From c609dd6a4b76eb7b7ff7537dab59d12f77744b07 Mon Sep 17 00:00:00 2001
From: "seqan-actions[bot]" <seqan-actions@users.noreply.github.com>
Date: Wed, 23 Oct 2024 20:21:42 +0200
Subject: [PATCH 1/3] [INFRA] Update CPM Packages

---
 cmake/package-lock.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/package-lock.cmake b/cmake/package-lock.cmake
index 79536268..7ad93b6b 100644
--- a/cmake/package-lock.cmake
+++ b/cmake/package-lock.cmake
@@ -6,7 +6,7 @@
 # This file should be committed to version control
 
 # hibf
-set (CHOPPER_HIBF_VERSION 25539c9654508cd531b7c4ccdda2d817addcbd73)
+set (CHOPPER_HIBF_VERSION 6e1fd5adf9aa1ba129b05e56da53ae843ef1f072)
 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 30bdf8d0a5d59b79342b472504b95ae50c33da6d)
+set (CHOPPER_SEQAN3_VERSION 31a3b14ccd79c04ce72f4727dc53740378c0c112)
 CPMDeclarePackage (seqan3
                    NAME seqan3
                    GIT_TAG ${CHOPPER_SEQAN3_VERSION} # main

From 3a7128d3d8832a7484340235965e3f640b2d1001 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 23 Oct 2024 20:29:59 +0200
Subject: [PATCH 2/3] [INFRA] Change linkage order

Such that hibf's std flag overwrites seqan3's flag
---
 src/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 55680001..47a3e2ea 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -12,7 +12,7 @@ if (TARGET chopper::interface)
 endif ()
 
 add_library (chopper_interface INTERFACE)
-target_link_libraries (chopper_interface INTERFACE seqan::hibf sharg::sharg seqan3::seqan3)
+target_link_libraries (chopper_interface INTERFACE sharg::sharg seqan3::seqan3 seqan::hibf)
 target_include_directories (chopper_interface INTERFACE "${PROJECT_SOURCE_DIR}/include")
 target_compile_options (chopper_interface INTERFACE "-pedantic" "-Wall" "-Wextra")
 add_library (chopper::interface ALIAS chopper_interface)

From 1f0943aad7c6a53356b1cbbedad7c352fcc21942 Mon Sep 17 00:00:00 2001
From: Enrico Seiler <enrico.seiler@hotmail.de>
Date: Wed, 23 Oct 2024 20:48:31 +0200
Subject: [PATCH 3/3] [FIX] missing include

---
 src/util/display_layout/general.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/util/display_layout/general.cpp b/src/util/display_layout/general.cpp
index 893ce5fb..70f6ee50 100644
--- a/src/util/display_layout/general.cpp
+++ b/src/util/display_layout/general.cpp
@@ -14,6 +14,7 @@
 #include <fstream>
 #include <functional>
 #include <iostream>
+#include <mutex>
 #include <stdexcept>
 #include <string>
 #include <tuple>