Merge branch 'cherry-pick-e91695c5' into 'release-v0.6'

Cherry-pick 'DOR-670-homebrew-dylibs' into 'release-v0.6'

See merge request machine-learning/dorado!968

CMakeLists.txt

@@ -341,6 +341,7 @@ if(NOT DORADO_DISABLE_DORADO)
     endif()
 
     enable_warnings_as_errors(dorado)
+    check_linked_libs(dorado)
 
     if (DORADO_ENABLE_PCH)
         target_precompile_headers(dorado REUSE_FROM dorado_lib)

DEV.md

@@ -35,5 +35,5 @@ $ brew link autoconf@2.69
 
 The following other packages need to be available as well
 ```bash
-brew install openssl zstd hdf5
+brew install openssl zstd
 ```

README.md

@@ -452,8 +452,6 @@ On macOS, the equivalent export would be (change path as appropriate):
 $ export DYLD_LIBRARY_PATH=<PATH_TO_DORADO>/dorado-x.y.z-osx-arm64/lib:$DYLD_LIBRARY_PATH
 ```
 
-This will let the Dorado binary pick up the shipped libraries and you will not need to manually install `libaec` and `zstd`. 
-
 ### Improving the Speed of Duplex Basecalling
 
 Duplex basecalling is an IO-intensive process and can perform poorly if using networked storage or HDD. This can generally be improved by splitting up POD5 files appropriately.

cmake/HDF5.cmake

@@ -1,21 +1,16 @@
-set(HDF_VER hdf5-1.12.1-3)
-set(ZLIB_VER 1.2.12)
-
 option(DYNAMIC_HDF "Link HDF as dynamic libs" OFF)
 
 if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_SYSTEM_PROCESSOR STREQUAL "aarch64"))
     # download the pacakge for arm, we want to package this due to hdf5's dependencies
-
     set(DYNAMIC_HDF ON)
     set(HDF_VER hdf5-1.10.0-aarch64)
-    if(EXISTS ${DORADO_3RD_PARTY_DOWNLOAD}/${HDF_VER})
-        message(STATUS "Found ${HDF_VER}")
-    else()    
-        download_and_extract(https://cdn.oxfordnanoportal.com/software/analysis/${HDF_VER}.zip ${HDF_VER})
-    endif()
+    download_and_extract(https://cdn.oxfordnanoportal.com/software/analysis/${HDF_VER}.zip ${HDF_VER})
     list(PREPEND CMAKE_PREFIX_PATH ${DORADO_3RD_PARTY_DOWNLOAD}/${HDF_VER}/${HDF_VER})
 
 elseif(WIN32)
+    set(HDF_VER hdf5-1.12.1-3)
+    set(ZLIB_VER 1.2.12)
+
     # On windows, we need to build HDF5
     set(HDF5_ZLIB_INSTALL_DIR ${CMAKE_BINARY_DIR}/zlib-${ZLIB_VER}/install)
     if(EXISTS ${DORADO_3RD_PARTY_DOWNLOAD}/${HDF_VER} AND EXISTS ${HDF5_ZLIB_INSTALL_DIR})
@@ -42,9 +37,21 @@ elseif(WIN32)
     list(APPEND CMAKE_PREFIX_PATH ${DORADO_3RD_PARTY_DOWNLOAD}/${HDF_VER}/${HDF_VER})
 
     install(FILES ${HDF5_ZLIB_INSTALL_DIR}/bin/zlib.dll DESTINATION bin)
+
 elseif (IOS)
     # iOS doesn't make use of HDF5.
     return()
+
+elseif (APPLE)
+    set(HDF_VER 1.14.3)
+    if (CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        set(HDF_ARCH "x86_64")
+    else()
+        set(HDF_ARCH "armv8")
+    endif()
+    download_and_extract(https://cdn.oxfordnanoportal.com/software/analysis/hdf5-${HDF_VER}-${HDF_ARCH}.zip hdf5-${HDF_VER}-${HDF_ARCH})
+    list(PREPEND CMAKE_PREFIX_PATH ${DORADO_3RD_PARTY_DOWNLOAD}/hdf5-${HDF_VER}-${HDF_ARCH}/${HDF_VER}_${HDF_ARCH})
+
 endif()
 
 if(DYNAMIC_HDF)

cmake/Warnings.cmake

@@ -30,3 +30,22 @@ function(disable_warnings TARGET_NAME)
         )
     endif()
 endfunction()
+
+function(check_linked_libs TARGET_NAME)
+    if (ECM_ENABLE_SANITIZERS)
+        # We don't ship these, so no need to check them.
+        return()
+    endif()
+
+    if (APPLE)
+        add_custom_command(
+            TARGET ${TARGET_NAME}
+            POST_BUILD
+            COMMAND echo "Checking linked libs..."
+            # We shouldn't be linking to anything from homebrew.
+            COMMAND sh -c "otool -L $<TARGET_FILE:${TARGET_NAME}> | grep -i /opt/homebrew ; test $? -eq 1"
+            COMMAND sh -c "otool -L $<TARGET_FILE:${TARGET_NAME}> | grep -i /usr/local/opt ; test $? -eq 1"
+            VERBATIM
+        )
+    endif()
+endfunction()