Merge branch 'staging-next' into staging

In python-packages.nix, resolve conflict between 50d604314e and 187d0371ab.

pkgs/tools/misc/hdf5/1.10.nix

@@ -0,0 +1,50 @@
+{ lib, stdenv
+, fetchurl
+, removeReferencesTo
+, zlib ? null
+, enableShared ? !stdenv.hostPlatform.isStatic
+}:
+
+let inherit (lib) optional optionals; in
+
+stdenv.mkDerivation rec {
+  version = "1.10.7";
+  pname = "hdf5";
+  src = fetchurl {
+    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${lib.versions.majorMinor version}/${pname}-${version}/src/${pname}-${version}.tar.bz2";
+    sha256 = "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082";
+  };
+
+  outputs = [ "out" "dev" ];
+
+  nativeBuildInputs = [ removeReferencesTo ];
+
+  propagatedBuildInputs = optional (zlib != null) zlib;
+
+  configureFlags = optional enableShared "--enable-shared";
+
+  patches = [
+    ./bin-mv.patch
+  ];
+
+  postInstall = ''
+    find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
+    moveToOutput 'bin/h5cc' "''${!outputDev}"
+    moveToOutput 'bin/h5c++' "''${!outputDev}"
+    moveToOutput 'bin/h5fc' "''${!outputDev}"
+    moveToOutput 'bin/h5pcc' "''${!outputDev}"
+  '';
+
+  meta = {
+    description = "Data model, library, and file format for storing and managing data";
+    longDescription = ''
+      HDF5 supports an unlimited variety of datatypes, and is designed for flexible and efficient
+      I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing
+      applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and
+      applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
+    '';
+    license = lib.licenses.bsd3; # Lawrence Berkeley National Labs BSD 3-Clause variant
+    homepage = "https://www.hdfgroup.org/HDF5/";
+    platforms = lib.platforms.unix;
+  };
+}

pkgs/tools/misc/hdf5/default.nix

@@ -10,6 +10,7 @@
 , enableShared ? !stdenv.hostPlatform.isStatic
 , javaSupport ? false
 , jdk
+, usev110Api ? false
 }:
 
 # cpp and mpi options are mutually exclusive
@@ -50,7 +51,8 @@ stdenv.mkDerivation rec {
     ++ optional (szip != null) "--with-szlib=${szip}"
     ++ optionals mpiSupport ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
     ++ optional enableShared "--enable-shared"
-    ++ optional javaSupport "--enable-java";
+    ++ optional javaSupport "--enable-java"
+    ++ optional usev110Api "--with-default-api-version=v110";
 
   patches = [
     ./bin-mv.patch

pkgs/tools/misc/topgrade/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "topgrade";
-  version = "6.7.0";
+  version = "6.8.0";
 
   src = fetchFromGitHub {
     owner = "r-darwish";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-UikJZFSnkYGGGMm6hrOqs+ax9HwUsZPht9wV79rJBgE=";
+    sha256 = "sha256-PPOsb9bne0q/WGAL3W2RGo/0yxyz/XXU3xYXKcCIqX0=";
   };
 
-  cargoSha256 = "sha256-8MvXpJVwiIThwq8Du/9nQ0QINpqgemwiRpunzIUqkXk=";
+  cargoSha256 = "sha256-IirU/4hE+jo5A9pB7RnePhqcbCZXBCe0Ki6i7eEWIbk=";
 
   buildInputs = lib.optional stdenv.isDarwin Foundation;
 

pkgs/tools/misc/yubikey-manager/default.nix

@@ -3,11 +3,11 @@
 
 python3Packages.buildPythonPackage rec {
   pname = "yubikey-manager";
-  version = "3.1.2";
+  version = "4.0.1";
 
   srcs = fetchurl {
     url = "https://developers.yubico.com/${pname}/Releases/${pname}-${version}.tar.gz";
-    hash = "sha256-dwnIOuu0QyWRl6RSdyQw7dGsAZ4xpXpx6jOpCkp4efE=";
+    hash = "sha256-OxbKo5vwOBabU6/2hO4RMWiifo4IVIxz+DlcwP9xO/E=";
   };
 
   propagatedBuildInputs =
@@ -42,8 +42,7 @@ python3Packages.buildPythonPackage rec {
       --replace 'compdef _ykman_completion ykman;' '_ykman_completion "$@"'
   '';
 
-  # See https://github.com/NixOS/nixpkgs/issues/29169
-  doCheck = false;
+  checkInputs = with python3Packages; [ pytestCheckHook makefun ];
 
   meta = with lib; {
     homepage = "https://developers.yubico.com/yubikey-manager";