Merge staging-next into staging

maintainers/maintainer-list.nix

···
     githubId = 37017396;
     name = "gbtb";
   };
+  gdinh = {
+    email = "[e-mail]";
+    github = "gdinh";
+    githubId = 34658064;
+    name = "Grace Dinh";
+  };
   gebner = {
     email = "[e-mail]";
     github = "gebner";

pkgs/applications/audio/squeezelite/default.nix

···
   pname = binName;
   # versions are specified in `squeezelite.h`
   # see https://github.com/ralph-irving/squeezelite/issues/29
-  version = "1.9.9.1401";
+  version = "1.9.9.1403";
 
   src = fetchFromGitHub {
     owner = "ralph-irving";
     repo = "squeezelite";
-    rev = "894df3ea80f66a27a9ae5fab918acf62a6798b8b";
-    hash = "sha256-LIi+9vb0+56AGvVrLx4gQaUkUNjIi6PmqrLViLT1DSU=";
+    rev = "bc72c0de3fff771540a2a45aaafafed539387b3c";
+    hash = "sha256-205i61mbeQG2MzSE9NtPHSuNeyMbjZzbZVCFFzjqKqQ=";
   };
 
   buildInputs = [ flac libmad libvorbis mpg123 ]

pkgs/applications/misc/1password/default.nix

···
   pname = "1password-cli";
   version = "2.6.1";
   sources = rec {
-    aarch64-linux = fetch "linux_arm64" "sha256-2V3/F7/HEOvk2T1dv4rnS0xu6Z5EqGSV/9erED7ZS1w=" "zip";
-    i686-linux = fetch "linux_386" "sha256-z4pKZY5DQ2oDHHuet1S/p7GM+rXS8/8xmTrN+rqCUBo=" "zip";
+    aarch64-linux = fetch "linux_arm64" "sha256-udKcojp7CUz5mXIFeLiXKJ7X1A/fejoeLUc+2zlnlKo=" "zip";
+    i686-linux = fetch "linux_386" "sha256-gJpwZrtgzC+fD8dqc2hgfsAiYmVkAY3xSmIQnsC5naw=" "zip";
     x86_64-linux = fetch "linux_amd64" "sha256-X+VyoXg7HRq70b9qRhk2N/UvBlhIkvCWM6kadaGDhsU=" "zip";
-    aarch64-darwin = fetch "apple_universal" "sha256-YPidRXNzNNuDoM2Gd5dEsCDxwosBJFKSzjoP0SPkQZs=" "pkg";
+    aarch64-darwin = fetch "apple_universal" "sha256-Z8MKp9fQBsvg1nQ0QSrnMV0Bxy6LmnwHb5WIrhGjxv8=" "pkg";
     x86_64-darwin = aarch64-darwin;
   };
   platforms = builtins.attrNames sources;

pkgs/applications/networking/browsers/offpunk/default.nix

···
   offpunk,
   python3,
   stdenv,
-  testVersion,
+  testers,
   timg,
   xdg-utils,
   xsel,
···
    runHook postInstall
   '';
 
-  passthru.tests.version = testVersion { package = offpunk; };
+  passthru.tests.version = testers.testVersion { package = offpunk; };
 
   meta = with lib; {
     description = "An Offline-First browser for the smolnet ";

pkgs/applications/networking/instant-messengers/telegram/tdesktop/default.nix

···
 in
 env.mkDerivation rec {
   pname = "telegram-desktop";
-  version = "4.0.2";
+  version = "4.1.0";
   # Note: Update via pkgs/applications/networking/instant-messengers/telegram/tdesktop/update.py
 
   # Telegram-Desktop with submodules
···
     repo = "tdesktop";
     rev = "v${version}";
     fetchSubmodules = true;
-    sha256 = "07fhm36394171w0rvay1x9x1br3z36z4dlpi57bkq23dvi331pxj";
+    sha256 = "06va1b5dac7a2av6vc0xin27y1hfnf4xbafy10myv33am8l5222m";
   };
 
   postPatch = ''

pkgs/applications/networking/instant-messengers/telegram/tdesktop/tg_owt.nix

···
 
 stdenv.mkDerivation {
   pname = "tg_owt";
-  version = "unstable-2022-05-08";
+  version = "unstable-2022-08-11";
 
   src = fetchFromGitHub {
     owner = "desktop-app";
     repo = "tg_owt";
-    rev = "10d5f4bf77333ef6b43516f90d2ce13273255f41";
-    sha256 = "02sky7sx73rj8xm1f70vy94zxaab6qiif742fv0vi4y6pfqrngn7";
+    rev = "a5fbc9123e056e611e69acf0ceb4252ddd838adb";
+    sha256 = "1hzck63spjjkqzkj0mlrxygrix4lw0n3i5cmc0vkxaphfzawz74n";
     fetchSubmodules = true;
   };
 

pkgs/applications/science/biology/mni_autoreg/default.nix

···
-{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, perlPackages, libminc }:
+{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }:
 
 stdenv.mkDerivation rec {
   pname = "mni_autoreg";
-  version = "unstable-2017-09-22";
+  version = "unstable-2022-05-20";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
     repo = pname;
-    rev = "ab99e29987dc029737785baebf24896ec37a2d76";
-    sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq";
+    rev = "be7bd25bf7776974e0f2c1d90b6e7f8ccc0c8874";
+    sha256 = "sGMZbCrdV6yAOgGiqvBFOUr6pGlTCqwy8yNrPxMoKco=";
   };
-
-  patches = [
-    # Pull upstream workaround for -fno-common toolchains:
-    #  https://github.com/BIC-MNI/mni_autoreg/pull/28
-    (fetchpatch {
-      name = "fno-common.patch";
-      url = "https://github.com/BIC-MNI/mni_autoreg/commit/06adfacbd84369ea3bcc4376596ac1c0f2e49af9.patch";
-      sha256 = "004sdrbx9kcj1qqwjly6p03svakl0x2sbv83salyg63fv67jynx8";
-    })
-  ];
 
   nativeBuildInputs = [ cmake makeWrapper ];
   buildInputs = [ libminc ];

