Merge master into staging-next

nixos/doc/manual/from_md/release-notes/rl-2111.section.xml

@@ -2013,6 +2013,16 @@ Superuser created successfully.
           file.
         </para>
       </listitem>
+      <listitem>
+        <para>
+          hydrus has been upgraded from version <literal>438</literal>
+          to <literal>463</literal>. Since upgrading between releases
+          this old is advised against, be sure to have a backup of your
+          data before upgrading. For details, see
+          <link xlink:href="https://hydrusnetwork.github.io/hydrus/help/getting_started_installing.html#big_updates">the
+          hydrus manual</link>.
+        </para>
+      </listitem>
     </itemizedlist>
   </section>
 </section>

nixos/doc/manual/release-notes/rl-2111.section.md

@@ -547,3 +547,5 @@ In addition to numerous new and upgraded packages, this release has the followin
 - `julia` now refers to `julia-stable` instead of `julia-lts`. In practice this means it has been upgraded from `1.0.4` to `1.5.4`.
 
 - RetroArch has been upgraded from version `1.8.5` to `1.9.13.2`. Since the previous release was quite old, if you're having issues after the upgrade, please delete your `$XDG_CONFIG_HOME/retroarch/retroarch.cfg` file.
+
+- hydrus has been upgraded from version `438` to `463`. Since upgrading between releases this old is advised against, be sure to have a backup of your data before upgrading. For details, see [the hydrus manual](https://hydrusnetwork.github.io/hydrus/help/getting_started_installing.html#big_updates).

nixos/modules/services/networking/monero.nix

@@ -222,7 +222,7 @@ in
       serviceConfig = {
         User  = "monero";
         Group = "monero";
-        ExecStart = "${pkgs.monero}/bin/monerod --config-file=${configFile} --non-interactive";
+        ExecStart = "${pkgs.monero-cli}/bin/monerod --config-file=${configFile} --non-interactive";
         Restart = "always";
         SuccessExitStatus = [ 0 1 ];
       };

pkgs/applications/audio/pulseaudio-dlna/0001-setup.py-remove-dbus-python-from-list.patch

@@ -0,0 +1,25 @@
+From a4bf7df795146c843696daee8c02826ba0034298 Mon Sep 17 00:00:00 2001
+From: Florian Klink <flokli@flokli.de>
+Date: Sun, 21 Nov 2021 12:04:48 +0100
+Subject: [PATCH] setup.py: remove dbus-python from list
+
+I wasn't able to convince setuptools to find this.
+---
+ setup.py | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 61d6831..013fff3 100644
+--- a/setup.py
++++ b/setup.py
+@@ -42,7 +42,6 @@ setuptools.setup(
+     install_requires=[
+     'docopt',
+     'chardet',
+-    'dbus-python',
+     'docopt',
+     'requests',
+     'setproctitle',
+-- 
+2.33.1
+

pkgs/applications/audio/pulseaudio-dlna/default.nix

@@ -1,43 +1,64 @@
-{ fetchFromGitHub, lib, pythonPackages
+{ fetchFromGitHub
-, mp3Support ? true, lame ? null
+, lib
-, opusSupport ? true, opusTools ? null
+, python3Packages
-, faacSupport ? false, faac ? null
+, mp3Support ? true
-, flacSupport ? true, flac ? null
+, lame
-, soxSupport ? true, sox ? null
+, opusSupport ? true
-, vorbisSupport ? true, vorbis-tools ? null
+, opusTools
+, faacSupport ? false
+, faac
+, flacSupport ? true
+, flac
+, soxSupport ? true
+, sox
+, vorbisSupport ? true
+, vorbis-tools
+, pulseaudio
 }:
 
-assert mp3Support -> lame != null;
+python3Packages.buildPythonApplication {
-assert opusSupport -> opusTools != null;
-assert faacSupport -> faac != null;
-assert flacSupport -> flac != null;
-assert soxSupport -> sox != null;
-assert vorbisSupport -> vorbis-tools != null;
-
-let
-  zeroconf = pythonPackages.callPackage ./zeroconf.nix { };
-in
-pythonPackages.buildPythonApplication {
   pname = "pulseaudio-dlna";
-  version = "unstable-2017-11-01";
+  version = "unstable-2021-11-09";
 
   src = fetchFromGitHub {
-    owner = "masmu";
+    owner = "Cygn";
     repo = "pulseaudio-dlna";
-    rev = "4472928dd23f274193f14289f59daec411023ab0";
+    rev = "637a2e7bba2277137c5f12fb58e63100dab7cbe6";
-    sha256 = "1dfn7036vrq49kxv4an7rayypnm5dlawsf02pfsldw877hzdamqk";
+    sha256 = "sha256-Oda+zQQJE2D3fiNWTzxYvI8cZVHG5JAoV2Wf5Z6IU3M=";
   };
 
-  propagatedBuildInputs = with pythonPackages; [
+  patches = [
-    dbus-python docopt requests setproctitle protobuf psutil futures
+    ./0001-setup.py-remove-dbus-python-from-list.patch
-    chardet notify2 netifaces pyroute2 pygobject2 lxml setuptools ]
+  ];
-    ++ [ zeroconf ]
+
-    ++ lib.optional mp3Support lame
+  propagatedBuildInputs = with python3Packages; [
-    ++ lib.optional opusSupport opusTools
+    dbus-python
-    ++ lib.optional faacSupport faac
+    docopt
-    ++ lib.optional flacSupport flac
+    requests
-    ++ lib.optional soxSupport sox
+    setproctitle
-    ++ lib.optional vorbisSupport vorbis-tools;
+    protobuf
+    psutil
+    chardet
+    netifaces
+    notify2
+    pyroute2
+    pygobject3
+    PyChromecast
+    lxml
+    setuptools
+    zeroconf
+  ]
+  ++ lib.optional mp3Support lame
+  ++ lib.optional opusSupport opusTools
+  ++ lib.optional faacSupport faac
+  ++ lib.optional flacSupport flac
+  ++ lib.optional soxSupport sox
+  ++ lib.optional vorbisSupport vorbis-tools;
+
+  # pulseaudio-dlna shells out to pactl to configure sinks and sources.
+  # As pactl might not be in $PATH, add --suffix it (so pactl configured by the
+  # user get priority)
+  makeWrapperArgs = [ "--suffix PATH : ${lib.makeBinPath [ pulseaudio ]}" ];
 
   # upstream has no tests
   checkPhase = ''
@@ -46,7 +67,7 @@ pythonPackages.buildPythonApplication {
 
   meta = with lib; {
     description = "A lightweight streaming server which brings DLNA / UPNP and Chromecast support to PulseAudio and Linux";
-    homepage = "https://github.com/masmu/pulseaudio-dlna";
+    homepage = "https://github.com/Cygn/pulseaudio-dlna";
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ mog ];
     platforms = platforms.linux;

pkgs/applications/blockchains/monero-cli/default.nix

@@ -8,7 +8,7 @@
 }:
 
 stdenv.mkDerivation rec {
-  pname = "monero";
+  pname = "monero-cli";
   version = "0.17.2.3";
 
   src = fetchFromGitHub {

pkgs/applications/blockchains/monero-gui/default.nix

@@ -5,7 +5,7 @@
 , qtmultimedia, qtxmlpatterns
 , qtquickcontrols, qtquickcontrols2
 , qtmacextras
-, monero, miniupnpc, unbound, readline
+, monero-cli, miniupnpc, unbound, readline
 , boost, libunwind, libsodium, pcsclite
 , randomx, zeromq, libgcrypt, libgpg-error
 , hidapi, rapidjson, quirc
@@ -32,7 +32,7 @@ stdenv.mkDerivation rec {
     qtbase qtdeclarative qtgraphicaleffects
     qtmultimedia qtquickcontrols qtquickcontrols2
     qtxmlpatterns
-    monero miniupnpc unbound readline
+    monero-cli miniupnpc unbound readline
     randomx libgcrypt libgpg-error
     boost libunwind libsodium pcsclite
     zeromq hidapi rapidjson quirc
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
   postUnpack = ''
     # copy monero sources here
     # (needs to be writable)
-    cp -r ${monero.source}/* source/monero
+    cp -r ${monero-cli.source}/* source/monero
     chmod -R +w source/monero
   '';
 
@@ -58,7 +58,7 @@ stdenv.mkDerivation rec {
 
     # use monerod from the monero package
     substituteInPlace src/daemon/DaemonManager.cpp \
-      --replace 'QApplication::applicationDirPath() + "' '"${monero}/bin'
+      --replace 'QApplication::applicationDirPath() + "' '"${monero-cli}/bin'
 
