From 9af5a7ecbe4fabf1f3885f938ddf07af0b609de3 Mon Sep 17 00:00:00 2001
From: Dusan Baran <work.dusanbaran@gmail.com>
Date: Tue, 22 Oct 2024 15:31:30 +0200
Subject: [PATCH] Fixing auditwheel issues

---
 apis/python/CMakeLists.txt      | 12 +-----
 libtiledbvcf/CMakeLists.txt     |  2 +
 libtiledbvcf/src/CMakeLists.txt | 68 ++++++++++++++++-----------------
 3 files changed, 38 insertions(+), 44 deletions(-)

diff --git a/apis/python/CMakeLists.txt b/apis/python/CMakeLists.txt
index c3c8b4551..376d4149d 100644
--- a/apis/python/CMakeLists.txt
+++ b/apis/python/CMakeLists.txt
@@ -62,22 +62,14 @@ target_link_libraries(${VCF_TARGET_NAME} PRIVATE tiledbvcf)
 if (APPLE)
     set_target_properties(${VCF_TARGET_NAME} PROPERTIES INSTALL_RPATH "@loader_path/lib")
 else()
-    set_target_properties(${VCF_TARGET_NAME} PROPERTIES INSTALL_RPATH "$ORIGIN/")
-    set_target_properties(tiledbvcf PROPERTIES INSTALL_RPATH "$ORIGIN/")
+    set_target_properties(${VCF_TARGET_NAME} PROPERTIES INSTALL_RPATH "$ORIGIN/lib")
 endif()
 
-install(
-        IMPORTED_RUNTIME_ARTIFACTS
-        TileDB::tiledb_shared
-        RUNTIME DESTINATION tiledbvcf
-        LIBRARY DESTINATION tiledbvcf
-)
-
 # Install the extension module
 install(
         TARGETS ${VCF_TARGET_NAME}
         RUNTIME DESTINATION tiledbvcf
-        LIBRARY DESTINATION tiledbvcf
+        LIBRARY DESTINATION tiledbvcf # MODULE
         ARCHIVE DESTINATION tiledbvcf
         INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
         PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/tiledbvcf
diff --git a/libtiledbvcf/CMakeLists.txt b/libtiledbvcf/CMakeLists.txt
index f153c6b14..1bf6c28da 100644
--- a/libtiledbvcf/CMakeLists.txt
+++ b/libtiledbvcf/CMakeLists.txt
@@ -50,6 +50,8 @@ find_package(TileDB REQUIRED)
 find_package(CLI11 REQUIRED)
 find_package(spdlog REQUIRED)
 
+# TODO: Add simple find_package for Conda builds
+
 if (WIN32)
   FetchContent_Declare(
           htslib
diff --git a/libtiledbvcf/src/CMakeLists.txt b/libtiledbvcf/src/CMakeLists.txt
index e0f1e4e78..8f78914b1 100644
--- a/libtiledbvcf/src/CMakeLists.txt
+++ b/libtiledbvcf/src/CMakeLists.txt
@@ -250,56 +250,56 @@ else()
   set_target_properties(tiledbvcf PROPERTIES INSTALL_RPATH "$ORIGIN/")
 endif()
 
-set_property(
-        TARGET tiledbvcf-bin
-        PROPERTY INSTALL_RPATH
-        "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}"
-        "${CMAKE_INSTALL_PREFIX}/lib"
-)
+#set_property(
+#        TARGET tiledbvcf-bin
+#        PROPERTY INSTALL_RPATH
+#        "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}"
+#        "${CMAKE_INSTALL_PREFIX}/lib"
+#)
+
+#if(WIN32)
+#  # Having the .dll and the .exe with the same name was resulting in a .exp
+#  # file for the .exe being 'last out' (replacing one of same name for the .dll)
+#  # and was causing the python api extension
+#  # to link to the .exe, which was not functional.
+#  # So, tiledbvcf-bin now sets an output (above somewhere) of tiledbvcfcli.exe
+#  # and we install it here RENAMEing it to match the known name in pre-existing
+#  # *nix world.
+#  install(PROGRAMS $<TARGET_FILE:tiledbvcf-bin>
+#          RENAME tiledbvcf.exe
+#          DESTINATION tiledbvcf
+#  )
+#else()
+#  install(
+#          TARGETS tiledbvcf-bin
+#          RUNTIME DESTINATION tiledbvcf
+#  )
+#endif()
 
-if(WIN32)
-  # Having the .dll and the .exe with the same name was resulting in a .exp
-  # file for the .exe being 'last out' (replacing one of same name for the .dll)
-  # and was causing the python api extension
-  # to link to the .exe, which was not functional.
-  # So, tiledbvcf-bin now sets an output (above somewhere) of tiledbvcfcli.exe
-  # and we install it here RENAMEing it to match the known name in pre-existing
-  # *nix world.
-  install(PROGRAMS $<TARGET_FILE:tiledbvcf-bin>
-          RENAME tiledbvcf.exe
-          DESTINATION ${CMAKE_INSTALL_BINDIR}
-  )
-else()
+if(TILEDBVCF_INSTALL_TILEDB)
   install(
-          TARGETS tiledbvcf-bin
-          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+          IMPORTED_RUNTIME_ARTIFACTS
+          TileDB::tiledb_shared
+          RUNTIME DESTINATION tiledbvcf
+          LIBRARY DESTINATION tiledbvcf/lib
   )
 endif()
 
-#if(TILEDBVCF_INSTALL_TILEDB)
-#  install(
-#          IMPORTED_RUNTIME_ARTIFACTS
-#          TileDB::tiledb_shared
-#          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-#          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-#  )
-#endif()
-
 install(
         TARGETS tiledbvcf
         RUNTIME DESTINATION tiledbvcf
-        LIBRARY DESTINATION tiledbvcf
-        ARCHIVE DESTINATION tiledbvcf
+        LIBRARY DESTINATION tiledbvcf/lib
+        ARCHIVE DESTINATION tiledbvcf/lib
         INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
         PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/tiledbvcf
 )
 
 if (TILEDBVCF_ENABLE_PYTHON)
   if (APPLE)
-    set_target_properties(tiledbvcf-bin PROPERTIES INSTALL_RPATH "@loader_path/../lib")
+#    set_target_properties(tiledbvcf-bin PROPERTIES INSTALL_RPATH "@loader_path/..")
     set_target_properties(tiledbvcf PROPERTIES INSTALL_RPATH "@loader_path")
   else()
-    set_target_properties(tiledbvcf-bin PROPERTIES INSTALL_RPATH "\$ORIGIN/../lib")
+#    set_target_properties(tiledbvcf-bin PROPERTIES INSTALL_RPATH "\$ORIGIN/..")
     set_target_properties(tiledbvcf PROPERTIES INSTALL_RPATH "\$ORIGIN")
   endif()
 endif()