pkgs/applications/virtualization/krunvm/default.nix

···
+{ lib
+, stdenv
+, rustPlatform
+, fetchFromGitHub
+, asciidoctor
+, libkrun
+}:
+
+stdenv.mkDerivation rec {
+  pname = "krunvm";
+  version = "0.2.1";
+
+  src = fetchFromGitHub {
+    owner = "containers";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-rR762L8P+7ebE0u4MVCJoXc5mmqXlDFfSas+lFBMVFQ=";
+  };
+
+  cargoDeps = rustPlatform.fetchCargoTarball {
+    inherit src;
+    hash = "sha256-3WiXm90XiQHpCbhlkigg/ZATQeDdUKTstN7hwcsKm4o=";
+  };
+
+  nativeBuildInputs = with rustPlatform;[
+    cargoSetupHook
+    rust.cargo
+    rust.rustc
+    asciidoctor
+  ];
+
+  buildInputs = [ libkrun ];
+
+  makeFlags = [ "PREFIX=${placeholder "out"}" ];
+
+  meta = with lib; {
+    description = "A CLI-based utility for creating microVMs from OCI images";
+    homepage = "https://github.com/containers/krunvm";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ nickcao ];
+  };
+}

pkgs/applications/virtualization/kvmtool/default.nix

···
 
 stdenv.mkDerivation {
   pname = "kvmtool";
-  version = "unstable-2022-04-04";
+  version = "unstable-2022-06-09";
 
   src = fetchgit {
     url = "https://git.kernel.org/pub/scm/linux/kernel/git/will/kvmtool.git";
-    rev = "5657dd3e48b41bc6db38fa657994bc0e030fd31f";
-    sha256 = "1y1j44lk9957f2dmyrscbxl4zncp4ibvvcdj6bwylb8jsvmd5fs2";
+    rev = "f44af23e3a62e46158341807b0d2d132249b96a8";
+    sha256 = "sha256-M83dCCXU/fkh21x10vx6BLg9Wja1714qW7yxl5zY6z0=";
   };
 
   enableParallelBuilding = true;

pkgs/development/libraries/irrlichtmt/default.nix

···
 }:
 stdenv.mkDerivation rec {
   pname = "irrlichtmt";
-  version = "1.9.0mt5";
+  version = "1.9.0mt7";
 
   src = fetchFromGitHub {
     owner = "minetest";
     repo = "irrlicht";
     rev = version;
-    sha256 = "sha256-ocsO4nKab2YxHY1qqZbF4OErpBKmG4V+psgC40APs8s=";
+    sha256 = "sha256-Eu7zW3mXl7GPRmLnKjt/dPoZ64HPYulI7MO1dJfj+10=";
   };
 
   nativeBuildInputs = [
···
   ];
 
   # https://github.com/minetest/minetest/pull/10729
-  postPatch = lib.optionalString withTouchSupport ''
-    substituteInPlace include/IrrCompileConfig.h \
-      --replace '//#define _IRR_LINUX_X11_XINPUT2_' '#define _IRR_LINUX_X11_XINPUT2_'
+  postPatch = lib.optionalString (!withTouchSupport) ''
+    sed -i '1i #define NO_IRR_LINUX_X11_XINPUT2_' include/IrrCompileConfig.h
+
+    # HACK: Fix mistake in build script
+    sed -i '/''${X11_Xi_LIB}/d' source/Irrlicht/CMakeLists.txt
   '';
 
   buildInputs = [

pkgs/development/libraries/libkrun/default.nix

···
+{ lib
+, stdenv
+, fetchFromGitHub
+, rustPlatform
+, pkg-config
+, glibc
+, openssl
+, libkrunfw
+, sevVariant ? false
+}:
+
+stdenv.mkDerivation rec {
+  pname = "libkrun";
+  version = "1.3.0";
+
+  src = fetchFromGitHub {
+    owner = "containers";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-qVyEqiqaQ8wfZhL5u+Bsaa1yXlgHUitSj5bo7FJ5Y8c=";
+  };
+
+  cargoDeps = rustPlatform.fetchCargoTarball {
+    inherit src;
+    hash = "sha256-jxSzhj1iU8qY+sZEVCYTaUqpaA4egjJi9qxrapASQF0=";
+  };
+
+  nativeBuildInputs = with rustPlatform;[
+    cargoSetupHook
+    rust.cargo
+    rust.rustc
+  ] ++ lib.optional sevVariant pkg-config;
+
+  buildInputs = [
+    glibc
+    glibc.static
+    (libkrunfw.override { inherit sevVariant; })
+  ] ++ lib.optional sevVariant openssl;
+
+  makeFlags = [ "PREFIX=${placeholder "out"}" ]
+    ++ lib.optional sevVariant "SEV=1";
+
+  meta = with lib; {
+    description = "A dynamic library providing Virtualization-based process isolation capabilities";
+    homepage = "https://github.com/containers/libkrun";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ nickcao ];
+  };
+}

pkgs/development/libraries/libkrunfw/default.nix

···
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchurl
+, flex
+, bison
+, bc
+, elfutils
+, python3
+, sevVariant ? false
+}:
+
+assert sevVariant -> stdenv.isx86_64;
+stdenv.mkDerivation rec {
+  pname = "libkrunfw";
+  version = "3.3.0";
+
+  src = fetchFromGitHub {
+    owner = "containers";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-ay+E5AgJeA0i3T4JDosDawwtezDGquzAvYEWHGbPidg=";
+  };
+
+  kernelSrc = fetchurl {
+    url = "https://cdn.kernel.org/pub/linux/kernel/v5.x/linux-5.15.59.tar.xz";
+    hash = "sha256-5t3GQgVzQNsGs7khwrMb/tLGETWejxRMPlz5w6wzvMs=";
+  };
+
+  preBuild = ''
+    substituteInPlace Makefile --replace 'curl $(KERNEL_REMOTE) -o $(KERNEL_TARBALL)' 'ln -s $(kernelSrc) $(KERNEL_TARBALL)'
+  '';
+
+  nativeBuildInputs = [ flex bison bc python3 python3.pkgs.pyelftools ];
+  buildInputs = [ elfutils ];
+
+  makeFlags = [ "PREFIX=${placeholder "out"}" ]
+    ++ lib.optional sevVariant "SEV=1";
+
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "A dynamic library bundling the guest payload consumed by libkrun";
+    homepage = "https://github.com/containers/libkrunfw";
+    license = with licenses; [ lgpl2Only lgpl21Only ];
+    maintainers = with maintainers; [ nickcao ];
+    platforms = [ "x86_64-linux" "aarch64-linux" ];
+  };
+}