     # 1: only build external deps, *not* the full monero
     # 2: use nixpkgs libraries

pkgs/applications/editors/cudatext/default.nix

@@ -38,13 +38,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "cudatext";
-  version = "1.148.0";
+  version = "1.150.0";
 
   src = fetchFromGitHub {
     owner = "Alexey-T";
     repo = "CudaText";
     rev = version;
-    sha256 = "sha256-/wvtIPF/1HneW0zuT7+VCixemkw91MdU0S66bz2y48U=";
+    sha256 = "sha256-6XG4v2S7InKA6OVrV+q1lT/CzNxmzVQfmAAo2cqbqBY=";
   };
 
   postPatch = ''

pkgs/applications/editors/cudatext/deps.json

@@ -11,13 +11,13 @@
   },
   "ATFlatControls": {
     "owner": "Alexey-T",
-    "rev": "2021.10.19",
+    "rev": "2021.11.11",
-    "sha256": "sha256-NO1q4qDXZ0x0G6AtcRP9xnFDWuBzOvxq8G7I76LgaBw="
+    "sha256": "sha256-lbRRiA8CHWmosJefTHrP2cTgU8nlK1SmNcppG6Bl54I="
   },
   "ATSynEdit": {
     "owner": "Alexey-T",
-    "rev": "2021.10.27",
+    "rev": "2021.11.25",
-    "sha256": "sha256-7DlnO7IeCFLU1A+HJt4CFXoHWfhAr52tBvfPNHieXMM="
+    "sha256": "sha256-CbH0C+UOJ9X2wKG5IEbgitda06lazujYM8l961k7C7g="
   },
   "ATSynEdit_Cmp": {
     "owner": "Alexey-T",
@@ -31,8 +31,8 @@
   },
   "ATSynEdit_Ex": {
     "owner": "Alexey-T",
-    "rev": "2021.09.03",
+    "rev": "2021.11.25",
-    "sha256": "sha256-XYFnTfRa0n9XF9l/hL6z5RFZgdpVP9o1If4qln905Yc="
+    "sha256": "sha256-6hk9wNdoz1d3VpuW7yHyIQnnYseEAfgjCNGl6+o0Hjs="
   },
   "Python-for-Lazarus": {
     "owner": "Alexey-T",

pkgs/applications/graphics/hydrus/default.nix

@@ -10,14 +10,14 @@
 
 python3Packages.buildPythonPackage rec {
   pname = "hydrus";
-  version = "462";
+  version = "463";
   format = "other";
 
   src = fetchFromGitHub {
     owner = "hydrusnetwork";
     repo = "hydrus";
     rev = "v${version}";
-    sha256 = "sha256-eHUztpnDs1kxaBlTO7BRbO3eH+On9m7aJtbNw2b9Ado=";
+    sha256 = "sha256-GT5aIMskOVn4eAd4612YYA8uAQC8tuJzpEHNhc7pMuc=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/cherrytree/default.nix

@@ -18,13 +18,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cherrytree";
-  version = "0.99.42";
+  version = "0.99.43";
 
   src = fetchFromGitHub {
     owner = "giuspen";
     repo = "cherrytree";
     rev = version;
-    sha256 = "sha256-PKjl9n6J0iNdcA56CZ/nAzvgRNwqRLTHjwi3HQYWIMU=";
+    sha256 = "sha256-KSIdA585WbmvHXituCJoHpVRobfCZ62m5t7BWI6jIYk=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/todoist/default.nix

@@ -2,19 +2,23 @@
 
 buildGoModule rec {
   pname = "todoist";
-  version = "0.15.0";
+  version = "0.16.0";
 
   src = fetchFromGitHub {
     owner = "sachaos";
     repo = "todoist";
     rev = "v${version}";
-    sha256 = "0d3c621jaqxd6i58xm6nvi0avrh5mk23r169i95bn73igzw62w33";
+    sha256 = "sha256-cfhwbL7RaeD5LWxlfqnHfPPPkC5AA3Z034p+hlFBWtg=";
   };
 
-  vendorSha256 = "0cznb8glh36dwyyn1gx1ggkwa9zffrrxg52k78brnaczsl0rsmky";
+  vendorSha256 = "sha256-ly+OcRo8tGeNX4FnqNVaqjPx/A1FALOnScxs04lIOiU=";
 
   doCheck = false;
 
+  postPatch = ''
+    substituteInPlace main.go --replace '0.15.0' '${version}'
+  '';
+
   meta = {
     homepage = "https://github.com/sachaos/todoist";
     description = "Todoist CLI Client";

pkgs/applications/misc/wtf/default.nix

@@ -8,16 +8,16 @@
 
 buildGoModule rec {
   pname = "wtf";
-  version = "0.39.2";
+  version = "0.40.0";
 
   src = fetchFromGitHub {
     owner = "wtfutil";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-nP56HzjtIg9EIOBda9TQl8soUqlGfRmixidWrmQ7+vs=";
+    sha256 = "0hd5gnydxfncsmm7c58lvhkpnyxknvicc8f58xfh74azf363wcvm";
-   };
+  };
 
-  vendorSha256 = "sha256-yD4BUauYvyGk/D0Gr5Z15xWPtI/ZR9xTbmeS6RAxw1o=";
+  vendorSha256 = "1pkdfg042kg3b6m5rf044gz5yg6vp3bbsay1mrrbaysnb3gs51dq";
 
   doCheck = false;
 
@@ -35,6 +35,7 @@ buildGoModule rec {
   meta = with lib; {
     description = "The personal information dashboard for your terminal";
     homepage = "https://wtfutil.com/";
+    changelog = "https://github.com/wtfutil/wtf/raw/v${version}/CHANGELOG.md";
     license = licenses.mpl20;
     maintainers = with maintainers; [ kalbasit ];
     platforms = platforms.linux ++ platforms.darwin;

pkgs/applications/networking/appgate-sdp/default.nix

@@ -87,11 +87,11 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "appgate-sdp";
-  version = "5.4.2";
+  version = "5.5.0";
 
   src = fetchurl {
     url = "https://bin.appgate-sdp.com/${versions.majorMinor version}/client/appgate-sdp_${version}_amd64.deb";
-    sha256 = "sha256-wAhcTRO/Cd4MG1lfPNDq92yGcu3NOfymucddy92VaXo=";
+    sha256 = "sha256-lWInks3DBkSpKQh+dcNyn43iY5vvE67FLadohBbF6n4=";
   };
 
   # just patch interpreter
@@ -156,4 +156,3 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ ymatsiuk ];
   };
 }
-

pkgs/applications/science/molecular-dynamics/gromacs/default.nix

@@ -14,7 +14,7 @@ let
     if stdenv.hostPlatform.system == "i686-linux" then "SSE2" else
     if stdenv.hostPlatform.system == "x86_64-linux" then "SSE4.1" else
     if stdenv.hostPlatform.system == "x86_64-darwin" then "SSE4.1" else
-    if stdenv.hostPlatform.system == "aarch64-linux" then "ARM_NEON" else
+    if stdenv.hostPlatform.system == "aarch64-linux" then "ARM_NEON_ASIMD" else
     "None";
 
 in stdenv.mkDerivation rec {

pkgs/applications/version-management/git-review/default.nix

@@ -1,24 +1,31 @@
 { lib
-, fetchurl
+, fetchFromGitea
 , buildPythonApplication
 , pbr
 , requests
 , setuptools
+, genericUpdater
+, common-updater-scripts
 }:
 
 buildPythonApplication rec {
   pname = "git-review";
-  version = "2.1.0";
+  version = "2.2.0";
 
   # Manually set version because prb wants to get it from the git
   # upstream repository (and we are installing from tarball instead)
   PBR_VERSION = version;
 
-  src = fetchurl {
+  src = fetchFromGitea {
-    url = "https://opendev.org/opendev/${pname}/archive/${version}.tar.gz";
+    domain = "opendev.org";
-    hash = "sha256-3A1T+/iXhNeMS2Aww5jISoiNExdv9N9/kwyATSuwVTE=";
+    owner = "opendev";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-2+X5fPxB2FIp1fwqEUc+W0gH2NjhF/V+La+maE+XEpo=";
   };
 
+  outputs = [ "out" "man" ];
+
   nativeBuildInputs = [
     pbr
   ];
@@ -35,6 +42,11 @@ buildPythonApplication rec {
 
   pythonImportsCheck = [ "git_review" ];
 
