python3Packages.hdf5plugin: build using system libraries; bzip2_1_1: drop (#526391)

pkgs/by-name/c-/c-blosc/package.nix

@@ -7,8 +7,10 @@
   testers,
 
   static ? stdenv.hostPlatform.isStatic,
+  snappySupport ? false,
 
   lz4,
+  snappy,
   zlib,
   zstd,
 }:
@@ -51,7 +53,8 @@ stdenv.mkDerivation (finalAttrs: {
     lz4
     zlib
     zstd
-  ];
+  ]
+  ++ lib.optional snappySupport snappy;
 
   cmakeFlags = [
     "-DBUILD_STATIC=${if static then "ON" else "OFF"}"
@@ -64,7 +67,8 @@ stdenv.mkDerivation (finalAttrs: {
     "-DBUILD_EXAMPLES=OFF"
     "-DBUILD_BENCHMARKS=OFF"
     "-DBUILD_TESTS=${if finalAttrs.finalPackage.doCheck then "ON" else "OFF"}"
-  ];
+  ]
+  ++ lib.optional snappySupport "-DDEACTIVATE_SNAPPY=OFF";
 
   doCheck = !static;
 

pkgs/by-name/zf/zfp/package.nix

@@ -10,6 +10,7 @@
   stdenv,
   config,
   testers,
+  bitStreamWordSize ? 64,
   enableCfp ? true,
   enableCuda ? config.cudaSupport,
   enableFortran ? builtins.elem stdenv.hostPlatform.system gfortran.meta.platforms,
@@ -70,6 +71,7 @@ effectiveStdenv.mkDerivation (finalAttrs: {
 
   cmakeFlags = [
   ]
+  ++ lib.optional (bitStreamWordSize != 64) "-DZFP_BIT_STREAM_WORD_SIZE=${toString bitStreamWordSize}"
   ++ lib.optional enableCfp "-DBUILD_CFP=ON"
   ++ lib.optional enableCuda "-DZFP_WITH_CUDA=ON"
   ++ lib.optional enableFortran "-DBUILD_ZFORP=ON"
@@ -79,6 +81,11 @@ effectiveStdenv.mkDerivation (finalAttrs: {
 
   doCheck = true;
 
+  # the testzfp regression test only supports the default 64-bit bitstream word
+  preCheck = lib.optionalString (bitStreamWordSize != 64) ''
+    checkFlagsArray+=(ARGS="--exclude-regex testzfp")
+  '';
+
   passthru.tests = {
     cmake-config = testers.hasCmakeConfigModules {
       moduleNames = [ "zfp" ];

pkgs/development/python-modules/hdf5plugin/default.nix

@@ -6,9 +6,12 @@
   py-cpuinfo,
   h5py,
   pkgconfig,
+  c-blosc,
   c-blosc2,
+  bzip2,
   charls,
   lz4,
+  zfp,
   zlib,
   zstd,
   stdenv,
@@ -18,7 +21,12 @@
   avx512Support ? stdenv.hostPlatform.avx512Support,
 }:
 
-buildPythonPackage rec {
+let
+  c-blosc' = c-blosc.override { snappySupport = true; };
+  # H5Z-ZFP needs an 8-bit bitstream word so the compressed HDF5 data is byte-portable
+  zfp' = zfp.override { bitStreamWordSize = 8; };
+in
+buildPythonPackage (finalAttrs: {
   pname = "hdf5plugin";
   version = "6.0.0";
   pyproject = true;
@@ -26,7 +34,7 @@ buildPythonPackage rec {
   src = fetchFromGitHub {
     owner = "silx-kit";
     repo = "hdf5plugin";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-LW6rY+zLta4hENBbTll+1amf9TYJiuAumwzgpk1LZ3M=";
   };
 
@@ -39,27 +47,25 @@ buildPythonPackage rec {
   dependencies = [ h5py ];
 
   buildInputs = [
-    #c-blosc
+    c-blosc'
     c-blosc2
-    # bzip2_1_1
+    bzip2
     charls
     lz4
-    # snappy
-    # zfp
+    zfp'
     zlib
     zstd
   ];
 