pkgs/development/libraries/libminc/default.nix

···
 
 stdenv.mkDerivation rec {
   pname   = "libminc";
-  version = "unstable-2020-07-17";
+  version = "2.4.05";
 
   owner = "BIC-MNI";
 
   src = fetchFromGitHub {
     inherit owner;
     repo   = pname;
-    rev    = "ffb5fb234a852ea7e8da8bb2b3b49f67acbe56ca";
-    sha256 = "0yr4ksghpvxh9zg0a4p7hvln3qirsi08plvjp5kxx2qiyj96zsdm";
+    rev    = "aa08255f0856e70fb001c5f9ee1f4e5a8c12d47d";  # new release, but no git tag
+    sha256 = "XMTO6/HkyrrQ0s5DzJLCmmWheye2DGMnpDbcGdP6J+A=";
   };
 
   postPatch = ''
···
   cmakeFlags = [
     "-DLIBMINC_MINC1_SUPPORT=ON"
     "-DLIBMINC_BUILD_SHARED_LIBS=ON"
+    "-DLIBMINC_USE_NIFTI=ON"
     "-DLIBMINC_USE_SYSTEM_NIFTI=ON"
   ];
 
   doCheck = !stdenv.isDarwin;
+    # -j1: see https://github.com/BIC-MNI/libminc/issues/110
   checkPhase = ''
-    ctest -j1 -E 'ezminc_rw_test' --output-on-failure
-    # -j1: see https://github.com/BIC-MNI/libminc/issues/110
-    # ezminc_rw_test: can't find libminc_io.so.5.2.0
+    ctest -j1 --output-on-failure
   '';
 
   meta = with lib; {

pkgs/development/libraries/science/biology/ciftilib/default.nix

···
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, boost
+, libxmlxx
+, pkg-config
+, zlib
+}:
+
+stdenv.mkDerivation rec {
+  pname = "ciftilib";
+  version = "1.6.0";
+
+  src = fetchFromGitHub {
+    owner = "Washington-University";
+    repo = "CiftiLib";
+    rev = "v${version}";
+    hash = "sha256-xc2dpMse4SozYEV/w3rXCrh1LKpTThq5nHB2y5uAD0A=";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ boost libxmlxx zlib ];
+
+  cmakeFlags = [ "-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;'big|datatype-md5'" ];
+
+  doCheck = true;
+
+  meta = with lib; {
+    homepage = "https://github.com/Washington-University/CiftiLib";
+    description = "Library for reading and writing CIFTI files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license = licenses.bsd2;
+  };
+}

pkgs/development/libraries/science/math/scalapack/default.nix

···
   checkInputs = [ openssh ];
   buildInputs = [ blas lapack ];
   propagatedBuildInputs = [ mpi ];
+  hardeningDisable = lib.optionals (stdenv.isAarch64 && stdenv.isDarwin) [ "stackprotector" ];
 
-  doCheck = true;
+  # xslu and xsllt tests seem to time out on x86_64-darwin.
+  # this line is left so those who force installation on x86_64-darwin can still build
+  doCheck = !(stdenv.isx86_64 && stdenv.isDarwin);
 
   preConfigure = ''
     cmakeFlagsArray+=(
···
     homepage = "http://www.netlib.org/scalapack/";
     description = "Library of high-performance linear algebra routines for parallel distributed memory machines";
     license = licenses.bsd3;
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ costrouc markuskowa ];
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ costrouc markuskowa gdinh ];
+    # xslu and xsllt tests fail on x86 darwin
+    broken = stdenv.isDarwin && stdenv.isx86_64;
   };
 }

pkgs/development/libraries/vtk/9.x.nix

···
 import ./generic.nix {
-  majorVersion = "9.0";
-  minorVersion = "3";
-  sourceSha256 = "vD65Ylsrjb/stgUqKrCR/JFAXeQzOw7GjzMjgVFU7Yo=";
-
-  patchesToFetch = [
-    # Add missing header includes.
-    # https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7611
-    {
-     url = "https://gitlab.kitware.com/vtk/vtk/-/commit/e066c3f4fbbfe7470c6207db0fc3f3952db633cb.patch";
-     sha256 = "ggmDisS3qoMquOqrmIYlCIT7TLxP/DUtW29ktjaEnlM=";
-    }
-  ];
+  majorVersion = "9.1";
+  minorVersion = "0";
+  sourceSha256 = "sha256-j+1C9Pjx64CDEHto6qmtcdoHEQFhoxFq2Af0PlylzpY=";
 }

pkgs/development/libraries/vtk/generic.nix

···
 { majorVersion, minorVersion, sourceSha256, patchesToFetch ? [] }:
 { stdenv, lib, fetchurl, cmake, libGLU, libGL, libX11, xorgproto, libXt, libpng, libtiff
 , fetchpatch
-, enableQt ? false, wrapQtAppsHook, qtbase, qtx11extras, qttools
+, enableQt ? false, qtbase, qtx11extras, qttools, qtdeclarative, qtEnv
 , enablePython ? false, pythonInterpreter ? throw "vtk: Python support requested, but no python interpreter was given."
 # Darwin support
 , Cocoa, CoreServices, DiskArbitration, IOKit, CFNetwork, Security, GLUT, OpenGL
···
   nativeBuildInputs = [ cmake ];
 
   buildInputs = [ libpng libtiff ]
-    ++ optionals enableQt [ qtbase qtx11extras qttools ]
+    ++ optionals enableQt (if lib.versionOlder majorVersion "9"
+                           then [ qtbase qtx11extras qttools ]
+                           else  [ (qtEnv "qvtk-qt-env" [ qtx11extras qttools qtdeclarative ]) ])
     ++ optionals stdenv.isLinux [
       libGLU
       libGL

