biology/spoa: update 4.0.7 → 4.1.0

Reported by:	portscout

4 files changed, 21 insertions, 128 deletions

diff --git a/biology/spoa/Makefile b/biology/spoa/Makefile
index bf258c57ffe4..378002e2f801 100644
--- a/biology/spoa/Makefile
+++ b/biology/spoa/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	spoa
-DISTVERSION=	4.0.7
-PORTREVISION=	4
+DISTVERSION=	4.1.0
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -11,7 +10,7 @@ LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	bioparser>0:biology/bioparser \
-		${LOCALBASE}/include/biosoup/nucleic_acid.hpp:biology/biosoup \
+		biosoup>0:biology/biosoup \
 		cereal>0:devel/cereal \
 		simde>0:devel/simde
 LIB_DEPENDS=	libcpu_features.so:devel/cpu_features
@@ -24,8 +23,17 @@ USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	rvaser
 
-CMAKE_ON=	BUILD_SHARED_LIBS spoa_optimize_for_portability spoa_build_executable spoa_use_simde spoa_use_simde_nonvec spoa_use_simde_openmp
-CMAKE_OFF=	spoa_optimize_for_native
+CMAKE_ON=	BUILD_SHARED_LIBS \
+		spoa_build_exe \
+		spoa_optimize_for_portability \
+		spoa_build_executable \
+		spoa_use_simde \
+		spoa_use_simde_nonvec \
+		spoa_use_simde_openmp \
+		spoa_use_cereal \
+		spoa_use_simde_openmp
+CMAKE_OFF=	spoa_optimize_for_native \
+		spoa_build_tests
 
