From 2623b4081a1b299f0593ecf1c437f9577672f06a Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 18 Sep 2024 15:00:37 +0200
Subject: [PATCH 1/3] [INFRA] Use macos-14

macos-14 uses ARM processors (M1)
---
 .github/workflows/ci_macos.yml     | 2 +-
 .github/workflows/ci_sanitizer.yml | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index cf582456..c9ac3a07 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -27,7 +27,7 @@ defaults:
 jobs:
   build:
     name: ${{ matrix.compiler }}
-    runs-on: macos-12
+    runs-on: macos-14
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     strategy:
       fail-fast: false
diff --git a/.github/workflows/ci_sanitizer.yml b/.github/workflows/ci_sanitizer.yml
index 190ef61f..ac8d7085 100644
--- a/.github/workflows/ci_sanitizer.yml
+++ b/.github/workflows/ci_sanitizer.yml
@@ -32,11 +32,11 @@ jobs:
       fail-fast: false
       matrix:
         name: [ASan, TSan, UBSan]
-        os: [ubuntu-latest, macos-12]
+        os: [ubuntu-latest, macos-14]
         build_type: [Release, RelWithDebInfo, Debug]
         exclude:
           - name: "TSan"
-            os: macos-12
+            os: macos-14
 
         include:
           - name: "ASan"
@@ -46,14 +46,14 @@ jobs:
             cxx_flags: "-fno-omit-frame-pointer -fsanitize=thread"
 
           - name: "UBSan"
-            os: macos-12
+            os: macos-14
             cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,implicit-conversion,local-bounds,nullability -Wno-pass-failed"
 
           - name: "UBSan"
             os: ubuntu-latest
             cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero"
 
-          - os: macos-12
+          - os: macos-14
             compiler: clang-18
 
           - os: ubuntu-latest

From e409f0bbf8cfe0069f70154f3269f53943b5df87 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 18 Sep 2024 16:22:39 +0200
Subject: [PATCH 2/3] [INFRA] Do not use native on M1 with gcc < 14

---
 cmake/configuration.cmake | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/cmake/configuration.cmake b/cmake/configuration.cmake
index a04a565e..19a62da3 100644
--- a/cmake/configuration.cmake
+++ b/cmake/configuration.cmake
@@ -228,8 +228,19 @@ else ()
     set (HIBF_IS_DEBUG FALSE)
 endif ()
 
+# Apple M1 with GCC sets `march=apple-m1` when using `-march=native`. This option is only available with GCC >= 14.
+if ("${CMAKE_SYSTEM_PROCESSOR}" MATCHES "arm64"
+    AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU"
+    AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 14)
+    set (HIBF_M1_NO_NATIVE TRUE)
+else ()
+    set (HIBF_M1_NO_NATIVE FALSE)
+endif ()
+
 option (HIBF_NATIVE_BUILD "Optimize build for current architecture." ON)
-if (HIBF_IS_DEBUG)
+if (HIBF_M1_NO_NATIVE)
+    hibf_config_print ("Optimize build:             disabled (Apple M1 with GCC < 14)")
+elseif (HIBF_IS_DEBUG)
     hibf_config_print ("Optimize build:             disabled")
 elseif (HIBF_NATIVE_BUILD)
     set (HIBF_CXX_FLAGS "${HIBF_CXX_FLAGS} -march=native")

From 7bc188b324d71fc7f10543dc25146b8d6a88b1a5 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 18 Sep 2024 19:01:40 +0200
Subject: [PATCH 3/3] [INFRA] Patch M1 GCC

---
 .github/workflows/ci_macos.yml     | 7 ++++---
 .github/workflows/ci_sanitizer.yml | 6 ++++++
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml
index c9ac3a07..51a801ec 100644
--- a/.github/workflows/ci_macos.yml
+++ b/.github/workflows/ci_macos.yml
@@ -43,10 +43,11 @@ jobs:
           compiler: ${{ matrix.compiler }}
           ccache_size: 75M
 
-      - name: Install CMake
-        uses: seqan/actions/setup-cmake@main
+      - name: Patch M1 GCC
+        if: contains(matrix.compiler, 'gcc') && matrix.compiler != 'gcc-14'
+        uses: seqan/actions/patch-m1-gcc@main
         with:
-          cmake: 3.28.5
+          compiler: ${{ matrix.compiler }}
 
       - name: Configure tests
         run: |
diff --git a/.github/workflows/ci_sanitizer.yml b/.github/workflows/ci_sanitizer.yml
index ac8d7085..a5e5bfcb 100644
--- a/.github/workflows/ci_sanitizer.yml
+++ b/.github/workflows/ci_sanitizer.yml
@@ -78,6 +78,12 @@ jobs:
         with:
           compiler: ${{ matrix.compiler }}
 
+      - name: Patch M1 GCC
+        if: contains(matrix.os, 'macos') && contains(matrix.compiler, 'gcc') && matrix.compiler != 'gcc-14'
+        uses: seqan/actions/patch-m1-gcc@main
+        with:
+          compiler: ${{ matrix.compiler }}
+
       - name: Configure tests
         run: |
           mkdir build && cd build