From 3111f21eec2fdc26cd3d1489d22aea8be3b84e49 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 27 Feb 2026 12:35:11 +0000
Subject: [PATCH] kalign: 3.4.0 -> 3.5.1

---
 .../ka/kalign/macos-openmp-config.patch       | 46 +++++++++++++++++++
 pkgs/by-name/ka/kalign/package.nix            | 12 ++++-
 2 files changed, 56 insertions(+), 2 deletions(-)
 create mode 100644 pkgs/by-name/ka/kalign/macos-openmp-config.patch

diff --git a/pkgs/by-name/ka/kalign/macos-openmp-config.patch b/pkgs/by-name/ka/kalign/macos-openmp-config.patch
new file mode 100644
index 000000000000..c24f2cb4f0df
--- /dev/null
+++ b/pkgs/by-name/ka/kalign/macos-openmp-config.patch
@@ -0,0 +1,46 @@
+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)
diff --git a/pkgs/by-name/ka/kalign/package.nix b/pkgs/by-name/ka/kalign/package.nix
index 86a75dd384ed..fc1d0818490d 100644
--- a/pkgs/by-name/ka/kalign/package.nix
+++ b/pkgs/by-name/ka/kalign/package.nix
@@ -11,15 +11,23 @@
 
 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
   ];