+  passthru.updateScript = genericUpdater {
+    inherit pname version;
+    versionLister = "${common-updater-scripts}/bin/list-git-tags ${src.meta.homepage}";
+  };
+
   meta = with lib; {
     description = "Tool to submit code to Gerrit";
     homepage = "https://opendev.org/opendev/git-review";

pkgs/data/fonts/recursive/default.nix

@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 
 let
-  version = "1.082";
+  version = "1.084";
 in
 fetchzip {
   name = "recursive-${version}";
@@ -14,7 +14,7 @@ fetchzip {
     unzip -j $downloadedFile \*.ttf -d $out/share/fonts/truetype
   '';
 
-  sha256 = "1hjyjvzhfgqw58py4gk58fwyp5pxr3j8j76ppj6apg4dndfhs0lp";
+  sha256 = "sha256-YL09RVU9pgP0/aGRKECHzd5t1VmNDPtOFcRygWqIisg=";
 
   meta = with lib; {
     homepage = "https://recursive.design/";

pkgs/data/fonts/sudo/default.nix

@@ -1,11 +1,11 @@
 { lib, fetchzip }:
 
 let
-  version = "0.60";
+  version = "0.61";
 in fetchzip {
   name = "sudo-font-${version}";
   url = "https://github.com/jenskutilek/sudo-font/releases/download/v${version}/sudo.zip";
-  sha256 = "1zhl9yhx0dzkzc31i60lmcrizq8f3rkc7dbng5fal6iy8dwhnkmg";
+  sha256 = "sha256-4GDlx2zhwkcsxJPq0IrS1owmw+RKy09X3Q0zzA9l79w=";
 
   postFetch = ''
     mkdir -p $out/share/fonts/

pkgs/data/icons/numix-cursor-theme/default.nix

@@ -1,28 +1,18 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, inkscape, xcursorgen }:
+{ lib, stdenv, fetchFromGitHub, inkscape, xcursorgen }:
 
 stdenv.mkDerivation rec {
-  version = "1.1";
+  pname = "numix-cursor-theme";
-  package-name = "numix-cursor-theme";
+  version = "1.2";
-  name = "${package-name}-${version}";
 
   src = fetchFromGitHub {
     owner = "numixproject";
-    repo = package-name;
+    repo = pname;
     rev = "v${version}";
-    sha256 = "0p8h48wsy3z5dz9vdnp01fpn6q8ky0h74l5qgixlip557bsa1spi";
+    sha256 = "1q3w5i0h3ly6i7s9pqjdrb14kp89i78s0havri7lhiqyxizjvcvh";
   };
 
   nativeBuildInputs = [ inkscape xcursorgen ];
 
-  patches = [
-    # Remove when https://github.com/numixproject/numix-cursor-theme/pull/7 is merged
-    (fetchpatch {
-      url = "https://github.com/stephaneyfx/numix-cursor-theme/commit/3b647bf768cebb8f127b88e3786f6a9640460197.patch";
-      sha256 = "174kmhlvv76wwvndkys78aqc32051sqg3wzc0xg6b7by4agrbg76";
-      name = "support-inkscape-1-in-numix-cursor-theme.patch";
-    })
-  ];
-
   buildPhase = ''
     patchShebangs .
     HOME=$TMP ./build.sh

pkgs/desktops/pantheon/apps/elementary-code/default.nix

@@ -21,7 +21,6 @@
 , libsoup
 , vte
 , webkitgtk
-, zeitgeist
 , ctags
 , libgit2-glib
 , wrapGAppsHook
@@ -74,7 +73,6 @@ stdenv.mkDerivation rec {
     libsoup
     vte
     webkitgtk
-    zeitgeist
   ];
 
   # install script fails with UnicodeDecodeError because of printing a fancy elipsis character

pkgs/desktops/pantheon/apps/switchboard/default.nix

@@ -13,7 +13,6 @@
 , libhandy
 , granite
 , gettext
-, clutter-gtk
 , elementary-icon-theme
 , wrapGAppsHook
 }:
@@ -46,7 +45,6 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    clutter-gtk
     elementary-icon-theme
     granite
     gtk3

pkgs/development/compilers/fstar/default.nix

@@ -1,36 +1,20 @@
 { lib, stdenv, fetchFromGitHub, z3, ocamlPackages, makeWrapper, installShellFiles }:
 
-let
-  # FStar requires sedlex < 2.4
-  # see https://github.com/FStarLang/FStar/issues/2343
-  sedlex-2_3 = ocamlPackages.sedlex_2.overrideAttrs (_: rec {
-    pname = "sedlex";
-    version = "2.3";
-    src = fetchFromGitHub {
-       owner = "ocaml-community";
-       repo = "sedlex";
-       rev = "v${version}";
-       sha256 = "WXUXUuIaBUrFPQOKtZ7dgDZYdpEVnoJck0dkrCi8g0c=";
-    };
-  });
-in
-
 stdenv.mkDerivation rec {
   pname = "fstar";
-  version = "2021.10.16";
+  version = "2021.11.27";
 
   src = fetchFromGitHub {
     owner = "FStarLang";
     repo = "FStar";
     rev = "v${version}";
-    sha256 = "03b693s7s7dzflv5qkf61gd8ji9bn6fq4pxd8pd3a6ppkwj6b5vc";
+    sha256 = "sha256-OpY7vDb37ym4srsmD+deXiuofUJKRyKXG7g3zsJKvHo=";
   };
 
   nativeBuildInputs = [ makeWrapper installShellFiles ];
 
   buildInputs = [
     z3
-    sedlex-2_3
   ] ++ (with ocamlPackages; [
     ocaml
     findlib
@@ -43,6 +27,7 @@ stdenv.mkDerivation rec {
     menhir
     menhirLib
     pprint
+    sedlex_2
     ppxlib
     ppx_deriving
     ppx_deriving_yojson

pkgs/development/compilers/julia/1.6-bin.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "julia-bin";
-  version = "1.6.3";
+  version = "1.6.4";
 
   src = {
     x86_64-linux = fetchurl {
       url = "https://julialang-s3.julialang.org/bin/linux/x64/${lib.versions.majorMinor version}/julia-${version}-linux-x86_64.tar.gz";
-      sha256 = "0jrijj9snfx70692z2301rjassvwjcsjbxdsjyif9hyp9hrrqif7";
+      sha256 = "0ci1dd8g1pgpp6j1v971zg8xpw120hdjblf9zcyhgs4pfvj4l92j";
     };
   }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
 
@@ -19,7 +19,6 @@ stdenv.mkDerivation rec {
   '';
   patches = [
     # Source release Nix patch(es) relevant for binary releases as well.
-    ./patches/1.6-bin/0002-nix-Skip-tempname-test-broken-in-sandbox.patch
     ./patches/1.6-bin/0005-nix-Enable-parallel-unit-tests-for-sandbox.patch
   ];
   postPatch = ''

pkgs/development/compilers/julia/patches/1.6-bin/0002-nix-Skip-tempname-test-broken-in-sandbox.patch

@@ -1,28 +0,0 @@
-From ffe227676352a910754d96d92e9b06e475f28ff1 Mon Sep 17 00:00:00 2001
-From: Pontus Stenetorp <pontus@stenetorp.se>
-Date: Thu, 8 Apr 2021 04:25:19 +0000
-Subject: [PATCH 2/6] nix: Skip `tempname` test broken in sandbox
-
-Reported upstream:
-
-    https://github.com/JuliaLang/julia/issues/38873
----
- test/file.jl | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/test/file.jl b/test/file.jl
-index 0f39bc7c14..bd4dd78f62 100644
---- a/test/file.jl
-+++ b/test/file.jl
-@@ -95,7 +95,7 @@ end
-     @test dirname(t) == tempdir()
-     mktempdir() do d
-         t = tempname(d)
--        @test dirname(t) == d
-+        @test_skip dirname(t) == d
-     end
-     @test_throws ArgumentError tempname(randstring())
- end
--- 
-2.29.3
-

pkgs/development/interpreters/php/7.4.nix

@@ -2,8 +2,8 @@
 
 let
   base = callPackage ./generic.nix (_args // {
-    version = "7.4.25";
+    version = "7.4.26";
-    sha256 = "sha256-J5klcMrz4uUyOrezeFPETBUpsdMeqU2Xdu+pHVp4ExM=";
+    sha256 = "0k803j5wf4jv72px0zqz2z2hxyk2w3jr6xyczy568dx4z2l8i2yn";
   });
 