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

···
 
 buildPythonPackage rec {
   pname = "batchgenerators";
-  version = "0.21";
+  version = "0.24";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
···
     owner = "MIC-DKFZ";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-q8mBWcy+PkJcfiKtq8P2bnTw56FE1suVS0zUgUEmc5k=";
+    hash = "sha256-47jAeHMJPBk7GpUvXtQuJchgiSy6M50anftsuXWk2ag=";
   };
 
   propagatedBuildInputs = [
···
     threadpoolctl
   ];
 
-  checkInputs = [
-    pytestCheckHook
-  ];
-
-  patches = [
-    # Remove deprecated unittest2, https://github.com/MIC-DKFZ/batchgenerators/pull/78
-    (fetchpatch {
-      name = "remove-unittest2.patch";
-      url = "https://github.com/MIC-DKFZ/batchgenerators/commit/87a9437057df8a7550aa3b3eaf840871cc0d5cef.patch";
-      sha256 = "sha256-vozBK7g2dLxx9din/R2vU28Mm+LoGAO/BmQlt/ShmEo=";
-    })
-  ];
-
+  # see https://github.com/MIC-DKFZ/batchgenerators/pull/78
   postPatch = ''
     substituteInPlace setup.py \
       --replace '"unittest2",' ""
   '';
 
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  # see https://github.com/MIC-DKFZ/batchgenerators/pull/78
+  disabledTestPaths = [ "tests/test_axis_mirroring.py" ];
+
   pythonImportsCheck = [
     "batchgenerators"
+    "batchgenerators.augmentations"
+    "batchgenerators.dataloading"
+    "batchgenerators.datasets"
+    "batchgenerators.transforms"
+    "batchgenerators.utilities"
   ];
 
   meta = with lib; {

pkgs/development/python-modules/bleak-retry-connector/default.nix

···
 
 buildPythonPackage rec {
   pname = "bleak-retry-connector";
-  version = "1.7.1";
+  version = "1.7.2";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
···
     owner = "Bluetooth-Devices";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-ql7j+m8g7ZgkgqJGUVE903n1b73kqWDExgSbnDpKQwc=";
+    hash = "sha256-qRUS+JJWd2MPXa5Bs2WzZIHk6VcPe75yBoArFGk2yHQ=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/govee-ble/default.nix

···
 
 buildPythonPackage rec {
   pname = "govee-ble";
-  version = "0.14.0";
+  version = "0.14.1";
   format = "pyproject";
 
   disabled = pythonOlder "3.9";
···
     owner = "Bluetooth-Devices";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-iJ3fvbQBIk2fpCfz9/uvxk6WcGaL8OVDsNQux+pTBhM=";
+    hash = "sha256-gAhrhHTPwNipAFS22GXKjeVXqx0AGorvsqqEWKwRLzA=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/json-schema-for-humans/default.nix

···
 
 buildPythonPackage rec {
   pname = "json-schema-for-humans";
-  version = "0.41.6";
+  version = "0.41.8";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
···
     owner = "coveooss";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-t5t+tZwhzOHpI2nc69baWtZamEOeouseMuVBnCQyjzQ=";
+    hash = "sha256-lz08+T8ITsCI0qjcd/JcgXG4o87UjoP1NQa01FJ7fO0=";
   };
 
   postPatch = ''

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

···
 { lib
+, stdenv
 , fetchFromGitHub
 , buildPythonPackage
 , poetry-core
···
 
 buildPythonPackage rec {
   pname = "libtmux";
-  version = "0.11.0";
+  version = "0.13.0";
   format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "tmux-python";
     repo = pname;
-    rev = "v${version}";
-    hash = "sha256-QbKqS40la6UGZENyGEw5kXigzexp3q7ff43fKlQ9GqE=";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-u08lxVMuyO5CwFbmxn69QqdSWcvGaSMZgizRJlsHa0k=";
   };
 
   nativeBuildInputs = [
···
     pytestCheckHook
   ];
 
+  pytestFlagsArray = lib.optionals stdenv.isDarwin [ "--ignore=tests/test_test.py" ];
+
+  pythonImportsCheck = [ "libtmux" ];
+
   meta = with lib; {
-    description = "Scripting library for tmux";
-    homepage = "https://libtmux.readthedocs.io/";
-    license = licenses.bsd3;
+    description = "Typed scripting library / ORM / API wrapper for tmux";
+    homepage = "https://libtmux.git-pull.com/";
+    changelog = "https://github.com/tmux-python/libtmux/raw/v${version}/CHANGES";
+    license = licenses.mit;
     maintainers = with maintainers; [ ];
   };
 }

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

···
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, ninja
+, ignite
+, numpy
+, pybind11
+, pytorch
+, which
+}:
+
+buildPythonPackage rec {
+  pname = "monai";
+  version = "0.9.0";
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "Project-MONAI";
+    repo = "MONAI";
+    rev = version;
+    sha256 = "sha256-HxW9WYxt2a7fS9/1E9DtiH+SCTTJoxYBfgZqskYdcvI=";
+  };
+
+  # Ninja is not detected by setuptools for some reason even though it's present:
+  postPatch = ''
+    substituteInPlace "setup.cfg" --replace "ninja" ""
+  '';
+
+  preBuild = ''
+    export MAX_JOBS=$NIX_BUILD_CORES;
+  '';
+
+  nativeBuildInputs = [ ninja which ];
+  buildInputs = [ pybind11 ];
+  propagatedBuildInputs = [ numpy pytorch ignite ];
+
+  BUILD_MONAI = 1;
+
+  doCheck = false;  # takes too long; numerous dependencies, some not in Nixpkgs
+
+  pythonImportsCheck = [
+    "monai"
+    "monai.apps"
+    "monai.data"
+    "monai.engines"
+    "monai.handlers"
+    "monai.inferers"
+    "monai.losses"
+    "monai.metrics"
+    "monai.optimizers"
+    "monai.networks"
+    "monai.transforms"
+    "monai.utils"
+    "monai.visualize"
+  ];
+
+  meta = with lib; {
+    description = "Pytorch framework (based on Ignite) for deep learning in medical imaging";
+    homepage = "https://github.com/Project-MONAI/MONAI";
+    license = licenses.asl20;
+    maintainers = [ maintainers.bcdarwin ];
+  };
+}

