tiledb: 2.18.2 -> 2.27.2 (#394875)
This commit is contained in:
Ivan Mincik
@@ -1,14 +0,0 @@
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diff --git a/FindMagic_EP.cmake b/FindMagic_EP.cmake
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--- a/cmake/Modules/FindMagic_EP.cmake
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+++ b/cmake/Modules/FindMagic_EP.cmake
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@@ -126,9 +126,7 @@ if(NOT TILEDB_LIBMAGIC_EP_BUILT)
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# that was modified by tiledb to also build with cmake for nix
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ExternalProject_Add(ep_magic
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PREFIX "externals"
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- GIT_REPOSITORY "https://github.com/TileDB-Inc/file-windows.git"
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- GIT_TAG "5.38.2.tiledb"
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- GIT_SUBMODULES_RECURSE TRUE
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+ DOWNLOAD_COMMAND true
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UPDATE_COMMAND ""
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CMAKE_ARGS
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-DCMAKE_INSTALL_PREFIX=${TILEDB_EP_INSTALL_PREFIX}
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@@ -0,0 +1,14 @@
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--- a/tiledb/sm/misc/generate_embedded_data_header.script.cmake
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+++ b/tiledb/sm/misc/generate_embedded_data_header.script.cmake
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@@ -40,11 +40,7 @@
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string(MAKE_C_IDENTIFIER ${INPUT_FILENAME} INPUT_VARIABLE)
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message(DEBUG "Compressing ${INPUT_FILE} to ${compressed_file}")
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-file(ARCHIVE_CREATE OUTPUT "${compressed_file}" PATHS ${INPUT_FILE} FORMAT raw COMPRESSION Zstd
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- # Level 12 was found to have the best balance between compression ratio and speed
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- # but is available in CMake 3.26+.
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- COMPRESSION_LEVEL 9
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-)
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+execute_process(COMMAND zstd -9 -c "${INPUT_FILE}" OUTPUT_FILE "${compressed_file}")
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file(SIZE ${compressed_file} COMPRESSED_SIZE)
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message(DEBUG "Compressed size: ${COMPRESSED_SIZE} bytes")
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@@ -2,7 +2,6 @@
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lib,
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stdenv,
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fetchFromGitHub,
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cmake,
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zlib,
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lz4,
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@@ -16,70 +15,58 @@
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clang-tools,
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catch2_3,
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python3,
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gtest,
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doxygen,
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fixDarwinDylibNames,
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gtest,
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rapidcheck,
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libpng,
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file,
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runCommand,
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catch2,
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useAVX2 ? stdenv.hostPlatform.avx2Support,
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}:
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let
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# pre-fetch ExternalProject from cmake/Modules/FindMagic_EP.cmake
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ep-file-windows = fetchFromGitHub {
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owner = "TileDB-Inc";
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repo = "file-windows";
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rev = "5.38.2.tiledb";
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hash = "sha256-TFn30VCuWZr252VN1T5NNCZe2VEN3xQSomS7XxxKGF8=";
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fetchSubmodules = true;
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};
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rapidcheck' = runCommand "rapidcheck" { } ''
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cp -r ${rapidcheck.out} $out
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chmod -R +w $out
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cp -r ${rapidcheck.dev}/* $out
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'';
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in
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stdenv.mkDerivation rec {
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pname = "tiledb";
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version = "2.18.2";
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version = "2.27.2";
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src = fetchFromGitHub {
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owner = "TileDB-Inc";
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repo = "TileDB";
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rev = version;
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hash = "sha256-uLiXhigYz3v7NgY38twot3sBHxZS5QCrOiPfME4wWzE=";
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tag = version;
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hash = "sha256-zk4jkXJMh6wpuEKaCvuKUDod+F8B/6W5Lw8gwelcPEM=";
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};
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patches = [
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./FindMagic_EP.cmake.patch
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];
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patches = lib.optionals stdenv.hostPlatform.isDarwin [ ./generate_embedded_data_header.patch ];
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postPatch =
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''
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# copy pre-fetched external project to directory where it is expected to be
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mkdir -p build/externals/src
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cp -a ${ep-file-windows} build/externals/src/ep_magic
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chmod -R u+w build/externals/src/ep_magic
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# libcxx (as of llvm-19) does not yet support `stop_token` and `jthread`
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# without the -fexperimental-library flag. Tiledb adds its own
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# implementations in the std namespace which conflict with libcxx. This
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# test can be re-enabled once libcxx supports stop_token and jthread.