 in

pkgs/development/interpreters/php/8.0.nix

@@ -2,8 +2,8 @@
 
 let
   base = callPackage ./generic.nix (_args // {
-    version = "8.0.12";
+    version = "8.0.13";
-    sha256 = "sha256-tIhtsd8yLcj7Eo2LNK5+lPb8aC7LKf9PWlkdTen+rb8=";
+    sha256 = "0djqh650clz4fy1zifazf0jq383znksydx23f1s48prrlixrshf2";
   });
 
 in

pkgs/development/libraries/getdata/default.nix

@@ -1,19 +1,15 @@
-{ lib, stdenv, fetchurl, fetchpatch, libtool }:
+{ lib, stdenv, fetchFromGitHub, autoreconfHook, libtool }:
 stdenv.mkDerivation rec {
   pname = "getdata";
-  version = "0.10.0";
+  version = "0.11.0";
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "mirror://sourceforge/getdata/${pname}-${version}.tar.xz";
+    owner = "ketiltrout";
-    sha256 = "18xbb32vygav9x6yz0gdklif4chjskmkgp06rwnjdf9myhia0iym";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-fuFakbkxDwDp6Z9VITPIB8NiYRSp98Ub1y5SC6W5S1E=";
   };
 
-  patches = [
+  nativeBuildInputs = [ autoreconfHook ];
-    (fetchpatch {
-      url = "https://sources.debian.org/data/main/libg/libgetdata/0.10.0-10/debian/patches/CVE-2021-20204.patch";
-      sha256 = "1lvp1c2pkk9kxniwlvax6d8fsmjrkpxawf71c7j4rfjm6dgvivzm";
-    })
-  ];
-
   buildInputs = [ libtool ];
 
   meta = with lib; {

pkgs/development/libraries/libcint/default.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libcint";
-  version = "4.4.0";
+  version = "4.4.6";
 
   src = fetchFromGitHub {
     owner = "sunqm";
     repo = "libcint";
     rev = "v${version}";
-    hash = "sha256-nsIyosn8dBf217UmjXSKLTM2RhIQHCSvPlrvlqo5KLc=";
+    sha256 = "sha256-eWUuORMZs6Bl/zFGYZkpgNAgJPIei+k0cQoWl+v+zxo=";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -24,6 +24,9 @@ stdenv.mkDerivation rec {
     "-DENABLE_TEST=1"
     "-DQUICK_TEST=1"
     "-DCMAKE_INSTALL_PREFIX=" # ends up double-adding /nix/store/... prefix, this avoids issue
+    "-DWITH_RANGE_COULOMB:STRING=1"
+    "-DWITH_FORTRAN:STRING=1"
+    "-DMIN_EXPCUTOFF:STRING=20"
   ];
 
   strictDeps = true;

pkgs/development/libraries/libxc/default.nix

@@ -17,7 +17,15 @@ stdenv.mkDerivation rec {
     patchShebangs ./
   '';
 
-  cmakeFlags = [ "-DENABLE_FORTRAN=ON" "-DBUILD_SHARED_LIBS=ON" ];
+  cmakeFlags = [
+    "-DENABLE_FORTRAN=ON"
+    "-DBUILD_SHARED_LIBS=ON"
+    # Force compilation of higher derivatives
+    "-DDISABLE_VXC=0"
+    "-DDISABLE_FXC=0"
+    "-DDISABLE_KXC=0"
+    "-DDISABLE_LXC=0"
+  ];
 
   preCheck = ''
     export LD_LIBRARY_PATH=$(pwd)
@@ -29,7 +37,7 @@ stdenv.mkDerivation rec {
     description = "Library of exchange-correlation functionals for density-functional theory";
     homepage = "https://www.tddft.org/programs/Libxc/";
     license = licenses.mpl20;
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.unix;
     maintainers = with maintainers; [ markuskowa ];
   };
 }

pkgs/development/libraries/science/chemistry/cppe/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, lib, fetchFromGitHub, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "cppe";
+  version = "0.3.1";
+
+  src = fetchFromGitHub {
+    owner = "maxscheurer";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-guM7+ZWDJLcAUJtPkKLvC4LYSA2eBvER7cgwPZ7FxHw=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  cmakeFlags = [ "-DCMAKE_INSTALL_LIBDIR=lib" ];
+
+  meta = with lib; {
+    description = "C++ and Python library for Polarizable Embedding";
+    homepage = "https://github.com/maxscheurer/cppe";
+    license = licenses.lgpl3Only;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/libraries/science/chemistry/xcfun/default.nix

@@ -8,7 +8,7 @@ stdenv.mkDerivation rec {
     owner = "dftlibs";
     repo = pname;
     rev = "v${version}";
-    sha256= "1bj70cnhbh6ziy02x988wwl7cbwaq17ld7qwhswqkgnnx8rpgxid";
+    sha256 = "1bj70cnhbh6ziy02x988wwl7cbwaq17ld7qwhswqkgnnx8rpgxid";
   };
 
   nativeBuildInputs = [

pkgs/development/lisp-modules/quicklisp-to-nix-output/cl-shellwords.nix

@@ -0,0 +1,29 @@
+/* Generated file. */
+args @ { fetchurl, ... }:
+rec {
+  baseName = "cl-shellwords";
+  version = "20150923-git";
+
+  description = "Common Lisp port of Ruby's shellwords.rb, for escaping and
+splitting strings to be passed to a shell.";
+
+  deps = [ args."cl-ppcre" ];
+
+  src = fetchurl {
+    url = "http://beta.quicklisp.org/archive/cl-shellwords/2015-09-23/cl-shellwords-20150923-git.tgz";
+    sha256 = "1rb0ajpl2lai6bj4x0p3wf0cnf51nnyidhca4lpqp1w1wf1vkcqk";
+  };
+
+  packageName = "cl-shellwords";
+
+  asdFilesToKeep = ["cl-shellwords.asd"];
+  overrides = x: x;
+}
+/* (SYSTEM cl-shellwords DESCRIPTION
+    Common Lisp port of Ruby's shellwords.rb, for escaping and
+splitting strings to be passed to a shell.
+    SHA256 1rb0ajpl2lai6bj4x0p3wf0cnf51nnyidhca4lpqp1w1wf1vkcqk URL
+    http://beta.quicklisp.org/archive/cl-shellwords/2015-09-23/cl-shellwords-20150923-git.tgz
+    MD5 c2c62c6a2ce4ed2590d60707ead2e084 NAME cl-shellwords FILENAME
+    cl-shellwords DEPS ((NAME cl-ppcre FILENAME cl-ppcre)) DEPENDENCIES
+    (cl-ppcre) VERSION 20150923-git SIBLINGS (cl-shellwords-test) PARASITES NIL) */

pkgs/development/lisp-modules/quicklisp-to-nix-systems.txt

@@ -71,6 +71,7 @@ cl-prevalence
 cl-protobufs
 cl-qprint
 cl-reexport
+cl-shellwords
 cl-slice
 cl-smt-lib
 cl-smtp

pkgs/development/lisp-modules/quicklisp-to-nix.nix

@@ -4024,6 +4024,15 @@ let quicklisp-to-nix-packages = rec {
        }));
 
 
+  "cl-shellwords" = buildLispPackage
+    ((f: x: (x // (f x)))
+       (qlOverrides."cl-shellwords" or (x: {}))
+       (import ./quicklisp-to-nix-output/cl-shellwords.nix {
+         inherit fetchurl;
+           "cl-ppcre" = quicklisp-to-nix-packages."cl-ppcre";
+       }));
+
+
   "cl-reexport" = buildLispPackage
     ((f: x: (x // (f x)))
        (qlOverrides."cl-reexport" or (x: {}))

pkgs/development/ocaml-modules/lwt_ssl/default.nix

@@ -1,4 +1,4 @@
-{ lib, fetchzip, buildDunePackage, ssl, lwt }:
+{ lib, fetchFromGitHub, buildDunePackage, ssl, lwt }:
 
 buildDunePackage rec {
   pname = "lwt_ssl";
@@ -7,9 +7,11 @@ buildDunePackage rec {
   minimumOCamlVersion = "4.02";
   useDune2 = true;
 