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

···
 
 buildPythonPackage rec {
   pname = "pyswitchbot";
-  version = "0.18.6";
+  version = "0.18.7";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
···
     owner = "Danielhiversen";
     repo = "pySwitchbot";
     rev = "refs/tags/${version}";
-    hash = "sha256-4mVKs3Lycb9DVdFcG1gzM4FjJiQTcV7aT/OLpBacZjU=";
+    hash = "sha256-TAFrrCwlcbKoQk6puoSx2sk1WeucThf7614RNQ1NFbM=";
   };
 
   propagatedBuildInputs = [

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

···
 
 buildPythonPackage rec {
   pname = "readme-renderer";
-  version = "35.0";
+  version = "36.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
···
   src = fetchPypi {
     pname = "readme_renderer";
     inherit version;
-    sha256 = "sha256-pyeZms/CIvwh2CoS7UjJV8SYl4XlhlgHxlpIfSFndJc=";
+    sha256 = "sha256-9xru+aWI/L7R9MwAG6YRNw6UoM0nx1sRQFN2GOx48KI=";
   };
 
   propagatedBuildInputs = [

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

···
 
 buildPythonPackage rec {
   pname = "threadpoolctl";
-  version = "3.0.0";
+  version = "3.1.0";
 
   disabled = pythonOlder "3.6";
   format = "flit";
···
     owner = "joblib";
     repo = pname;
     rev = version;
-    sha256 = "02zccsiq4gvawy7q2fh3m3hvr40hl2ylmwwny6dv0lqsr2iwgnmn";
+    sha256 = "sha256-/qt7cgFbvpc1BLZC7a4S0RToqSggKXAqF1Xr6xOqzw8=";
   };
 
   checkInputs = [ pytestCheckHook numpy scipy ];

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

···
 
 buildPythonPackage rec {
   pname = "zigpy";
-  version = "0.49.0";
+  version = "0.49.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
···
     owner = "zigpy";
     repo = "zigpy";
     rev = "refs/tags/${version}";
-    sha256 = "sha256-mCqRqi7AUsrvfSOHyfK+WVj/4D7/4RDOYFWveS+tS/A=";
+    sha256 = "sha256-ai0qWKgsh8kIS4juvzpE+amsnIbEOJbhGutV75yRGog=";
   };
 
   propagatedBuildInputs = [

pkgs/development/tools/analysis/brakeman/Gemfile.lock

···
 GEM
   remote: https://rubygems.org/
   specs:
-    brakeman (5.2.3)
+    brakeman (5.3.1)
 
 PLATFORMS
   ruby
···
   brakeman
 
 BUNDLED WITH
-   2.3.9
+   2.3.20

pkgs/development/tools/analysis/brakeman/gemset.nix

···
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1m188ypcl2lb1hin21fmyk9d4fbjw4w7cr2k6l37jasw3rmgnvjv";
+      sha256 = "0zr2p0w4ckv65cv3vdwnk9f3yydmjdmw75x7dskx1gqr9j9q3306";
       type = "gem";
     };
-    version = "5.2.3";
+    version = "5.3.1";
   };
 }

pkgs/development/tools/dapr/cli/default.nix

···
 
 buildGoModule rec {
   pname = "dapr-cli";
-  version = "1.8.0";
+  version = "1.8.1";
 
   src = fetchFromGitHub {
     owner = "dapr";
     repo = "cli";
     rev = "v${version}";
-    sha256 = "sha256-ytn7fG84Wu4+fcgkV5B9djCw8KgAJWgffoNbV7wveK4=";
+    sha256 = "sha256-NzHg/pn0Gek3JhcdOBFilmmw0xaKtjTote11LLr4oj8=";
   };
 
   vendorSha256 = "sha256-ZsuDaFcBPZuyt5rmjeBkzkrphCCcraLZCrMiQ2FtAUc=";

pkgs/development/tools/esbuild/default.nix

···
 
 buildGoModule rec {
   pname = "esbuild";
-  version = "0.15.0";
+  version = "0.15.2";
 
   src = fetchFromGitHub {
     owner = "evanw";
     repo = "esbuild";
     rev = "v${version}";
-    sha256 = "sha256-ZQRU3UlUkvTgbRMGg+BVNy+0BSUYGYUysgZ69YTeqiA=";
+    sha256 = "sha256-VYW3XQvwxeUnfNMXFcqB6xhh45YgTv4Iu6ce6MEclpw=";
   };
 
   vendorSha256 = "sha256-+BfxCyg0KkDQpHt/wycy/8CTG6YBA/VJvJFhhzUnSiQ=";

pkgs/development/tools/memray/default.nix

···
+{ lib
+, fetchFromGitHub
+, libunwind
+, lz4
+, pkg-config
+, python3
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "memray";
+  version = "1.2.0";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "bloomberg";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-MZOKo0VaCJM/YyvCByM5Yg7H/8onDKNSufBzr+GsFlo=";
+  };
+
+  buildInputs = [
+    libunwind
+    lz4
+    pkg-config
+  ] ++ (with python3.pkgs; [
+    cython
+  ]);
+
+  propagatedBuildInputs = with python3.pkgs; [
+    jinja2
+    rich
+  ];
+
+  checkInputs = with python3.pkgs; [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "memray"
+  ];
+
+  pytestFlagsArray = [
+    "tests"
+  ];
+
+  disabledTests = [
+    # Import issue
+    "test_header_allocator"
+  ];
+
+  disabledTestPaths = [
+    # Very time-consuming and some tests fails (performance-related?)
+    "tests/integration/test_main.py"
+  ];
+
+  meta = with lib; {
+    description = "Memory profiler for Python";
+    homepage = "https://bloomberg.github.io/memray/";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+    platforms = platforms.linux;
+  };
+}

pkgs/development/tools/rust/cargo-public-api/default.nix

···
 
 rustPlatform.buildRustPackage rec {
   pname = "cargo-public-api";
-  version = "0.12.4";
+  version = "0.13.0";
 
   src = fetchCrate {
     inherit pname version;
-    sha256 = "sha256-URCKsI7q0/b8KkCooKeYr342m7C8ukJJITRDgOUmcEM=";
+    sha256 = "sha256-e+HM4pO0bLszlcSklsiRPamr/GUVckuw7uBSgDSK7d0=";
   };
 
