git: f89bdf93a963 - main - biology/hyphy: Update to 2.5.76

The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f89bdf93a96342d8e2798cf670670ea8bf90fb08

commit f89bdf93a96342d8e2798cf670670ea8bf90fb08
Author:     Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2025-08-15 20:59:53 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2025-08-16 17:48:10 +0000

    biology/hyphy: Update to 2.5.76
    
    Release notes:  https://github.com/veg/hyphy/releases/tag/2.5.76
    Sponsored by:   The FreeBSD Foundation
---
 biology/hyphy/Makefile                   |  2 +-
 biology/hyphy/distinfo                   |  6 +++---
 biology/hyphy/files/patch-CMakeLists.txt | 27 +++++++++++++++++++++++++++
 3 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 62e26956129f..9c44e24985ad 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.75
+DISTVERSION=	2.5.76
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index c62a818945c5..3bcc8e9eb6fe 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1755287249
-SHA256 (veg-hyphy-2.5.75_GH0.tar.gz) = 0acfc26d428cf2b9b8ff070528a22e40529d614bf114ce05c49b5d7a51ebda30
-SIZE (veg-hyphy-2.5.75_GH0.tar.gz) = 4093653
+TIMESTAMP = 1755289798
+SHA256 (veg-hyphy-2.5.76_GH0.tar.gz) = d3f649b304e6ed408ee25f568de8361d43fb0a20d689243eba227d63fe6926ae
+SIZE (veg-hyphy-2.5.76_GH0.tar.gz) = 4027248
diff --git a/biology/hyphy/files/patch-CMakeLists.txt b/biology/hyphy/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..0c926e529c55
--- /dev/null
+++ b/biology/hyphy/files/patch-CMakeLists.txt
@@ -0,0 +1,27 @@
+--- CMakeLists.txt.orig	2025-08-15 20:40:45 UTC
++++ CMakeLists.txt
+@@ -83,7 +83,7 @@ int main() {
+     if(HYPHY_HAVE_NEON)
+         add_compile_definitions(_SLKP_USE_ARM_NEON)
+         if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+-            list(APPEND HYPHY_SIMD_FLAGS "-mcpu=native;-mtune=native")
++            list(APPEND HYPHY_SIMD_FLAGS "-mtune=native")
+         endif()
+     endif()
+     set(CMAKE_REQUIRED_FLAGS ${OLD_CMAKE_REQUIRED_FLAGS})
+@@ -91,7 +91,7 @@ if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_CO
+ 
+ if(CMAKE_CXX_COMPILER_ID MATCHES "GNU" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+     if(NOT HYPHY_HAVE_NEON AND NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
+-        list(APPEND COMMON_COMPILE_FLAGS "-march=native" "-mcpu=native" "-mtune=native")
++        list(APPEND COMMON_COMPILE_FLAGS "-march=native" "-mtune=native")
+     endif()
+     if(NOT NOAVX)
+         set(OLD_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
+@@ -332,4 +332,4 @@ add_test(NAME GARD COMMAND hyphy tests/hbltests/libv3/
+ add_test(CONTRAST-FEL hyphy tests/hbltests/libv3/CFEL.wbf)
+ add_test(FADE hyphy tests/hbltests/libv3/FADE.wbf)
+ add_test(NAME GARD COMMAND hyphy tests/hbltests/libv3/GARD.wbf "ENV=TOLERATE_NUMERICAL_ERRORS=1;")
+-add_test(ABSREL hyphy tests/hbltests/libv3/ABSREL.wbf)
+\ No newline at end of file
++add_test(ABSREL hyphy tests/hbltests/libv3/ABSREL.wbf)