-  src = fetchzip {
+  src = fetchFromGitHub {
-    url = "https://github.com/aantron/${pname}/archive/${version}.tar.gz";
+    owner = "aantron";
-    sha256 = "0v417ch5zn0yknj156awa5mrq3mal08pbrvsyribbn63ix6f9y3p";
+    repo = "lwt_ssl";
+    rev = version;
+    sha256 = "sha256-d/jkTI/D2LVi9nrndRGgqg6ca1FcmRKknR7YXyA7gWw=";
   };
 
   propagatedBuildInputs = [ ssl lwt ];

pkgs/development/ocaml-modules/macaque/default.nix

@@ -1,12 +1,14 @@
-{ lib, stdenv, fetchzip, ocaml, findlib, ocamlbuild, pgocaml, camlp4 }:
+{ lib, stdenv, fetchFromGitHub, ocaml, findlib, ocamlbuild, pgocaml, camlp4 }:
 
 stdenv.mkDerivation rec {
   pname = "ocaml-macaque";
   version = "0.7.2";
 
-  src = fetchzip {
+  src = fetchFromGitHub {
-    url = "https://github.com/ocsigen/macaque/archive/${version}.tar.gz";
+    owner = "ocsigen";
-    sha256 = "14i0a8cndzndjmlkyhf31r451q99cnkndgxcj0id4qjqhdl4bmjv";
+    repo = "macaque";
+    rev = version;
+    sha256 = "sha256-W9ZFaINYYtIikKy/ZqdlKeFQSA7DQT9plc3+ZhlSIJI=";
   };
 
   buildInputs = [ ocaml findlib ocamlbuild camlp4 ];

pkgs/development/ocaml-modules/markup/default.nix

@@ -1,4 +1,4 @@
-{ lib, buildDunePackage, fetchzip, ocaml, uchar, uutf, ounit2 }:
+{ lib, buildDunePackage, fetchFromGitHub, ocaml, uchar, uutf, ounit2 }:
 
 buildDunePackage rec {
   pname = "markup";
@@ -6,9 +6,11 @@ buildDunePackage rec {
 
   useDune2 = true;
 
-  src = fetchzip {
+  src = fetchFromGitHub {
-    url = "https://github.com/aantron/markup.ml/archive/${version}.tar.gz";
+    owner = "aantron";
-    sha256 = "09hkrf9pw6hpb9j06p5bddklpnjwdjpqza3bx2179l970yl67an9";
+    repo = "markup.ml";
+    rev = version;
+    sha256 = "sha256-yapjqAcn0XSC6Guoj69sXNpLZ2urXANkWhcafpPLEyY=";
   };
 
   propagatedBuildInputs = [ uchar uutf ];

pkgs/development/ocaml-modules/ocplib-endian/default.nix

@@ -1,11 +1,13 @@
-{ lib, buildDunePackage, fetchzip, cppo }:
+{ lib, buildDunePackage, fetchFromGitHub, cppo }:
 
 buildDunePackage rec {
   version = "1.1";
   pname = "ocplib-endian";
 
-  src = fetchzip {
+  src = fetchFromGitHub {
-    url = "https://github.com/OCamlPro/ocplib-endian/archive/${version}.tar.gz";
+    owner = "OCamlPro";
+    repo = "ocplib-endian";
+    rev = version;
     sha256 = "sha256-zKsSkhlZBXSqPtw+/WN3pwo9plM9rDZfMbGVfosqb10=";
   };
 

pkgs/development/ocaml-modules/ocsigen-deriving/default.nix

@@ -1,4 +1,12 @@
-{ stdenv, lib, fetchzip, ocaml, findlib, ocamlbuild, oasis, ocaml_optcomp, camlp4
+{ stdenv
+, lib
+, fetchFromGitHub
+, ocaml
+, findlib
+, ocamlbuild
+, oasis
+, ocaml_optcomp
+, camlp4
 , num
 }:
 
@@ -19,23 +27,27 @@ let inherit (param) version; in
 stdenv.mkDerivation {
   pname = "ocsigen-deriving";
   inherit version;
-  src = fetchzip {
+
-    url = "https://github.com/ocsigen/deriving/archive/${version}.tar.gz";
+  src = fetchFromGitHub {
+    owner = "ocsigen";
+    repo = "deriving";
+    rev = version;
     inherit (param) sha256;
   };
 
   buildInputs = [ ocaml findlib ocamlbuild oasis ocaml_optcomp camlp4 ]
-  ++ (param.buildInputs or []);
+    ++ (param.buildInputs or [ ]);
 
   createFindlibDestdir = true;
 
-  meta =  {
+  meta = {
     homepage = "https://github.com/ocsigen/deriving";
     description = "Extension to OCaml for deriving functions from type declarations";
     license = lib.licenses.mit;
-    platforms = ocaml.meta.platforms or [];
+    platforms = ocaml.meta.platforms or [ ];
     maintainers = with lib.maintainers; [
-      gal_bolle vbgl
+      gal_bolle
+      vbgl
     ];
   };
 

pkgs/development/ocaml-modules/ocsigen-start/default.nix

@@ -5,7 +5,7 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "ocaml${ocaml.version}-ocsigen-start-${version}";
+  pname = "ocaml${ocaml.version}-ocsigen-start";
   version = "4.3.0";
 
   buildInputs = [ ocaml findlib ];

pkgs/development/ocaml-modules/optcomp/default.nix

@@ -1,12 +1,14 @@
-{ stdenv, lib, fetchurl, fetchpatch, ocaml, findlib, ocamlbuild, camlp4 }:
+{ stdenv, lib, fetchFromGitHub, fetchpatch, ocaml, findlib, ocamlbuild, camlp4 }:
 
 stdenv.mkDerivation rec {
   pname = "ocaml-optcomp";
   version = "1.6";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/diml/optcomp/archive/${version}.tar.gz";
+    owner = "diml";
-    sha256 = "0hhhb2gisah1h22zlg5iszbgqxdd7x85cwd57bd4mfkx9l7dh8jh";
+    repo = "optcomp";
+    rev = version;
+    sha256 = "sha256-UCLYDk19ukraOqVxVlA/rXX81texPPqFgAEqHZ9YEEI=";
   };
 
   patches =

pkgs/development/ocaml-modules/pa_bench/default.nix

@@ -1,4 +1,4 @@
-{lib, buildOcaml, fetchurl, type_conv, pa_ounit}:
+{ lib, buildOcaml, fetchFromGitHub, type_conv, pa_ounit }:
 
 buildOcaml rec {
   pname = "pa_bench";
@@ -6,9 +6,11 @@ buildOcaml rec {
 
   minimumSupportedOcamlVersion = "4.00";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/janestreet/pa_bench/archive/${version}.tar.gz";
+    owner = "janestreet";
-    sha256 = "1cd6291gdnk6h8ziclg6x3if8z5xy67nfz9gx8sx4k2cwv0j29k5";
+    repo = "pa_bench";
+    rev = version;
+    sha256 = "sha256-WaXB3lgNPHy/z6D7uHxfD5W4HYuTZ+ieRbxxHlPao7c=";
   };
 
   buildInputs = [ pa_ounit ];

pkgs/development/ocaml-modules/pa_ounit/default.nix

@@ -1,4 +1,4 @@
-{ lib, buildOcaml, ocaml, fetchurl, ounit }:
+{ lib, buildOcaml, ocaml, fetchFromGitHub, ounit }:
 
 if lib.versionAtLeast ocaml.version "4.06"
 then throw "pa_ounit is not available for OCaml ${ocaml.version}"
@@ -8,9 +8,11 @@ buildOcaml rec {
   pname = "pa_ounit";
   version = "113.00.00";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/janestreet/pa_ounit/archive/${version}.tar.gz";
+    owner = "janestreet";
-    sha256 = "0vi0p2hxcrdsl0319c9s8mh9hmk2i4ir6c6vrj8axkc37zkgc437";
+    repo = "pa_ounit";
+    rev = version;
+    sha256 = "sha256-zzXN+mSJtlnQ3e1QoEukCiyfDEoe8cBdkAQ3U1dkvEk=";
   };
 
   propagatedBuildInputs = [ ounit ];

pkgs/development/ocaml-modules/pipebang/default.nix

@@ -1,4 +1,4 @@
-{lib, buildOcaml, fetchurl}:
+{ lib, buildOcaml, fetchFromGitHub }:
 