-  cargoSha256 = "sha256-qXJeNbGvC6zoxdn2QmApw1m7gn4CI1eUC3Cqhrn8dpU=";
+  cargoSha256 = "sha256-RKO/YMVWKVtparAfDUtpQ3mbRWataNnjnFUUQozQghs=";
 
   nativeBuildInputs = [ pkg-config ];
 

pkgs/development/tools/sq/default.nix

···
 { lib, buildGoModule, fetchFromGitHub, installShellFiles, testers, sq }:
 buildGoModule rec {
   pname = "sq";
-  version = "0.15.4";
+  version = "0.15.6";
 
   src = fetchFromGitHub {
     owner = "neilotoole";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-4CINLOHUVXQ+4e5I1fMqog6LubMm8RnbFmeuBOwALaw=";
+    sha256 = "sha256-QEg80di2DmMfIrvsRFp7nELs7LiJRVa/wENDnf1zQ2Y=";
   };
 
   nativeBuildInputs = [ installShellFiles ];
 
-  vendorSha256 = "sha256-lNpWXKtnzwySzinNPxAKuaLqweWuS6zz8s2W4xXWlqM=";
+  vendorSha256 = "sha256-P1NxcjRA0g9NK2EaEG5E9G2TywTp5uvHesQE7+EG4ag=";
 
   # Some tests violates sandbox constraints.
   doCheck = false;

pkgs/development/web/flyctl/default.nix

···
 
 buildGoModule rec {
   pname = "flyctl";
-  version = "0.0.370";
+  version = "0.0.372";
 
   src = fetchFromGitHub {
     owner = "superfly";
     repo = "flyctl";
     rev = "v${version}";
-    sha256 = "sha256-Med1B6E6e1oLkpaL8aNtT/qoHZtkCOwSRVkVQRPNRpI=";
+    sha256 = "sha256-KsSaBzAjiexyhUmYEFEHhWuRROt553Lhkm1idlT8n5s=";
   };
 
-  vendorSha256 = "sha256-CloCB7El/fSlBXVzBstm1wgMEobBNKPIQJCilS/PhX8=";
+  vendorSha256 = "sha256-E6QeWu88MXMMfZAM7vMIGXpJQuduX6GTj3tXvlE9hFo=";
 
   subPackages = [ "." ];
 

pkgs/games/minetest/default.nix

···
   };
 
   v5 = {
-    version = "5.5.1";
-    sha256 = "sha256-ssaDy6tYxhXGZ1+05J5DwoKYnfhKIKtZj66DOV84WxA=";
-    dataSha256 = "sha256-SI6I1wXbB0CgTmIemm3VY9DNnWMoI5bt/hqRwHlUl4k=";
+    version = "5.6.0";
+    sha256 = "sha256-wcbYcVHs4L0etOwUBjKvzsmZtnpOxpFgLV8nx3UfJQI=";
+    dataSha256 = "sha256-TVaDHYstFEuT0nBExwLE1PtM1CZh71t9CRxC9rEYTd4=";
   };
 
+  mkClient = version: generic (version // { buildClient = true; buildServer = false; });
+  mkServer = version: generic (version // { buildClient = false; buildServer = true; });
 in {
-  minetestclient_5 = generic (v5 // { buildClient = true; buildServer = false; });
-  minetestserver_5 = generic (v5 // { buildClient = false; buildServer = true; });
+  minetestclient_5 = mkClient v5;
+  minetestserver_5 = mkServer v5;
 }

pkgs/os-specific/linux/cpuid/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "cpuid";
-  version = "20220620";
+  version = "20220812";
 
   src = fetchurl {
     url = "http://etallen.com/cpuid/${pname}-${version}.src.tar.gz";
-    sha256 = "sha256-kVmhwJWm5ExspjBsUIC/4qe83iXo3Bbwb1+HTXcyyxo=";
+    sha256 = "sha256-O/aPuX2UcU+QdjzK2BDfjcX3/pwfmjZSQ2SR/XVBWr8=";
   };
 
   # For pod2man during the build process.

pkgs/servers/home-assistant/component-packages.nix

···
 # Do not edit!
 
 {
-  version = "2022.8.3";
+  version = "2022.8.4";
   components = {
     "abode" = ps: with ps; [
       abodepy

pkgs/servers/home-assistant/default.nix

···
   extraPackagesFile = writeText "home-assistant-packages" (lib.concatMapStringsSep "\n" (pkg: pkg.pname) extraBuildInputs);
 
   # Don't forget to run parse-requirements.py after updating
-  hassVersion = "2022.8.3";
+  hassVersion = "2022.8.4";
 
 in python.pkgs.buildPythonApplication rec {
   pname = "homeassistant";
···
     owner = "home-assistant";
     repo = "core";
     rev = version;
-    hash = "sha256-Wx5l51+vcByOqdwqcnOn1+yYgp98kXggRmgO/wtiI+U=";
+    hash = "sha256-x6W69oGCPXK7OLN/XaF4A+OSubSnhFYof1SvLwy9+jY=";
   };
 
   # leave this in, so users don't have to constantly update their downstream patch handling

pkgs/servers/minio/default.nix

···
 in
 buildGoModule rec {
   pname = "minio";
-  version = "2022-08-08T18-34-09Z";
+  version = "2022-08-11T04-37-28Z";
 
   src = fetchFromGitHub {
     owner = "minio";
     repo = "minio";
     rev = "RELEASE.${version}";
-    sha256 = "sha256-HuKfpQY6dllxkrictCMBczHTg2oCLQtZrJQqPG2l6N8=";
+    sha256 = "sha256-gxDTHy/CDqeQhf/RZaaoloGEfAOg9djjIWdWyb+7fhM=";
   };
 