   # opt-in to use use system libs instead
   env.HDF5PLUGIN_SYSTEM_LIBRARIES = lib.concatStringsSep "," [
-    #"blosc" # AssertionError: 4000 not less than 4000
+    "blosc"
     "blosc2"
-    # "bz2" # only works with bzip2_1_1
+    "bz2"
     "charls"
     "lz4"
-    # "snappy" # snappy tests fail
     # "sperr" # not packaged?
-    # "zfp" #  pkgconfig: (lib)zfp not found
+    "zfp"
     "zlib"
     "zstd"
   ];
@@ -82,6 +88,19 @@ buildPythonPackage rec {
 
   preBuild = ''
     mkdir src/hdf5plugin/plugins
+
+    mkdir -p pkg-config
+    ln -s ${lib.getDev bzip2}/lib/pkgconfig/bzip2.pc pkg-config/bz2.pc
+    # zfp ships only a CMake config; synthesise the pkg-config module hdf5plugin probes for
+    {
+      echo "includedir=${lib.getDev zfp'}/include"
+      echo "Name: zfp"
+      echo "Version: ${zfp'.version}"
+      echo "Description: zfp"
+      echo "Libs: -L${lib.getLib zfp'}/lib -lzfp"
+      echo "Cflags: -I${lib.getDev zfp'}/include"
+    } > pkg-config/zfp.pc
+    export PKG_CONFIG_PATH="$PWD/pkg-config''${PKG_CONFIG_PATH:+:$PKG_CONFIG_PATH}"
   '';
 
   meta = {
@@ -94,4 +113,4 @@ buildPythonPackage rec {
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ pbsds ];
   };
-}
+})

pkgs/tools/compression/bzip2/1_1.nix

@@ -1,55 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchFromGitLab,
-  meson,
-  python3,
-  ninja,
-  testers,
-}:
-
-stdenv.mkDerivation (finalAttrs: {
-  pname = "bzip2-unstable";
-  version = "2020-08-11";
-
-  src = fetchFromGitLab {
-    owner = "federicomenaquintero";
-    repo = "bzip2";
-    rev = "15255b553e7c095fb7a26d4dc5819a11352ebba1";
-    hash = "sha256-BAyz35D62LWi47B/gNcCSKpdaECHBGSpt21vtnk3fKs=";
-  };
-
-  postPatch = ''
-    patchShebangs install_links.py
-  '';
-
-  nativeBuildInputs = [
-    meson
-    python3
-    ninja
-  ];
-
-  outputs = [
-    "bin"
-    "dev"
-    "out"
-    "man"
-  ];
-
-  mesonFlags = [
-    "-Ddocs=disabled"
-  ];
-
-  strictDeps = true;
-
-  passthru.tests.pkg-config = testers.testMetaPkgConfig finalAttrs.finalPackage;
-
-  meta = {
-    description = "High-quality data compression program";
-    homepage = "https://gitlab.com/federicomenaquintero/bzip2";
-    license = lib.licenses.bzip2;
-    pkgConfigModules = [ "bz2" ];
-    platforms = lib.platforms.all;
-    maintainers = [ ];
-  };
-})

pkgs/top-level/aliases.nix

@@ -423,6 +423,7 @@ mapAliases {
   buildXenPackage = throw "'buildXenPackage' has been removed as a custom Xen build can now be achieved by simply overriding 'xen'."; # Added 2025-05-12
   bullet-roboschool = throw "'bullet-roboschool' has been removed as its build was broken and it was deprecated with its last update in 2019."; # Added 2025-11-15
   bwidget = throw "'bwidget' has been renamed to/replaced by 'tclPackages.bwidget'"; # Converted to throw 2025-10-27
+  bzip2_1_1 = throw "'bzip2_1_1' has been removed as it was an unmaintained 2020 snapshot with no remaining users; use 'bzip2' instead"; # Added 2026-05-31
   bzrtp = throw "'bzrtp' has been moved to 'linphonePackages.bzrtp'"; # Added 2025-09-20
   c0 = throw "'c0' has been removed due to being broken for more than a year; see RFC 180"; # Added 2026-02-05
   caido = warnAlias "'caido' has been split into 'caido-cli' and 'caido-desktop'." caido-desktop; # Added 2026-03-03

pkgs/top-level/all-packages.nix

@@ -1885,8 +1885,6 @@ with pkgs;
 
   bzip2 = callPackage ../tools/compression/bzip2 { };
 
-  bzip2_1_1 = callPackage ../tools/compression/bzip2/1_1.nix { };
-
   davix-copy = davix.override { enableThirdPartyCopy = true; };
 
   libceph = ceph.lib;