From c7cd5d83eec198354cbb14cf548ef48247d8c83c Mon Sep 17 00:00:00 2001
From: Ben Lawrence <ben.lawrence@nanoporetech.com>
Date: Tue, 23 Apr 2024 12:10:59 +0000
Subject: [PATCH] Merge branch 'DOR-670-homebrew-dylibs' into 'master'

[DOR-670] Change to using a CDN hosted HDF5

Closes DOR-670

See merge request machine-learning/dorado!964

(cherry picked from commit e91695c5c6a3a26442dc384cbcbadf9c673eee84)

f1701fd1 [DOR-670] Add post-build check that dorado doesn't link to brew dylibs
ad75e886 [DOR-670] Skip checks for sanitizer builds
29399c7f [DOR-670] Add macOS Intel homebrew path to the search too
3daead45 [DOR-670] Add macOS hdf5 libs
12509cfb [DOR-670] Simplify download_and_extract() call
c3ece9ae [DOR-670] Remove references to hdf5 and libaec
---
 CMakeLists.txt       |  1 +
 DEV.md               |  2 +-
 README.md            |  2 --
 cmake/HDF5.cmake     | 25 ++++++++++++++++---------
 cmake/Warnings.cmake | 19 +++++++++++++++++++
 5 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8a88adef..59faa587 100755
--- a/CMakeLists.txt
+++ b/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)
diff --git a/DEV.md b/DEV.md
index ffd8a8a7..35badf8e 100644
--- a/DEV.md
+++ b/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
 ```
diff --git a/README.md b/README.md
index 57d53490..6dee444e 100644
--- a/README.md
+++ b/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.
diff --git a/cmake/HDF5.cmake b/cmake/HDF5.cmake
index a9d6b733..d1b9432b 100644
--- a/cmake/HDF5.cmake
+++ b/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)
diff --git a/cmake/Warnings.cmake b/cmake/Warnings.cmake
index b7ce071a..c3a8bbd6 100644
--- a/cmake/Warnings.cmake
+++ b/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()