 buildOcaml rec {
   pname = "pipebang";
@@ -6,9 +6,11 @@ buildOcaml rec {
 
   minimumSupportedOcamlVersion = "4.00";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/janestreet/pipebang/archive/${version}.tar.gz";
+    owner = "janestreet";
-    sha256 = "0acm2y8wxvnapa248lkgm0vcc44hlwhrjxqkx1awjxzcmarnxhfk";
+    repo = "pipebang";
+    rev = version;
+    sha256 = "sha256-9A3X/ciL5HtuKQ5awS+hDDBLL5ytOr12wHsmJLNRn+Q=";
   };
 
   meta = with lib; {

pkgs/development/ocaml-modules/reactivedata/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, ocaml, findlib, ocamlbuild, react, opaline }:
+{ lib, stdenv, fetchFromGitHub, ocaml, findlib, ocamlbuild, react, opaline }:
 
 if !lib.versionAtLeast ocaml.version "4.04"
 then throw "reactiveData is not available for OCaml ${ocaml.version}"
@@ -8,9 +8,11 @@ stdenv.mkDerivation rec {
   pname = "ocaml${ocaml.version}-reactiveData";
   version = "0.2.2";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://github.com/ocsigen/reactiveData/archive/${version}.tar.gz";
+    owner = "ocsigen";
-    sha256 = "0jzagyp4zla28wykvcgqwd8df71ir0vb4s8akp02cfacd5v86sng";
+    repo = "reactiveData";
+    rev = version;
+    sha256 = "sha256-YLkacIbjxZQ/ThgSxjTqviBYih6eW2GX5H7iybQDv1A=";
   };
 
   buildInputs = [ ocaml findlib ocamlbuild opaline ];

pkgs/development/python-modules/cppe/default.nix

@@ -0,0 +1,47 @@
+{ buildPythonPackage
+, lib
+, cmake
+, cppe
+, eigen
+, python
+, pybind11
+, numpy
+, h5py
+, numba
+, scipy
+, pandas
+, polarizationsolver
+, pytest
+}:
+
+buildPythonPackage rec {
+  inherit (cppe) pname version src meta;
+
+  # The python interface requires eigen3, but builds from a checkout in tree.
+  # Using the nixpkgs version instead.
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "external/eigen3" "${eigen}/include/eigen3"
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    eigen
+  ];
+
+  dontUseCmakeConfigure = true;
+
+  buildInputs = [ pybind11 ];
+
+  checkInputs = [
+    pytest
+    h5py
+    numba
+    numpy
+    pandas
+    polarizationsolver
+    scipy
+  ];
+
+  pythonImportsCheck = [ "cppe" ];
+}

pkgs/development/python-modules/crownstone-sse/default.nix

@@ -1,6 +1,5 @@
 { lib
 , aiohttp
-, asynctest
 , buildPythonPackage
 , certifi
 , fetchFromGitHub
@@ -9,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "crownstone-sse";
-  version = "2.0.2";
+  version = "2.0.3";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
@@ -18,20 +17,14 @@ buildPythonPackage rec {
     owner = "crownstone";
     repo = "crownstone-lib-python-sse";
     rev = version;
-    sha256 = "0rrr92j8pi5annrfa22k1hggsyyacl9asi9i8yrj4jqdjvwjn2gc";
+    sha256 = "sha256-O1joOH7HCXYCro26p6foMMpg0UXfOgXD0BXuN50OK7U=";
   };
 
   propagatedBuildInputs = [
     aiohttp
-    asynctest
     certifi
   ];
 
-  postPatch = ''
-    substituteInPlace requirements.txt \
-      --replace "aiohttp~=3.7.4" "aiohttp>=3.7.4"
-  '';
-
   # Tests are only providing coverage
   doCheck = false;
 

pkgs/development/python-modules/fields/default.nix

@@ -0,0 +1,20 @@
+{ buildPythonPackage, lib, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "fields";
+  version = "5.0.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "sha256-MdSqA9jUTjXfE8Qx3jUTaZfwR6kkpZfYT3vCCeG+Vyc=";
+  };
+
+  pythonImportsCheck = [ "fields" ];
+
+  meta = with lib; {
+    description = "Container class boilerplate killer";
+    homepage = "https://github.com/ionelmc/python-fields";
+    license = licenses.bsd2;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/python-modules/flux-led/default.nix

@@ -8,7 +8,7 @@
 
 buildPythonPackage rec {
   pname = "flux-led";
-  version = "0.25.0";
+  version = "0.25.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -17,7 +17,7 @@ buildPythonPackage rec {
     owner = "Danielhiversen";
     repo = "flux_led";
     rev = version;
-    sha256 = "sha256-FLea34jhjGnCr02stCkszLgKdemufzmqYBIGegKXAL0=";
+    sha256 = "sha256-+GgA7ma27dah8G/ITsy84jZHpktJHnGSMjzMfAvvuJg=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/polarizationsolver/default.nix

@@ -0,0 +1,38 @@
+{ buildPythonPackage
+, lib
+, fetchFromGitLab
+, python
+, numpy
+, scipy
+, periodictable
+, fields
+}:
+
+buildPythonPackage rec {
+  pname = "polarizationsolver";
+  version = "unstable-2021-11-02";
+
+  src = fetchFromGitLab {
+    owner = "reinholdt";
+    repo = pname;
+    rev = "00424ac4d1862257a55e4b16543f63ace3fe8c22";
+    sha256 = "sha256-LACf8Xw+o/uJ3+PD/DE/o7nwKY7fv3NyYbpjCrTTnBU=";
+  };
+
+  propagatedBuildInputs = [
+    numpy
+    periodictable
+    scipy
+  ];
+
+  checkInputs = [ fields ];
+
+  pythonImportsCheck = [ "polarizationsolver" ];
+
+  meta = with lib; {
+    description = "Multipole moment solver for quantum chemistry and polarisable embedding";
+    homepage = "https://gitlab.com/reinholdt/polarizationsolver";
+    license = licenses.gpl3Plus;
+    maintainers = [ maintainers.sheepforce ];
+  };
+}

pkgs/development/python-modules/pyscf/default.nix

@@ -1,45 +1,109 @@
-{ buildPythonPackage, lib, fetchFromGitHub, libcint, libxc, xcfun, blas
+{ buildPythonPackage
-, numpy, scipy, h5py
+, python3
+, lib
+, fetchFromGitHub
+, cmake
+, blas
+, libcint
+, libxc
+, xcfun
+, cppe
+, h5py
+, numpy
+, scipy
+, nose
+, nose-exclude
 }:
 
 buildPythonPackage rec {
   pname = "pyscf";
-  version = "1.7.6.post1";
+  version = "2.0.1";
 
   src = fetchFromGitHub {
     owner = "pyscf";
     repo = pname;
-    rev = "f6c9c6654dd9609c5e467a1edd5c2c076f793acc";
+    rev = "v${version}";
-    sha256  = "0xbwkjxxysfpqz72qn6n4a0zr2h6sprbcal8j7kzymh7swjy117w";
+    sha256 = "sha256-nwnhaqSn/9WHBjUPaEabK4x23fJ83WwEYvz6aCcvsDw=";
   };
 
-  # Backport from the 2.0.0 alpha releases of PySCF.
+  # setup.py calls Cmake and passes the arguments in CMAKE_CONFIGURE_ARGS to cmake.
-  # H5Py > 3.3 deprecates the file modes, that PySCF sets.
+  nativeBuildInputs = [ cmake ];
-  patches = [ ./h5py.patch ];
+  dontUseCmakeConfigure = true;
+  preConfigure = ''
+    export CMAKE_CONFIGURE_ARGS="-DBUILD_LIBCINT=0 -DBUILD_LIBXC=0 -DBUILD_XCFUN=0"
+    PYSCF_INC_DIR="${libcint}:${libxc}:${xcfun}";
+  '';
 
   buildInputs = [
+    blas
     libcint
     libxc
     xcfun
-    blas
   ];
 
   propagatedBuildInputs = [
+    cppe
+    h5py
     numpy
     scipy
-    h5py
   ];
 
-  PYSCF_INC_DIR="${libcint}:${libxc}:${xcfun}";
+  checkInputs = [ nose nose-exclude ];
 