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postPatch = lib.optionalString (stdenv.cc.libcxx != null) ''
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truncate -s0 tiledb/stdx/test/CMakeLists.txt
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'';
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# add openssl on path
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sed -i '49i list(APPEND OPENSSL_PATHS "${openssl.dev}" "${openssl.out}")' \
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cmake/Modules/FindOpenSSL_EP.cmake
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''
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# libcxx (as of llvm-19) does not yet support `stop_token` and `jthread`
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# without the -fexperimental-library flag. Tiledb adds its own
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# implementations in the std namespace which conflict with libcxx. This
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# test can be re-enabled once libcxx supports stop_token and jthread.
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+ lib.optionalString (stdenv.cc.libcxx != null) ''
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truncate -s0 tiledb/stdx/test/CMakeLists.txt
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'';
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# upstream will hopefully fix this in some newer release
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env.CXXFLAGS = "-include random";
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env.TILEDB_DISABLE_AUTO_VCPKG = "1";
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# (bundled) blosc headers have a warning on some archs that it will be using
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# unaccelerated routines.
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cmakeFlags = [
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"-DTILEDB_VCPKG=OFF"
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"-DTILEDB_WEBP=OFF"
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"-DTILEDB_WERROR=OFF"
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# https://github.com/NixOS/nixpkgs/issues/144170
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"-DCMAKE_INSTALL_INCLUDEDIR=include"
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"-DCMAKE_INSTALL_LIBDIR=lib"
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] ++ lib.optional (!useAVX2) "-DCOMPILER_SUPPORTS_AVX2=FALSE";
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nativeBuildInputs = [
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ep-file-windows
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catch2_3
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clang-tools
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cmake
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@@ -87,10 +74,6 @@ stdenv.mkDerivation rec {
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doxygen
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] ++ lib.optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames;
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nativeCheckInputs = [
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gtest
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];
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buildInputs = [
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zlib
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lz4
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@@ -101,20 +84,34 @@ stdenv.mkDerivation rec {
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openssl
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boost
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libpqxx
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libpng
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file
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rapidcheck'
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catch2
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];
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# fatal error: catch.hpp: No such file or directory
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doCheck = false;
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nativeCheckInputs = [
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gtest
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catch2
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];
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# test commands taken from
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# https://github.com/TileDB-Inc/TileDB/blob/dev/.github/workflows/unit-test-runs.yml
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checkPhase = ''
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runHook preCheck
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make -C tiledb tests -j$NIX_BUILD_CORES
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make -C tiledb test ARGS="-R '^unit_'" -R "test_assert"
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make -C tiledb test ARGS="-R 'test_ci_asserts'"
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pushd ..
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cmake --build build --target tests
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ctest --test-dir build -R '(^unit_|test_assert)' --no-tests=error
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ctest --test-dir build -R 'test_ci_asserts'
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popd
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runHook postCheck
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'';
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doCheck = true;
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installTargets = [
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"install-tiledb"
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"doc"
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@@ -124,11 +121,11 @@ stdenv.mkDerivation rec {
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install_name_tool -add_rpath ${tbb}/lib $out/lib/libtiledb.dylib
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'';
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meta = with lib; {
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meta = {
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description = "TileDB allows you to manage the massive dense and sparse multi-dimensional array data";
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homepage = "https://github.com/TileDB-Inc/TileDB";
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license = licenses.mit;
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platforms = platforms.unix;
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maintainers = with maintainers; [ rakesh4g ];
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license = lib.licenses.mit;
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platforms = lib.platforms.unix;
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maintainers = with lib.maintainers; [ rakesh4g ];
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};
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}
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@@ -50,6 +50,8 @@ buildPythonPackage rec {
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disabledTestPaths = [
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"mapclassify/tests/test_greedy.py"
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"mapclassify/tests/test_rgba.py"
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# Abort trap: 6
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"mapclassify/tests/test_mapclassify.py"
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];
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pythonImportsCheck = [ "mapclassify" ];
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