kalign: 3.4.0 -> 3.5.1 (#492312)

From fb223fceeb81f481316694560ceacc473ad04b4a Mon Sep 17 00:00:00 2001

From: natsukium <tomoya.otabi@gmail.com>

Date: Thu, 23 Apr 2026 16:46:54 +0900

Subject: [PATCH] cmake: allow overriding hardcoded libomp path on macOS

The OpenMP workaround hardcoded /opt/homebrew/opt/libomp, which locked

out a custom build.

Introduce LIBOMP_ROOT (defaulting to Homebrew) so the prefix can be

overridden on the cmake command line.

While here, restrict the block to AppleClang. The flags inside are

AppleClang-specific (-Xpreprocessor -fopenmp, linking against the LLVM

libomp runtime) and were previously forced on any compiler targeting

Apple Silicon, silently breaking GCC and mis-configuring Homebrew LLVM

Clang builds.

---

 CMakeLists.txt | 14 +++++++-------

 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt

index 5a7d3f0..d76453d 100644

--- a/CMakeLists.txt

+++ b/CMakeLists.txt

@@ -75,15 +75,15 @@ set(KALIGN_KMEANS_UPGMA_THRESHOLD "50" CACHE STRING "Number of sequences thresho

 if(USE_OPENMP)

-  # Configure OpenMP for macOS with Homebrew (only for arm64 native builds)

-  if(APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "arm64" AND NOT CMAKE_OSX_ARCHITECTURES MATCHES "x86_64")

-    list(APPEND CMAKE_PREFIX_PATH /opt/homebrew)

-    # Set OpenMP flags for Apple Clang + Homebrew libomp

-    set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")

+  # Configure OpenMP for macOS with external libomp (only for Apple Clang on arm64 native builds)

+  if(APPLE AND CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "arm64" AND NOT CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" AND CMAKE_C_COMPILER_ID STREQUAL "AppleClang")

+    # Defaults to Homebrew

+    set(LIBOMP_ROOT "/opt/homebrew/opt/libomp" CACHE PATH "libomp install prefix")

+    set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I${LIBOMP_ROOT}/include")

     set(OpenMP_C_LIB_NAMES "omp")

-    set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include")

+    set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${LIBOMP_ROOT}/include")

     set(OpenMP_CXX_LIB_NAMES "omp")

-    set(OpenMP_omp_LIBRARY /opt/homebrew/opt/libomp/lib/libomp.dylib)

+    set(OpenMP_omp_LIBRARY "${LIBOMP_ROOT}/lib/libomp.dylib")

   endif()

   find_package(OpenMP)

stdenv.mkDerivation (finalAttrs: {

  pname = "kalign";

  version = "3.4.0";

  version = "3.5.1";

  src = fetchFromGitHub {

    owner = "TimoLassmann";

    repo = "kalign";

    tag = "v${finalAttrs.version}";

    hash = "sha256-QcFNaCTqj6CFiOzQ6ezfBL0mu8PDU11hyNdkcsLOPzA=";

    hash = "sha256-wcVzKedd8IFKql+TU4wJ4jEGDPdDfpyC5iGXrPYa0oY=";

  };

  patches = [

    # Allow overriding the hardcoded Homebrew libomp path on macOS and

    # restrict the workaround to AppleClang so other compilers fall back

    # to the standard OpenMP detection path.

    # https://github.com/TimoLassmann/kalign/pull/65

    ./macos-openmp-config.patch

  ];

  nativeBuildInputs = [

    cmake

  ];