-  doCheck = false;
   pythonImportsCheck = [ "pyscf" ];
+  preCheck = ''
+    # Set config used by tests to ensure reproducibility
+    echo 'pbc_tools_pbc_fft_engine = "NUMPY"' > pyscf/pyscf_config.py
+    export OMP_NUM_THREADS=1
+    ulimit -s 20000
+    export PYSCF_CONFIG_FILE=$(pwd)/pyscf/pyscf_config.py
+  '';
+  # As defined for the PySCF CI at https://github.com/pyscf/pyscf/blob/master/.github/workflows/run_tests.sh
+  # minus some additionally numerically instable tests, that are sensitive to BLAS, FFTW, etc.
+  checkPhase = ''
+    runHook preCheck
+
+    nosetests pyscf/ -v \
+      --exclude-dir=examples --exclude-dir=pyscf/pbc/grad \
+      --exclude-dir=pyscf/x2c \
+      --exclude-dir=pyscf/pbc/tdscf \
+      -e test_bz \
+      -e h2o_vdz \
+      -e test_mc2step_4o4e \
+      -e test_ks_noimport \
+      -e test_jk_hermi0 \
+      -e test_j_kpts \
+      -e test_k_kpts \
+      -e high_cost \
+      -e skip \
+      -e call_in_background \
+      -e libxc_cam_beta_bug \
+      -e test_finite_diff_rks_eph \
+      -e test_finite_diff_uks_eph \
+      -e test_pipek \
+      -e test_n3_cis_ewald \
+      -I test_kuccsd_supercell_vs_kpts\.py \
+      -I test_kccsd_ghf\.py \
+      -I test_h_.*\.py \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondKSTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondKSTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_krhf_slow_supercell.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_hf.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_ks.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_hf.DiamondTestSupercell3 \
+      --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_ks.DiamondTestSupercell3 \
+      -I .*_slow.*py -I .*_kproxy_.*py -I test_proxy.py tdscf/*_slow.py gw/*_slow.py
+
+    runHook postCheck
+  '';
 
   meta = with lib; {
     description = "Python-based simulations of chemistry framework";
     homepage = "https://github.com/pyscf/pyscf";
     license = licenses.asl20;
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     maintainers = [ maintainers.sheepforce ];
   };
 }

pkgs/development/python-modules/pyscf/h5py.patch

@@ -1,13 +0,0 @@
-diff --git a/pyscf/lib/misc.py b/pyscf/lib/misc.py
-index ed43689ff..a8a0d0e20 100644
---- a/pyscf/lib/misc.py
-+++ b/pyscf/lib/misc.py
-@@ -42,8 +42,6 @@ if h5py.version.version[:4] == '2.2.':
-     sys.stderr.write('h5py-%s is found in your environment. '
-                      'h5py-%s has bug in threading mode.\n'
-                      'Async-IO is disabled.\n' % ((h5py.version.version,)*2))
--if h5py.version.version[:2] == '3.':
--    h5py.get_config().default_file_mode = 'a'
- 
- c_double_p = ctypes.POINTER(ctypes.c_double)
- c_int_p = ctypes.POINTER(ctypes.c_int)

pkgs/development/python-modules/slicer/default.nix

@@ -5,6 +5,7 @@
 , pytestCheckHook
 , pandas
 , pytorch
+, scipy
 }:
 
 buildPythonPackage rec {
@@ -17,7 +18,7 @@ buildPythonPackage rec {
     sha256 = "f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec";
   };
 
-  checkInputs = [ pytestCheckHook pandas pytorch ];
+  checkInputs = [ pytestCheckHook pandas pytorch scipy ];
 
   meta = with lib; {
     description = "Wraps tensor-like objects and provides a uniform slicing interface via __getitem__";

pkgs/misc/emulators/mame/default.nix

@@ -33,13 +33,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "mame";
-  version = "0.237";
+  version = "0.238";
 
   src = fetchFromGitHub {
     owner = "mamedev";
     repo = "mame";
     rev = "mame${builtins.replaceStrings [ "." ] [ "" ] version}";
-    sha256 = "sha256-0GOzpE8YP32ixz+c4dtDur9K0Szf7cl/dkWzPcJRFAM=";
+    sha256 = "sha256-kh0kvtl+zPJjBWUXyzb/LSbPoJRxh55vUwF2G06tzoo=";
   };
 
   hardeningDisable = [ "fortify" ];

pkgs/os-specific/darwin/apple-sdk/default.nix

@@ -271,7 +271,7 @@ in rec {
 
   overrides = super: {
     AppKit = lib.overrideDerivation super.AppKit (drv: {
-      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps ++ [
+      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps or [] ++ [
         "/System/Library/PrivateFrameworks/"
       ];
     });
@@ -285,13 +285,13 @@ in rec {
     });
 
     CoreMedia = lib.overrideDerivation super.CoreMedia (drv: {
-      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps ++ [
+      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps or [] ++ [
         "/System/Library/Frameworks/CoreImage.framework"
       ];
     });
 
     CoreMIDI = lib.overrideDerivation super.CoreMIDI (drv: {
-      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps ++ [
+      __propagatedImpureHostDeps = drv.__propagatedImpureHostDeps or [] ++ [
         "/System/Library/PrivateFrameworks/"
       ];
       setupHook = ./private-frameworks-setup-hook.sh;

pkgs/servers/computing/storm/default.nix

@@ -7,12 +7,12 @@
 
 stdenv.mkDerivation rec {
   pname = "apache-storm";
-  version = "2.2.0";
+  version = "2.3.0";
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://apache/storm/${name}/${name}.tar.gz";
-    sha256 = "0xc6lfilfkkjyds59b6c770gj21v9srzpln31c9qb3ls6hzic8gn";
+    sha256 = "sha256-ScIlWyZjPG/ZY5nFIDOeRZ/NopoOfm0Mh3XO/P9sNjY=";
   };
 
   nativeBuildInputs = [ zip unzip ];

pkgs/shells/bash/update-patch-set.sh

@@ -28,7 +28,7 @@ md5sum -c gpgkey.asc.md5
 gpg --import ./gpgkey.asc
 rm gpgkey.asc{,.md5}
 
-( echo "# Automatically generated by \`$(basename $0)'; do not edit." ;	\
+( echo "# Automatically generated by \`$(basename "$0")'; do not edit." ;	\
   echo "" ;								\
   echo "patch: [" )							\
 >> "$PATCH_LIST"

pkgs/tools/misc/cpufetch/default.nix

@@ -1,17 +1,23 @@
-{ stdenv, lib, fetchFromGitHub, installShellFiles }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, installShellFiles
+}:
 
 stdenv.mkDerivation rec {
   pname = "cpufetch";
-  version = "1.00";
+  version = "1.01";
 
   src = fetchFromGitHub {
-    owner  = "Dr-Noob";
+    owner = "Dr-Noob";
-    repo   = "cpufetch";
+    repo = "cpufetch";
-    rev    = "v${version}";
+    rev = "v${version}";
-    sha256 = "sha256-2Iar7RwL3T4DrFbqKJFys/R+VENRg2lmYFkslEaZeVE=";
+    sha256 = "sha256-vae/59eEDuZUDsTHE93mi+L8WBr3H4zp+mzXg7WWusA=";
   };
 
-  nativeBuildInputs = [ installShellFiles ];
+  nativeBuildInputs = [
+    installShellFiles
+  ];
 
   installPhase = ''
     runHook preInstall

pkgs/tools/misc/mbuffer/default.nix

@@ -1,32 +1,40 @@
-{ lib, stdenv, fetchurl,
+{ lib
-  openssl,
+, stdenv
- } :
+, fetchurl
+, openssl
+, which
+}:
 
 stdenv.mkDerivation rec {
-  version = "20210328";
   pname = "mbuffer";
+  version = "20211018";
 
   src = fetchurl {
     url = "http://www.maier-komor.de/software/mbuffer/mbuffer-${version}.tgz";
-    sha256 = "sha256-UbW42EiJkaVf4d/OkBMPnke8HOKGugO09ijAS3hP3F0=";
+    sha256 = "sha256-4kDB5OSsFMKL6MZg7EfUTOFrHo7JKqkHrRMAT/1dtuM=";
   };
 
-  buildInputs = [ openssl ];
+  buildInputs = [
+    openssl
+    which
+  ];
 
   # The mbuffer configure scripts fails to recognize the correct
   # objdump binary during cross-building for foreign platforms.
   # The correct objdump is exposed via the environment variable
   # $OBJDUMP, which should be used in such cases.
   preConfigure = lib.optionalString (stdenv.hostPlatform != stdenv.buildPlatform) ''
-    substituteInPlace configure --replace "OBJDUMP=$ac_cv_path_OBJDUMP" 'OBJDUMP=''${OBJDUMP}'
+    substituteInPlace configure \
+      --replace "OBJDUMP=$ac_cv_path_OBJDUMP" 'OBJDUMP=''${OBJDUMP}'
   '';
+
   doCheck = true;
 
