From 60cc59d1679634231d33ba25e2dbd6f1023a50e6 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 21 Oct 2024 21:52:48 +0200
Subject: [PATCH] Fix OpenMP stub patch used for FastANI on MacOS

---
 src/FastANI/CMakeLists.txt         | 3 ++-
 src/{pyfastani => FastANI}/omp.cpp | 2 ++
 src/{pyfastani => FastANI}/omp.h   | 1 +
 src/pyfastani/CMakeLists.txt       | 2 +-
 4 files changed, 6 insertions(+), 2 deletions(-)
 rename src/{pyfastani => FastANI}/omp.cpp (88%)
 rename src/{pyfastani => FastANI}/omp.h (86%)

diff --git a/src/FastANI/CMakeLists.txt b/src/FastANI/CMakeLists.txt
index 92dd225..f2ac771 100644
--- a/src/FastANI/CMakeLists.txt
+++ b/src/FastANI/CMakeLists.txt
@@ -33,7 +33,8 @@ foreach(_header ${FASTANI_HEADERS})
     set(FASTANI_GENERATED_HEADERS ${FASTANI_GENERATED_HEADERS} ${CMAKE_CURRENT_BINARY_DIR}/include/${_header})
 endforeach()
 
-add_library(fastani src/cgi/core_genome_identity.cpp ${FASTANI_GENERATED_HEADERS})
+file(COPY omp.h DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/include/src)
+add_library(fastani src/cgi/core_genome_identity.cpp omp.cpp ${FASTANI_GENERATED_HEADERS})
 target_compile_definitions(fastani PUBLIC USE_BOOST=1 BOOST_NO_EXCEPTIONS=1)
 target_include_directories(fastani PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/include/src)
 
diff --git a/src/pyfastani/omp.cpp b/src/FastANI/omp.cpp
similarity index 88%
rename from src/pyfastani/omp.cpp
rename to src/FastANI/omp.cpp
index f6c6889..54fe02a 100644
--- a/src/pyfastani/omp.cpp
+++ b/src/FastANI/omp.cpp
@@ -9,3 +9,5 @@ int omp_get_thread_num(void) {
 int omp_get_num_threads(void) {
     return 1;
 }
+
+void omp_set_num_threads(int) {}
diff --git a/src/pyfastani/omp.h b/src/FastANI/omp.h
similarity index 86%
rename from src/pyfastani/omp.h
rename to src/FastANI/omp.h
index d55ee42..5c80f12 100644
--- a/src/pyfastani/omp.h
+++ b/src/FastANI/omp.h
@@ -8,6 +8,7 @@ extern "C" {
 
 extern int omp_get_thread_num(void);
 extern int omp_get_num_threads(void);
+extern void omp_set_num_threads(int);
 
 #ifdef __cplusplus
 }
diff --git a/src/pyfastani/CMakeLists.txt b/src/pyfastani/CMakeLists.txt
index 336e0e9..62510f5 100644
--- a/src/pyfastani/CMakeLists.txt
+++ b/src/pyfastani/CMakeLists.txt
@@ -1,4 +1,4 @@
 add_subdirectory(_sequtils)
 
 cython_extension(_fasta   LINKS sequtils         )
-cython_extension(_fastani LINKS fastani sequtils SOURCES omp.cpp _utils.cpp)
\ No newline at end of file
+cython_extension(_fastani LINKS fastani sequtils SOURCES _utils.cpp)
\ No newline at end of file