tiledb: 2.18.2 -> 2.27.2 (#394875)

diff --git a/FindMagic_EP.cmake b/FindMagic_EP.cmake

--- a/cmake/Modules/FindMagic_EP.cmake

+++ b/cmake/Modules/FindMagic_EP.cmake

@@ -126,9 +126,7 @@ if(NOT TILEDB_LIBMAGIC_EP_BUILT)

     # that was modified by tiledb to also build with cmake for nix

     ExternalProject_Add(ep_magic

       PREFIX "externals"

-      GIT_REPOSITORY "https://github.com/TileDB-Inc/file-windows.git"

-      GIT_TAG "5.38.2.tiledb"

-      GIT_SUBMODULES_RECURSE TRUE

+      DOWNLOAD_COMMAND true

       UPDATE_COMMAND ""

       CMAKE_ARGS

         -DCMAKE_INSTALL_PREFIX=${TILEDB_EP_INSTALL_PREFIX}

--- a/tiledb/sm/misc/generate_embedded_data_header.script.cmake

+++ b/tiledb/sm/misc/generate_embedded_data_header.script.cmake

@@ -40,11 +40,7 @@

 string(MAKE_C_IDENTIFIER ${INPUT_FILENAME} INPUT_VARIABLE)

 message(DEBUG "Compressing ${INPUT_FILE} to ${compressed_file}")

-file(ARCHIVE_CREATE OUTPUT "${compressed_file}" PATHS ${INPUT_FILE} FORMAT raw COMPRESSION Zstd

-    # Level 12 was found to have the best balance between compression ratio and speed

-    # but is available in CMake 3.26+.

-    COMPRESSION_LEVEL 9

-)

+execute_process(COMMAND zstd -9 -c "${INPUT_FILE}" OUTPUT_FILE "${compressed_file}")

 file(SIZE ${compressed_file} COMPRESSED_SIZE)

 message(DEBUG "Compressed size: ${COMPRESSED_SIZE} bytes")

  lib,

  stdenv,

  fetchFromGitHub,

  cmake,

  zlib,

  lz4,

  clang-tools,

  catch2_3,

  python3,

  gtest,

  doxygen,

  fixDarwinDylibNames,

  gtest,

  rapidcheck,

  libpng,

  file,

  runCommand,

  catch2,

  useAVX2 ? stdenv.hostPlatform.avx2Support,

}:

let

  # pre-fetch ExternalProject from cmake/Modules/FindMagic_EP.cmake

  ep-file-windows = fetchFromGitHub {

    owner = "TileDB-Inc";

    repo = "file-windows";

    rev = "5.38.2.tiledb";

    hash = "sha256-TFn30VCuWZr252VN1T5NNCZe2VEN3xQSomS7XxxKGF8=";

    fetchSubmodules = true;

  };

  rapidcheck' = runCommand "rapidcheck" { } ''

    cp -r ${rapidcheck.out} $out

    chmod -R +w $out

    cp -r ${rapidcheck.dev}/* $out

  '';

in

stdenv.mkDerivation rec {

  pname = "tiledb";

  version = "2.18.2";

  version = "2.27.2";

  src = fetchFromGitHub {

    owner = "TileDB-Inc";

    repo = "TileDB";

    rev = version;

    hash = "sha256-uLiXhigYz3v7NgY38twot3sBHxZS5QCrOiPfME4wWzE=";

    tag = version;

    hash = "sha256-zk4jkXJMh6wpuEKaCvuKUDod+F8B/6W5Lw8gwelcPEM=";

  };

  patches = [

    ./FindMagic_EP.cmake.patch

  ];

  patches = lib.optionals stdenv.hostPlatform.isDarwin [ ./generate_embedded_data_header.patch ];

  postPatch =

    ''

      # copy pre-fetched external project to directory where it is expected to be

      mkdir -p build/externals/src

      cp -a ${ep-file-windows} build/externals/src/ep_magic

      chmod -R u+w build/externals/src/ep_magic

      # add openssl on path

      sed -i '49i list(APPEND OPENSSL_PATHS "${openssl.dev}" "${openssl.out}")' \

        cmake/Modules/FindOpenSSL_EP.cmake

    ''

  # libcxx (as of llvm-19) does not yet support `stop_token` and `jthread`

  # without the -fexperimental-library flag. Tiledb adds its own

  # implementations in the std namespace which conflict with libcxx. This

  # test can be re-enabled once libcxx supports stop_token and jthread.

    + lib.optionalString (stdenv.cc.libcxx != null) ''

  postPatch = lib.optionalString (stdenv.cc.libcxx != null) ''

    truncate -s0 tiledb/stdx/test/CMakeLists.txt

  '';

  # upstream will hopefully fix this in some newer release

  env.CXXFLAGS = "-include random";

  env.TILEDB_DISABLE_AUTO_VCPKG = "1";

  # (bundled) blosc headers have a warning on some archs that it will be using

  # unaccelerated routines.

  cmakeFlags = [

    "-DTILEDB_VCPKG=OFF"

    "-DTILEDB_WEBP=OFF"

    "-DTILEDB_WERROR=OFF"

    # https://github.com/NixOS/nixpkgs/issues/144170

    "-DCMAKE_INSTALL_INCLUDEDIR=include"

    "-DCMAKE_INSTALL_LIBDIR=lib"

  ] ++ lib.optional (!useAVX2) "-DCOMPILER_SUPPORTS_AVX2=FALSE";

  nativeBuildInputs = [

    ep-file-windows

    catch2_3

    clang-tools

    cmake

    doxygen

  ] ++ lib.optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames;

  nativeCheckInputs = [

    gtest

  ];

  buildInputs = [

    zlib

    lz4

    openssl

    boost

    libpqxx

    libpng

    file

    rapidcheck'

    catch2

  ];

  # fatal error: catch.hpp: No such file or directory

  doCheck = false;

  nativeCheckInputs = [

    gtest

    catch2

  ];

  # test commands taken from

  # https://github.com/TileDB-Inc/TileDB/blob/dev/.github/workflows/unit-test-runs.yml

  checkPhase = ''

    runHook preCheck

    make -C tiledb tests -j$NIX_BUILD_CORES

    make -C tiledb test ARGS="-R '^unit_'" -R "test_assert"

    make -C tiledb test ARGS="-R 'test_ci_asserts'"

    pushd ..

    cmake --build build --target tests

    ctest --test-dir build -R '(^unit_|test_assert)' --no-tests=error

    ctest --test-dir build -R 'test_ci_asserts'

    popd

    runHook postCheck

  '';

  doCheck = true;

  installTargets = [

    "install-tiledb"

    "doc"

    install_name_tool -add_rpath ${tbb}/lib $out/lib/libtiledb.dylib

  '';

  meta = with lib; {

  meta = {

    description = "TileDB allows you to manage the massive dense and sparse multi-dimensional array data";

    homepage = "https://github.com/TileDB-Inc/TileDB";

    license = licenses.mit;

    platforms = platforms.unix;

    maintainers = with maintainers; [ rakesh4g ];

    license = lib.licenses.mit;

    platforms = lib.platforms.unix;

    maintainers = with lib.maintainers; [ rakesh4g ];

  };

}

  disabledTestPaths = [

    "mapclassify/tests/test_greedy.py"

    "mapclassify/tests/test_rgba.py"

    # Abort trap: 6

    "mapclassify/tests/test_mapclassify.py"

  ];

  pythonImportsCheck = [ "mapclassify" ];