[INFRA] clang-19 and CPM package update

.github/workflows/ci_header.yml

@@ -29,10 +29,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-18", "gcc-14", "gcc-12", "intel"]
+        compiler: ["clang-19", "gcc-14", "gcc-12", "intel"]
         include:
           - cxx_flags: "-Wno-interference-size"
-          - compiler: "clang-18"
+          - compiler: "clang-19"
             cxx_flags: ""
           - compiler: "intel"
             cxx_flags: "-fp-model=strict -Wno-overriding-option"

.github/workflows/ci_linux.yml

@@ -29,9 +29,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
+        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12", "intel"]
         include:
           - cxx_flags: "-Wno-interference-size"
+          - compiler: "clang-19"
+            cxx_flags: ""
           - compiler: "clang-18"
             cxx_flags: ""
           - compiler: "clang-17"

.github/workflows/ci_macos.yml

@@ -29,9 +29,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        compiler: ["clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
+        compiler: ["clang-19", "clang-18", "clang-17", "gcc-14", "gcc-13", "gcc-12"]
         include:
           - cxx_flags: "-Wno-interference-size"
+          - compiler: "clang-19"
+            cxx_flags: ""
           - compiler: "clang-18"
             cxx_flags: ""
           - compiler: "clang-17"

.github/workflows/ci_sanitizer.yml

@@ -55,16 +55,16 @@ jobs:
             cxx_flags: "-fno-omit-frame-pointer -fsanitize=undefined,float-divide-by-zero,local-bounds,nullability -fno-sanitize=function -Wno-pass-failed"
 
           - os: macos-14
-            compiler: clang-18
+            compiler: clang-19
 
           - os: ubuntu-latest
             compiler: gcc-14
             image: ghcr.io/seqan/gcc-14
 
           - name: "TSan"
             os: ubuntu-latest
-            compiler: clang-18
-            image: ghcr.io/seqan/clang-18
+            compiler: clang-19
+            image: ghcr.io/seqan/clang-19
     container:
       image: ${{ matrix.image || '' }}
       volumes:

CMakeLists.txt

@@ -17,8 +17,12 @@ project (chopper
 
 ## BUILD
 
-# Optimization
-option (CHOPPER_NATIVE_BUILD "Optimize build for current architecture." ON)
+# LTO
+include (CheckIPOSupported)
+check_ipo_supported (RESULT CHOPPER_HAS_LTO OUTPUT CHOPPER_HAS_LTO_OUTPUT)
+if (CHOPPER_HAS_LTO)
+    set (CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+endif ()
 
 # Make Release default build type
 if (NOT CMAKE_BUILD_TYPE)

cmake/package-lock.cmake

@@ -6,7 +6,7 @@
 # This file should be committed to version control
 
 # hibf
-set (CHOPPER_HIBF_VERSION 9e631fd792a35e369ea3385c04e299db3a00859c)
+set (CHOPPER_HIBF_VERSION 2c1488a460c6a136332286f6efeaad26b1d8daac)
 CPMDeclarePackage (hibf
                    NAME hibf
                    GIT_TAG ${CHOPPER_HIBF_VERSION} # main
@@ -26,7 +26,7 @@ CPMDeclarePackage (sharg
                    OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "BUILD_TESTING OFF"
 )
 # seqan3
-set (CHOPPER_SEQAN3_VERSION 0b86c6567f910c943c13f40944ab737524a2ecf6)
+set (CHOPPER_SEQAN3_VERSION f500cf7fbe128636c6e50a99519b5eb2532ab70e)
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    GIT_TAG ${CHOPPER_SEQAN3_VERSION} # main
@@ -38,7 +38,7 @@ CPMDeclarePackage (seqan3
 # googletest
 set (CHOPPER_GOOGLETEST_VERSION 1.15.2)
 CPMDeclarePackage (googletest
-                   NAME googletest
+                   NAME GTest
                    VERSION ${CHOPPER_GOOGLETEST_VERSION}
                    GITHUB_REPOSITORY google/googletest
                    SYSTEM TRUE

src/layout/ibf_query_cost.cpp

@@ -8,6 +8,7 @@
 #include <array>
 #include <bit>
 #include <cassert>
+#include <cmath>
 #include <cstddef>
 #include <map>
 #include <stdexcept>

test/api/layout/CMakeLists.txt

@@ -17,5 +17,12 @@ target_use_datasources (execute_with_estimation_test FILES seq3.fa)
 target_use_datasources (execute_with_estimation_test FILES small.fa)
 
 add_api_test (hibf_statistics_test.cpp)
+# Bogus LTO warning on gcc-12
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU"
+    AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 12
+    AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13
+)
+    target_link_options (hibf_statistics_test PRIVATE -Wno-stringop-overflow)
+endif ()
 add_api_test (user_bin_io_test.cpp)
 add_api_test (input_test.cpp)