-  meta = {
+  meta = with lib; {
-    homepage = "https://www.maier-komor.de/mbuffer.html";
     description  = "A tool for buffering data streams with a large set of unique features";
-    license = lib.licenses.gpl3Only;
+    homepage = "https://www.maier-komor.de/mbuffer.html";
-    maintainers = with lib.maintainers; [ tokudan ];
+    license = licenses.gpl3Only;
-    platforms = lib.platforms.linux; # Maybe other non-darwin Unix
+    maintainers = with maintainers; [ tokudan ];
+    platforms = platforms.linux; # Maybe other non-darwin Unix
   };
 }

pkgs/tools/misc/pspg/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pspg";
-  version = "5.4.1";
+  version = "5.5.0";
 
   src = fetchFromGitHub {
     owner = "okbob";
     repo = pname;
     rev = version;
-    sha256 = "1pi9dbjhd2mj11p3hx74f3rr8ysriq7sy2x012r0kil3b5xzpv2p";
+    sha256 = "sha256-zrnmhv+dc2Om1FE5TeoYCOjKGs2+mfMqcaRaTakHxAQ=";
   };
 
   nativeBuildInputs = [ pkg-config installShellFiles ];

pkgs/tools/security/exploitdb/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "exploitdb";
-  version = "2021-11-25";
+  version = "2021-11-27";
 
   src = fetchFromGitHub {
     owner = "offensive-security";
     repo = pname;
     rev = version;
-    sha256 = "sha256-kvkbWsdWMxDwMehOUoqccrVMzerPV5F6S0cNm6xrX2E";
+    sha256 = "sha256-gELHYX1gaNtQtDIyIa3cJOWilf02PknlSyMI4a7pOX4=";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/tools/security/hashcat/default.nix

@@ -8,11 +8,11 @@
 
 stdenv.mkDerivation rec {
   pname   = "hashcat";
-  version = "6.2.4";
+  version = "6.2.5";
 
   src = fetchurl {
     url = "https://hashcat.net/files/hashcat-${version}.tar.gz";
-    sha256 = "sha256-kCA5b/kzaT4xC0ebZB6G8Xg9mBnWDR2Qd1KtjSSmDDE=";
+    sha256 = "sha256-b2iZ162Jlln3tDpNaAmFQ6tUbSFx+OUdaR0Iplk3iWk=";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/tools/system/hwinfo/default.nix

@@ -1,16 +1,33 @@
-{ lib, stdenv, fetchFromGitHub, libx86emu, flex, perl, libuuid }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, flex
+, libuuid
+, libx86emu
+, perl
+}:
 
 stdenv.mkDerivation rec {
   pname = "hwinfo";
-  version = "21.76";
+  version = "21.78";
 
   src = fetchFromGitHub {
     owner = "opensuse";
     repo = "hwinfo";
     rev = version;
-    sha256 = "sha256-C0aYEgJC+ITxWcYBLPehNz9J1Y25gS1+UDVc3+7nIKQ=";
+    sha256 = "sha256-uYI7nFwUJwuxAoa6+ZxYcFb3kI2DtxTobgxAetuvemw=";
   };
 
+  nativeBuildInputs = [
+    flex
+  ];
+
+  buildInputs = [
+    libuuid
+    libx86emu
+    perl
+  ];
+
   postPatch = ''
     # VERSION and changelog are usually generated using Git
     # unless HWINFO_VERSION is defined (see Makefile)
@@ -22,13 +39,13 @@ stdenv.mkDerivation rec {
     substituteInPlace hwinfo.pc.in --replace "prefix=/usr" "prefix=$out"
   '';
 
-  nativeBuildInputs = [ flex ];
+  makeFlags = [
-  buildInputs = [ libx86emu perl libuuid ];
+    "LIBDIR=/lib"
+  ];
 
-  makeFlags = [ "LIBDIR=/lib" ];
+  installFlags = [
-  #enableParallelBuilding = true;
+    "DESTDIR=$(out)"
-
+  ];
-  installFlags = [ "DESTDIR=$(out)" ];
 
   meta = with lib; {
     description = "Hardware detection tool from openSUSE";

pkgs/top-level/aliases.nix

@@ -550,6 +550,7 @@ mapAliases ({
   minergate = throw "minergate has been removed from nixpkgs, because the package is unmaintained and the site has a bad reputation"; # added 2021-08-13
   minergate-cli = throw "minergatecli has been removed from nixpkgs, because the package is unmaintained and the site has a bad reputation"; # added 2021-08-13
   minetime = throw "minetime has been removed from nixpkgs, because it was discontinued 2021-06-22"; # added 2021-10-14
+  monero = monero-cli; # added 2021-11-28
   mopidy-gmusic = throw "mopidy-gmusic has been removed because Google Play Music was discontinued"; # added 2021-03-07
   mopidy-local-images = throw "mopidy-local-images has been removed as it's unmaintained. Its functionality has been merged into the mopidy-local extension."; # added 2020-10-18
   mopidy-local-sqlite = throw "mopidy-local-sqlite has been removed as it's unmaintained. Its functionality has been merged into the mopidy-local extension."; # added 2020-10-18

pkgs/top-level/all-packages.nix

@@ -15960,6 +15960,8 @@ with pkgs;
 
   ctpl = callPackage ../development/libraries/ctpl { };
 
+  cppe = callPackage ../development/libraries/science/chemistry/cppe { };
+
   cppdb = callPackage ../development/libraries/cppdb { };
 
   cpp-utilities = callPackage ../development/libraries/cpp-utilities { };
@@ -29750,16 +29752,16 @@ with pkgs;
 
   lndmanage = callPackage ../applications/blockchains/lndmanage { };
 
-  monero = callPackage ../applications/blockchains/monero {
+  monero-cli = callPackage ../applications/blockchains/monero-cli {
     inherit (darwin.apple_sdk.frameworks) CoreData IOKit PCSC;
     boost = boost17x;
   };
 
-  oxen = callPackage ../applications/blockchains/oxen {
+  monero-gui = libsForQt5.callPackage ../applications/blockchains/monero-gui {
     boost = boost17x;
   };
 
-  monero-gui = libsForQt5.callPackage ../applications/blockchains/monero-gui {
+  oxen = callPackage ../applications/blockchains/oxen {
     boost = boost17x;
   };
 
@@ -32435,12 +32437,6 @@ with pkgs;
 
   mame = libsForQt514.callPackage ../misc/emulators/mame {
     inherit (darwin.apple_sdk.frameworks) CoreAudioKit ForceFeedback;
-    # TODO: remove it on mame 0.238
-    stdenv =
-      if stdenv.cc.isClang then
-        overrideCC stdenv clang_6
-      else
-        stdenv;
   };
 
   martyr = callPackage ../development/libraries/martyr { };

pkgs/top-level/php-packages.nix

@@ -565,6 +565,7 @@ lib.makeScope pkgs.newScope (self: with self; {
           buildInputs = [ libxml2 ];
           internalDeps = [ php.extensions.dom ];
           NIX_CFLAGS_COMPILE = [ "-I../.." "-DHAVE_DOM" ];
+          doCheck = false;
           configureFlags = [ "--enable-xmlreader" ]
             # Required to build on darwin.
             ++ lib.optionals (lib.versionOlder php.version "7.4") [ "--with-libxml-dir=${libxml2.dev}" ];

pkgs/top-level/python-packages.nix

@@ -1769,6 +1769,10 @@ in {
 
   cozy = callPackage ../development/python-modules/cozy { };
 
+  cppe = callPackage ../development/python-modules/cppe {
+    cppe = pkgs.cppe;
+  };
+
   cppheaderparser = callPackage ../development/python-modules/cppheaderparser { };
 
   cppy = callPackage ../development/python-modules/cppy { };
@@ -2703,6 +2707,8 @@ in {
 
   fido2 = callPackage ../development/python-modules/fido2 { };
 
+  fields = callPackage ../development/python-modules/fields { };
+
   filebrowser_safe = callPackage ../development/python-modules/filebrowser_safe { };
 
   filebytes = callPackage ../development/python-modules/filebytes { };
@@ -5943,6 +5949,8 @@ in {
 
   poezio = callPackage ../applications/networking/instant-messengers/poezio { };
 
+  polarizationsolver = callPackage ../development/python-modules/polarizationsolver { };
+
   polib = callPackage ../development/python-modules/polib { };
 
   policy-sentry = callPackage ../development/python-modules/policy-sentry { };