 CXXFLAGS+=	-I${LOCALBASE}/include/cpu_features
 LDFLAGS+=	-lz -lcpu_features
diff --git a/biology/spoa/distinfo b/biology/spoa/distinfo
index b004cd66001d..09296c5fd3cf 100644
--- a/biology/spoa/distinfo
+++ b/biology/spoa/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1611045674
-SHA256 (rvaser-spoa-4.0.7_GH0.tar.gz) = f8cb409adcca20ca6cc0025371743b915790879957cf001ca5e155ed16fd14e0
-SIZE (rvaser-spoa-4.0.7_GH0.tar.gz) = 43574
+TIMESTAMP = 1693289273
+SHA256 (rvaser-spoa-4.1.0_GH0.tar.gz) = 43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8
+SIZE (rvaser-spoa-4.1.0_GH0.tar.gz) = 47814
diff --git a/biology/spoa/files/patch-CMakeLists.txt b/biology/spoa/files/patch-CMakeLists.txt
deleted file mode 100644
index a5e7af7845e8..000000000000
--- a/biology/spoa/files/patch-CMakeLists.txt
+++ /dev/null
@@ -1,118 +0,0 @@
---- CMakeLists.txt.orig	2021-01-15 03:44:02 UTC
-+++ CMakeLists.txt
-@@ -44,9 +44,10 @@ if (spoa_use_simde OR
-   endif ()
- endif ()
- 
--if (NOT TARGET cereal)
--  add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL)
--endif ()
-+#if (NOT TARGET cereal)
-+#  add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL)
-+#endif ()
-+find_package(cereal REQUIRED)
- 
- add_library(${PROJECT_NAME}
-   src/alignment_engine.cpp
-@@ -55,19 +56,19 @@ add_library(${PROJECT_NAME}
-   src/dispatcher.cpp)
- target_include_directories(${PROJECT_NAME} PUBLIC
-   $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
--  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
--  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
-+  #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
-+  #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include>
-   $<INSTALL_INTERFACE:include>)
- target_link_libraries(${PROJECT_NAME}
--  cereal)
-+  cereal::cereal)
- if (BUILD_SHARED_LIBS)
-   set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0")
- endif ()
- 
- if (spoa_generate_dispatch)
--  if (NOT TARGET cpu_features)
--    add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL)
--  endif ()
-+  #if (NOT TARGET cpu_features)
-+  #  add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL)
-+  #endif ()
- 
-   list(APPEND ARCHITECTURES avx2 sse4.1 sse2)
-   foreach(arch IN LISTS ARCHITECTURES)
-@@ -78,7 +79,7 @@ if (spoa_generate_dispatch)
-       $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde>
-       $<INSTALL_INTERFACE:include>)
-     target_link_libraries(${PROJECT_NAME}_${arch}
--      cereal)
-+      cereal::cereal)
-     set_target_properties(${PROJECT_NAME}_${arch} PROPERTIES
-       COMPILE_FLAGS "-m${arch}")
-     if (BUILD_SHARED_LIBS)
-@@ -92,8 +93,8 @@ if (spoa_generate_dispatch)
-     ${PROJECT_NAME}_sse4.1
-     ${PROJECT_NAME}_sse2)
- 
--  target_link_libraries(${PROJECT_NAME}
--    cpu_features)
-+  #target_link_libraries(${PROJECT_NAME}
-+  #  cpu_features)
- endif ()
- 
- include(GNUInstallDirs)
-@@ -110,18 +111,19 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/spoa-1.pc
- 
- option(spoa_build_executable "Build spoa standalone tool" OFF)
- if (spoa_build_executable)
--  if (NOT TARGET biosoup)
--    add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
--  endif ()
--  if (NOT TARGET bioparser)
--    add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
--  endif ()
-+  #if (NOT TARGET biosoup)
-+  #  add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
-+  #endif ()
-+  #if (NOT TARGET bioparser)
-+  #  add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
-+  #endif ()
-   add_executable(${PROJECT_NAME}_exe
-     src/main.cpp)
-   target_link_libraries(${PROJECT_NAME}_exe
-     ${PROJECT_NAME}
--    bioparser
--    biosoup)
-+    #bioparser
-+    #biosoup
-+  )
-   target_compile_definitions(${PROJECT_NAME}_exe PRIVATE
-     SPOA_VERSION="v${PROJECT_VERSION}")
-   set_property(TARGET ${PROJECT_NAME}_exe PROPERTY
-@@ -134,19 +136,19 @@ endif ()
- option(spoa_build_tests "Build spoa unit tests" OFF)
- if (spoa_build_tests)
-   find_package(GTest REQUIRED)
--  if (NOT TARGET biosoup)
--    add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
--  endif ()
--  if (NOT TARGET bioparser)
--    add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
--  endif ()
-+  #if (NOT TARGET biosoup)
-+  #  add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
-+  #endif ()
-+  #if (NOT TARGET bioparser)
-+  #  add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
-+  #endif ()
-   include_directories(${PROJECT_SOURCE_DIR}/src)
-   add_executable(${PROJECT_NAME}_test
-     test/spoa_test.cpp)
-   target_link_libraries(${PROJECT_NAME}_test
-     ${PROJECT_NAME}
--    bioparser
--    biosoup
-+    #bioparser
-+    #biosoup
-     GTest::Main)
-   target_compile_definitions(${PROJECT_NAME}_test PRIVATE
-     SPOA_DATA_PATH="${PROJECT_SOURCE_DIR}/test/data/sample.fastq.gz")
diff --git a/biology/spoa/pkg-plist b/biology/spoa/pkg-plist
index 7883602bf5f0..397027fc2850 100644
--- a/biology/spoa/pkg-plist
+++ b/biology/spoa/pkg-plist
@@ -1,8 +1,11 @@
 bin/spoa
 include/spoa/alignment_engine.hpp
-include/spoa/architectures.hpp
 include/spoa/graph.hpp
 include/spoa/spoa.hpp
+include/spoa/version.hpp
+lib/cmake/spoa/spoaConfig.cmake
+lib/cmake/spoa/spoaConfigVersion.cmake
+lib/cmake/spoa/spoaTargets-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/spoa/spoaTargets.cmake
 lib/libspoa.so
 lib/libspoa.so.7.0.0
-libdata/pkgconfig/spoa-1.pc