-  vendorSha256 = "sha256-uoavsixaLQg0gL70m4ea5fgH5R06YyIZHy1oxDSA0ko=";
+  vendorSha256 = "sha256-LSAB+0+yNsxi5qCXEBVf3aE8Rt+UP63AIGBV5OhWJDY=";
 
   doCheck = false;
 

pkgs/tools/misc/smug/default.nix

···
 
 buildGoModule rec {
   pname = "smug";
-  version = "0.2.7";
+  version = "0.3.2";
 
   subPackages = [ "." ];
 
···
     owner = "ivaaaan";
     repo = "smug";
     rev = "v${version}";
-    sha256 = "178125835dhnaq9k42yv4pfxpyhgb5179wrxkimb59fy0nk8jzx8";
+    sha256 = "sha256-JZV4UfrmvcM7d8Ld4m/jC3GvzJCUgXqsGBSSnz81fXk=";
   };
 
-  vendorSha256 = "1rba5rpvlr8dyhj145b5i57pm4skfpj3vm7vydkn79k6ak6x985x";
+  vendorSha256 = "sha256-vaDUzVRmpmNn8/vUPeR1U5N6T4llFRIk9A1lum8uauU=";
 
   nativeBuildInputs = [ installShellFiles ];
 
···
 
   postInstall = ''
     installManPage ./man/man1/smug.1
+    installShellCompletion completion/smug.{bash,fish}
   '';
 
   meta = with lib; {

pkgs/tools/misc/tmuxp/default.nix

···
-{ lib, python3Packages }:
+{ lib, python3Packages, installShellFiles }:
 
 let
   pypkgs = python3Packages;
···
 in
 pypkgs.buildPythonApplication rec {
   pname = "tmuxp";
-  version = "1.11.0";
+  version = "1.12.1";
 
   src = pypkgs.fetchPypi {
     inherit pname version;
-    sha256 = "sha256-N5kZ+e17ZgLOCvV/lcT/hdG1VNqLxh98QOQyM0BmZCA=";
+    sha256 = "078624c5ac7aa4142735f856fadb9281fcebb10e6b98d1be2b2f2bbd106613b9";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "libtmux>=0.12.0,<0.13.0" "libtmux"
+  '';
+
   # No tests in archive
   doCheck = false;
+
+  nativeBuildInputs = [ installShellFiles ];
 
   propagatedBuildInputs = with pypkgs; [
     click
···
     libtmux
   ];
 
+  postInstall = ''
+    installShellCompletion --cmd tmuxp \
+      --bash <(_TMUXP_COMPLETE=bash_source $out/bin/tmuxp) \
+      --fish <(_TMUXP_COMPLETE=fish_source $out/bin/tmuxp) \
+      --zsh <(_TMUXP_COMPLETE=zsh_source $out/bin/tmuxp)
+  '';
+
   meta = with lib; {
-    description = "Manage tmux workspaces from JSON and YAML";
+    description = "tmux session manager";
     homepage = "https://tmuxp.git-pull.com/";
-    license = licenses.bsd3;
+    changelog = "https://github.com/tmux-python/tmuxp/raw/v${version}/CHANGES";
+    license = licenses.mit;
     maintainers = with maintainers; [ peterhoeg ];
   };
 }

pkgs/tools/networking/htpdate/default.nix

···
 { stdenv, lib, fetchFromGitHub }:
 
 stdenv.mkDerivation rec {
-  version = "1.3.5";
+  version = "1.3.6";
   pname = "htpdate";
 
   src = fetchFromGitHub {
     owner = "twekkel";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-L3CKBgGk9R8qJFWOS98Tm1j/s/5t6+/Vt2EcZ+or0Ng=";
+    sha256 = "sha256-0NLlBNYTJ+hmQLH/UYwIOIbq3G1sDo/A03xFHsXdzig=";
   };
 
   makeFlags = [

pkgs/tools/networking/minio-client/default.nix

···
 
 buildGoModule rec {
   pname = "minio-client";
-  version = "2022-08-05T08-01-28Z";
+  version = "2022-08-11T00-30-48Z";
 
   src = fetchFromGitHub {
     owner = "minio";
     repo = "mc";
     rev = "RELEASE.${version}";
-    sha256 = "sha256-XtRpRp5KtqM+VwaouzbcjoiwuUDo4NtgaQ/bsCmwP58=";
+    sha256 = "sha256-wv/Y4MIJFISf+fvV3BYbA5kQqETsYe4vt2lp36DfFrE=";
   };
 
-  vendorSha256 = "sha256-0WljjAgL//PqooHwAusMQwJpLRYzjpDUNcrmCHUGyNs=";
+  vendorSha256 = "sha256-5kpE0jtE3ljnUsXQY2cWvABVpegrTSYZCIYy0pz4iz8=";
 
   subPackages = [ "." ];
 

pkgs/tools/security/cirrusgo/default.nix

···
+{ lib
+, stdenv
+, buildGoModule
+, fetchFromGitHub
+}:
+
+buildGoModule rec {
+  pname = "cirrusgo";
+  version = "0.1.0";
+
+  src = fetchFromGitHub {
+    owner = "Ph33rr";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-FYI/Ldu91YB/4wCiVADeYxYQOeBGro1msY5VXsnixw4=";
+  };
+
+  vendorSha256 = "sha256-KCf2KQ8u+nX/+zMGZ6unWb/Vz6zPNkKtMioFo1FlnVI=";
+
+  meta = with lib; {
+    description = "Tool to scan SAAS and PAAS applications";
+    homepage = "https://github.com/Ph33rr/cirrusgo";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}

pkgs/tools/system/hwinfo/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "hwinfo";
-  version = "22.0";
+  version = "22.1";
 
   src = fetchFromGitHub {
     owner = "opensuse";
     repo = "hwinfo";
     rev = version;
-    sha256 = "sha256-hjKF/fyV7/uQF6iJNOsRpX4Iw7aDURkdb7hbwfIDBPo=";
+    sha256 = "sha256-nGWpUqBkpiiNuH5kEHWR1/+0aYIeLf9k3AmzQR85Swk=";
   };
 
   nativeBuildInputs = [

pkgs/tools/text/colordiff/default.nix

···
-{ lib, stdenv, fetchFromGitHub, docbook_xml_dtd_412, docbook_xsl, perl, w3m, xmlto, diffutils }:
+{ lib, stdenv, fetchFromGitHub, docbook_xml_dtd_412, docbook_xsl, perl, w3m-batch, xmlto, diffutils }:
 
 stdenv.mkDerivation rec {
   pname = "colordiff";
···
     sha256 = "sha256-+TtVnUX88LMd8zmhLsKTyR9JlgR7IkUB18PF3LRgPB0=";
   };
 
