Fix OpenMP stub patch used for FastANI on MacOS

althonos · Oct 21, 2024 · 4765f51 · 4765f51
1 parent 450898f
commit 4765f51
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Showing 5 changed files with 9 additions and 5 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -8,7 +8,7 @@ jobs:
 
   test_linux:
     name: Test (Linux)
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       OS: Linux
     strategy:
@@ -70,7 +70,7 @@ jobs:
 
   test_osx:
     name: Test (OSX)
-    runs-on: macos-latest
+    runs-on: macos-12
     env:
       OS: OSX
     strategy:
@@ -109,7 +109,7 @@ jobs:
           python-impl: PyPy
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         submodules: true
     - name: Setup Python ${{ matrix.python-version }}

diff --git 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 → src/FastANI/omp.cpp b/src/pyfastani/omp.cpp → 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 → src/FastANI/omp.h b/src/pyfastani/omp.h → 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
@@ -1,4 +1,4 @@
 add_subdirectory(_sequtils)
 
 cython_extension(_fasta   LINKS sequtils         )
-cython_extension(_fastani LINKS fastani sequtils SOURCES omp.cpp _utils.cpp)
+cython_extension(_fastani LINKS fastani sequtils SOURCES _utils.cpp)