw9v2k3zibwksl7j57yb51bxaa2sa1cx";
   };
 
   nativeBuildInputs = [ pkgconfig ];

diff --git a/pkgs/tools/filesystems/squashfs-tools-ng/default.nix b/pkgs/tools/filesystems/squashfs-tools-ng/default.nix
@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation rec {
   pname = "squashfs-tools-ng";
-  version = "0.9.1";
+  version = "1.0.0";
 
   src = fetchurl {
     url = "https://infraroot.at/pub/squashfs/squashfs-tools-ng-${version}.tar.xz";
-    sha256 = "1ilxkrqbpb5whv7xfwfvph76jwyjzf988njjpyyr99h6jv2r77q1";
+    sha256 = "1dpx0a200s46s1dxp64hkn765vap0hzmyyvmq7wrmcs81mvlrd0l";
   };
 
   nativeBuildInputs = [ doxygen graphviz pkgconfig perl ];