-  nativeBuildInputs = [ docbook_xml_dtd_412 docbook_xsl perl w3m xmlto ];
+  nativeBuildInputs = [ docbook_xml_dtd_412 docbook_xsl perl w3m-batch xmlto ];
 
   buildInputs = [ perl ];
 

pkgs/tools/text/ugrep/default.nix

···
 
 stdenv.mkDerivation rec {
   pname = "ugrep";
-  version = "3.8.3";
+  version = "3.9.0";
 
   src = fetchFromGitHub {
     owner = "Genivia";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-p2x3WQIzM1FJBn9mvqfisjTLgjtkZouV/fr/waCiYw0=";
+    sha256 = "sha256-9tHSdO9VlsbLqFFA/CKhbPvstU3+26jBaBw/tX5qJnw=";
   };
 
   buildInputs = [

pkgs/tools/wayland/wayout/default.nix

···
+{ lib
+, stdenv
+, fetchFromSourcehut
+, rustPlatform
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "wayout";
+  version = "1.1.3";
+
+  src = fetchFromSourcehut {
+    owner = "~shinyzenith";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-EzRetxx0NojhBlBPwhQ7p9rGXDUBlocVqxcEVGIF3+0=";
+  };
+
+  cargoSha256 = "sha256-QlxXbfeWJdCythYRRLSpJbTzKkwrL4kmAfyL3tRt194=";
+
+  meta = with lib; {
+    description = "Simple output management tool for wlroots based compositors implementing";
+    homepage = "https://git.sr.ht/~shinyzenith/wayout";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ onny ];
+    broken = stdenv.isDarwin; # Build failed on Darwin
+  };
+
+}

pkgs/top-level/all-packages.nix

···
 
   wayland-proxy-virtwl = callPackage ../tools/wayland/wayland-proxy-virtwl { };
 
+  wayout = callPackage ../tools/wayland/wayout { };
+
   way-displays = callPackage ../tools/wayland/way-displays { };
 
   wev = callPackage ../tools/wayland/wev { };
···
   circus = callPackage ../tools/networking/circus { };
 
   cirrus-cli = callPackage ../development/tools/continuous-integration/cirrus-cli { };
+
+  cirrusgo = callPackage ../tools/security/cirrusgo { };
 
   inherit (callPackage ../applications/networking/remote/citrix-workspace { })
     citrix_workspace_21_01_0
···
   krename = libsForQt5.callPackage ../applications/misc/krename { };
 
   krunner-pass = libsForQt5.callPackage ../tools/security/krunner-pass { };
+
+  krunvm = callPackage ../applications/virtualization/krunvm { };
 
   kronometer = libsForQt5.callPackage ../tools/misc/kronometer { };
 
···
 
   libmilter = callPackage ../development/libraries/libmilter { };
 
-  libminc = callPackage ../development/libraries/libminc {
-    hdf5 = hdf5_1_10;
-  };
+  libminc = callPackage ../development/libraries/libminc { };
 
   libmkv = callPackage ../development/libraries/libmkv { };
 
···
     deps = [ memorymapping ];
   } ../development/libraries/memorymapping/setup-hook.sh;
 
+  memray = callPackage ../development/tools/memray { };
+
   memstream = callPackage ../development/libraries/memstream { };
   memstreamHook = makeSetupHook {
     deps = [ memstream ];
···
   libatasmart = callPackage ../os-specific/linux/libatasmart { };
 
   libcgroup = callPackage ../os-specific/linux/libcgroup { };
+
+  libkrun = callPackage ../development/libraries/libkrun { };
+
+  libkrun-sev = callPackage ../development/libraries/libkrun { sevVariant = true; };
+
+  libkrunfw = callPackage ../development/libraries/libkrunfw { };
 
   libnl = callPackage ../os-specific/linux/libnl { };
 
···
 
   cd-hit = callPackage ../applications/science/biology/cd-hit {
     inherit (llvmPackages) openmp;
+  };
+
+  ciftilib = callPackage ../development/libraries/science/biology/ciftilib {
+    boost = boost16x;
   };
 
   cmtk = callPackage ../applications/science/biology/cmtk { };

pkgs/top-level/perl-packages.nix

···
     };
   };
 
+  ObjectPad = buildPerlModule {
+    pname = "Object-Pad";
+    version = "0.68";
+    src = fetchurl {
+      url = "mirror://cpan/authors/id/P/PE/PEVANS/Object-Pad-0.68.tar.gz";
+      sha256 = "sha256-xN5jBIQxMJZNrskozF99HphTnu/X7azHvn4Yg0XhnXE=";
+    };
+    buildInputs = [ TestFatal TestRefcount ];
+    perlPreHook = lib.optionalString stdenv.isDarwin "export LD=$CC";
+    propagatedBuildInputs = [ XSParseKeyword XSParseSublike ];
+    meta = {
+      description = "simple syntax for lexical field-based objects";
+      license = with lib.licenses; [ artistic1 gpl1Plus ];
+      maintainers = [ maintainers.zakame ];
+    };
+  };
+
   ObjectSignature = buildPerlPackage {
     pname = "Object-Signature";
     version = "1.08";

pkgs/top-level/python-packages.nix

···
 
   moku = callPackage ../development/python-modules/moku { };
 
+  monai = callPackage ../development/python-modules/monai { };
+
   monero = callPackage ../development/python-modules/monero { };
 
   mongomock = callPackage ../development/python-modules/mongomock { };
···
 
   tableaudocumentapi = callPackage ../development/python-modules/tableaudocumentapi { };
 
-  tables = callPackage ../development/python-modules/tables {
-    hdf5 = pkgs.hdf5_1_10;
-  };
+  tables = callPackage ../development/python-modules/tables { };
 
   tablib = callPackage ../development/python-modules/tablib { };